4 results on '"Vladyslav Bondarenko"'
Search Results
2. Genomic analysis of P elements in natural populations of Drosophila melanogaster
- Author
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Casey M. Bergman, Shunhua Han, Michael G. Nelson, Vladyslav Bondarenko, and Iryna Kozeretska
- Subjects
P element ,Drosophila melanogaster ,Transposable elements ,Population genomics ,Hybrid dysgenesis ,Medicine ,Biology (General) ,QH301-705.5 - Abstract
The Drosophila melanogaster P transposable element provides one of the best cases of horizontal transfer of a mobile DNA sequence in eukaryotes. Invasion of natural populations by the P element has led to a syndrome of phenotypes known as P-M hybrid dysgenesis that emerges when strains differing in their P element composition mate and produce offspring. Despite extensive research on many aspects of P element biology, many questions remain about the genomic basis of variation in P-M dysgenesis phenotypes across populations. Here we compare estimates of genomic P element content with gonadal dysgenesis phenotypes for isofemale strains obtained from three worldwide populations of D. melanogaster to illuminate the molecular basis of natural variation in cytotype status. We show that P element abundance estimated from genome sequences of isofemale strains is highly correlated across different bioinformatics approaches, but that abundance estimates are sensitive to method and filtering strategies as well as incomplete inbreeding of isofemale strains. We find that P element content varies significantly across populations, with strains from a North American population having fewer P elements but a higher proportion of full-length elements than strains from populations sampled in Europe or Africa. Despite these geographic differences in P element abundance and structure, neither the number of P elements nor the ratio of full-length to internally-truncated copies is strongly correlated with the degree of gonadal dysgenesis exhibited by an isofemale strain. Thus, variation in P element abundance and structure across different populations does not necessarily lead to corresponding geographic differences in gonadal dysgenesis phenotypes. Finally, we confirm that population differences in the abundance and structure of P elements that are observed from isofemale lines can also be observed in pool-seq samples from the same populations. Our work supports the view that genomic P element content alone is not sufficient to explain variation in gonadal dysgenesis across strains of D. melanogaster, and informs future efforts to decode the genomic basis of geographic and temporal differences in P element induced phenotypes.
- Published
- 2017
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3. The degree of enhancer or promoter activity is reflected by the levels and directionality of eRNA transcription
- Author
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Rebecca Rodríguez Viales, Olga Mikhaylichenko, Ignacio E. Schor, Eileen E. M. Furlong, Matilda Males, Vladyslav Bondarenko, and Dermot Harnett
- Subjects
0301 basic medicine ,SPATIO ,Enhancer RNAs ,EMBRYONIC DEVELOPMENT] ,Biology ,Ciencias Biológicas ,PROMOTERS ,purl.org/becyt/ford/1 [https] ,03 medical and health sciences ,Transcription (biology) ,Gene expression ,Genetics ,Directionality ,ERNA ,Enhancer ,purl.org/becyt/ford/1.6 [https] ,NCRNA ,Drosophila embryogenesis ,Promoter ,TEMPORAL EXPRESSION ,Bioquímica y Biología Molecular ,Non-coding RNA ,Cell biology ,030104 developmental biology ,DEVELOPMENTAL ENHANCERS ,CIENCIAS NATURALES Y EXACTAS ,Developmental Biology - Abstract
Gene expression is regulated by promoters, which initiate transcription, and enhancers, which control their temporal and spatial activity. However, the discovery that mammalian enhancers also initiate transcription questions the inherent differences between enhancers and promoters. Here, we investigate the transcriptional properties of enhancers during Drosophila embryogenesis using characterized developmental enhancers. We show that while the timing of enhancer transcription is generally correlated with enhancer activity, the levels and directionality of transcription are highly varied among active enhancers. To assess how this impacts function, we developed a dual transgenic assay to simultaneously measure enhancer and promoter activities from a single element in the same embryo. Extensive transgenic analysis revealed a relationship between the direction of endogenous transcription and the ability to function as an enhancer or promoter in vivo, although enhancer RNA (eRNA) production and activity are not always strictly coupled. Some enhancers (mainly bidirectional) can act as weak promoters, producing overlapping spatio–temporal expression. Conversely, bidirectional promoters often act as strong enhancers, while unidirectional promoters generally cannot. The balance between enhancer and promoter activity is generally reflected in the levels and directionality of eRNA transcription and is likely an inherent sequence property of the elements themselves. Fil: Mikhaylichenko, Olga. European Molecular Biology Laboratory; Alemania Fil: Bondarenko, Vladyslav. European Molecular Biology Laboratory; Alemania Fil: Harnett, Dermot. European Molecular Biology Laboratory; Alemania Fil: Schor, Ignacio Esteban. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina Fil: Males, Matilda. European Molecular Biology Laboratory; Alemania Fil: Viales, Rebecca R.. European Molecular Biology Laboratory; Alemania Fil: Furlong, Eileen E. M.. European Molecular Biology Laboratory; Alemania
- Published
- 2018
4. Toward predictive R-loop computational biology: genome-scale prediction of R-loops reveals their association with complex promoter structures, G-quadruplexes and transcriptionally active enhancers
- Author
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Surya Pavan Yenamandra, Vladimir A. Kuznetsov, Vladyslav Bondarenko, Thidathip Wongsurawat, and Piroon Jenjaroenpun
- Subjects
0301 basic medicine ,Transcription, Genetic ,R-loop ,Computational biology ,Biology ,Genome ,03 medical and health sciences ,chemistry.chemical_compound ,Transcription (biology) ,Genetics ,Humans ,Enhancer ,Promoter Regions, Genetic ,Gene ,030102 biochemistry & molecular biology ,Genome, Human ,Computational Biology ,Promoter ,DNA ,G-Quadruplexes ,Gene Expression Regulation, Neoplastic ,030104 developmental biology ,Enhancer Elements, Genetic ,chemistry ,Nucleic Acid Conformation ,RNA ,Human genome ,Erratum ,K562 Cells - Abstract
R-loops are three-stranded RNA:DNA hybrid structures essential for many normal and pathobiological processes. Previously, we generated a quantitative R-loop forming sequence (RLFS) model, quantitative model of R-loop-forming sequences (QmRLFS) and predicted ∼660 000 RLFSs; most of them located in genes and gene-flanking regions, G-rich regions and disease-associated genomic loci in the human genome. Here, we conducted a comprehensive comparative analysis of these RLFSs using experimental data and demonstrated the high performance of QmRLFS predictions on the nucleotide and genome scales. The preferential co-localization of RLFS with promoters, U1 splice sites, gene ends, enhancers and non-B DNA structures, such as G-quadruplexes, provides evidence for the mechanical linkage between DNA tertiary structures, transcription initiation and R-loops in critical regulatory genome regions. We introduced and characterized an abundant class of reverse-forward RLFS clusters highly enriched in non-B DNA structures, which localized to promoters, gene ends and enhancers. The RLFS co-localization with promoters and transcriptionally active enhancers suggested new models for in cis and in trans regulation by RNA:DNA hybrids of transcription initiation and formation of 3D-chromatin loops. Overall, this study provides a rationale for the discovery and characterization of the non-B DNA regulatory structures involved in the formation of the RNA:DNA interactome as the basis for an emerging quantitative R-loop biology and pathobiology.
- Published
- 2018
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