148 results on '"Lahn, Bruce T."'
Search Results
102. Trak1 mutation disrupts GABAA receptor homeostasis in hypertonic mice
- Author
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Gilbert, Sandra L, primary, Zhang, Li, additional, Forster, Michele L, additional, Iwase, Tamaki, additional, Soliven, Betty, additional, Donahue, Leah Rae, additional, Sweet, Hope O, additional, Bronson, Roderick T, additional, Davisson, Muriel T, additional, Wollmann, Robert L, additional, and Lahn, Bruce T, additional
- Published
- 2005
- Full Text
- View/download PDF
103. Selective Constraint on Noncoding Regions of Hominid Genomes
- Author
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Bush, Eliot C, primary and Lahn, Bruce T, additional
- Published
- 2005
- Full Text
- View/download PDF
104. Robust signals of coevolution of interacting residues in mammalian proteomes identified by phylogeny-aided structural analysis
- Author
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Shim Choi, Sun, primary, Li, Weimin, additional, and Lahn, Bruce T, additional
- Published
- 2005
- Full Text
- View/download PDF
105. A highly unexpected strong correlation between fixation probability of nonsynonymous mutations and mutation rate
- Author
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Wyckoff, Gerald J., primary, Malcom, Christine M., additional, Vallender, Eric J., additional, and Lahn, Bruce T., additional
- Published
- 2005
- Full Text
- View/download PDF
106. The X chromosome: not just her brother's keeper
- Author
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Vallender, Eric J, primary, Pearson, Nathaniel M, additional, and Lahn, Bruce T, additional
- Published
- 2005
- Full Text
- View/download PDF
107. The Evolution of Word Composition in Metazoan Promoter Sequence
- Author
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Bush, Eliot C., primary and Lahn, Bruce T., additional
- Published
- 2005
- Full Text
- View/download PDF
108. Rate of molecular evolution of the seminal protein gene SEMG2 correlates with levels of female promiscuity
- Author
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Dorus, Steve, primary, Evans, Patrick D, additional, Wyckoff, Gerald J, additional, Choi, Sun Shim, additional, and Lahn, Bruce T, additional
- Published
- 2004
- Full Text
- View/download PDF
109. Effects of chromosomal rearrangements on human-chimpanzee molecular evolution
- Author
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Vallender, Eric J., primary and Lahn, Bruce T., additional
- Published
- 2004
- Full Text
- View/download PDF
110. Diverse fates of paralogs following segmental duplication of telomeric genes☆☆☆
- Author
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Wong, Andrew, primary, Vallender, Eric J., additional, Heretis, Konstantina, additional, Ilkin, Yesim, additional, Lahn, Bruce T., additional, Martin, Christa Lese, additional, and Ledbetter, David H., additional
- Published
- 2004
- Full Text
- View/download PDF
111. Localized methylation in the key regulator gene endothelin- 1 is associated with cell type-specific transcriptional silencing
- Author
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Vallender, Tammy W. and Lahn, Bruce T.
- Published
- 2006
- Full Text
- View/download PDF
112. The human Y chromosome, in the light of evolution
- Author
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Lahn, Bruce T., primary, Pearson, Nathaniel M., additional, and Jegalian, Karin, additional
- Published
- 2001
- Full Text
- View/download PDF
113. Erratum: Retroposition of autosomal mRNA yielded testis-specific gene family on human Y chromosome
- Author
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Lahn, Bruce T, primary and Page, David C, additional
- Published
- 1999
- Full Text
- View/download PDF
114. Retroposition of autosomal mRNA yielded testis-specific gene family on human Y chromosome
- Author
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Lahn, Bruce T, primary and Page, David C, additional
- Published
- 1999
- Full Text
- View/download PDF
115. Functional Coherence of the Human Y Chromosome
- Author
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Lahn, Bruce T., primary and Page, David C., additional
- Published
- 1998
- Full Text
- View/download PDF
116. Xq–Yq interchange resulting in supernormal X-linked gene expression in severely retarded males with 46,XYq- karyotype
- Author
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Lahn, Bruce T., primary, Ma, Nancy, additional, Breg, W. Roy, additional, Stratton, Robert, additional, Surti, Urvashi, additional, and Page, David C., additional
- Published
- 1994
- Full Text
- View/download PDF
117. Evidence for a critical role of gene occlusion in cell fate restriction.
- Author
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Gaetz, Jedidiah, Clift, Kayla L, Fernandes, Croydon J, Mao, Frank Fuxiang, Lee, Jae Hyun, Zhang, Li, Baker, Samuel W, Looney, Timothy J, Foshay, Kara M, Yu, Wei-Hua, Xiang, Andy Peng, and Lahn, Bruce T
- Subjects
CELL determination ,CELL fusion ,EPIGENETICS ,BACTERIAL artificial chromosomes ,CHROMATIN - Abstract
The progressive restriction of cell fate during lineage differentiation is a poorly understood phenomenon despite its ubiquity in multicellular organisms. We recently used a cell fusion assay to define a mode of epigenetic silencing that we termed 'occlusion', wherein affected genes are silenced by cis-acting chromatin mechanisms irrespective of whether trans-acting transcriptional activators are present. We hypothesized that occlusion of lineage-inappropriate genes could contribute to cell fate restriction. Here, we test this hypothesis by introducing bacterial artificial chromosomes (BACs), which are devoid of chromatin modifications necessary for occlusion, into mouse fibroblasts. We found that BAC transgenes corresponding to occluded endogenous genes are expressed in most cases, whereas BAC transgenes corresponding to silent but non-occluded endogenous genes are not expressed. This indicates that the cellular milieu in trans supports the expression of most occluded genes in fibroblasts, and that the silent state of these genes is solely the consequence of occlusion in cis. For the BAC corresponding to the occluded myogenic master regulator Myf5, expression of the Myf5 transgene on the BAC triggered fibroblasts to acquire a muscle-like phenotype. These results provide compelling evidence for a critical role of gene occlusion in cell fate restriction. [ABSTRACT FROM AUTHOR]
- Published
- 2012
- Full Text
- View/download PDF
118. Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine.
- Author
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Chun-Xiao Song, Szulwach, Keith E., Ye Fu, Qing Dai, Chengqi Yi, Xuekun Li, Yujing Li, Chih-Hsin Chen, Wen Zhang, Xing Jian, Jing Wang, Li Zhang, Looney, Timothy J., Baichen Zhang, Godley, Lucy A., Hicks, Leslie M., Lahn, Bruce T., Peng Jin, and Chuan He
- Subjects
GENOMES ,AZIDES ,BACTERIOPHAGES ,GLYCOSYLTRANSFERASES ,NEURODEGENERATION - Abstract
In contrast to 5-methylcytosine (5-mC), which has been studied extensively, little is known about 5-hydroxymethylcytosine (5-hmC), a recently identified epigenetic modification present in substantial amounts in certain mammalian cell types. Here we present a method for determining the genome-wide distribution of 5-hmC. We use the T4 bacteriophage β-glucosyltransferase to transfer an engineered glucose moiety containing an azide group onto the hydroxyl group of 5-hmC. The azide group can be chemically modified with biotin for detection, affinity enrichment and sequencing of 5-hmC-containing DNA fragments in mammalian genomes. Using this method, we demonstrate that 5-hmC is present in human cell lines beyond those previously recognized. We also find a gene expression level-dependent enrichment of intragenic 5-hmC in mouse cerebellum and an age-dependent acquisition of this modification in specific gene bodies linked to neurodegenerative disorders. [ABSTRACT FROM AUTHOR]
- Published
- 2011
- Full Text
- View/download PDF
119. A Stem Cell-Based Tool for Small Molecule Screening in Adipogenesis.
- Author
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Jie Qin, Wei-Qiang Li, Li Zhang, Fei Chen, Wen-Hua Liang, Frank Fuxiang Mao, Xiu-Ming Zhang, Lahn, Bruce T., Wei-Hua Yu, and Andy Peng Xiang
- Subjects
STEM cells ,MESENCHYMAL stem cells ,FLUORESCENCE ,REPORTER genes ,FAT cells ,PROTEINS ,SPECTROPHOTOMETERS ,ADIPOSE tissues ,CARDIOVASCULAR diseases ,TYPE 2 diabetes - Abstract
Techniques for small molecule screening are widely used in biological mechanism study and drug discovery. Here, we reported a novel adipocyte differentiation assay for small molecule selection, based on human mesenchymal stem cells (hMSCs) transduced with fluorescence reporter gene driven by adipogenic specific promoter - adipocyte Protein 2 (aP2; also namely Fatty Acid Binding Protein 4, FABP4). During normal adipogenic induction as well as adipogenic inhibition by Ly294002, we confirmed that the intensity of green fluorescence protein corresponded well to the expression level of aP2 gene. Furthermore, this variation of green fluorescence protein intensity can be read simply through fluorescence spectrophotometer. By testing another two small molecules in adipogenesis -Troglitazone and CHIR99021, we proved that this is a simple and sensitive method, which could be applied in adipocyte biology, drug discovery and toxicological study in the future. [ABSTRACT FROM AUTHOR]
- Published
- 2010
- Full Text
- View/download PDF
120. Systematic Comparison of Constitutive Promoters and the Doxycycline-Inducible Promoter.
- Author
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Jane Yuxia Qin, Li Zhang, Clift, Kayla L., Hulur, Imge, Xiang, Andy Peng, Bing-Zhong Ren, and Lahn, Bruce T.
- Subjects
PROMOTERS (Genetics) ,GENETIC transcription ,GENE expression ,GENETIC regulation ,MAMMAL genetics ,DROSOPHILA genetics ,CELLS ,GENETIC code ,NUCLEOTIDES - Abstract
Constitutive promoters are used routinely to drive ectopic gene expression. Here, we carried out a systematic comparison of eight commonly used constitutive promoters (SV40, CMV, UBC, EF1A, PGK and CAGG for mammalian systems, and COPIA and ACT5C for Drosophila systems). We also included in the comparison the TRE promoter, which can be activated by the rtTA transcriptional activator in a doxycycline-inducible manner. To make our findings representative, we conducted the comparison in a variety of cell types derived fromseveral species. We found that these promoters vary considerably from one another in their strength. Most promoters have fairly consistent strengths across different cell types, but the CMV promoter can vary considerably from cell type to cell type. At maximal induction, the TRE promoter is comparable to a strong constitutive promoter. These results should facilitate more rational choices of promoters in ectopic gene expression studies. [ABSTRACT FROM AUTHOR]
- Published
- 2010
- Full Text
- View/download PDF
121. Generation of functional hepatocytes from mouse induced pluripotent stem cells.
- Author
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WEIQIANG LI, DING WANG, JIE QIN, CHANG LIU, QI ZHANG, XIUMING ZHANG, XINBING YU, LAHN, BRUCE T., MAO, FRANK FUXIANG, and XIANG, ANDY PENG
- Subjects
STEM cells ,SOMATIC cells ,TRANSCRIPTION factors ,CHROMATIN ,LIVER cells ,EMBRYONIC stem cells - Abstract
Induced pluripotent stem cells are derived from somatic cells by forced expression of several transcriptional factors. Induced pluripotent stem cells resemble embryonic stem cells in many aspects, such as the expression of certain stem cell markers, chromatin methylation patterns, embryoid body formation and teratoma formation. Therefore, induced pluripotent stem cells provide a powerful tool for study of developmental biology and unlimited resources for transplantation therapy. Here we reported the successful induction of mouse induced pluripotent stem cells and a simple and efficient process for generation of functional hepatocytes from mouse induced pluripotent stem cells by sequential addition of inducing factors. These induced pluripotent stem cell-derived hepatocytes, just as mouse embryonic stem cell-derived hepatocytes, expressed hepatic lineage markers including CK7, CK8, CK18, CK19, alpha-fetoprotein, albumin, Cyp7a1, and exhibited functional hepatic characteristics, including glycogen storage, indocyanine green (ICG) uptake and release, low-density lipoprotein (LDL) uptake and urea secretion. Although we observed some variations in the efficiency of hepatic differentiation between induced pluripotent stem cells and common mouse embryonic stem cell lines, our results indicate that mouse induced pluripotent stem cells can efficiently differentiate into functional hepatocytes in vitro, which may be helpful for the study of liver development and regenerative medicine. J. Cell. Physiol. 222: 492–501, 2010. © 2009 Wiley-Liss, Inc. [ABSTRACT FROM AUTHOR]
- Published
- 2010
- Full Text
- View/download PDF
122. Multiple mesodermal lineage differentiation ofApodemus sylvaticus embryonic stem cells in vitro.
- Author
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Tao Wang, Frank Fuxiang Mao, Wenyu Lai, Weiqiang Li, Weihua Yu, Zifei Wang, Lirong Zhang, Jinli Zhang, Jin Niu, Xiuming Zhang, Lahn, Bruce T., and Andy Peng Xiang
- Subjects
EMBRYONIC stem cell research ,APODEMUS sylvaticus ,BIOLOGICAL reagents ,FAT cells ,HEART cells - Abstract
Background: Embryonic stem (ES) cells have attracted significant attention from researchers around the world because of their ability to undergo indefinite self-renewal and produce derivatives from the three cell lineages, which has enormous value in research and clinical applications. Until now, many ES cell lines of different mammals have been established and studied. In addition, recently, AS-ES1 cells derived from Apodemus sylvaticus were established and identified by our laboratory as a new mammalian ES cell line. Hence further research, in the application of AS-ES1 cells, is warranted. Results: Herein we report the generation of multiple mesodermal AS-ES1 lineages via embryoid body (EB) formation by the hanging drop method and the addition of particular reagents and factors for induction at the stage of EB attachment. The AS-ES1 cells generated separately in vitro included: adipocytes, osteoblasts, chondrocytes and cardiomyocytes. Histochemical staining, immunofluorescent staining and RT-PCR were carried out to confirm the formation of multiple mesodermal lineage cells. Conclusions: The appropriate reagents and culture milieu used in mesodermal differentiation of mouse ES cells also guide the differentiation of in vitro AS-ES1 cells into distinct mesoderm-derived cells. This study provides a better understanding of the characteristics of AS-ES1 cells, a new species ES cell line and promotes the use of Apodemus ES cells as a complement to mouse ES cells in future studies. [ABSTRACT FROM AUTHOR]
- Published
- 2010
- Full Text
- View/download PDF
123. Trak1 mutation disrupts GABAA receptor homeostasis in hypertonic mice.
- Author
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Gilbert, Sandra L., Li Zhang, Forster, Michele L., Iwase, Tamaki, Soliven, Betty, Donahue, Leah Rae, Sweet, Hope O., Bronson, Roderick T., Davisson, Muriel T., Wollmann, Robert L., and Lahn, Bruce T.
- Subjects
CENTRAL nervous system ,NERVOUS system ,CEREBRAL palsy ,DEVELOPMENTAL disabilities ,CEREBROVASCULAR disease ,SPINAL cord injuries ,PARAPLEGIA ,PARALYSIS ,DYSTONIA ,PARKINSON'S disease - Abstract
Hypertonia, which results from motor pathway defects in the central nervous system (CNS), is observed in numerous neurological conditions, including cerebral palsy, stroke, spinal cord injury, stiff-person syndrome, spastic paraplegia, dystonia and Parkinson disease. Mice with mutation in the hypertonic (hyrt) gene exhibit severe hypertonia as their primary symptom. Here we show that hyrt mutant mice have much lower levels of γ-aminobutyric acid type A (GABA
A ) receptors in their CNS, particularly the lower motor neurons, than do wild-type mice, indicating that the hypertonicity of the mutants is likely to be caused by deficits in GABA-mediated motor neuron inhibition. We cloned the responsible gene, trafficking protein, kinesin binding 1 (Trak1), and showed that its protein product interacts with GABAA receptors. Our data implicate Trak1 as a crucial regulator of GABAA receptor homeostasis and underscore the importance of hyrt mice as a model for studying the molecular etiology of hypertonia associated with human neurological diseases. [ABSTRACT FROM AUTHOR]- Published
- 2006
- Full Text
- View/download PDF
124. Robust signals of coevolution of interacting residues in mammalian proteomes identified by phylogeny-aided structural analysis.
- Author
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Sun Shim Choi, Weimin Li, and Lahn, Bruce T.
- Subjects
COEVOLUTION ,BIOLOGICAL evolution ,PHYLOGENY ,PROTEOMICS ,MOLECULAR phylogeny ,CONVERGENT evolution ,MOLECULAR biology ,GENETICS - Abstract
The structure of a protein depends critically on the complex interactions among its amino acid residues. It has long been hypothesized that interacting residues might tend to coevolve, but it is not known whether such coevolution is a general phenomenon across the proteome. Here, we describe a novel methodology called phylogeny-aided structural analysis, which uncovers robust signals of interacting-residue coevolution in mammalian proteomes. Furthermore, this new method allows the magnitude of coevolution to be quantified. Finally, it facilitates a comprehensive evaluation of various factors that affect interacting-residue coevolution, such as the physicochemical properties of the interactions between residues, solvent accessibility of the residues and their secondary structure context. [ABSTRACT FROM AUTHOR]
- Published
- 2005
- Full Text
- View/download PDF
125. Opinion: Genetic links between brain development and brain evolution.
- Author
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Gilbert, Sandra L., Dobyns, William B., and Lahn, Bruce T.
- Subjects
BRAIN ,GENETICS ,GENES ,BIOLOGICAL evolution ,CENTRAL nervous system - Abstract
The most defining biological attribute of Homo sapiens is its enormous brain size and accompanying cognitive prowess. How this was achieved by means of genetic changes over the course of human evolution has fascinated biologists and the general public alike. Recent studies have shown that genes controlling brain development — notably those implicated in microcephaly (a congenital defect that is characterized by severely reduced brain size) — are favoured targets of natural selection during human evolution. We propose that genes that regulate brain size during development, such as microcephaly genes, are chief contributors in driving the evolutionary enlargement of the human brain. Based on the synthesis of recent studies, we propose a general methodological template for the genetic analysis of human evolution. [ABSTRACT FROM AUTHOR]
- Published
- 2005
- Full Text
- View/download PDF
126. Adaptive Evolution of MRG, a Neuron-Specific Gene Family Implicated in Nociception.
- Author
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Sun Shim Choi and Lahn, Bruce T.
- Subjects
- *
GENES , *EXTRACELLULAR space , *CELL membranes - Abstract
Shows that the ratio between nonsynonymous and synonymous substitution rates displays distinct profiles along the coding regions of the MRG gene family, with peaks corresponding to extracellular domains and valleys corresponding to transmembrane and cytoplasmic domains. Excess of radical amino acid changes characterizing the extracellular domains; Characteristics of the MRG gene family.
- Published
- 2003
- Full Text
- View/download PDF
127. A human sex-chromosomal gene family expressed in male germ cells and encoding variably charged proteins.
- Author
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Lahn, Bruce T.
- Abstract
Presents a study which describes a family of human X-Y genes that can be assigned to neither the category in which the X and Y homologs are ubiquitously expressed, nor the category in which the X homolog is ubiquitously expressed and the Y homolog is expressed exclusively in the testis. Expression of the germ family, designated VCX/Y, exclusively in male germ cells.
- Published
- 2000
- Full Text
- View/download PDF
128. Derivation, characterization and gene modification of cynomolgus monkey mesenchymal stem cells
- Author
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Ke, Hui, Wang, Peng, Yu, Weihua, Liu, Xiaoming, Liu, Chang, Yang, Fan, Mao, Frank Fuxiang, Zhang, Liangming, Zhang, Xiuming, Lahn, Bruce T., and Xiang, Andy Peng
- Abstract
Mesenchymal stem cells (MSCs) have received considerable attention in recent years. Particularly exciting is the prospect that MSCs could be differentiated into specialized cells of interest, which could then be used for cell therapy and tissue engineering. MSCs derived from nonhuman primates could be a powerful tool for investigating the differentiation potential in vitro and in vivo for preclinical research. The purpose of this study was to isolate cynomolgus mesenchymal stem cells (cMSCs) from adult bone marrow and characterize their growth properties and multipotency. Mononuclear cells were isolated from cynomolgus monkey bone marrow by density-gradient centrifugation, and adherent fibroblast-like cells grew well in the complete growth medium with 10μM Tenofovir. cMSCs expressed mesenchymal markers, such as CD29, CD105, CD166 and were negative for hematopoietic markers such as CD34, CD45. Furthermore, the cells were capable of differentiating into osteogenic, chondrogenic, and adipogenic lineages under certain conditions, maintaining normal karyotype throughout extended culture. We also compared different methods (lipofection, nucleofection and lentivirus) for genetic modification of cMSCs and found lentivirus proved to be the most effective method with transduction efficiency of up to 44.6% and lowest level of cell death. The cells after transduction stably expressed green fluorescence protein (GFP) and maintained the abilities to differentiate down osteogenic and adipogenic lineages. In conclusion, these data showed that cMSCs isolated from cynomolgus bone marrow shared similar characteristics with human MSCs and might provide an attractive cell type for cell-based therapy in higher-order mammalian species disorder models.
- Published
- 2009
- Full Text
- View/download PDF
129. Uncovering the Mutation-Fixation Correlation in Short Lineages
- Author
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Lahn, Bruce T and Vallender, Eric
- Abstract
Background: We recently reported a highly unexpected positive correlation between the fixation probability of nonsynonymous mutations (estimated by \(\omega\)) and neutral mutation rate (estimated by \(K_s\)) in mammalian lineages. However, this positive correlation was observed for lineages with relatively long divergence time such as the human-mouse lineage, and was not found for very short lineages such as the human-chimpanzee lineage. It was previously unclear how to interpret this discrepancy. It may indicate that the positive correlation between \(\omega\) and \(K_s\) in long lineages is a false finding. Alternatively, it may reflect a biologically meaningful difference between various lineages. Finally, the lack of positive correlation in short lineages may be the result of methodological artifacts. Results: Here we show that a strong positive correlation can indeed be seen in short lineages when a method was introduced to correct for the inherently high levels of stochastic noise in the use of \(K_s\) as an estimator of neutral mutation rate. Thus, the previously noted lack of positive correlation between \(\omega\) and \(K_s\) in short lineages is due to stochastic noise in \(K_s\) that makes it a far less reliable estimator of neutral mutation rate in short lineages as compared to long lineages. Conclusion: A positive correlation between \(\omega\) and \(K_s\) can be observed in all mammalian lineages for which large amounts of sequence data are available, including very short lineages. It confirms the authenticity of this highly unexpected correlation, and argues that the correction likely applies broadly across all mammals and perhaps even non-mammalian species.
- Published
- 2007
- Full Text
- View/download PDF
130. The Key Masculinity.
- Author
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Lahn, Bruce T. and Jegalian, Karin
- Subjects
- *
Y chromosome , *SEX chromosomes , *GENES , *SPERMATOZOA , *EMBRYOS , *GAMETES - Abstract
This article reports that the Y chromosome causes an embryo to become male by directing the development of the testes. But new research indicates that the Y does much more. In humans, the tiny Y chromosome one of the smallest of the 46 chromosomes that carry all genes essentially dictates a person's sex. Genes on the Y chromosome trigger the development of male features everything from the formation of the testes and the ability to produce sperm to the emergence of secondary sexual characteristics, such as facial hair and a deep voice. Without a Y chromosome and its resident male-forming genes, an embryo will develop as a female.
- Published
- 1999
131. Systematically Assessing the Influence of 3-Dimensional Structural Context on the Molecular Evolution of Mammalian Proteomes.
- Author
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Sun Shim Choi, Vallender, Eric J., and Lahn, Bruce T.
- Published
- 2006
- Full Text
- View/download PDF
132. Authors' Reply.
- Author
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Bush, Eliot C. and Lahn, Bruce T.
- Subjects
- *
LETTERS to the editor , *GENOMES - Abstract
A response by Bush and others to a letter to the editor about their article "Selective constraint on noncoding regions of hominid genomes" in the 2005 issue is presented.
- Published
- 2006
- Full Text
- View/download PDF
133. Transcriptional Fingerprint of Hypomyelination in Zfp191null and Shiverer (Mbpshi) Mice.
- Author
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Aaker JD, Elbaz B, Wu Y, Looney TJ, Zhang L, Lahn BT, and Popko B
- Abstract
The transcriptional program that controls oligodendrocyte maturation and central nervous system (CNS) myelination has not been fully characterized. In this study, we use high-throughput RNA sequencing to analyze how the loss of a key transcription factor, zinc finger protein 191 (ZFP191), results in oligodendrocyte development abnormalities and CNS hypomyelination. Using a previously described mutant mouse that is deficient in ZFP191 protein expression (Zfp191
null ), we demonstrate that key transcripts are reduced in the whole brain as well as within oligodendrocyte lineage cells cultured in vitro To determine whether the loss of myelin seen in Zfp191null mice contributes indirectly to these perturbations, we also examined the transcriptome of a well-characterized mouse model of hypomyelination, in which the myelin structural protein myelin basic protein (MBP) is deficient. Interestingly, Mbpshi (shiverer) mice had far fewer transcripts perturbed with the loss of myelin alone. This study demonstrates that the loss of ZFP191 disrupts expression of genes involved in oligodendrocyte maturation and myelination, largely independent from the loss of myelin. Nevertheless, hypomyelination in both mouse mutants results in the perturbation of lipid synthesis pathways, suggesting that oligodendrocytes have a feedback system that allows them to regulate myelin lipid synthesis depending on their myelinating state. The data presented are of potential clinical relevance as the human orthologs of the Zfp191 and MBP genes reside on a region of Chromosome 18 that is deleted in childhood leukodystrophies., (© The Author(s) 2016.)- Published
- 2016
- Full Text
- View/download PDF
134. Systematic mapping of occluded genes by cell fusion reveals prevalence and stability of cis-mediated silencing in somatic cells.
- Author
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Looney TJ, Zhang L, Chen CH, Lee JH, Chari S, Mao FF, Pelizzola M, Zhang L, Lister R, Baker SW, Fernandes CJ, Gaetz J, Foshay KM, Clift KL, Zhang Z, Li WQ, Vallender EJ, Wagner U, Qin JY, Michelini KJ, Bugarija B, Park D, Aryee E, Stricker T, Zhou J, White KP, Ren B, Schroth GP, Ecker JR, Xiang AP, and Lahn BT
- Subjects
- Animals, Cell Fusion, Cell Line, Chromatin genetics, DNA Methylation genetics, Genome, Histones genetics, Histones metabolism, Mice, Rats, Gene Expression Regulation, Gene Silencing, Regulatory Sequences, Nucleic Acid, Trans-Activators genetics, Transcription, Genetic
- Abstract
Both diffusible factors acting in trans and chromatin components acting in cis are implicated in gene regulation, but the extent to which either process causally determines a cell's transcriptional identity is unclear. We recently used cell fusion to define a class of silent genes termed "cis-silenced" (or "occluded") genes, which remain silent even in the presence of trans-acting transcriptional activators. We further showed that occlusion of lineage-inappropriate genes plays a critical role in maintaining the transcriptional identities of somatic cells. Here, we present, for the first time, a comprehensive map of occluded genes in somatic cells. Specifically, we mapped occluded genes in mouse fibroblasts via fusion to a dozen different rat cell types followed by whole-transcriptome profiling. We found that occluded genes are highly prevalent and stable in somatic cells, representing a sizeable fraction of silent genes. Occluded genes are also highly enriched for important developmental regulators of alternative lineages, consistent with the role of occlusion in safeguarding cell identities. Alongside this map, we also present whole-genome maps of DNA methylation and eight other chromatin marks. These maps uncover a complex relationship between chromatin state and occlusion. Furthermore, we found that DNA methylation functions as the memory of occlusion in a subset of occluded genes, while histone deacetylation contributes to the implementation but not memory of occlusion. Our data suggest that the identities of individual cell types are defined largely by the occlusion status of their genomes. The comprehensive reference maps reported here provide the foundation for future studies aimed at understanding the role of occlusion in development and disease.
- Published
- 2014
- Full Text
- View/download PDF
135. Generation of functional hepatocytes from mouse induced pluripotent stem cells.
- Author
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Li W, Wang D, Qin J, Liu C, Zhang Q, Zhang X, Yu X, Lahn BT, Mao FF, and Xiang AP
- Subjects
- Albumins metabolism, Animals, Biomarkers metabolism, Butyrates pharmacology, Cells, Cultured, Cholesterol 7-alpha-Hydroxylase metabolism, Dimethyl Sulfoxide pharmacology, Embryonic Stem Cells drug effects, Embryonic Stem Cells metabolism, Glycogen metabolism, Hepatocytes drug effects, Hepatocytes metabolism, Indocyanine Green metabolism, Keratins metabolism, Lipoproteins, LDL metabolism, Mice, Pluripotent Stem Cells drug effects, Pluripotent Stem Cells metabolism, Time Factors, Transcription Factors genetics, Transcription Factors metabolism, Transfection, Urea metabolism, alpha-Fetoproteins metabolism, Cell Differentiation drug effects, Cell Lineage drug effects, Embryonic Stem Cells physiology, Hepatocytes physiology, Pluripotent Stem Cells physiology
- Abstract
Induced pluripotent stem cells are derived from somatic cells by forced expression of several transcriptional factors. Induced pluripotent stem cells resemble embryonic stem cells in many aspects, such as the expression of certain stem cell markers, chromatin methylation patterns, embryoid body formation and teratoma formation. Therefore, induced pluripotent stem cells provide a powerful tool for study of developmental biology and unlimited resources for transplantation therapy. Here we reported the successful induction of mouse induced pluripotent stem cells and a simple and efficient process for generation of functional hepatocytes from mouse induced pluripotent stem cells by sequential addition of inducing factors. These induced pluripotent stem cell-derived hepatocytes, just as mouse embryonic stem cell-derived hepatocytes, expressed hepatic lineage markers including CK7, CK8, CK18, CK19, alpha-fetoprotein, albumin, Cyp7a1, and exhibited functional hepatic characteristics, including glycogen storage, indocyanine green (ICG) uptake and release, low-density lipoprotein (LDL) uptake and urea secretion. Although we observed some variations in the efficiency of hepatic differentiation between induced pluripotent stem cells and common mouse embryonic stem cell lines, our results indicate that mouse induced pluripotent stem cells can efficiently differentiate into functional hepatocytes in vitro, which may be helpful for the study of liver development and regenerative medicine.
- Published
- 2010
- Full Text
- View/download PDF
136. Genetic basis of human brain evolution.
- Author
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Vallender EJ, Mekel-Bobrov N, and Lahn BT
- Subjects
- Animals, Humans, Brain physiology, Evolution, Molecular, Hominidae genetics, Nerve Tissue Proteins genetics
- Abstract
Human evolution is characterized by a rapid increase in brain size and complexity. Decades of research have made important strides in identifying anatomical and physiological substrates underlying the unique features of the human brain. By contrast, it has become possible only very recently to examine the genetic basis of human brain evolution. Through comparative genomics, tantalizing insights regarding human brain evolution have emerged. The genetic changes that potentially underlie human brain evolution span a wide range from single-nucleotide substitutions to large-scale structural alterations of the genome. Similarly, the functional consequences of these genetic changes vary greatly, including protein-sequence alterations, cis-regulatory changes and even the emergence of new genes and the extinction of existing ones. Here, we provide a general review of recent findings into the genetic basis of human brain evolution, highlight the most notable trends that have emerged and caution against over-interpretation of current data.
- Published
- 2008
- Full Text
- View/download PDF
137. Critical role of phosphoinositide 3-kinase cascade in adipogenesis of human mesenchymal stem cells.
- Author
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Yu W, Chen Z, Zhang J, Zhang L, Ke H, Huang L, Peng Y, Zhang X, Li S, Lahn BT, and Xiang AP
- Subjects
- Cell Proliferation drug effects, Enzyme Activation drug effects, Humans, Mesenchymal Stem Cells drug effects, Phosphoinositide-3 Kinase Inhibitors, Protein Kinase Inhibitors pharmacology, Protein Kinases metabolism, Proto-Oncogene Proteins c-akt antagonists & inhibitors, Ribosomal Protein S6 Kinases, 70-kDa antagonists & inhibitors, TOR Serine-Threonine Kinases, Transcription, Genetic drug effects, Adipogenesis drug effects, Mesenchymal Stem Cells cytology, Mesenchymal Stem Cells enzymology, Phosphatidylinositol 3-Kinases metabolism
- Abstract
Mesenchymal stem cells (MSCs) are multipotent stem cells capable of differentiating into adipocytes in the presence of a hormone cocktail. These cells thus provide a promising model for studying the early events of adipogenesis. Here, we examine the involvement of the PI3K/Akt and mTOR/p70S6K signaling pathways in human MSC adipogenesis. We found that the two pathways were strongly activated with a similar temporal profile under the adipogenesis-inducing hormone cocktail and this activation could be blocked by LY294002, a specific inhibitor of PI3K. Furthermore, rapamycin, a specific inhibitor of mTOR, blocked the activation of mTOR/p70S6K but not PI3K/Akt. Both LY294002 and rapamycin severely suppressed lipid accumulation, as well as the expression of adipogenic markers, including PPAR gamma 2 and C/EBP alpha, two master adipogenic transcription factors. Together, these data indicate that the mTOR/p70S6K pathway acts downstream of the PI3K/Akt pathway in mediating the adipogenic conversion of MSCs. In conclusion, our data suggest that the PI3K/Akt and mTOR/p70S6K signaling pathways are essential for adipogenesis of human MSCs.
- Published
- 2008
- Full Text
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138. Proteomic identification of differently expressed proteins responsible for osteoblast differentiation from human mesenchymal stem cells.
- Author
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Zhang AX, Yu WH, Ma BF, Yu XB, Mao FF, Liu W, Zhang JQ, Zhang XM, Li SN, Li MT, Lahn BT, and Xiang AP
- Subjects
- Cells, Cultured, Cluster Analysis, Electrophoresis, Gel, Two-Dimensional, Humans, Mesenchymal Stem Cells metabolism, Reverse Transcriptase Polymerase Chain Reaction, Cell Differentiation, Gene Expression Profiling methods, Mesenchymal Stem Cells cytology, Osteoblasts cytology, Osteoblasts metabolism, Proteomics
- Abstract
Human mesenchymal stem cells (hMSC) are a population of multipotent cells that can differentiate into osteoblasts, chondrocytes, adipocytes, and other cells. The exact mechanism governing the differentiation of hMSC into osteoblasts remains largely unknown. Here, we analyzed protein expression profiles of undifferentiated as well as osteogenic induced hMSC using 2-D gel electrophoresis (2-DE), mass spectrometry (MS), and peptide mass fingerprinting (PMF) to investigate the early gene expression in osteoblast differentiation. We have generated proteome maps of undifferentiated hMSC and osteogenic induced hMSC on day 3 and day 7. 2-DE revealed 102 spots with at least 2.0-fold changes in expression and 52 differently expressed proteins were successfully identified by MALDI-TOF-MS. These proteins were classified into 7 functional categories: metabolism, signal transduction, transcription, calcium-binding protein, protein degradation, protein folding and others. The expression of some identified proteins was confirmed by further RT-PCR analyses. This study clarifies the global proteome during osteoblast differentiation. Our results will play an important role in better elucidating the underlying molecular mechanism in hMSC differentiation into osteoblasts.
- Published
- 2007
- Full Text
- View/download PDF
139. What makes us human: revisiting an age-old question in the genomic era.
- Author
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Mekel-Bobrov N and Lahn BT
- Abstract
In 1970, Karl Pribram took on the immense challenge of asking the question, what makes us human? Nearly four decades later, the most significant finding has been the undeniable realization of how incredibly subtle and fine-scaled the unique biological features of our species must be. The recent explosion in the availability of large-scale sequence data, however, and the consequent emergence of comparative genomics, are rapidly transforming the study of human evolution. The field of comparative genomics is allowing us to reach unparalleled resolution, reframing our questions in reference to DNA sequence--the very unit that evolution operates on. But like any reductionist approach, it comes at a price. Comparative genomics may provide the necessary resolution for identifying rare DNA sequence differences in a vast sea of conservation, but ultimately we will have to face the challenge of figuring out how DNA sequence divergence translates into phenotypic divergence. Our goal here is to provide a brief outline of the major findings made in the study of human brain evolution since the Pribram lecture, focusing specifically on the field of comparative genomics. We then discuss the broader implications of these findings and the future challenges that are in store.
- Published
- 2006
- Full Text
- View/download PDF
140. Evidence that the adaptive allele of the brain size gene microcephalin introgressed into Homo sapiens from an archaic Homo lineage.
- Author
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Evans PD, Mekel-Bobrov N, Vallender EJ, Hudson RR, and Lahn BT
- Subjects
- Animals, Humans, Models, Genetic, Reproduction genetics, Adaptation, Biological genetics, Alleles, Biological Evolution, Brain metabolism, Hominidae genetics, Nerve Tissue Proteins genetics
- Abstract
At the center of the debate on the emergence of modern humans and their spread throughout the globe is the question of whether archaic Homo lineages contributed to the modern human gene pool, and more importantly, whether such contributions impacted the evolutionary adaptation of our species. A major obstacle to answering this question is that low levels of admixture with archaic lineages are not expected to leave extensive traces in the modern human gene pool because of genetic drift. Loci that have undergone strong positive selection, however, offer a unique opportunity to identify low-level admixture with archaic lineages, provided that the introgressed archaic allele has risen to high frequency under positive selection. The gene microcephalin (MCPH1) regulates brain size during development and has experienced positive selection in the lineage leading to Homo sapiens. Within modern humans, a group of closely related haplotypes at this locus, known as haplogroup D, rose from a single copy approximately 37,000 years ago and swept to exceptionally high frequency (approximately 70% worldwide today) because of positive selection. Here, we examine the origin of haplogroup D. By using the interhaplogroup divergence test, we show that haplogroup D likely originated from a lineage separated from modern humans approximately 1.1 million years ago and introgressed into humans by approximately 37,000 years ago. This finding supports the possibility of admixture between modern humans and archaic Homo populations (Neanderthals being one possibility). Furthermore, it buttresses the important notion that, through such adminture, our species has benefited evolutionarily by gaining new advantageous alleles. The interhaplogroup divergence test developed here may be broadly applicable to the detection of introgression at other loci in the human genome or in genomes of other species.
- Published
- 2006
- Full Text
- View/download PDF
141. Multiple independent origins of sex chromosomes in amniotes.
- Author
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Vallender EJ and Lahn BT
- Subjects
- Animals, Biological Evolution, Sex Determination Processes, Amnion metabolism, Origin of Life, Sex Chromosomes genetics
- Published
- 2006
- Full Text
- View/download PDF
142. Trak1 mutation disrupts GABA(A) receptor homeostasis in hypertonic mice.
- Author
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Gilbert SL, Zhang L, Forster ML, Anderson JR, Iwase T, Soliven B, Donahue LR, Sweet HO, Bronson RT, Davisson MT, Wollmann RL, and Lahn BT
- Subjects
- Adaptor Proteins, Vesicular Transport, Animals, Anterior Horn Cells pathology, Chromosomes, Mammalian genetics, Diazepam pharmacology, Electromyography, Gene Expression, Homozygote, Humans, Inclusion Bodies pathology, Inclusion Bodies ultrastructure, Mice, Molecular Sequence Data, Muscle Hypertonia genetics, Muscle Hypertonia pathology, Muscle, Skeletal drug effects, Physical Chromosome Mapping, Pons pathology, Pons ultrastructure, RNA, Messenger genetics, RNA, Messenger metabolism, Carrier Proteins genetics, Carrier Proteins metabolism, Homeostasis, Muscle Hypertonia metabolism, Mutation genetics, Receptors, GABA-A metabolism
- Abstract
Hypertonia, which results from motor pathway defects in the central nervous system (CNS), is observed in numerous neurological conditions, including cerebral palsy, stroke, spinal cord injury, stiff-person syndrome, spastic paraplegia, dystonia and Parkinson disease. Mice with mutation in the hypertonic (hyrt) gene exhibit severe hypertonia as their primary symptom. Here we show that hyrt mutant mice have much lower levels of gamma-aminobutyric acid type A (GABA(A)) receptors in their CNS, particularly the lower motor neurons, than do wild-type mice, indicating that the hypertonicity of the mutants is likely to be caused by deficits in GABA-mediated motor neuron inhibition. We cloned the responsible gene, trafficking protein, kinesin binding 1 (Trak1), and showed that its protein product interacts with GABA(A) receptors. Our data implicate Trak1 as a crucial regulator of GABA(A) receptor homeostasis and underscore the importance of hyrt mice as a model for studying the molecular etiology of hypertonia associated with human neurological diseases.
- Published
- 2006
- Full Text
- View/download PDF
143. Robust signals of coevolution of interacting residues in mammalian proteomes identified by phylogeny-aided structural analysis.
- Author
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Choi SS, Li W, and Lahn BT
- Subjects
- Amino Acid Sequence, Amino Acids chemistry, Animals, Dogs, Humans, Mice, Proteins chemistry, Rats, Evolution, Molecular, Phylogeny, Proteome chemistry, Proteomics methods
- Abstract
The structure of a protein depends critically on the complex interactions among its amino acid residues. It has long been hypothesized that interacting residues might tend to coevolve, but it is not known whether such coevolution is a general phenomenon across the proteome. Here, we describe a novel methodology called phylogeny-aided structural analysis, which uncovers robust signals of interacting-residue coevolution in mammalian proteomes. Furthermore, this new method allows the magnitude of coevolution to be quantified. Finally, it facilitates a comprehensive evaluation of various factors that affect interacting-residue coevolution, such as the physicochemical properties of the interactions between residues, solvent accessibility of the residues and their secondary structure context.
- Published
- 2005
- Full Text
- View/download PDF
144. Ongoing adaptive evolution of ASPM, a brain size determinant in Homo sapiens.
- Author
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Mekel-Bobrov N, Gilbert SL, Evans PD, Vallender EJ, Anderson JR, Hudson RR, Tishkoff SA, and Lahn BT
- Subjects
- Adaptation, Biological, Animals, Asian People genetics, Black People, Brain physiology, Gene Conversion, Gene Frequency, Genotype, Haplotypes, Humans, Linkage Disequilibrium, Models, Genetic, Organ Size, Pan troglodytes genetics, Phylogeny, Polymorphism, Genetic, Recombination, Genetic, Sequence Analysis, DNA, Time, White People, Biological Evolution, Brain anatomy & histology, Nerve Tissue Proteins genetics, Selection, Genetic
- Abstract
The gene ASPM (abnormal spindle-like microcephaly associated) is a specific regulator of brain size, and its evolution in the lineage leading to Homo sapiens was driven by strong positive selection. Here, we show that one genetic variant of ASPM in humans arose merely about 5800 years ago and has since swept to high frequency under strong positive selection. These findings, especially the remarkably young age of the positively selected variant, suggest that the human brain is still undergoing rapid adaptive evolution.
- Published
- 2005
- Full Text
- View/download PDF
145. Microcephalin, a gene regulating brain size, continues to evolve adaptively in humans.
- Author
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Evans PD, Gilbert SL, Mekel-Bobrov N, Vallender EJ, Anderson JR, Vaez-Azizi LM, Tishkoff SA, Hudson RR, and Lahn BT
- Subjects
- Adaptation, Biological, Alleles, Amino Acid Substitution, Asian People genetics, Black People genetics, Brain physiology, Cell Cycle Proteins, Cytoskeletal Proteins, Exons, Gene Conversion, Gene Frequency, Genetic Variation, Genotype, Haplotypes, Humans, Linkage Disequilibrium, Microcephaly genetics, Organ Size, Polymorphism, Genetic, Recombination, Genetic, Sequence Analysis, DNA, Time, White People genetics, Biological Evolution, Brain anatomy & histology, Nerve Tissue Proteins genetics, Selection, Genetic
- Abstract
The gene Microcephalin (MCPH1) regulates brain size and has evolved under strong positive selection in the human evolutionary lineage. We show that one genetic variant of Microcephalin in modern humans, which arose approximately 37,000 years ago, increased in frequency too rapidly to be compatible with neutral drift. This indicates that it has spread under strong positive selection, although the exact nature of the selection is unknown. The finding that an important brain gene has continued to evolve adaptively in anatomically modern humans suggests the ongoing evolutionary plasticity of the human brain. It also makes Microcephalin an attractive candidate locus for studying the genetics of human variation in brain-related phenotypes.
- Published
- 2005
- Full Text
- View/download PDF
146. Genetic links between brain development and brain evolution.
- Author
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Gilbert SL, Dobyns WB, and Lahn BT
- Subjects
- Animals, Humans, Phylogeny, Brain anatomy & histology, Evolution, Molecular, Microcephaly genetics, Nerve Tissue Proteins genetics
- Abstract
The most defining biological attribute of Homo sapiens is its enormous brain size and accompanying cognitive prowess. How this was achieved by means of genetic changes over the course of human evolution has fascinated biologists and the general public alike. Recent studies have shown that genes controlling brain development - notably those implicated in microcephaly (a congenital defect that is characterized by severely reduced brain size) - are favoured targets of natural selection during human evolution. We propose that genes that regulate brain size during development, such as microcephaly genes, are chief contributors in driving the evolutionary enlargement of the human brain. Based on the synthesis of recent studies, we propose a general methodological template for the genetic analysis of human evolution.
- Published
- 2005
- Full Text
- View/download PDF
147. Hereditary hyperekplexia caused by novel mutations of GLRA1 in Turkish families.
- Author
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Gilbert SL, Ozdag F, Ulas UH, Dobyns WB, and Lahn BT
- Subjects
- Alleles, Genetic Predisposition to Disease, Humans, Pedigree, Stiff-Person Syndrome ethnology, Turkey, Mutation, Receptors, Glycine genetics, Stiff-Person Syndrome genetics
- Abstract
Background: Hyperekplexia, also known as startle disease or stiff-person syndrome, is a neurological condition characterized by neonatal hypertonia and a highly exaggerated startle reflex. Genetic studies have linked mutations in the gene encoding glycine receptor alpha1 (GLRA1) with hereditary hyperekplexia., Methods: We analyzed four Turkish families with a history of hyperekplexia. Genomic DNA was obtained from members of these families, and the entire coding sequence of GLRA1 was amplified by PCR followed by the sequencing of PCR products. DNA sequences were analyzed by direct observation using an electropherogram and compared with a published reference sequence., Results: We identified three novel mutations in GLRA1. These included a large deletion removing the first 7 of 9 exons, a single-base deletion in exon 8 that results in protein truncation immediately after the deletion, and a missense mutation in exon 7 causing a tryptophan-to-cysteine change in the first transmembrane domain (M1). These mutant alleles have some distinct features as compared to previously identified GLRA1 mutations. Our data provides further evidence for mutational heterogeneity in GLRA1. The new mutant alleles reported here should advance our understanding of the etiology of hyperekplexia.
- Published
- 2004
- Full Text
- View/download PDF
148. Previously uncharacterized histone acetyltransferases implicated in mammalian spermatogenesis.
- Author
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Lahn BT, Tang ZL, Zhou J, Barndt RJ, Parvinen M, Allis CD, and Page DC
- Subjects
- Acetylation, Acetyltransferases metabolism, Amino Acid Sequence, Animals, Base Sequence, DNA Primers, Histone Acetyltransferases, Histones metabolism, Humans, Immunohistochemistry, Male, Mice, Molecular Sequence Data, Proteins genetics, Proteins metabolism, Reverse Transcriptase Polymerase Chain Reaction, Sequence Homology, Amino Acid, Spermatids metabolism, Acetyltransferases physiology, Nuclear Proteins, Saccharomyces cerevisiae Proteins, Spermatogenesis physiology
- Abstract
During spermiogenesis (the maturation of spermatids into spermatozoa) in many vertebrate species, protamines replace histones to become the primary DNA-packaging protein. It has long been thought that this process is facilitated by the hyperacetylation of histone H4. However, the responsible histone acetyltransferase enzymes are yet to be identified. CDY is a human Y-chromosomal gene family expressed exclusively in the testis and implicated in male infertility. Its mouse homolog Cdyl, which is autosomal, is expressed abundantly in the testis. Proteins encoded by CDY and its homologs bear the "chromodomain," a motif implicated in chromatin binding. Here, we show that (i) human CDY and mouse CDYL proteins exhibit histone acetyltransferase activity in vitro, with a strong preference for histone H4; (ii) expression of human CDY and mouse Cdyl genes during spermatogenesis correlates with the occurrence of H4 hyperacetylation; and (iii) CDY and CDYL proteins are localized to the nuclei of maturing spermatids where H4 hyperacetylation takes place. Taken together, these data link human CDY and mouse CDYL to the histone-to-protamine transition in mammalian spermiogenesis. This link offers a plausible mechanism to account for spermatogenic failure in patients bearing deletions of the CDY genes.
- Published
- 2002
- Full Text
- View/download PDF
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