914 results
Search Results
2. Development of microsatellite loci and optimization of a multiplex assay for Latibulus argiolus (Hymenoptera: Ichneumonidae), the specialized parasitoid of paper wasps
- Author
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Anna Siekiera, Magdalena Czajkowska, Jan J. Pomorski, Agata Kostro-Ambroziak, and Hanna Panagiotopoulou
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0106 biological sciences ,0301 basic medicine ,Genetic Markers ,Population ,Genome, Insect ,Wasps ,lcsh:Medicine ,Locus (genetics) ,Ectoparasitic Infestations ,Biology ,010603 evolutionary biology ,01 natural sciences ,03 medical and health sciences ,Animals ,Multiplex ,Genetic variability ,Allele ,education ,lcsh:Science ,Alleles ,education.field_of_study ,Multidisciplinary ,Polymorphism, Genetic ,lcsh:R ,biology.organism_classification ,Null allele ,Ichneumonidae ,030104 developmental biology ,Genetics, Population ,Evolutionary biology ,Genetic Loci ,Microsatellite ,lcsh:Q ,Multiplex Polymerase Chain Reaction ,Microsatellite Repeats - Abstract
Microsatellite loci are commonly used markers in population genetic studies. In this study, we present 40 novel and polymorphic microsatellite loci elaborated for the ichneumonid parasitoid Latibulus argiolus (Rossi, 1790). Reaction condition optimisation procedures allowed 14 of these loci to be co-amplified in two PCRs and loaded in two multiplex panels onto a genetic analyser. The assay was tested on 197 individuals of L. argiolus originating from ten natural populations obtained from the host nests of paper wasps. The validated loci were polymorphic with high allele numbers ranging from eight to 27 (average 17.6 alleles per locus). Both observed and expected heterozygosity values were high, ranging between 0.75 and 0.92 for HO (mean 0.83) and from 0.70 to 0.90 for HE (mean 0.85). The optimized assay showed low genotyping error rate and negligible null allele frequency. The designed multiplex panels could be successfully applied in relatedness analyses and genetic variability studies of L. argiolus populations, which would be particularly interesting considering the coevolutionary context of this species with its social host.
- Published
- 2020
3. Assessing false paternity risk in simulated motherless cases from more than 20 000 real exclusion trios.
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Aguiar VRC, de Castro AM, Pinto LM, Ferreira ACS, Dos Santos EVW, and Louro ID
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- Alleles, Computer Simulation, Female, Genotype, Humans, Male, Mothers, Mutation, Paternity, Probability, Genetic Loci, Microsatellite Repeats
- Abstract
Background: When the mother's DNA profile is not available for paternity testing, there is a smaller probability that a locus will exclude an alleged father. This study aims to evaluate the risk of potential false paternity inclusions in motherless cases., Study Design and Methods: More than 20 000 duos were generated by removing the maternal genotypes from exclusion trios. After recalculating paternity in these duos, any found inclusions would be false., Results: The use of an appropriate number of loci, mutation model, and mutation rates to analyze motherless paternity cases was robust against false inclusions. A single potential false inclusion was observed in a case wherein kinship plays a role. This result highlights the importance of testing the mother when available and of obtaining information on family circumstances for the proper handling of cases involving related individuals., Conclusion: The guidelines we used here were sufficient to avoid false inclusions in a data set of more than 20 000 motherless cases., (© 2020 AABB.)
- Published
- 2021
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- View/download PDF
4. Mating system and population structure in the natural distribution of Toona ciliata (Meliaceae) in South China.
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Zhou W, Zhang XX, Ren Y, Li P, Chen XY, and Hu XS
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- China, Crosses, Genetic, Endangered Species, Inbreeding, Meliaceae, Pollination genetics, Reproduction genetics, Genetic Loci genetics, Microsatellite Repeats genetics, Toona physiology
- Abstract
Most initially perfect flowers of Toona ciliata Roem subsequently develop into functionally unisexual flowers and their relative positions in the same inflorescence could enhance the outcrossing system in this species. Here we investigated the mating system of this species. We used eight nuclear microsatellite markers and investigated the progeny of 125 mother trees from six populations naturally distributed in South China, with sample sizes ranging from 64 to 300 seeds. The multilocus outcrossing rate was 0.970 ± 0.063, and the single locus outcrossing rate was 0.859 ± 0.106, indicating the pattern of predominant outcrossing. Selfing was present in one population, but biparental inbreeding occurred in five populations. Inbreeding was absent in maternal parents, and correlations of selfing among families or among loci were generally insignificant. Positive correlation of paternity at multiple loci was significant in four populations, but was not consistent with the results at single loci. Population substructure occurred in male similarity between outcrosses only in one population. Population genetic differentaitaion was significant (F
st = 34.5%) and the effects of isolation-by-distance at the eight loci were significant among the six populations. These results provide evidence that self-comptability and inbreeding naturally occur in T. ciliata and indicate that inbreeding avoidance is necessary during genetic improvement and breeding of this endangered tree species.- Published
- 2020
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- View/download PDF
5. Statistical correction of the Winner’s Curse explains replication variability in quantitative trait genome-wide association studies.
- Author
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Palmer, Cameron and Pe’er, Itsik
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GENOMES ,DATABASES ,REGRESSION analysis ,ANALYSIS of covariance ,DIFFERENTIAL psychology - Abstract
Genome-wide association studies (GWAS) have identified hundreds of SNPs responsible for variation in human quantitative traits. However, genome-wide-significant associations often fail to replicate across independent cohorts, in apparent inconsistency with their apparent strong effects in discovery cohorts. This limited success of replication raises pervasive questions about the utility of the GWAS field. We identify all 332 studies of quantitative traits from the NHGRI-EBI GWAS Database with attempted replication. We find that the majority of studies provide insufficient data to evaluate replication rates. The remaining papers replicate significantly worse than expected (p < 10
−14 ), even when adjusting for regression-to-the-mean of effect size between discovery- and replication-cohorts termed the Winner’s Curse (p < 10−16 ). We show this is due in part to misreporting replication cohort-size as a maximum number, rather than per-locus one. In 39 studies accurately reporting per-locus cohort-size for attempted replication of 707 loci in samples with similar ancestry, replication rate matched expectation (predicted 458, observed 457, p = 0.94). In contrast, ancestry differences between replication and discovery (13 studies, 385 loci) cause the most highly-powered decile of loci to replicate worse than expected, due to difference in linkage disequilibrium. [ABSTRACT FROM AUTHOR]- Published
- 2017
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6. Genome-wide association meta-analysis of individuals of European ancestry identifies new loci explaining a substantial fraction of hair color variation and heritability.
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Hysi PG, Valdes AM, Liu F, Furlotte NA, Evans DM, Bataille V, Visconti A, Hemani G, McMahon G, Ring SM, Smith GD, Duffy DL, Zhu G, Gordon SD, Medland SE, Lin BD, Willemsen G, Jan Hottenga J, Vuckovic D, Girotto G, Gandin I, Sala C, Concas MP, Brumat M, Gasparini P, Toniolo D, Cocca M, Robino A, Yazar S, Hewitt AW, Chen Y, Zeng C, Uitterlinden AG, Ikram MA, Hamer MA, van Duijn CM, Nijsten T, Mackey DA, Falchi M, Boomsma DI, Martin NG, Hinds DA, Kayser M, and Spector TD
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- Aged, Chromosomes, Human, X, Female, Genome-Wide Association Study methods, Humans, Male, Middle Aged, Phenotype, Genetic Loci, Hair Color genetics, Multifactorial Inheritance, Polymorphism, Single Nucleotide genetics, White People genetics
- Abstract
Hair color is one of the most recognizable visual traits in European populations and is under strong genetic control. Here we report the results of a genome-wide association study meta-analysis of almost 300,000 participants of European descent. We identified 123 autosomal and one X-chromosome loci significantly associated with hair color; all but 13 are novel. Collectively, single-nucleotide polymorphisms associated with hair color within these loci explain 34.6% of red hair, 24.8% of blond hair, and 26.1% of black hair heritability in the study populations. These results confirm the polygenic nature of complex phenotypes and improve our understanding of melanin pigment metabolism in humans.
- Published
- 2018
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7. Evolutionary games, climate and the generation of diversity.
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Friedman, Daniel, Magnani, Jacopo, Paranjpe, Dhanashree, and Sinervo, Barry
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BIODIVERSITY ,GAME theory in biology ,HEALTH outcome assessment ,MAXIMUM likelihood statistics ,ROCK-paper-scissors (Game) ,OSCILLATIONS - Abstract
Environmental stochasticity and climate affect outcomes in evolutionary games, which can thereby affect biological diversity. Our maximum likelihood (ML) estimates of replicator dynamics for morph frequency data from control (25 years) and three experimentally perturbed populations (14 years) of side-blotched lizards yield a 3 × 3 payoff matrix in the generalized Rock-Paper-Scissors family; it has intransitive best replies, and each strategy is its own worst reply. ML estimates indicate significant interactive effects of density and temperature on morph frequency. Implied dynamics feature a powerful interior attractor and recover (for the first time) observed 4-5 year oscillations. Our evolutionary experiment on morph frequency confirms that oscillations are driven by frequency dependent selection, but climate entrains the cycles across the perturbed and control populations within 10 generations. Applying the model across the species range, we find that climate also accounts for morph fixation and mating system diversity, suggesting climate may similarly impact ecosystem diversity. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
8. Many chronological aging clocks can be found throughout the epigenome: Implications for quantifying biological aging
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Chase A. Brown, Xiavan Roopnarinesingh, Jonathan D. Wren, Willard M. Freeman, Hunter Porter, Constantin Georgescu, and Cory B. Giles
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Adult ,Epigenomics ,Male ,Aging ,Age prediction ,Longevity ,Context (language use) ,Disease ,Computational biology ,epigenetic clocks ,Biology ,Epigenesis, Genetic ,Epigenome ,Basic research ,Biological Clocks ,Databases, Genetic ,Humans ,Epigenetics ,Aged ,Aged, 80 and over ,Original Paper ,epigenetics ,Brain ,Cell Biology ,bioinformatics ,DNA Methylation ,Middle Aged ,Original Papers ,Genetic Loci ,DNA methylation ,Weak association ,Female ,Biomarkers - Abstract
Epigenetic alterations are a hallmark of aging and age‐related diseases. Computational models using DNA methylation data can create “epigenetic clocks” which are proposed to reflect “biological” aging. Thus, it is important to understand the relationship between predictive clock sites and aging biology. To do this, we examined over 450,000 methylation sites from 9,699 samples. We found ~20% of the measured genomic cytosines can be used to make many different epigenetic clocks whose age prediction performance surpasses that of telomere length. Of these predictive sites, the average methylation change over a lifetime was small (~1.5%) and these sites were under‐represented in canonical regions of epigenetic regulation. There was only a weak association between “accelerated” epigenetic aging and disease. We also compare tissue‐specific and pan‐tissue clock performance. This is critical to applying clocks both to new sample sets in basic research, as well as understanding if clinically available tissues will be feasible samples to evaluate “epigenetic aging” in unavailable tissues (e.g., brain). Despite the reproducible and accurate age predictions from DNA methylation data, these findings suggest they may have limited utility as currently designed in understanding the molecular biology of aging and may not be suitable as surrogate endpoints in studies of anti‐aging interventions. Purpose‐built clocks for specific tissues age ranges or phenotypes may perform better for their specific purpose. However, if purpose‐built clocks are necessary for meaningful predictions, then the utility of clocks and their application in the field needs to be considered in that context., Epigenetic clocks show promise as a biomarker of aging. Our study identifies components of epigenetic clocks critical to understanding their uses and where improvements are still needed. We identified a parabolic trajectory of methylation aging and the extent to which epigenetic clocks are robust to removing the most age‐predictive loci. These data shape our understanding of epigenetic age acceleration and what epigenetic clocks can tell us about the biology of aging.
- Published
- 2021
9. Discovering the mechanism and involvement of the methylation of cyclin-dependent kinase inhibitor 2A (CDKN2A) gene and its special locus region in gastric cancer
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Ning Li, Wenying Deng, Jiye Xu, and Suxia Luo
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0301 basic medicine ,Adult ,Male ,cdkn2a ,Bioengineering ,Locus (genetics) ,Biology ,medicine.disease_cause ,Applied Microbiology and Biotechnology ,Cyclin-Dependent Kinase Inhibitor 2A ,03 medical and health sciences ,0302 clinical medicine ,gsea ,CDKN2A ,Stomach Neoplasms ,hemic and lymphatic diseases ,medicine ,Humans ,tcga ,Gene ,neoplasms ,Cyclin-Dependent Kinase Inhibitor p16 ,Aged ,Aged, 80 and over ,gastric cancer ,General Medicine ,Methylation ,DNA Methylation ,Middle Aged ,Prognosis ,Phenotype ,digestive system diseases ,Gene Expression Regulation, Neoplastic ,Survival Rate ,stomatognathic diseases ,030104 developmental biology ,Genetic Loci ,030220 oncology & carcinogenesis ,DNA methylation ,Cancer research ,Female ,KRAS ,methylation ,TP248.13-248.65 ,Research Article ,Research Paper ,Biotechnology - Abstract
Cyclin-dependent kinase inhibitor 2A (CDKN2A) gene methylation has been paramount in the development of malignant masses. The purpose of the conducted research was to evaluate the mechanism and involvement of methylation in regards to the CDKN2A gene and the specific locus region in gastric cancer (GC) with comprehensive statistical analysis utilizing statistics acquired from The Cancer Genome Atlas (TCGA) database. Gene Set Enrichment Analysis (GSEA) revealed that the level of CDKN2A gene methylation and its locus in GC tissues was increased compared to para-cancerous tissues. In multivariate analysis, low methylation of CDKN2A gene, cg03079681, cg04026675, cg07562918, and cg13601799 locus were independently linked to better OS. In addition, the methylation of CDKN2A gene, cg00718440, cg03079681, cg04026675, cg07562918, cg10848754, cg14069088 and cg14430974 locus were negative correlated with CDKN2A gene expression. Meanwhile, the methylation of cg12840719 locus was positively correlated with CDKN2A gene expression. GSEA showed that hallmark_kras_signaling_dn, hallmark_myogenesis, and hallmark_epithelial_mesenchymal_transition pathways were enriched in the CDKN2A gene hypermethylation phenotype. Taken together, the low methylation of CDKN2A gene, cg03079681, cg04026675, cg07562918, and cg13601799 locus indicated a better prognosis in GC. The methylation levels of cg14069088 were most negatively correlated with CDKN2A gene expression. Hallmark_kras_signaling_dn, Hallmark_myogenesis, and hallmark_epithelial_mesenchymal_transition pathways might be important in the regulation of CDKN2A gene hypermethylation., Graphical abstract
- Published
- 2021
10. DNA methylation in the promoters of PD-L1, MMP9, ARG1, galectin-9, TIM-3, VISTA and TGF-β genes in HLA-DR– myeloid cells, compared with HLA-DR+ antigen-presenting cells
- Author
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Saleh, Reem, Toor, Salman M., Taha, Rowaida Z., Al-Ali, Dana, Sasidharan Nair, Varun, and Elkord, Eyad
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DNA methylation ,immunosuppression ,B7 Antigens ,epigenetics ,Arginase ,MDSC ,Sialic Acid Binding Ig-like Lectin 3 ,Antigen-Presenting Cells ,HLA-DR Antigens ,B7-H1 Antigen ,Epigenesis, Genetic ,Matrix Metalloproteinase 9 ,Genetic Loci ,Transforming Growth Factor beta ,Humans ,Myeloid Cells ,Promoter Regions, Genetic ,Hepatitis A Virus Cellular Receptor 2 ,Research Article ,Research Paper - Abstract
Myeloid cells, including antigen-presenting cells (APCs) and myeloid-derived suppressor cells (MDSCs) play opposing roles to orchestrate innate and adaptive immune responses during physiological and pathological conditions. We investigated the role of DNA methylation in regulating the transcription of inhibitory/suppressive molecules in myeloid suppressive cells (identified as CD33+HLA-DR–) in comparison to APCs. We selected a number of immune checkpoints (ICs), IC ligands, and immunosuppressive molecules that have been implicated in MDSC function, including PD-L1, TIM-3, VISTA, galectin-9, TGF-β, ARG1 and MMP9. We examined their mRNA expression levels, and investigated whether DNA methylation regulates their transcription in sorted myeloid cell subpopulations. We found that mRNA levels of PD-L1, TIM-3, TGF-β, ARG1 and MMP9 in CD33+HLA-DR– cells were higher than APCs. However, VISTA and galectin-9 mRNA levels were relatively similar in both myeloid subpopulations. CpG islands in the promoter regions of TGF-β1, TIM-3 and ARG1 were highly unmethylated in CD33+HLA-DR–cells, compared with APCs, suggesting that DNA methylation is one of the key mechanisms, which regulate their expression. However, we did not find differences in the methylation status of PD-L1 and MMP9 between CD33+HLA-DR– and APCs, suggesting that their transcription could be regulated via other genetic and epigenetic mechanisms. The promoter methylation status of VISTA was relatively similar in both myeloid subpopulations. This study provides novel insights into the epigenetic mechanisms, which control the expression of inhibitory/suppressive molecules in circulating CD33+HLA-DR– cells in a steady-state condition, possibly to maintain immune tolerance and haemostasis.
- Published
- 2020
11. Genome-wide characterization of cytosine-specific 5-hydroxymethylation in normal breast tissue
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Owen M. Wilkins, E. Andres Houseman, Kevin C. Johnson, Brock C. Christensen, Jessica E. King, and Carmen J. Marsit
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0301 basic medicine ,Adult ,Cancer Research ,Adolescent ,Biology ,Epigenesis, Genetic ,03 medical and health sciences ,chemistry.chemical_compound ,Epigenome ,0302 clinical medicine ,Lactate oxidation ,Breast cancer ,medicine ,Humans ,Epigenetics ,5-hydroxymethylcytosine ,Mammary Glands, Human ,Molecular Biology ,Aged ,5-Hydroxymethylcytosine ,Transcriptionally active chromatin ,Regulation of gene expression ,Aged, 80 and over ,DNA methylation ,Middle Aged ,medicine.disease ,Cell biology ,030104 developmental biology ,chemistry ,CpG site ,Genetic Loci ,030220 oncology & carcinogenesis ,5-Methylcytosine ,CpG Islands ,Female ,Transcriptome ,Research Paper - Abstract
Despite recent evidence that 5-hydroxymethylcytosine (5hmC) possesses roles in gene regulation distinct from 5-methylcytosine (5mC), relatively little is known regarding the functions of 5hmC in mammalian tissues. To address this issue, we utilized an approach combining both paired bisulfite (BS) and oxidative bisulfite (oxBS) DNA treatment, to resolve genome-wide patterns of 5hmC and 5mC in normal breast tissue from disease-free women. Although less abundant than 5mC, 5hmC was differentially distributed, and consistently enriched among breast-specific enhancers and transcriptionally active chromatin. In contrast, regulatory regions associated with transcriptional inactivity, such as heterochromatin and repressed Polycomb regions, were relatively depleted of 5hmC. Gene regions containing abundant 5hmC were significantly associated with lactate oxidation, immune cell function, and prolactin signaling pathways. Furthermore, genes containing abundant 5hmC were enriched among those actively transcribed in normal breast tissue. Finally, in independent data sets, normal breast tissue 5hmC was significantly enriched among CpG loci demonstrated to have altered methylation in pre-invasive breast cancer and invasive breast tumors. Primarily, our findings identify genomic loci containing abundant 5hmC in breast tissues and provide a genome-wide map of nucleotide-level 5hmC in normal breast tissue. Additionally, these data suggest 5hmC may participate in gene regulatory programs that are dysregulated during breast-related carcinogenesis.
- Published
- 2019
12. Functional validation of the albinism-associated tyrosinase T373K SNP by CRISPR/Cas9-mediated homology-directed repair (HDR) in rabbits
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Mao Chen, Liangxue Lai, Jichao Deng, Tingting Sui, Zhanjun Li, Yuxin Zhang, and Yuning Song
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0301 basic medicine ,Research paper ,Tyrosinase ,Mutant ,Rabbit ,Biology ,medicine.disease_cause ,Polymorphism, Single Nucleotide ,General Biochemistry, Genetics and Molecular Biology ,Melanin ,Homology directed repair ,03 medical and health sciences ,medicine ,Animals ,Genetic Predisposition to Disease ,Gene ,CRISPR/Cas9 ,Cells, Cultured ,Genetic Association Studies ,Genetics ,OCA ,Gene Editing ,Melanins ,Mutation ,T373K ,Point mutation ,Monophenol Monooxygenase ,Recombinational DNA Repair ,General Medicine ,medicine.disease ,Oculocutaneous albinism ,Enzyme Activation ,Disease Models, Animal ,030104 developmental biology ,Amino Acid Substitution ,Albinism, Oculocutaneous ,Genetic Loci ,Albinism ,Female ,sense organs ,Rabbits ,CRISPR-Cas Systems - Abstract
Background Oculocutaneous albinism (OCA) is a group of autosomal recessive disorders characterized by reduced melanin that are caused by mutations in the gene encoding tyrosinase (TYR), which is the rate-limiting enzyme in the production of the pigment melanin. Many studies or meta-analyses have suggested an association between the TYR T373K SNP and OCA1, but there is limited biochemical and genetic evidence to support this association. Methods We overexpressed TYR-WT and TYR-T373K mutants on HK293T cells and tested the changes of melanin production and tyrosinase activity. Then we generated TYR-K373T knock-in (KI) rabbits by microinjection of ssDNA and synthesized RNAs targeting C1118A using CRISPR/Cas9-HDR to observe the formation of melanin. Findings We demonstrated that the T373K mutation in TYR can reduce tyrosinase activity, leading to an absence of melanin synthesis at the cell-level. The gene-edited TYR-K373T rabbits exhibited rescued melanin production in hair follicles and irises, as inferred from the evident decrease in pigmentation in TYR-T373K rabbits, thus providing functional validation of the albinism-associated T373K SNP at the animal level. Interpretation Our study provides the first animal-level functional validation of the albinism-associated TYR K373T SNP in rabbits, and these results will facilitate gene therapy of OCA1 in pre-clinical settings in the future. Fund The National Key Research and Development Program of China Stem Cell and Translational Research, the Strategic Priority Research Program of the Chinese Academy of Sciences, the Guangdong Province Science and Technology Plan Project, and the Program for JLU Science and Technology Innovative Research Team.
- Published
- 2018
13. AvrPm2 encodes an RNase‐like avirulence effector which is conserved in the two different specialized forms of wheat and rye powdery mildew fungus
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Francis Parlange, Luisa K. Schäfer, Dazhao Yu, Kaitlin E. McNally, Yang Lijun, Javier Sánchez-Martín, Rainer Boni, Xue Minfeng, Salim Bourras, Simone Oberhaensli, Coraline R. Praz, Roi Ben-David, Fabrizio Menardo, Gerard Herren, Stefan Roffler, Beat Keller, Zeng Fansong, Simon Flückiger, Thomas Wicker, University of Zurich, and Yu, Dazhao
- Subjects
Models, Molecular ,0301 basic medicine ,Secale ,Physiology ,Blumeria graminis ,Plant Science ,580 Plants (Botany) ,Conserved sequence ,Fungal Proteins ,03 medical and health sciences ,Ribonucleases ,Ascomycota ,10126 Department of Plant and Microbial Biology ,Gene Expression Regulation, Plant ,wheat ,Tobacco ,1110 Plant Science ,Gene family ,Amino Acid Sequence ,Gene ,Conserved Sequence ,Phylogeny ,Triticum ,Plant Diseases ,Plant Proteins ,Genetics ,Mildew ,Virulence ,biology ,Full Paper ,Research ,food and beverages ,Pm2 ,1314 Physiology ,Full Papers ,RNAse‐like ,Physical Chromosome Mapping ,biology.organism_classification ,030104 developmental biology ,avirulence gene ,Genetic Loci ,powdery mildew ,Gene pool ,Corrigendum ,Powdery mildew ,Genome-Wide Association Study - Abstract
Summary There is a large diversity of genetically defined resistance genes in bread wheat against the powdery mildew pathogen Blumeria graminis (B. g.) f. sp. tritici. Many confer race‐specific resistance to this pathogen, but until now only the mildew avirulence gene AvrPm3 a2/f2 that is recognized by Pm3a/f was known molecularly.We performed map‐based cloning and genome‐wide association studies to isolate a candidate for the mildew avirulence gene AvrPm2. We then used transient expression assays in Nicotiana benthamiana to demonstrate specific and strong recognition of AvrPm2 by Pm2.The virulent AvrPm2 allele arose from a conserved 12 kb deletion, while there is no protein sequence diversity in the gene pool of avirulent B. g. tritici isolates. We found one polymorphic AvrPm2 allele in B. g. triticale and one orthologue in B. g. secalis and both are recognized by Pm2. AvrPm2 belongs to a small gene family encoding structurally conserved RNase‐like effectors, including Avr a13 from B. g. hordei, the cognate Avr of the barley resistance gene Mla13.These results demonstrate the conservation of functional avirulence genes in two cereal powdery mildews specialized on different hosts, thus providing a possible explanation for successful introgression of resistance genes from rye or other grass relatives to wheat., See also the Commentary on this article by Spanu, 213: 969–971.
- Published
- 2016
14. Dominant inhibition of awn development by a putative zinc‐finger transcriptional repressor expressed at the B1 locus in wheat
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Nikolai M. Adamski, Catherine Chinoy, Paul Nicholson, Curt A. McCartney, Yasmina Bekkaoui, Sateesh Kagale, Qian Zheng, Frank M. You, Tancey Melchkart, J. Allan Feurtado, Martha Clarke, David Konkin, Daiqing Huang, Adrian J. Cutler, Martial Martucci, and A. Steed
- Subjects
0106 biological sciences ,0301 basic medicine ,Physiology ,Mutant ,Amino Acid Motifs ,Plant Science ,01 natural sciences ,Gene Expression Regulation, Plant ,Chromosome Segregation ,wheat ,Coding region ,B1 Locus ,Triticum ,Genes, Dominant ,Plant Proteins ,Zinc finger ,Genetics ,education.field_of_study ,C2H2 Zinc Finger ,Full Paper ,Chromosome Mapping ,food and beverages ,Genetic Pleiotropy ,Zinc Fingers ,Bread ,Full Papers ,awnletted ,Multigene Family ,Population ,Plant Development ,Locus (genetics) ,Biology ,03 medical and health sciences ,Open Reading Frames ,transcriptional repression ,Deletion mapping ,education ,Gene ,Cell Proliferation ,Polymorphism, Genetic ,Indoleacetic Acids ,zinc finger ,Research ,awn ,transcription repression ,Repressor Proteins ,030104 developmental biology ,Haplotypes ,C2H2 ,Genetic Loci ,Mutation ,EAR motif ,010606 plant biology & botany - Abstract
Summary Awns, bristle‐like structures extending from grass lemmas, provide protection against predators, contribute to photosynthesis and aid in grain dispersal. In wheat, selection of awns with minimal extension, termed awnletted, has occurred during domestication by way of loci that dominantly inhibit awn development, such as Tipped1 (B1), Tipped2 (B2), and Hooded (Hd). Here we identify and characterize the B1 gene. B1 was identified using bulked segregant RNA‐sequencing of an F2 durum wheat population and through deletion mapping of awned bread wheat mutants. Functional characterization was accomplished by gene overexpression while haplotype analyses assessed B1 polymorphisms and genetic variation.Located on chromosome 5A, B1 is a C2H2 zinc finger encoding gene with ethylene‐responsive element binding factor‐associated amphiphilic repression (EAR) motifs. Constitutive overexpression of B1 in awned wheat produced an awnletted phenotype with pleiotropic effects on plant height and fertility. Transcriptome analysis of B1 overexpression plants suggests a role as transcriptional repressor, putatively targeting pathways involved in cell proliferation. Haplotype analysis revealed a conserved B1 coding region with proximal polymorphisms and supported the contention that B1 is mainly responsible for awnletted wheats globally. B1, predominantly responsible for awn inhibition in wheat, encodes a C2H2 zinc finger protein with EAR motifs which putatively functions as a transcriptional repressor.
- Published
- 2019
15. Chromatin structure regulates cancer-specific alternative splicing events in primary HPV-related oropharyngeal squamous cell carcinoma
- Author
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Eli Winkler, Elana J. Fertig, Michael Considine, Alexander V. Favorov, Hildegard A. Wulf, Kristina Diana A. Zambo, Christopher Hopkins, Fernando T. Zamuner, Rossin Erbe, Daria A. Gaykalova, David Sidransky, Liliana Florea, Theresa Guo, Ludmila Danilova, Dylan Z. Kelley, and Tingting Ou
- Subjects
0301 basic medicine ,Cancer Research ,animal structures ,In silico ,Biology ,Alphapapillomavirus ,medicine.disease_cause ,Epigenesis, Genetic ,Histones ,03 medical and health sciences ,0302 clinical medicine ,Cell Line, Tumor ,medicine ,Humans ,Epigenetics ,Molecular Biology ,Head and neck cancer ,Alternative splicing ,Cancer ,medicine.disease ,Chromatin Assembly and Disassembly ,Chromatin ,Gene Expression Regulation, Neoplastic ,Histone Code ,Alternative Splicing ,Oropharyngeal Neoplasms ,030104 developmental biology ,Histone ,Genetic Loci ,030220 oncology & carcinogenesis ,Cancer research ,biology.protein ,Carcinoma, Squamous Cell ,Carcinogenesis ,Research Paper - Abstract
Human papillomavirus-related oropharyngeal squamous cell carcinoma (HPV+ OPSCC) represents a unique disease entity within head and neck cancer with rising incidence. Previous work has shown that alternative splicing events (ASEs) are prevalent in HPV+ OPSCC, but further validation is needed to understand the regulation of this process and its role in these tumours. In this study, eleven ASEs (GIT2, CTNNB1, MKNK2, MRPL33, SIPA1L3, SNHG6, SYCP2, TPRG1, ZHX2, ZNF331, and ELOVL1) were selected for validation from 109 previously published candidate ASEs to elucidate the post-transcriptional mechanisms of oncogenesis in HPV+ disease. In vitro qRT-PCR confirmed differential expression of 9 of 11 ASE candidates, and in silico analysis within the TCGA cohort confirmed 8 of 11 candidates. Six ASEs (MRPL33, SIPA1L3, SNHG6, TPRG1, ZHX2, and ELOVL1) showed significant differential expression across both methods. Further evaluation of chromatin modification revealed that ASEs strongly correlated with cancer-specific distribution of acetylated lysine 27 of histone 3 (H3K27ac). Subsequent epigenetic treatment of HPV+ HNSCC cell lines (UM-SCC-047 and UPCI-SCC-090) with JQ1 not only induced downregulation of cancer-specific ASE isoforms, but also growth inhibition in both cell lines. The UPCI-SCC-090 cell line, with greater ASE expression, also showed more significant growth inhibition after JQ1 treatment. This study confirms several novel cancer-specific ASEs in HPV+OPSCC and provides evidence for the role of chromatin modifications in regulation of alternative splicing in HPV+OPSCC. This highlights the role of epigenetic changes in the oncogenesis of HPV+OPSCC, which represents a unique, unexplored target for therapeutics that can alter the global post-transcriptional landscape.
- Published
- 2020
16. Population and evolutionary genetics of the PAH locus to uncover overdominance and adaptive mechanisms in phenylketonuria: Results from a multiethnic study
- Author
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Oussalah, Abderrahim, Jeannesson-Thivisol, Elise, Chery, Céline, Perrin, Pascal, Rouyer, Pierre, Josse, Thomas, Cano, Aline, Barth, Magalie, Fouilhoux, Alain, Mention, Karine, Labarthe, François, Arnoux, Jean-Baptiste, Maillot, François, Lenaerts, Catherine, Dumesnil, Cécile, Wagner, Kathy, Terral, Daniel, Broue, Pierre, de Parscau, Loïc, Gay, Claire, Kuster, Alice, Bedu, Antoine, Besson, Gérard, Lamireau, Delphine, Odent, Sylvie, Masurel, Alice, Rodriguez-Guéant, Rosa-Maria, Feillet, François, Guéant, Jean-Louis, Namour, Fares, Nutrition-Génétique et Exposition aux Risques Environnementaux (NGERE), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lorraine (UL), Centre de référence des maladies héréditaires du métabolisme (MaMEA Nancy-Brabois), Hôpital de la Timone [CHU - APHM] (TIMONE), Service de génétique [Angers], Université d'Angers (UA)-Centre Hospitalier Universitaire d'Angers (CHU Angers), PRES Université Nantes Angers Le Mans (UNAM)-PRES Université Nantes Angers Le Mans (UNAM), Centre Hospitalier Lyon Sud [CHU - HCL] (CHLS), Hospices Civils de Lyon (HCL), Hôpital Jeanne de Flandres, Université de Lille, Droit et Santé-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Centre Hospitalier Régional Universitaire de Tours (CHRU Tours), CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), CHU Amiens-Picardie, CHU Rouen, Normandie Université (NU), Hôpitaux Pédiatriques de Nice Lenval (CHU-Lenval), Centre Hospitalier Universitaire de Nice (CHU Nice), Service de Pédiatrie Générale [CHU Clermont-Ferrand], CHU Estaing [Clermont-Ferrand], CHU Clermont-Ferrand-CHU Clermont-Ferrand, Hôpital des Enfants, CHU Toulouse [Toulouse], CHRU de Brest - Département de Pédiatrie (CHU BREST Pédiatrie), Centre Hospitalier Régional Universitaire de Brest (CHRU Brest), Centre Hospitalier Universitaire de Saint-Etienne (CHU de Saint-Etienne), Centre hospitalier universitaire de Nantes (CHU Nantes), Service de Pédiatrie médicale - réanimation et néonatologie [CHU Limoges], CHU Limoges, Centre Hospitalier Universitaire [Grenoble] (CHU), Hôpital Pellegrin, CHU Bordeaux [Bordeaux]-Groupe hospitalier Pellegrin, CHU Pontchaillou [Rennes], Service de génétique, CHU Dijon, Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon)-Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), IMPACT GEENAGE, ANR-15-IDEX-0004,LUE,Isite LUE(2015), Centre Hospitalier Régional Universitaire de Tours (CHRU TOURS), DE CARVALHO, Philippe, ISITE - Isite LUE - - LUE2015 - ANR-15-IDEX-0004 - IDEX - VALID, and Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)
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Male ,Research paper ,[SDV]Life Sciences [q-bio] ,lcsh:Medicine ,Metabolic adaptation ,Gene Frequency ,Phenylketonurias ,Overdominance ,[SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology ,Ethnicity ,Humans ,Phenylketonuria ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,Exome ,Genetic Association Studies ,Phylogeny ,Principal Component Analysis ,lcsh:R5-920 ,Geography ,lcsh:R ,Phenylalanine Hydroxylase ,Biological Evolution ,[SDV] Life Sciences [q-bio] ,Balancing selection ,Genetics, Population ,Haplotypes ,Genetic Loci ,Population divergence ,Female ,France ,lcsh:Medicine (General) - Abstract
Background: Phenylketonuria (PKU) is the most common inborn error of amino acid metabolism in Europe. The reasons underlying the high prevalence of heterozygous carriers are not clearly understood. We aimed to look for pathogenic PAH variant enrichment according to geographical areas and patients’ ethnicity using a multiethnic nationwide cohort of patients with PKU in France. We subsequently appraised the population differentiation, balancing selection and the molecular evolutionary history of the PAH locus. Methods: The French nationwide PKU study included patients who have been referred at the national level to the University Hospital of Nancy, and for whom a molecular diagnosis of phenylketonuria was made by Sanger sequencing. We performed enrichment analyses by comparing alternative allele frequencies using Fisher's exact test with Bonferroni adjustment. We estimated the amount of genetic differentiation among populations using Wright's fixation index (Fst). To estimate the molecular evolutionary history of the PAH gene, we performed phylogenetic and evolutionary analyses using whole-genome and exome-sequencing data from healthy individuals and non-PKU patients, respectively. Finally, we used exome-wide association study to decipher potential genetic loci associated with population divergence on PAH. Findings: The study included 696 patients and revealed 132 pathogenic PAH variants. Three geographical areas showed significant enrichment for a pathogenic PAH variant: North of France (p.Arg243Leu), North-West of France (p.Leu348Val), and Mediterranean coast (p.Ala403Val). One PAH variant (p.Glu280Gln) was significantly enriched among North-Africans (OR = 23·23; 95% CI: 9·75–55·38). PAH variants exhibiting a strong genetic differentiation were significantly enriched in the ‘Biopterin_H’ domain (OR = 6·45; 95% CI: 1·99–20·84), suggesting a balancing selection pressure on the biopterin function of PAH. Phylogenetic and timetree analyses were consistent with population differentiation events on European-, African-, and Asian-ancestry populations. The five PAH variants most strongly associated with a high selection pressure were phylogenetically close and were located within the biopterin domain coding region of PAH or in its vicinity. Among the non-PAH loci potentially associated with population divergence, two reached exome-wide significance: SSPO (SCO-spondin) and DBH (dopamine beta-hydroxylase), involved in neuroprotection and metabolic adaptation, respectively. Interpretation: Our data provide evidence on the combination of evolutionary and adaptive events in populations with distinct ancestries, which may explain the overdominance of some genetic variants on PAH. Funding: French National Institute of Health and Medical Research (INSERM) UMR_S 1256. Keywords: Phenylketonuria, Balancing selection, Population divergence, Overdominance, Metabolic adaptation
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- 2020
17. Seed dormancy release accelerated by elevated partial pressure of oxygen is associated with DOG loci
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Jan Kodde, Leónie Bentsink, Gonda Buijs, and Steven P.C. Groot
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0106 biological sciences ,0301 basic medicine ,EPPO ,Arabidopsis thaliana ,Physiology ,Partial Pressure ,Quantitative Trait Loci ,Arabidopsis ,Germination ,Plant Science ,Common method ,elevated partial pressure of oxygen ,Quantitative trait locus ,Biology ,01 natural sciences ,03 medical and health sciences ,DOG ,BIOS Plant Development Systems ,Laboratorium voor Plantenfysiologie ,Arabidopsis Proteins ,Seed dormancy ,seed dormancy ,food and beverages ,Chromosome Mapping ,Partial pressure ,Delay of Germination ,Plant Dormancy ,Research Papers ,Oxygen ,Horticulture ,030104 developmental biology ,Stratification (seeds) ,Ageing ,Genetic Loci ,quantitative trait loci ,Seeds ,Dormancy ,After-ripening ,Growth and Development ,EPS ,Laboratory of Plant Physiology ,010606 plant biology & botany - Abstract
Storage of seeds under elevated partial pressure of oxygen mimics dry after-ripening at the genetic level, as indicated by identification of DELAY OF GERMINATION quantitative trait loci., Seed dormancy determines the timing of seed germination and may be released by dry storage, also referred to as after-ripening. Studies on dormancy-release mechanisms are often hampered by the long after-ripening requirements of seeds. After-ripening is thought to be mainly caused by oxidative processes during seed dry storage. These processes are also the main cause of seed ageing. Increasing partial oxygen pressure through the elevated partial pressure of oxygen (EPPO) system has been shown to mimic and accelerate dry seed ageing. In this study, we investigated whether the EPPO system may also release primary seed dormancy in Arabidopsis thaliana. EPPO mimics dry after-ripening at the genetic level, as quantitative trait locus (QTL) analysis after EPPO treatment identified the DELAY OF GERMINATION loci DOG1, DOG2, and DOG6 that were first described in a study using dry after-ripening to release seed dormancy. QTL analysis also showed that dormancy release by cold stratification (another common method to break seed dormancy) partly overlaps with release by after-ripening and EPPO treatment. We conclude that EPPO is an appropriate method to mimic and accelerate dormancy release and, as such, may have applications in both research and industry.
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- 2018
18. PhenotypeSimulator: A comprehensive framework for simulating multi-trait, multi-locus genotype to phenotype relationships
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Ewan Birney, Rakesh Choorikkadu, and Meyer Hannah
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0301 basic medicine ,Statistics and Probability ,Genotype ,Computer science ,Locus (genetics) ,Machine learning ,computer.software_genre ,Biochemistry ,Genetic analysis ,03 medical and health sciences ,Multi trait ,Molecular Biology ,business.industry ,Genetics and Population Analysis ,Phenotype ,Original Papers ,Computer Science Applications ,Computational Mathematics ,030104 developmental biology ,Computational Theory and Mathematics ,Genetic Loci ,Artificial intelligence ,Genotype to phenotype ,business ,computer ,Software - Abstract
Motivation Simulation is a critical part of method development and assessment. With the increasing sophistication of multi-trait and multi-locus genetic analysis techniques, it is important that the community has flexible simulation tools to challenge and explore the properties of these methods. Results We have developed PhenotypeSimulator, a comprehensive phenotype simulation scheme that can model multiple traits with multiple underlying genetic loci as well as complex covariate and observational noise structure. This package has been designed to work with many common genetic tools both for input and output. We describe the underlying components of this simulation tool and illustrate its use on an example dataset. Availability and implementation PhenotypeSimulator is available as a well documented R/CRAN package and the code is available on github: https://github.com/HannahVMeyer/PhenotypeSimulator. Supplementary information Supplementary data are available at Bioinformatics online.
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- 2018
19. A Genome-Wide Association Study Finds Genetic Associations with Broadly-Defined Headache in UK Biobank (N = 223,773)
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Ian J. Deary, Weihua Meng, Harry L. Hébert, Mark Adams, Blair H. Smith, and Andrew M. McIntosh
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0301 basic medicine ,medicine.medical_specialty ,Genome-wide association study ,LRP1 ,lcsh:Medicine ,Single-nucleotide polymorphism ,Polymorphism, Single Nucleotide ,Linkage Disequilibrium ,General Biochemistry, Genetics and Molecular Biology ,Cohort Studies ,03 medical and health sciences ,0302 clinical medicine ,Single entity ,Statistical significance ,Internal medicine ,Tissue expression ,Humans ,Medicine ,Genetic Predisposition to Disease ,Biological Specimen Banks ,lcsh:R5-920 ,business.industry ,Gene Expression Profiling ,lcsh:R ,Case-control study ,Headache ,General Medicine ,UK biobank ,Biobank ,United Kingdom ,3. Good health ,030104 developmental biology ,Genetic Loci ,Case-Control Studies ,Cohort ,business ,lcsh:Medicine (General) ,030217 neurology & neurosurgery ,Research Paper ,Cohort study - Abstract
Background Headache is the most common neurological symptom and a leading cause of years lived with disability. We sought to identify the genetic variants associated with a broadly-defined headache phenotype in 223,773 subjects from the UK Biobank cohort. Methods We defined headache based on a specific question answered by the UK Biobank participants. We performed a genome-wide association study of headache as a single entity, using 74,461 cases and 149,312 controls. Results We identified 3343 SNPs which reached the genome-wide significance level of P, Highlights • This genome-wide association study identified 28 genomic loci for broadly-defined headache, among which, 14 are new. • Through tissue expression analysis, brain tissues showed significant relationships to broadly-defined headache. • Broadly-defined headache shared common genetic components with many psychological traits such as neuroticism. This genetic study using the UK Biobank resource has identified 28 genomic loci for broadly-defined headache, among which, 14 are new loci. In addition, it has provided extra evidence that the functions of brain tissues are closely related to headache. Moreover, it has suggested that headache and many psychological disorders share common genetic factors. These findings will not only contribute to the understanding of the causes of headache (and its subtypes) and its relationships with psychological disorders, it might also bring potential genetic targets for drug treatment for patients with headache and psychological disorders.
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- 2018
20. Natural antisense transcripts drive a regulatory cascade controlling c-MYC transcription
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Sara Napoli, Giuseppina Pisignano, Sarah N. Mapelli, Carlo V. Catapano, and Valentina Piccinelli
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0301 basic medicine ,Ribonuclease III ,endocrine system ,RNA, Untranslated ,Transcription, Genetic ,Genes, myc ,natural antisense transcripts ,Models, Biological ,Epigenesis, Genetic ,Histones ,03 medical and health sciences ,Transcription (biology) ,small RNAs ,Cell Line, Tumor ,Transcriptional regulation ,Humans ,transcriptional regulation ,RNA, Antisense ,Small nucleolar RNA ,Cloning, Molecular ,Molecular Biology ,Gene ,3' Untranslated Regions ,Regulation of gene expression ,Genetics ,biology ,epigenetics ,fungi ,Acetylation ,Cell Biology ,Long non-coding RNA ,030104 developmental biology ,c-MYC ,Sense strand ,Gene Expression Regulation ,Genetic Loci ,long non coding RNA ,biology.protein ,Nucleic Acid Conformation ,Transcription Initiation Site ,Dicer ,Research Paper - Abstract
Cis-natural antisense transcripts (cis-NATs) are long noncoding RNAs transcribed from the opposite strand and overlapping coding and noncoding genes on the sense strand. cis-NATs are widely present in the human genome and can be involved in multiple mechanisms of gene regulation. Here, we describe the presence of cis-NATs in the 3′ distal region of the c-MYC locus and investigate their impact on transcriptional regulation of this key oncogene in human cancers. We found that cis-NATs are produced as consequence of the activation of cryptic transcription initiation sites in the 3′ distal region downstream of the c-MYC 3′UTR. The process is tightly regulated and leads to the formation of two main transcripts, NAT6531 and NAT6558, which differ in their ability to fold into stem-loop secondary structures. NAT6531 acts as a substrate for DICER and as a source of small RNAs capable of modulating c-MYC transcription. This complex system, based on the interplay between cis-NATs and NAT-derived small RNAs, may represent an important layer of epigenetic regulation of the expression of c-MYC and other genes in human cells.
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- 2017
21. Fbxw7 haploinsufficiency loses its protection against DNA damage and accelerates MNU-induced gastric carcinogenesis
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Jin Ren, Zhenggang Zhu, Xinming Qi, Jun Ji, Yannan Jiang, Xinyu Liu, Yingyan Yu, and Jun Zhang
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0301 basic medicine ,F-Box-WD Repeat-Containing Protein 7 ,DNA Repair ,Genes, myc ,Apoptosis ,Haploinsufficiency ,Gene Knockout Techniques ,Mice ,0302 clinical medicine ,Gene Order ,Mice, Knockout ,biology ,Fbxw7 ,Methylnitrosourea ,Ubiquitin ligase ,Gene Expression Regulation, Neoplastic ,medicine.anatomical_structure ,Cell Transformation, Neoplastic ,Oncology ,030220 oncology & carcinogenesis ,Knockout mouse ,N-Methyl-N-nitrosourea ,Gene Targeting ,Research Paper ,Genotype ,DNA damage ,DNA repair ,Models, Biological ,03 medical and health sciences ,Stomach Neoplasms ,Cell Line, Tumor ,Gastric mucosa ,medicine ,Animals ,Genetic Predisposition to Disease ,business.industry ,gastric cancer ,Cancer ,medicine.disease ,Comet assay ,Disease Models, Animal ,030104 developmental biology ,Gastric Mucosa ,Genetic Loci ,biology.protein ,Cancer research ,business ,knockout mouse - Abstract
// Yannan Jiang 1 , Xinming Qi 2 , Xinyu Liu 1 , Jun Zhang 1 , Jun Ji 1 , Zhenggang Zhu 1 , Jin Ren 2 , Yingyan Yu 1 1 Department of Surgery of Shanghai Ruijin Hospital, Shanghai Institute of Digestive Surgery, Shanghai Key Laboratory for Gastric Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China 2 Center for Drug Safety Evaluation and Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China Correspondence to: Yingyan Yu, email: yingyan3y@sjtu.edu.cn Keywords: Fbxw7, knockout mouse, N-Methyl-N-nitrosourea, gastric cancer, DNA damage Received: January 17, 2017 Accepted: March 22, 2017 Published: April 03, 2017 ABSTRACT Fbxw7, a subunit of the SCF E3 ubiquitin ligase, recognizes oncoprotein substrates and leads to their proteasomal degradation. Fbxw7 acts as a tumor suppressor via inducing apoptosis and growth arrest in various kinds of tumors. To clarify the initiating role in gastric carcinogenesis as well as the histologic characterization of tumor in Fbxw7 allele haploinsufficient mice, we generated Fbxw7 heterozygous knockout mice (Fbxw7 +/− ) and treated them with chemical carcinogen N-methyl-N-nitrosourea (MNU) at 5–6 weeks of age. We also treated mouse embryo fibroblasts (MEFs) from Fbxw7 +/− and Fbxw7 +/+ mice with MNU and examined cell DNA damage via comet assay. The protein expression of Fbxw7 and its substrate c-Myc from mouse tumors, as well as human tumors sampled from six patients, were detected by Western blot. As results, the tumor incidence was obviously higher in Fbxw7 +/− mice (13/20) than in Fbxw7 +/+ mice (6/20) after 35-week observation. Intestinal metaplasia ( P = 0.013) and dysplasia ( P = 0.036) were more severe in Fbxw7 +/− mice than in Fbxw7 +/+ mice. The repair potential of DNA damage was suppressed in MEFs from Fbxw7 +/− mice after MNU exposure. Increased c-Myc expression was accompanied by decreased Fbxw7 protein expression in tumor tissues from mouse and patients. In conclusion, Fbxw7 haploinsufficiency increased the risk of gastric carcinogenesis induced by MNU, which is associated with the accumulation of DNA damage as well as c-Myc oncoprotein.
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- 2017
22. Myostatin-deficiency in mice increases global gene expression at the Dlk1-Dio3 locus in the skeletal muscle
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Keisuke Hitachi and Kunihiro Tsuchida
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0301 basic medicine ,medicine.medical_specialty ,Locus (genetics) ,Myostatin ,Muscle Development ,Iodide Peroxidase ,Cell Line ,Epigenesis, Genetic ,03 medical and health sciences ,Mice ,Internal medicine ,Gene expression ,medicine ,Animals ,Epigenetics ,skeletal muscle ,IG-DMR ncRNA ,Muscle, Skeletal ,miRNA ,Mice, Knockout ,biology ,Calcium-Binding Proteins ,Skeletal muscle ,musculoskeletal system ,callipyge ,Molecular biology ,Chromosomes, Mammalian ,Up-Regulation ,MicroRNAs ,030104 developmental biology ,Endocrinology ,DLK1 ,medicine.anatomical_structure ,Oncology ,Genetic Loci ,GDF11 ,Knockout mouse ,biology.protein ,Intercellular Signaling Peptides and Proteins ,Research Paper - Abstract
// Keisuke Hitachi 1 , Kunihiro Tsuchida 1 1 Division for Therapies Against Intractable Diseases, Institute for Comprehensive Medical Science (ICMS), Fujita Health University, Toyoake, Aichi 470-1192, Japan Correspondence to: Kunihiro Tsuchida, email: tsuchida@fujita-hu.ac.jp Keywords: myostatin, miRNA, callipyge, IG-DMR ncRNA, skeletal muscle Received: July 20, 2016 Accepted: December 08, 2016 Published: December 15, 2016 ABSTRACT Myostatin, a member of the transforming growth factor-beta superfamily, is a negative regulator of skeletal muscle growth and development. Myostatin inhibition leads to increased skeletal muscle mass in mammals; hence, myostatin is considered a potential therapeutic target for skeletal muscle wasting. However, downstream molecules of myostatin in the skeletal muscle have not been fully elucidated. Here, we identified the Dlk1-Dio3 locus at the mouse chromosome 12qF1, also called as the callipyge locus in sheep, as a novel downstream target of myostatin. In skeletal muscle of myostatin knockout mice, the expression of mature miRNAs at the Dlk1-Dio3 locus was significantly increased. The increased miRNA levels are caused by the transcriptional activation of the Dlk1-Dio3 locus, because a significant increase in the primary miRNA transcript was observed in myostatin knockout mice. In addition, we found increased expression of coding and non-coding genes ( Dlk1 , Gtl2 , Rtl1/Rtl1as , and Rian ) at the Dlk1-Dio3 locus in myostatin-deficient skeletal muscle. Moreover, epigenetic changes, associated with the regulation of the Dlk1-Dio3 locus, were observed in myostatin knockout mice. Taken together, this is the first report demonstrating the role of myostatin in regulating the Dlk1-Dio3 (the callipyge ) locus in the skeletal muscle.
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- 2016
23. The VEGF-A exon 8 splicing-sensitive fluorescent reporter mouse is a novel tool to assess the effects of splicing regulatory compounds in vivo
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Eleanor Star, Matthew Lee, Elizabeth Bowler, Megan Stevens, E. Innes, Ling Li, Sebastian Oltean, David O. Bates, and Steven J. Harper
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Genetically modified mouse ,Vascular Endothelial Growth Factor A ,mouse model ,Green Fluorescent Proteins ,SRPK1 ,Biology ,Protein Serine-Threonine Kinases ,Eye ,Kidney ,Green fluorescent protein ,Animals, Genetically Modified ,03 medical and health sciences ,Exon ,chemistry.chemical_compound ,Mice ,angiogenesis ,0302 clinical medicine ,Genes, Reporter ,Animals ,Protein Isoforms ,vascular endothelial growth factor-A ,Muscle, Skeletal ,Molecular Biology ,Pancreas ,Protein Kinase Inhibitors ,030304 developmental biology ,0303 health sciences ,Messenger RNA ,Myocardium ,Alternative splicing ,Cell Biology ,Exons ,Introns ,3. Good health ,Cell biology ,Vascular endothelial growth factor ,Alternative Splicing ,Luminescent Proteins ,chemistry ,splicing-sensitive fluorescent reporter ,Genetic Loci ,030220 oncology & carcinogenesis ,RNA splicing ,Research Paper - Abstract
Vascular endothelial growth factor (VEGF)-A is differentially spliced to give two functionally different isoform families; pro-angiogenic, pro-permeability VEGF-Axxx and anti-angiogenic, anti-permeability VEGF-Axxxb. VEGF-A splicing is dysregulated in several pathologies, including cancer, diabetes, and peripheral arterial disease. The bichromatic VEGF-A splicing-sensitive fluorescent reporter harboured in a transgenic mouse is a novel approach to investigate the splicing patterns of VEGF-A in vivo. We generated a transgenic mouse harbouring a splicing-sensitive fluorescent reporter designed to mimic VEGF-A terminal exon splicing (VEGF8ab) by insertion into the ROSA26 genomic locus. dsRED expression denotes proximal splice site selection (VEGF-Axxx) and eGFP expression denotes distal splice site selection (VEGF-Axxxb). We investigated the tissue-specific expression patterns in the eye, skeletal muscle, cardiac muscle, kidney, and pancreas, and determined whether the splicing pattern could be manipulated in the same manner as endogenous VEGF-A by treatment with the SRPK1 inhibitor SPHINX 31. We confirmed expression of both dsRED and eGFP in the eye, skeletal muscle, cardiac muscle, kidney, and pancreas, with the highest expression of both fluorescent proteins observed in the exocrine pancreas. The ratio of dsRED and eGFP matched that of endogenous VEGF-Axxx and VEGF-Axxxb. Treatment of the VEGF8ab mice with SPHINX 31 increased the mRNA and protein eGFP/dsRED ratio in the exocrine pancreas, mimicking endogenous VEGF-A splicing. The VEGF-A exon 8 splicing-sensitive fluorescent reporter mouse is a novel tool to assess splicing regulation in the individual cell-types and tissues, which provides a useful screening process for potentially therapeutic splicing regulatory compounds in vivo.
- Published
- 2019
24. Associations between placental CpG methylation of metastable epialleles and childhood body mass index across ages one, two and ten in the Extremely Low Gestational Age Newborns (ELGAN) cohort
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Jeliyah Clark, Catherine M. Bulka, Lisa Smeester, Elizabeth M. Martin, Hudson P. Santos, T. Michael O'Shea, and Rebecca C. Fry
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0301 basic medicine ,Adult ,Male ,Cancer Research ,Placenta ,Biology ,Childhood obesity ,Body Mass Index ,Epigenesis, Genetic ,Andrology ,03 medical and health sciences ,0302 clinical medicine ,Pregnancy ,medicine ,Humans ,Infant, Very Low Birth Weight ,Epigenetics ,Molecular Biology ,Alleles ,Infant, Newborn ,Gestational age ,Methylation ,DNA Methylation ,medicine.disease ,030104 developmental biology ,In utero ,Genetic Loci ,030220 oncology & carcinogenesis ,DNA methylation ,CpG Islands ,Female ,Genomic imprinting ,Body mass index ,Research Paper - Abstract
The Developmental Origins of Health and Disease (DOHaD) hypothesis posits that in utero and early life conditions can disrupt normal fetal development and program susceptibility to later-life disease. Metastable epialleles are genomic loci in which CpG methylation patterning is responsive to maternal diet and conserved across time and tissues. Thus, these sites could serve as 'signatures' of gestational environment conditions. Here, we sought to determine if methylation of metastable epialleles was associated with changes in childhood body mass index (BMI) z-scores across ages one, two and ten in the Extremely Low Gestational Age Newborns (ELGAN) cohort. CpG methylation of 250 probes (corresponding to 111 genes) within metastable epiallele regions was measured in placental tissue. Linear mixed effects models were fit to evaluate the overall and sex-stratified associations between methylation and changes in BMI z-score over time. In total, 26 probes were associated (p < 0.05) with changes in BMI z-score overall, including probes within Mesoderm Specific Transcript (MEST) and Histone Deacetylase 4 (HDAC4), which have previously been associated with childhood obesity and adipogenesis. Sex-stratified analyses revealed a significant association, after adjusting for multiple comparisons (q < 0.05), within female placentas for one probe annotated to the imprinted gene PLAG1 Like Zinc Finger 1 (PLAGL1). These findings suggest epigenetic marks may be involved in programming susceptibility to obesity in utero and highlight the potential to use placental tissues in predicting growth rate trajectories among premature infants.
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- 2019
25. Powerful testing via hierarchical linkage disequilibrium in haplotype association studies
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Jeanine J. Houwing-Duistermaat, Stefan Böhringer, Brunilda Balliu, Balliu B., Houwing-Duistermaat J.J., and Bohringer S.
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Statistics and Probability ,Linkage disequilibrium ,Biometry ,Computer science ,Degrees of freedom (statistics) ,Genome-wide association study ,computer.software_genre ,Polymorphism, Single Nucleotide ,haplotype association study ,Arthritis, Rheumatoid ,03 medical and health sciences ,Humans ,030304 developmental biology ,Genetic association ,genome‐wide association study ,General Biometry ,0303 health sciences ,genome-wide association study ,Liver Cirrhosis, Biliary ,030305 genetics & heredity ,Haplotype ,Statistics ,General Medicine ,cis interaction ,Other Topics ,Nominal level ,Haplotypes ,cis interactions ,Genetic Loci ,Multinomial distribution ,Probability and Uncertainty ,Data mining ,Statistics, Probability and Uncertainty ,computer ,linkage disequilibrium ,Type I and type II errors ,Research Paper - Abstract
Marginal tests based on individual SNPs are routinely used in genetic association studies. Studies have shown that haplotype‐based methods may provide more power in disease mapping than methods based on single markers when, for example, multiple disease‐susceptibility variants occur within the same gene. A limitation of haplotype‐based methods is that the number of parameters increases exponentially with the number of SNPs, inducing a commensurate increase in the degrees of freedom and weakening the power to detect associations. To address this limitation, we introduce a hierarchical linkage disequilibrium model for disease mapping, based on a reparametrization of the multinomial haplotype distribution, where every parameter corresponds to the cumulant of each possible subset of a set of loci. This hierarchy present in the parameters enables us to employ flexible testing strategies over a range of parameter sets: from standard single SNP analyses through the full haplotype distribution tests, reducing degrees of freedom and increasing the power to detect associations. We show via extensive simulations that our approach maintains the type I error at nominal level and has increased power under many realistic scenarios, as compared to single SNP and standard haplotype‐based studies. To evaluate the performance of our proposed methodology in real data, we analyze genome‐wide data from the Wellcome Trust Case‐Control Consortium.
- Published
- 2019
26. Novel DNA methylation sites associated with cigarette smoking among African Americans
- Author
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Sharon L.R. Kardia, Yunfeng Huang, Jiaxuan Liu, Jennifer A. Smith, Yan V. Sun, Veronica Barcelona, Miao Yu, Kristen M. Brown, Jacquelyn Y. Taylor, and Wei Zhao
- Subjects
0301 basic medicine ,Adult ,Male ,Cancer Research ,Lung Neoplasms ,Heart disease ,Biology ,Health outcomes ,Affect (psychology) ,Cigarette Smoking ,Epigenesis, Genetic ,03 medical and health sciences ,0302 clinical medicine ,Cigarette smoking ,Environmental health ,medicine ,Humans ,Genetic Predisposition to Disease ,Child ,Molecular Biology ,Epigenomics ,DNA Methylation ,medicine.disease ,Obesity ,Black or African American ,030104 developmental biology ,Cardiovascular Diseases ,Genetic Loci ,030220 oncology & carcinogenesis ,Child, Preschool ,DNA methylation ,Female ,Research Paper - Abstract
Introduction: Cigarette smoking has been associated with adverse health outcomes for mothers and children and is a major contributor to heart disease. Although cigarette smoking is known to affect the epigenome, few studies have been done in African American populations. In this study, we investigated the association between cigarette smoking and DNA methylation (DNAm) among African Americans from the Intergenerational Impact of Genetic and Psychological Factors on Blood Pressure Study (InterGEN), and the Genetic Epidemiology Network of Arteriopathy (GENOA). Methods: The InterGEN study aims to examine the effects of genetic and psychological factors on blood pressure among African American women and their children. Current cigarette smoking was assessed at baseline. DNAm of saliva was assessed using the 850K EPIC Illumina BeadChip for Epigenome-Wide Association analyses. A replication study was conducted among 1100 participants in the GENOA study using the same BeadChip. Results: After controlling for age, body mass index, population structure and cell composition, 26 epigenome-wide significant sites (FDR q
- Published
- 2019
27. NOXA1-dependent NADPH oxidase regulates redox signaling and phenotype of vascular smooth muscle cell during atherogenesis
- Author
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Andrey Lozhkin, Nageswara R. Madamanchi, Chandrika Canugovi, Arihiro Sumida, Takayuki Hayami, Aleksandr E. Vendrov, and Marschall S. Runge
- Subjects
NOXA1 ,0301 basic medicine ,Vascular smooth muscle ,Clinical Biochemistry ,MMP2, matrix metalloproteinase 2 ,medicine.disease_cause ,Biochemistry ,Muscle, Smooth, Vascular ,Pathogenesis ,Mice ,0302 clinical medicine ,lcsh:QH301-705.5 ,Mice, Knockout ,chemistry.chemical_classification ,Neointimal hyperplasia ,lcsh:R5-920 ,NADPH oxidase ,biology ,CCL2, CC chemokine ligand 2 ,NOX, NADPH oxidase ,KLF4 ,Cell biology ,VSMC, vascular smooth muscle cells ,Phenotype ,VCAM1, vascular cell adhesion molecule 1 ,Smooth muscle cells ,Organ Specificity ,POVPC, 1-palmitoyl-2-(5-oxovaleroyl)-sn-glycero-3-phosphatidylcholine ,cardiovascular system ,medicine.symptom ,lcsh:Medicine (General) ,Oxidation-Reduction ,Research Paper ,NOXA1, Nox activator 1 ,Signal Transduction ,Myocytes, Smooth Muscle ,Mice, Transgenic ,Inflammation ,Lesion ,Kruppel-Like Factor 4 ,03 medical and health sciences ,ROS, reactive oxygen species ,Apolipoproteins E ,KLF4, Krüppel-like factor 4 ,medicine ,Animals ,Adaptor Proteins, Signal Transducing ,Reactive oxygen species ,Tumor Necrosis Factor-alpha ,Organic Chemistry ,NADPH Oxidases ,Proteins ,Macrophage-like cells ,Atherosclerosis ,medicine.disease ,Enzyme Activation ,030104 developmental biology ,Receptors, LDL ,chemistry ,lcsh:Biology (General) ,Oxidative stress ,Genetic Loci ,biology.protein ,APOE, apolipoprotein E ,Reactive Oxygen Species ,Biomarkers ,Gene Deletion ,030217 neurology & neurosurgery - Abstract
Increased reactive oxygen species (ROS) production and inflammation are key factors in the pathogenesis of atherosclerosis. We previously reported that NOX activator 1 (NOXA1) is the critical functional homolog of p67phox for NADPH oxidase activation in mouse vascular smooth muscle cells (VSMC). Here we investigated the effects of systemic and SMC-specific deletion of Noxa1 on VSMC phenotype during atherogenesis in mice. Neointimal hyperplasia following endovascular injury was lower in Noxa1-deficient mice versus the wild-type following endovascular injury. Noxa1 deletion in Apoe-/- or Ldlr-/- mice fed a Western diet showed 50% reduction in vascular ROS and 30% reduction in aortic atherosclerotic lesion area and aortic sinus lesion volume (P, Graphical abstract fx1, Highlights • NOXA1 is a VSMC-specific regulator of NADPH oxidase 1 activity and downstream cell signaling. • NOX1 NADPH oxidase-dependent ROS generation is required for VSMC proliferation and migration after endovascular injury. • NOXA1-dependent NOX1 activation of KLF4 in atherosclerotic lesions induces SMC phenotypic switch to macrophage-like cells. • Atherosclerotic lesion macrophage-like cells promote plaque inflammation, matrix remodeling and increase volume expansion.
- Published
- 2019
28. Integration of genetic and physical maps of the Primula vulgaris S locus and localization by chromosome in situ hybridization
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Matthew C. Smith, Jinhong Li, Pat Heslop-Harrison, Philip M. Gilmartin, Farah Badakshi, Margaret A. Webster, Jonathan M. Wright, and Jonathan M. Cocker
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0106 biological sciences ,Genetic Markers ,Chromosomes, Artificial, Bacterial ,Primula vulgaris ,DNA, Plant ,Physiology ,Genetic Linkage ,Plant Development ,Locus (genetics) ,Plant Science ,Flowers ,Biology ,Genes, Plant ,01 natural sciences ,DNA sequencing ,Chromosomes, Plant ,S locus ,Evolution, Molecular ,03 medical and health sciences ,Contig Mapping ,Gene mapping ,chromosome in situ ,Centromere ,genetic map ,Gene ,In Situ Hybridization ,030304 developmental biology ,Genetics ,0303 health sciences ,Contig ,Gene map ,Full Paper ,Base Sequence ,Research ,Chromosome ,food and beverages ,Chromosome Mapping ,Full Papers ,Phenotype ,Primula ,Genetic Loci ,Mutation ,heterostyly ,Genome, Plant ,010606 plant biology & botany - Abstract
Summary Heteromorphic flower development in Primula is controlled by the S locus. The S locus genes, which control anther position, pistil length and pollen size in pin and thrum flowers, have not yet been characterized. We have integrated S‐linked genes, marker sequences and mutant phenotypes to create a map of the P. vulgaris S locus region that will facilitate the identification of key S locus genes. We have generated, sequenced and annotated BAC sequences spanning the S locus, and identified its chromosomal location.We have employed a combination of classical genetics and three‐point crosses with molecular genetic analysis of recombinants to generate the map. We have characterized this region by Illumina sequencing and bioinformatic analysis, together with chromosome in situ hybridization.We present an integrated genetic and physical map across the P. vulgaris S locus flanked by phenotypic and DNA sequence markers. BAC contigs encompass a 1.5‐Mb genomic region with 1 Mb of sequence containing 82 S‐linked genes anchored to overlapping BACs. The S locus is located close to the centromere of the largest metacentric chromosome pair.These data will facilitate the identification of the genes that orchestrate heterostyly in Primula and enable evolutionary analyses of the S locus.
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- 2015
29. CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci
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Fabrizio Costa, Roger A. Garrett, Omer S. Alkhnbashi, Shiraz A. Shah, Sita J. Saunders, and Rolf Backofen
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Statistics and Probability ,Sequence analysis ,Computational biology ,Biology ,Biochemistry ,Conserved sequence ,CRISPR ,Clustered Regularly Interspaced Short Palindromic Repeats ,Repeated sequence ,Molecular Biology ,Conserved Sequence ,Genetics ,Trans-activating crRNA ,Base Sequence ,Molecular Sequence Annotation ,Sequence Analysis, DNA ,Original Papers ,Structural Bioinformatics ,Archaea ,Computer Science Applications ,Computational Mathematics ,Computational Theory and Mathematics ,Genetic Loci ,Mutation (genetic algorithm) ,CRISPR Loci ,RNA ,CRISPR-Cas Systems ,Eccb 2014 Proceedings Papers Committee ,Software - Abstract
Motivation: The discovery of CRISPR-Cas systems almost 20 years ago rapidly changed our perception of the bacterial and archaeal immune systems. CRISPR loci consist of several repetitive DNA sequences called repeats, inter-spaced by stretches of variable length sequences called spacers. This CRISPR array is transcribed and processed into multiple mature RNA species (crRNAs). A single crRNA is integrated into an interference complex, together with CRISPR-associated (Cas) proteins, to bind and degrade invading nucleic acids. Although existing bioinformatics tools can recognize CRISPR loci by their characteristic repeat-spacer architecture, they generally output CRISPR arrays of ambiguous orientation and thus do not determine the strand from which crRNAs are processed. Knowledge of the correct orientation is crucial for many tasks, including the classification of CRISPR conservation, the detection of leader regions, the identification of target sites (protospacers) on invading genetic elements and the characterization of protospacer-adjacent motifs. Results: We present a fast and accurate tool to determine the crRNA-encoding strand at CRISPR loci by predicting the correct orientation of repeats based on an advanced machine learning approach. Both the repeat sequence and mutation information were encoded and processed by an efficient graph kernel to learn higher-order correlations. The model was trained and tested on curated data comprising >4500 CRISPRs and yielded a remarkable performance of 0.95 AUC ROC (area under the curve of the receiver operator characteristic). In addition, we show that accurate orientation information greatly improved detection of conserved repeat sequence families and structure motifs. We integrated CRISPRstrand predictions into our CRISPRmap web server of CRISPR conservation and updated the latter to version 2.0. Availability: CRISPRmap and CRISPRstrand are available at http://rna.informatik.uni-freiburg.de/CRISPRmap. Contact: backofen@informatik.uni-freiburg.de Supplementary information: Supplementary data are available at Bioinformatics online.
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- 2014
30. Insights into islet development and biology through characterization of a human iPSC-derived endocrine pancreas model
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van de Bunt, M, Lako, M, Barrett, A, Gloyn, A, Hansson, M, McCarthy, M, Beer, N, and Honoré, C
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Adult ,Pluripotent Stem Cells ,diabetes ,Gene Expression ,differentiation ,Models, Biological ,Islets of Langerhans ,Genetic Loci ,Humans ,Receptors, Leptin ,RNA, Messenger ,Pancreas ,transcriptional profiling ,Embryonic Stem Cells ,Research Paper ,endocrine pancreas - Abstract
Directed differentiation of stem cells offers a scalable solution to the need for human cell models recapitulating islet biology and T2D pathogenesis. We profiled mRNA expression at 6 stages of an induced pluripotent stem cell (iPSC) model of endocrine pancreas development from 2 donors, and characterized the distinct transcriptomic profiles associated with each stage. Established regulators of endodermal lineage commitment, such as SOX17 (log2 fold change [FC] compared to iPSCs = 14.2, p-value = 4.9 × 10−5) and the pancreatic agenesis gene GATA6 (log2 FC = 12.1, p-value = 8.6 × 10−5), showed transcriptional variation consistent with their known developmental roles. However, these analyses highlighted many other genes with stage-specific expression patterns, some of which may be novel drivers or markers of islet development. For example, the leptin receptor gene, LEPR, was most highly expressed in published data from in vivo-matured cells compared to our endocrine pancreas-like cells (log2 FC = 5.5, p-value = 2.0 × 10−12), suggesting a role for the leptin pathway in the maturation process. Endocrine pancreas-like cells showed significant stage-selective expression of adult islet genes, including INS, ABCC8, and GLP1R, and enrichment of relevant GO-terms (e.g. “insulin secretion”; odds ratio = 4.2, p-value = 1.9 × 10−3): however, principal component analysis indicated that in vitro-differentiated cells were more immature than adult islets. Integration of the stage-specific expression information with genetic data from T2D genome-wide association studies revealed that 46 of 82 T2D-associated loci harbor genes present in at least one developmental stage, facilitating refinement of potential effector transcripts. Together, these data show that expression profiling in an iPSC islet development model can further understanding of islet biology and T2D pathogenesis.
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- 2016
31. chewBBACA: A complete suite for gene-by-gene schema creation and strain identification
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Miguel P. Machado, Mário Ramirez, Jacob Moran-Gilad, Mickael Silva, Sérgio A. A. Santos, Mirko Rossi, Diogo N. Silva, João A. Carriço, Mirko Rossi Research Group, Food Hygiene and Environmental Health, Departments of Faculty of Veterinary Medicine, and Faculty of Veterinary Medicine
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0301 basic medicine ,business.product_category ,Microbial Evolution and Epidemiology: Population Genomics ,Computer science ,030106 microbiology ,Methods Paper ,multilocus sequence typing ,Genome ,Polymorphism, Single Nucleotide ,World Wide Web ,03 medical and health sciences ,Software ,schema ,Schema (psychology) ,Allele ,Gene ,1183 Plant biology, microbiology, virology ,Alleles ,computer.programming_language ,030304 developmental biology ,0303 health sciences ,business.industry ,030306 microbiology ,Suite ,Strain (biology) ,allele calling ,General Medicine ,Python (programming language) ,gene-by-gene ,3142 Public health care science, environmental and occupational health ,Identification (information) ,030104 developmental biology ,ComputingMethodologies_PATTERNRECOGNITION ,chewBBACA ,Genetic Loci ,Laptop ,Scalability ,Software engineering ,business ,computer ,Algorithms ,Genome, Bacterial - Abstract
Gene-by-gene approaches are becoming increasingly popular in bacterial genomic epidemiology and outbreak detection. However, there is a lack of open-source scalable software for schema definition and allele calling for these methodologies. The chewBBACA suite was designed to assist users in the creation and evaluation of novel whole-genome or core-genome gene-by-gene typing schemas and subsequent allele calling in bacterial strains of interest. The software can run in a laptop or in high performance clusters making it useful for both small laboratories and large reference centers. ChewBBACA is available athttps://github.com/B-UMMI/chewBBACAor as a docker image athttps://hub.docker.com/r/ummidock/chewbbaca/.DATA SUMMARYAssembled genomes used for the tutorial were downloaded from NCBI in August 2016 by selecting those submitted asStreptococcus agalactiaetaxon or sub-taxa. All the assemblies have been deposited as a zip file in FigShare (https://figshare.com/s/9cbe1d422805db54cd52), where a file with the original ftp link for each NCBI directory is also available.Code for the chewBBACA suite is available athttps://github.com/B-UMMI/chewBBACAwhile the tutorial example is found athttps://github.com/B-UMMI/chewBBACA_tutorial.I/We confirm all supporting data, code and protocols have been provided within the article or through supplementary data files. ⊠IMPACT STATEMENTThe chewBBACA software offers a computational solution for the creation, evaluation and use of whole genome (wg) and core genome (cg) multilocus sequence typing (MLST) schemas. It allows researchers to develop wg/cgMLST schemes for any bacterial species from a set of genomes of interest. The alleles identified by chewBBACA correspond to potential coding sequences, possibly offering insights into the correspondence between the genetic variability identified and phenotypic variability. The software performs allele calling in a matter of seconds to minutes per strain in a laptop but is easily scalable for the analysis of large datasets of hundreds of thousands of strains using multiprocessing options. The chewBBACA software thus provides an efficient and freely available open source solution for gene-by-gene methods. Moreover, the ability to perform these tasks locally is desirable when the submission of raw data to a central repository or web services is hindered by data protection policies or ethical or legal concerns.
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- 2018
32. Diffuse gliomas classified by 1p/19q co-deletion, TERT promoter and IDH mutation status are associated with specific genetic risk loci
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Labreche, Karim, Kinnersley, Ben, Berzero, Giulia, Di Stefano, Anna Luisa, Rahimian, Amithys, Detrait, Ines, Marie, Yannick, Grenier-Boley, Benjamin, Hoang-Xuan, Khe, Delattre, Jean-Yves, Idbaih, Ahmed, Houlston, Richard S., Sanson, Marc, Institut du Cerveau et de la Moëlle Epinière = Brain and Spine Institute (ICM), Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), University of Pavia, Sorbonne Université (SU), Facteurs de Risque et Déterminants Moléculaires des Maladies liées au Vieillissement - U 1167 (RID-AGE), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Sorbonne Université - Département de neurologie 2 - Mazarin, Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Institut du Cerveau = Paris Brain Institute (ICM), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Università degli Studi di Pavia = University of Pavia (UNIPV), CHU Pitié-Salpêtrière [AP-HP], and Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)
- Subjects
Original Paper ,Brain Neoplasms ,[SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology ,[SDV.CAN]Life Sciences [q-bio]/Cancer ,Glioma ,Polymorphism, Single Nucleotide ,Isocitrate Dehydrogenase ,White People ,Proto-Oncogene Proteins c-myc ,Chromosomes, Human, Pair 1 ,Genetic Loci ,Case-Control Studies ,Mutation ,Humans ,Stathmin ,Genetic Predisposition to Disease ,RNA, Messenger ,Promoter Regions, Genetic ,Chromosomes, Human, Pair 19 ,Telomerase ,Genetic Association Studies ,Preliminary Data - Abstract
Recent genome-wide association studies of glioma have led to the discovery of single nucleotide polymorphisms (SNPs) at 25 loci influencing risk. Gliomas are heterogeneous, hence to investigate the relationship between risk SNPs and glioma subtype we analysed 1659 tumours profiled for IDH mutation, TERT promoter mutation and 1p/19q co-deletion. These data allowed definition of five molecular subgroups of glioma: triple-positive (IDH mutated, 1p/19q co-deletion, TERT promoter mutated); TERT-IDH (IDH mutated, TERT promoter mutated, 1p/19q-wild-type); IDH-only (IDH mutated, 1p/19q wild-type, TERT promoter wild-type); triple-negative (IDH wild-type, 1p/19q wild-type, TERT promoter wild-type) and TERT-only (TERT promoter mutated, IDH wild-type, 1p/19q wild-type). Most glioma risk loci showed subtype specificity: (1) the 8q24.21 SNP for triple-positive glioma; (2) 5p15.33, 9p21.3, 17p13.1 and 20q13.33 SNPs for TERT-only glioma; (3) 1q44, 2q33.3, 3p14.1, 11q21, 11q23.3, 14q12, and 15q24.2 SNPs for IDH mutated glioma. To link risk SNPs to target candidate genes we analysed Hi-C and gene expression data, highlighting the potential role of IDH1 at 2q33.3, MYC at 8q24.21 and STMN3 at 20q13.33. Our observations provide further insight into the nature of susceptibility to glioma. Electronic supplementary material The online version of this article (10.1007/s00401-018-1825-z) contains supplementary material, which is available to authorized users.
- Published
- 2018
33. Genomic amplification of 9p24.1 targeting JAK2, PD-L1, and PD-L2 is enriched in high-risk triple negative breast cancer
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Elizabeth Lenkiewicz, Christine L. Klassen, Ann E. McCullough, Karen S. Anderson, Srikanth K. Reddy, Amylou C. Dueck, Barbara A. Pockaj, Ramesh K. Ramanathan, Donald W. Northfelt, Michael T. Barrett, Mariacarla Andreozzi, and Heather E. Cunliffe
- Subjects
Oncology ,Male ,Time Factors ,Gene Dosage ,Triple Negative Breast Neoplasms ,Kaplan-Meier Estimate ,Bioinformatics ,B7-H1 Antigen ,Continuous variable ,0302 clinical medicine ,Surgical oncology ,Triple-negative breast cancer ,Oligonucleotide Array Sequence Analysis ,0303 health sciences ,Comparative Genomic Hybridization ,Amplicon ,Middle Aged ,Flow Cytometry ,flow sorting ,3. Good health ,Up-Regulation ,Flow sorting ,Gene Expression Regulation, Neoplastic ,Phenotype ,Treatment Outcome ,Array-Based Comparative Genomic Hybridization ,JAK2 ,030220 oncology & carcinogenesis ,Female ,Chromosomes, Human, Pair 9 ,Colorectal Neoplasms ,Research Paper ,Carcinoma, Pancreatic Ductal ,PD-L1 ,Adult ,medicine.medical_specialty ,Poor prognosis ,Biology ,Disease-Free Survival ,Gene Expression Regulation, Enzymologic ,03 medical and health sciences ,Internal medicine ,medicine ,Biomarkers, Tumor ,Humans ,Genetic Predisposition to Disease ,030304 developmental biology ,Aged ,Gene Expression Profiling ,Janus Kinase 2 ,Programmed Cell Death 1 Ligand 2 Protein ,Pancreatic Neoplasms ,9p24.1 amplicon ,Genetic Loci ,triple negative breast cancer ,Glioblastoma - Abstract
// Michael T. Barrett 1 , Karen S. Anderson 2 , Elizabeth Lenkiewicz 1 , Mariacarla Andreozzi 1 , Heather E. Cunliffe 3 , Christine L. Klassen 4 , Amylou C. Dueck 5 , Ann E. McCullough 6 , Srikanth K. Reddy 7 , Ramesh K. Ramanathan 8 , Donald W. Northfelt 8 , Barbara A. Pockaj 4 1 Department of Research, Mayo Clinic in Arizona, Scottsdale, Arizona, United States of America 2 Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America 3 Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand 4 Division of General Surgery, Section of Surgical Oncology, Mayo Clinic in Arizona, Phoenix, Arizona, United States of America 5 Section of Biostatistics, Mayo Clinic in Arizona, Scottsdale, Arizona, United States of America 6 Department of Pathology and Laboratory Medicine, Mayo Clinic in Arizona, Scottsdale, Arizona, United States of America 7 Vanderbilt University, Nashville, Tennessee, United States of America 8 Division of Hematology-Oncology, Mayo Clinic in Arizona, Scottsdale, Arizona, United States of America Correspondence to: Michael T. Barrett, e-mail: Barrett.michael@mayo.edu Keywords: 9p24.1 amplicon, flow sorting, triple negative breast cancer, JAK2, PD-L1 Received: May 05, 2015 Accepted: June 22, 2015 Published: July 03, 2015 ABSTRACT We used DNA content flow cytometry followed by oligonucleotide array based comparative genomic hybridization to survey the genomes of 326 tumors, including 41 untreated surgically resected triple negative breast cancers (TNBC). A high level (log 2 ratio ≥1) 9p24 amplicon was found in TNBC (12/41), glioblastomas (2/44), and colon carcinomas (2/68). The shortest region of overlap for the amplicon targets 9p24.1 and includes the loci for PD-L1 , PD-L2 , and JAK2 (PDJ amplicon). In contrast this amplicon was absent in ER+ (0/8) and HER2+ (0/15) breast tumors, and in pancreatic ductal adenocarcinomas (0/150). The PDJ amplicon in TNBCs was correlated with clinical outcomes in group comparisons by two-sample t -tests for continuous variables and chi-squared tests for categorical variables. TNBC patients with the PDJ amplicon had a worse outcome with worse disease-free and overall survival. Quantitative RT-PCR confirmed that the PDJ amplicon in TNBC is associated with elevated expression of JAK2 and of the PD-1 ligands. These initial findings demonstrate that the PDJ amplicon is enriched in TNBC, targets signaling pathways that activate the PD-1 mediated immune checkpoint, and identifies patients with a poor prognosis.
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- 2015
34. IgNAR characterization and gene loci identification in whitespotted bamboo shark (Chiloscyllium plagiosum) genome.
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Jia L, Wang Y, Shen Y, Zhong B, Luo Z, Yang J, Chen G, Jiang X, Chen J, and Lyu Z
- Subjects
- Animals, Sharks genetics, Genetic Loci
- Abstract
Single domain antibodies (sdAb) are promising candidates in cancer and anti-virus biotherapies for their unique structure characters. Though VHH and IgNAR have been discovered in camelidae and nurse shark (Ginlymostoma cirratum) respectively serval decades ago, expense of these large animals still limits the studies and applications of sdAb. Recently, IgNAR has been found in whitespotted bamboo shark (Chiloscyllium plagiosum), a small-sized sharks, while how to characterize and achieved the IgNAR of whitespotted bamboo shark is still unclear. In our research, we identified four IgNAR coding gene loci in whitespotted bamboo shark chromosome 44 (NC_057753.1), and primers were designed for single domain variable regions of IgNAR (VNAR) libraries preparation. Following sequencing results revealed that all plasmids constructed with our predicted VNAR libraries contained VNAR coding sequences, which confirmed the specificities of our primers in VNAR amplification. To our surprise, ≥90% VNAR sequences were encoded by IgNAR1, which suggests IgNAR1 is the most active IgNAR transcription locus in whitespotted bamboo shark. Interestingly, we found IgNAR(ΔC2-C3) were encoded by IgNAR3. Our findings gave a new sight of whitespotted bamboo shark IgNAR, which would broad the way of IgNAR studies and applications in biotherapies., Competing Interests: Declaration of competing interest The authors declare that there is no conflict of interest regarding the publication of this paper., (Copyright © 2023. Published by Elsevier Ltd.)
- Published
- 2023
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35. miRCat2: Accurate prediction of plant and animal microRNAs from next-generation sequencing datasets
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Paicu, Claudia, Mohorianu, Irina, Stocks, Matthew, Xu, Ping, Coince, Aurore, Billmeier, Martina, Dalmay, Tamas, Moulton, Vincent, and Moxon, Simon
- Subjects
MicroRNAs ,Genetic Loci ,Sequence Analysis, RNA ,Entropy ,Animals ,Computational Biology ,High-Throughput Nucleotide Sequencing ,Sequence Analysis, DNA ,Plants ,Genome Analysis ,Original Papers ,Algorithms ,Software - Abstract
Motivation MicroRNAs are a class of ∼21–22 nt small RNAs which are excised from a stable hairpin-like secondary structure. They have important gene regulatory functions and are involved in many pathways including developmental timing, organogenesis and development in eukaryotes. There are several computational tools for miRNA detection from next-generation sequencing datasets. However, many of these tools suffer from high false positive and false negative rates. Here we present a novel miRNA prediction algorithm, miRCat2. miRCat2 incorporates a new entropy-based approach to detect miRNA loci, which is designed to cope with the high sequencing depth of current next-generation sequencing datasets. It has a user-friendly interface and produces graphical representations of the hairpin structure and plots depicting the alignment of sequences on the secondary structure. Results We test miRCat2 on a number of animal and plant datasets and present a comparative analysis with miRCat, miRDeep2, miRPlant and miReap. We also use mutants in the miRNA biogenesis pathway to evaluate the predictions of these tools. Results indicate that miRCat2 has an improved accuracy compared with other methods tested. Moreover, miRCat2 predicts several new miRNAs that are differentially expressed in wild-type versus mutants in the miRNA biogenesis pathway. Availability and Implementation miRCat2 is part of the UEA small RNA Workbench and is freely available from http://srna-workbench.cmp.uea.ac.uk/. Contact v.moulton@uea.ac.uk or s.moxon@uea.ac.uk Supplementary information Supplementary data are available at Bioinformatics online.
- Published
- 2017
36. De novo methylation in male germ cells of the common marmoset monkey occurs during postnatal development and is maintained in vitro
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Jörg Gromoll, Nina Neuhaus, Joachim Wistuba, Daniel Langenstroth-Röwer, Sandra Laurentino, Ina Tröndle, and Stefan Schlatt
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0301 basic medicine ,Male ,Cancer Research ,endocrine system ,Alu element ,Epigenesis, Genetic ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Alu Elements ,biology.animal ,medicine ,Animals ,Imprinting (psychology) ,Molecular Biology ,Cells, Cultured ,030219 obstetrics & reproductive medicine ,biology ,Marmoset ,Gene Expression Regulation, Developmental ,Callithrix ,Methylation ,DNA Methylation ,biology.organism_classification ,Molecular biology ,Research Papers ,Spermatozoa ,030104 developmental biology ,medicine.anatomical_structure ,chemistry ,Genetic Loci ,DNA methylation ,Germ cell ,DNA - Abstract
The timing of de novo DNA methylation in male germ cells during human testicular development is yet unsolved. Apart from that, the stability of established imprinting patterns in vitro is controversially discussed. This study aimed at determining the timing of DNA de novo methylation and at assessing the stability of the methylation status in vitro. We employed the marmoset monkey (Callithrix jacchus) as it is considered the best non-human primate model for human testicular development. We selected neonatal, pre-pubertal, pubertal, and adult animals (n = 3, each) and assessed germ cell global DNA methylation levels by 5-methyl cytosine staining, and Alu elements and gene-specific methylation (H19, LIT1, SNRPN, MEST, OCT4, MAGE-A4, and DDX-4) by pyrosequencing. De novo methylation is progressively established during postnatal primate development and continues until adulthood, a process that is different in most other species. Importantly, once established, methylation patterns remained stable, as demonstrated using in vitro cultures. Thus, the marmoset monkey is a unique model for the study of postnatal DNA methylation mechanisms in germ cells and for the identification of epimutations and their causes.
- Published
- 2016
37. Potential application of elastic nets for shared polygenicity detection with adapted threshold selection.
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John M and Lencz T
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- Phenotype, Alleles, Multifactorial Inheritance, Polymorphism, Single Nucleotide, Genome-Wide Association Study, Genetic Loci
- Abstract
Current research suggests that hundreds to thousands of single nucleotide polymorphisms (SNPs) with small to modest effect sizes contribute to the genetic basis of many disorders, a phenomenon labeled as polygenicity. Additionally, many such disorders demonstrate polygenic overlap, in which risk alleles are shared at associated genetic loci. A simple strategy to detect polygenic overlap between two phenotypes is based on rank-ordering the univariate p -values from two genome-wide association studies (GWASs). Although high-dimensional variable selection strategies such as Lasso and elastic nets have been utilized in other GWAS analysis settings, they are yet to be utilized for detecting shared polygenicity. In this paper, we illustrate how elastic nets, with polygenic scores as the dependent variable and with appropriate adaptation in selecting the penalty parameter, may be utilized for detecting a subset of SNPs involved in shared polygenicity. We provide theory to better understand our approaches, and illustrate their utility using synthetic datasets. Results from extensive simulations are presented comparing the elastic net approaches with the rank ordering approach, in various scenarios. Results from simulations studies exhibit one of the elastic net approaches to be superior when the correlations among the SNPs are high. Finally, we apply the methods on two real datasets to illustrate further the capabilities, limitations and differences among the methods., (© 2022 Walter de Gruyter GmbH, Berlin/Boston.)
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- 2022
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38. A new three-locus model for rootstock-induced dwarfing in apple revealed by genetic mapping of root bark percentage
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Marzena Lipska, Richard J. Harrison, Emma Cascant-Lopez, Nuria Barber-Perez, Felicidad Fernández-Fernández, Rebeca Conde-Ruíz, Peter J. Gregory, Magdalena Cobo-Medina, Nicola Harrison, and Philip Brain
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0106 biological sciences ,0301 basic medicine ,Genetic Linkage ,Physiology ,root bark percentage ,Plant Science ,Plant Roots ,01 natural sciences ,Malus × domestica ,root cortex ,education.field_of_study ,Plant Stems ,biology ,Chromosome Mapping ,food and beverages ,Malus - domestica ,Dwarfing ,Phenotype ,Malus ,Plant Bark ,Seasons ,Rootstock ,scion ,Research Paper ,Genetic Markers ,Genotype ,Quantitative Trait Loci ,Population ,Locus (genetics) ,Quantitative trait locus ,Polymorphism, Single Nucleotide ,complex mixtures ,root anatomy ,03 medical and health sciences ,Botany ,education ,Models, Genetic ,Apple ,rootstock ,biology.organism_classification ,grafting ,030104 developmental biology ,Genetic Loci ,Genetic marker ,rootstock-induced dwarfing ,010606 plant biology & botany - Abstract
Highlight Identification of three quantitative trait loci associated with root bark percentage in apple rootstocks is predictive of rootstock-induced dwarfing of the scion., Rootstock-induced dwarfing of apple scions revolutionized global apple production during the twentieth century, leading to the development of modern intensive orchards. A high root bark percentage (the percentage of the whole root area constituted by root cortex) has previously been associated with rootstock-induced dwarfing in apple. In this study, the root bark percentage was measured in a full-sib family of ungrafted apple rootstocks and found to be under the control of three loci. Two quantitative trait loci (QTLs) for root bark percentage were found to co-localize to the same genomic regions on chromosome 5 and chromosome 11 previously identified as controlling dwarfing, Dw1 and Dw2, respectively. A third QTL was identified on chromosome 13 in a region that has not been previously associated with dwarfing. The development of closely linked sequence-tagged site markers improved the resolution of allelic classes, thereby allowing the detection of dominance and epistatic interactions between loci, with high root bark percentage only occurring in specific allelic combinations. In addition, we report a significant negative correlation between root bark percentage and stem diameter (an indicator of tree vigour), measured on a clonally propagated grafted subset of the mapping population. The demonstrated link between root bark percentage and rootstock-induced dwarfing of the scion leads us to propose a three-locus model that is able to explain levels of dwarfing from the dwarf ‘M.27’ to the semi-invigorating rootstock ‘M.116’. Moreover, we suggest that the QTL on chromosome 13 (Rb3) might be analogous to a third dwarfing QTL, Dw3, which has not previously been identified.
- Published
- 2016
39. MYB controls erythroid versus megakaryocyte lineage fate decision through the miR-486-3p-mediated downregulation of MAF
- Author
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Sebastiano Rontauroli, Elisa Bianchi, Valentina Pennucci, Jenny Bulgarelli, Rossella Manfredini, Roberta Zini, Ruggiero Norfo, Giorgia Sacchi, Simona Salati, Zelia Prudente, Sergio Ferrari, and Samantha Ruberti
- Subjects
LMO2 ,Ankyrins ,Cells ,Oligonucleotides ,Down-Regulation ,Antigens, CD34 ,KLF1 ,Biology ,Promoter Regions ,Transactivation ,Proto-Oncogene Proteins c-myb ,Erythroid Cells ,Genetic ,Genes, Reporter ,Humans ,MYB ,Cell Lineage ,3' Untranslated Regions ,Cell Differentiation ,Cells, Cultured ,Chondrogenesis ,Genetic Loci ,Hematopoietic Stem Cells ,Megakaryocytes ,MicroRNAs ,Oligonucleotides, Antisense ,Promoter Regions, Genetic ,Proto-Oncogene Proteins c-maf ,RNA Interference ,Antigens ,Antisense ,Molecular Biology ,Reporter ,Megakaryopoiesis ,Original Paper ,Cultured ,Cell Biology ,Genes ,Cancer research ,Erythropoiesis ,CD34 - Abstract
The transcription factor MYB has a key role in hematopoietic progenitor cells (HPCs) lineage choice, by enhancing erythropoiesis at the expense of megakaryopoiesis. We previously demonstrated that MYB controls erythroid versus megakaryocyte lineage decision by transactivating KLF1 and LMO2 expression. To further unravel the molecular mechanisms through which MYB affects lineage fate decision, we performed the integrative analysis of miRNA and mRNA changes in MYB-silenced human primary CD34+ HPCs. Among the miRNAs with the highest number of predicted targets, we focused our studies on hsa-miR-486-3p by demonstrating that MYB controls miR-486-3p expression through the transactivation of its host gene, ankyrin-1 (ANK1) and that miR-486-3p affects HPCs commitment. Indeed, overexpression and knockdown experiments demonstrated that miR-486-3p supports the erythropoiesis while restraining the megakaryopoiesis. Of note, miR-486-3p also favors granulocyte differentiation while repressing the macrophage differentiation. To shed some light on the molecular mechanisms through which miR-486-3p affects HPCs lineage commitment, we profiled the gene expression changes upon miR-486-3p overexpression in CD34+ cells. Among the genes downregulated in miR-486-3p-overexpressing HPCs and computationally predicted to be miR-486-3p targets, we identified MAF as a miR-486-3p target by 3'UTR luciferase reporter assay. Noteworthy, MAF overexpression was able to partially reverse the effects of miR-486-3p overexpression on erythroid versus megakaryocyte lineage choice. Moreover, the MYB/MAF co-silencing constrained the skewing of erythroid versus megakaryocyte lineage commitment in MYB-silenced CD34+ cells, by restraining the expansion of megakaryocyte lineage while partially rescuing the impairment of erythropoiesis. Therefore, our data collectively demonstrate that MYB favors erythropoiesis and restrains megakaryopoiesis through the transactivation of miR-486-3p expression and the subsequent downregulation of MAF. As a whole, our study uncovers the MYB/miR-486-3p/MAF axis as a new mechanism underlying the MYB-driven control of erythroid versus megakaryocyte lineage fate decision.
- Published
- 2015
40. Enhancer Dependent Repositioning of TCRb Locus with Respect to the Chromosome Territory.
- Author
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Yadav M, Jalan M, and Srivastava M
- Subjects
- Animals, Chromatin metabolism, Chromosomes metabolism, Mice, Enhancer Elements, Genetic, Genetic Loci, Receptors, Antigen, T-Cell, alpha-beta genetics, Thymocytes metabolism, V(D)J Recombination
- Abstract
Intranuclear position of several genes is dynamically altered during development concordant with their activation. To understand this dynamic, but non-random, nuclear organization, it is important to identify the relevant regulatory elements and trans acting factors. Murine TCRb locus gets activated during thymic development. Enhancer Eb is important for VDJ recombination at TCRb locus as it is critically required for establishment of recombination center. Our analysis revealed that TCRb locus gets located out of the chromosome territory specifically in developing thymocytes. Further, CRISPR/Cas9 based deletion mutagenesis established an unambiguous role of enhancer Eb in defining TCRb location relative to chromosome territory. The ability to reposition the target locus relative to chromosome territory highlights a novel aspect pertaining to activity of enhancers which may contribute to their ability to regulate gene expression. Additionally, our observations have implications for understanding the role of enhancers in three-dimensional genome organization and function., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier Ltd. All rights reserved.)
- Published
- 2022
- Full Text
- View/download PDF
41. Association of Bw4/Bw6 mismatch across class I HLA loci with renal graft outcomes in first time transplants.
- Author
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Tang MS, Wang M, Chang SH, Alhamad T, and Liu C
- Subjects
- Adolescent, Adult, Epitopes chemistry, Epitopes genetics, Epitopes immunology, Female, Genotype, Graft Rejection genetics, Graft Rejection immunology, Graft Survival genetics, Graft Survival immunology, HLA-B Antigens immunology, Histocompatibility immunology, Histocompatibility Antigens Class I immunology, Histocompatibility Testing, Humans, Male, Middle Aged, Odds Ratio, Peptides chemistry, Peptides genetics, Peptides immunology, Phenotype, Prognosis, Risk Factors, Young Adult, Alleles, Genetic Loci, HLA-B Antigens genetics, Histocompatibility genetics, Histocompatibility Antigens Class I genetics, Kidney Transplantation methods
- Abstract
Bw4 and Bw6 are strongly immunogenic epitopes routinely assigned based on HLA-B typing results per Organ Procurement and Transplantation Network (OPTN) policies. These public epitopes and their variants are shared by some cross-reactive HLA-A and -C antigens. Although epitope mismatch has been associated with poor transplant outcomes, previous studies did not find such associations for Bw4/6 mismatch as defined by HLA-B antigens only. We hypothesized that a broader definition for Bw4/Bw6 mismatch that includes cross-reactive HLA-A and -C antigens may reveal the risk associated with these epitopes. In this retrospective cohort study, we examined kidney transplantations between 2000 and 2016 in the OPTN database and determined the association of Bw4/6 mismatch across all class I HLA antigens and renal graft outcomes. Even by this broader definition, Bw4/6 mismatch was not independently associated with 1-year graft rejection (adjusted OR: 0.99, 95%CI 0.93-1.06) or death-censored graft survival (adjusted HR: 1.02, 95%CI 1.00-1.05). There was no significant association among recipients who were already sensitized at transplant either. Our findings suggest that Bw4/6 mismatch alone is not associated with poor renal graft outcomes despite their strong immunogenicity, and the load of epitope mismatches over a certain threshold is likely required to cause adverse clinical consequences., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved.)
- Published
- 2021
- Full Text
- View/download PDF
42. Can a reference 'match' an evidence profile if these have no loci in common?
- Author
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Taylor D and Buckleton J
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- Apolipoproteins B genetics, Forensic Genetics, HLA-DQ alpha-Chains genetics, Humans, Likelihood Functions, Time Factors, DNA Fingerprinting, Genetic Loci
- Abstract
Cold case reinvestigations are a common occurrence. Occasionally some of the original work was conducted up to 30 years ago using profiling systems of the early 1990s, which targeted HLA-DQA1, ApoB, D1S80 and D17S5. When contemporary work is carried out, if a suspect is identified they will be profiled in contemporary profiling kits such as GlobalFiler. It would be common to then also attempt to profile the evidence profiles in the same contemporary profiling kit. Imagine a scenario where two evidence samples, E
1 and E2 , had previously produced single-source profiles, but only E2 had any DNA extract left to re-profile with GlobalFiler. At the old loci E1 matched E2 , and at the new loci E2 matched the suspect reference. Of interest to the investigation was whether anything could be said about the suspect being a donor of DNA to E1 even though the reference of the suspect and the profile from E1 had no loci in common, by using the information from the profile of E2 . This paper explores that possibility., (Copyright © 2021 Elsevier B.V. All rights reserved.)- Published
- 2021
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43. miRNAs generated from Meg3-Mirg locus are downregulated during aging.
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Lupan AM, Rusu EG, Preda MB, Marinescu CI, Ivan C, and Burlacu A
- Subjects
- Animals, Fibroblasts metabolism, Gene Expression Profiling, Genome, High-Throughput Nucleotide Sequencing, Mice, Inbred C57BL, Multigene Family, Myocardium cytology, Myocytes, Cardiac metabolism, Organ Specificity genetics, Up-Regulation genetics, Mice, Aging genetics, Down-Regulation genetics, Genetic Loci, MicroRNAs genetics
- Abstract
Aging determines a multilevel functional decline and increases the risk for cardiovascular pathologies. MicroRNAs are recognized as fine tuners of all cellular functions, being involved in various cardiac diseases. The heart is one of the most affected organs in aged individuals, however little is known about the extent and robustness to which miRNA profiles are modulated in cardiac cells during aging. This paper provides a comprehensive characterization of the aging-associated miRNA profile in the murine cardiac fibroblasts, which are increasingly recognized for their active involvement in the cardiac physiology and pathology. Next-generation sequencing of cardiac fibroblasts isolated from young and old mice revealed that an important fraction of the miRNAs generated by the Meg3-Mirg locus was downregulated during aging. To address the specificity of this repression, four miRNAs selected as representative for this locus were further assessed in other cells and organs isolated from aged mice. The results suggested that the repression of miRNAs generated by the Meg3-Mirg locus was a general feature of aging in multiple organs. Bioinformatic analysis of the predicted target genes identified Integrin Beta-2 as an aged-upregulated gene, which was thereafter confirmed in multiple mouse organs. In conclusion, our study provides new data concerning the mechanisms of natural aging and highlights the robustness of the miRNA modulation during this process.
- Published
- 2021
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- View/download PDF
44. The association of HLA-DP loci with autoimmune diabetes in Chinese.
- Author
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Xia Y, Li X, Huang G, Lin J, Luo S, Xie Z, and Zhou Z
- Subjects
- Adolescent, Adult, Aged, Child, Child, Preschool, China, Female, Humans, Infant, Male, Middle Aged, Young Adult, Diabetes Mellitus, Type 1 genetics, Gene Frequency genetics, Genetic Loci genetics, HLA-DP beta-Chains genetics, Latent Autoimmune Diabetes in Adults genetics
- Abstract
Aims: To determine if HLA-DP loci independently contribute to classic type 1 diabetes (T1D) of all ages, childhood-onset T1D and latent autoimmune diabetes in adults (LADA) among Chinese Han population., Methods: A total of 518 patients with classic T1D (Among them 180 participants manifested T1D between 1 and 14 years), 519 patients with LADA and 527 normal controls were genotyped for both HLA-DPA1 and -DPB1 loci. The frequencies of DP alleles and haplotypes in patients were directly compared to those in controls, followed by adjustment for linkage disequilibrium (LD) with DR-DQ haplotypes., Results: In the direct comparison, DPA1*01:03, DPB1*04:01 and DPA1*01:03-DPB1*04:01 showed disease-predisposing effects in both the overall T1D group and the childhood-onset T1D group mainly due to their conjunction with the known susceptible DR3 haplotype. Conditioning on DR-DQ haplotypes, only DPA1*02:02-DPB1*02:02 significantly increased T1D risk among those diagnosed during childhood (OR = 2.02, 95% CI = 1.35-3.01). Whether or not adjusted for LD, no statistically significant HLA-DP association could be observed for LADA., Conclusion: HLA-DP is implicated in the pathogenesis of childhood-onset T1D in Chinese, independent of the predominant DR-DQ loci and might serve as additional markers in genetic models for the recognition of those genetically at-risk individuals., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020. Published by Elsevier B.V.)
- Published
- 2021
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- View/download PDF
45. Spatial statistical tools for genome-wide mutation cluster detection under a microarray probe sampling system.
- Author
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Luo, Bin, Edge, Alanna K., Tolg, Cornelia, Turley, Eva A., Dean, C. B., Hill, Kathleen A., and Kulperger, R. J.
- Subjects
GENETIC disorder diagnosis ,MICROARRAY technology ,GENETIC mutation ,SPATIAL analysis (Statistics) ,POISSON processes - Abstract
Mutation cluster analysis is critical for understanding certain mutational mechanisms relevant to genetic disease, diversity, and evolution. Yet, whole genome sequencing for detection of mutation clusters is prohibitive with high cost for most organisms and population surveys. Single nucleotide polymorphism (SNP) genotyping arrays, like the Mouse Diversity Genotyping Array, offer an alternative low-cost, screening for mutations at hundreds of thousands of loci across the genome using experimental designs that permit capture of de novo mutations in any tissue. Formal statistical tools for genome-wide detection of mutation clusters under a microarray probe sampling system are yet to be established. A challenge in the development of statistical methods is that microarray detection of mutation clusters is constrained to select SNP loci captured by probes on the array. This paper develops a Monte Carlo framework for cluster testing and assesses test statistics for capturing potential deviations from spatial randomness which are motivated by, and incorporate, the array design. While null distributions of the test statistics are established under spatial randomness via the homogeneous Poisson process, power performance of the test statistics is evaluated under postulated types of Neyman-Scott clustering processes through Monte Carlo simulation. A new statistic is developed and recommended as a screening tool for mutation cluster detection. The statistic is demonstrated to be excellent in terms of its robustness and power performance, and useful for cluster analysis in settings of missing data. The test statistic can also be generalized to any one dimensional system where every site is observed, such as DNA sequencing data. The paper illustrates how the informal graphical tools for detecting clusters may be misleading. The statistic is used for finding clusters of putative SNP differences in a mixture of different mouse genetic backgrounds and clusters of de novo SNP differences arising between tissues with development and carcinogenesis. [ABSTRACT FROM AUTHOR]
- Published
- 2018
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- View/download PDF
46. High resolution allele genotyping and haplotype frequencies for NGS based HLA 11 loci of 5266 Hong Kong Chinese bone marrow donors.
- Author
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Kwok J, Tang WH, Chu WK, Chan YS, Liu Z, Yang W, Ip P, Ma W, Lee CK, and Middleton D
- Subjects
- Asian People genetics, Bone Marrow Transplantation, Genotyping Techniques methods, High-Throughput Nucleotide Sequencing methods, Histocompatibility Antigens Class I genetics, Histocompatibility Antigens Class II genetics, Histocompatibility Testing methods, Hong Kong, Humans, Alleles, Bone Marrow immunology, Gene Frequency, Genetic Loci, HLA Antigens genetics, Haplotypes, Registries, Unrelated Donors
- Abstract
Next-generation sequencing (NGS) at the HLA-A, -B, -C, -DRB1, -DRB3/4/5, -DQA1, -DQB1, -DPA1, and -DPB1 loci was performed on 5,266 southern Chinese unrelated donors of the Hong Kong Bone Marrow Donor Registry. High-resolution HLA genotypes defined by full sequencing of class I loci and extended coverage of class II loci were attained to determine allele frequencies and estimate haplotype frequencies. This study provides allele and haplotype frequencies on 11 loci estimated for the first time in the Hong Kong Chinese population. These results describe extended haplotypes including the less frequently typed HLA-DPA1, -DPB1 and -DQA1 loci and distinctive haplotype associations. The present data are timely in that they allow the permissible matching in HLA-DPB1 for Chinese patients awaiting haematopoietic stem cell transplantation upon applying the latest requirement of NMDP matching guidelines. Overall, these results provide a useful reference source for population genetics studies, HLA-disease association studies and for improving donor recruitment and selection strategies of bone marrow registries. The allele and haplotype data are available in the Allele Frequencies Net Database under the population name ''Hong Kong Chinese HKBMDR, HLA 11 loci'' and the identifier (AFND3724) [1]., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved.)
- Published
- 2020
- Full Text
- View/download PDF
47. A multilocus phylogeny of the non-photosynthetic parasitic plant Cistanche (Orobanchaceae) refutes current taxonomy and identifies four major morphologically distinct clades.
- Author
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Ataei N, Schneeweiss GM, García MA, Krug M, Lehnert M, Valizadeh J, and Quandt D
- Subjects
- Bayes Theorem, DNA, Plant genetics, Introns genetics, Likelihood Functions, Sequence Analysis, DNA, Cistanche anatomy & histology, Cistanche classification, Genetic Loci, Photosynthesis, Phylogeny
- Abstract
Phylogenetic relationships of and within non-photosynthetic parasitic lineages are notoriously poorly known, which negatively affects our understanding of parasitic plants. This is also the case for Cistanche (Orobanchaceae), an Old World genus with about two dozen species, whose relationships have not yet been addressed using molecular phylogenetic approaches. Here we infer phylogenetic relationships within the genus, employing a taxonomically and geographically broad sampling covering all previously distinguished infrageneric groups and most of the currently recognized species. A combined matrix of three plastid markers (trnL-trnF, including the trnL intron and the intergenic spacer (IGS), trnS-trnfM IGS and psbA-trnH IGS) and one nuclear marker (ITS) was analyzed using maximum parsimony, maximum likelihood and Bayesian inference. Cistanche falls into four well-supported and geographically differentiated clades: East Asian Clade, Northwest African Clade, Southwest Asian Clade and Widespread Clade. Of those, only the East Asian Clade corresponds to a previously recognized taxonomic section, whereas the others either contain members of two or three sections (Widespread Clade and Southwest Asian Clade, respectively) or have not been taxonomically recognized so far (Northwest African Clade). Whereas the Southwest Asian Clade exhibits strong phylogenetic structure among and partly within species (the East Asian Clade and the Northwest African Clade are monospecific), phylogenetic resolution within the Widespread Clade is often low and hampered by discrepancies between nuclear and plastid markers. Both molecular and morphological data indicate that species diversity in Cistanche is currently underestimated., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier Inc. All rights reserved.)
- Published
- 2020
- Full Text
- View/download PDF
48. Next-generation sequencing of 11 HLA loci in a large dengue vaccine cohort from the Philippines.
- Author
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Geretz A, Cofer L, Ehrenberg PK, Currier JR, Yoon IK, Alera MTP, Jarman R, Rothman AL, and Thomas R
- Subjects
- Alleles, Clinical Trials, Phase III as Topic, Exons genetics, Gene Frequency genetics, Genotype, Genotyping Techniques methods, High-Throughput Nucleotide Sequencing methods, Humans, Introns genetics, Philippines, Prospective Studies, Dengue genetics, Dengue immunology, Dengue Vaccines immunology, Genetic Loci genetics, HLA Antigens genetics
- Abstract
HLA genotyping by next-generation sequencing (NGS) has evolved with significant advancements in the last decade. Here we describe full-length HLA genotyping of 11 loci in 612 individuals comprising a dengue vaccine cohort from Cebu province in the Philippines. The multi-locus individual tagging NGS (MIT-NGS) method that we developed initially for genotyping 4-6 loci in one MiSeq run was expanded to 11 loci including HLA-A, B, C, DPA1, DPB1, DQA1, DQB1, DRB1, and DRB3/4/5. This change did not affect the overall coverage or depth of the sequencing reads. HLA alleles with frequencies greater than 10% were A*11:01:01, A*24:02:01, A*24:07:01, A*34:01:01, B*38:02:01, B*15:35, B*35:05:01, C*07:02:01, C*04:01:01, DPA1*02:02:02, DPB1*05:01:01, DPB1*01:01:01, DQA1*01:02:01, DQA1*06:01:01, DQB1*05:02:01, DQB1*03:01:01, DRB1*15:02:01, DRB1*12:02:01, DRB3*03:01:03, DRB4*01:03:01, and DRB5*01:01:01. Improvements in sequencing library preparation provide uniform and even coverage across all exons and introns. This has led to a marked reduction in allele imbalance and dropout. Furthermore, including more loci, such as DRB3/4/5, decreases cross-mapping and incorrect allele assignment at the DRB1 locus. The increased number of loci sequenced for each sample does not reduce the number of samples that can be multiplexed on a single MiSeq run and is therefore more cost-efficient. We believe that such improvements will help HLA genotyping by NGS to gain momentum over other conventional methods by increasing confidence in the calls., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 American Society for Histocompatibility and Immunogenetics. All rights reserved.)
- Published
- 2020
- Full Text
- View/download PDF
49. Investigating the utility of traditional and genomic multi-locus datasets to resolve relationships in Lipaugus and Tijuca (Cotingidae).
- Author
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Settlecowski AE, Cuervo AM, Tello JG, Harvey MG, Brumfield RT, and Derryberry EP
- Subjects
- Animals, Biological Evolution, Genetic Speciation, Geography, Phylogeny, Sequence Analysis, DNA, Databases, Genetic, Genetic Loci, Genomics, Passeriformes genetics
- Abstract
Rapid diversification limits our ability to resolve evolutionary relationships and examine diversification history, as in the case of the Neotropical cotingas. Here we present an analysis with complete taxon sampling for the cotinga genera Lipaugus and Tijuca, which include some of the most range-restricted (e.g., T. condita) and also the most widespread and familiar (e.g., L. vociferans) forest birds in the Neotropics. We used two datasets: (1) Sanger sequencing data sampled from eight loci in 34 individuals across all described taxa and (2) sequence capture data linked to 1,079 ultraconserved elements and conserved exons sampled from one or two individuals per species. Phylogenies estimated from the Sanger sequencing data failed to resolve three nodes, but the sequence capture data produced a well-supported tree. Lipaugus and Tijuca formed a single, highly supported clade, but Tijuca species were not sister and were embedded within Lipaugus. A dated phylogeny confirmed Lipaugus and Tijuca diversified rapidly in the Miocene. Our study provides a detailed evolutionary hypothesis for Lipaugus and Tijuca and demonstrates that increasing genomic sampling can prove instrumental in resolving the evolutionary history of recent radiations., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier Inc. All rights reserved.)
- Published
- 2020
- Full Text
- View/download PDF
50. New insights about species delimitation in red snappers (Lutjanus purpureus and L. campechanus) using multilocus data.
- Author
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da Silva R, Pedraza-Marrón CDR, Sampaio I, Betancur-R R, Gomes G, and Schneider H
- Subjects
- Animals, Databases, Genetic, Genetics, Population, Genome, Geography, Haplotypes genetics, Phylogeny, Species Specificity, Genetic Loci, Perciformes classification, Perciformes genetics
- Abstract
Lutjanus campechanus and Lutjanus purpureus are two commercially important lutjanid fishes (snappers) with non-sympatric distribution throughout Western Atlantic. Even though both taxa have traditionally been regarded as valid species, their taxonomic status remains under debate. In the present study, we used phylogeographic approaches and molecular methods of species delimitation to elucidate the taxonomic issues between both species, based on 1478 base pairs from four genomic regions. We found haplotypes shared between the two species, particularly in relation to nuclear DNA (nuDNA) sequences. The molecular delimitation of species supported the discrimination of L. purpureus and L. campechanus as distinct evolutionary units. Nonetheless, a unidirectional gene flow was found from L. campechanus towards L. purpureus. Therefore, it seems plausible to infer that L. campechanus and L. purpureus are two evolutionary units in which the apparent sharing of haplotypes should be driven by introgression., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier Inc. All rights reserved.)
- Published
- 2020
- Full Text
- View/download PDF
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