Distinct DNA sequence preference for histone occupancy in primary and transformed cells

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dc.contributor.author Datta, Subhamoy
dc.contributor.author Patel, Manthan
dc.contributor.author Patel, Divyesh
dc.contributor.author Singh, Umashankar
dc.date.accessioned 2019-06-19T11:12:55Z
dc.date.available 2019-06-19T11:12:55Z
dc.date.issued 2019-04
dc.identifier.citation Datta, Subhamoy; Patel, Manthan; Patel, Divyesh and Singh, Umashankar, "Distinct DNA sequence preference for histone occupancy in primary and transformed cells", Cancer Informatics, DOI: 10.1177/1176935119843835, vol. 18, Apr. 2019. en_US
dc.identifier.uri https://doi.org/10.1177/1176935119843835
dc.identifier.uri https://repository.iitgn.ac.in/handle/123456789/4488
dc.description.abstract Genome-wide occupancy of several histone modifications in various cell types has been studied using chromatin immunoprecipitation (ChIP) sequencing. Histone occupancy depends on DNA sequence features like inter-strand symmetry of base composition and periodic occurrence of TT/AT. However, whether DNA sequence motifs act as an additional effector of histone occupancy is not known. We have analyzed the presence of DNA sequence motifs in publicly available ChIP-sequence datasets for different histone modifications. Our results show that DNA sequence motifs are associated with histone occupancy, some of which are different between primary and transformed cells. The motifs for primary and transformed cells showed different levels of GC-richness and proximity to transcription start sites (TSSs). The TSSs associated with transformed or primary cell-specific motifs showed different levels of TSS flank transcription in primary and transformed cells. Interestingly, TSSs with a motif-linked occupancy of H2AFZ, a component of positioned nucleosomes, showed a distinct pattern of RNA Polymerase II (POLR2A) occupancy and TSS flank transcription in primary and transformed cells. These results indicate that DNA sequence features dictate differential histone occupancy in primary and transformed cells, and the DNA sequence motifs affect transcription through regulation of histone occupancy.
dc.description.statementofresponsibility by Subhamoy Datta, Manthan Patel, Divyesh Patel and Umashankar Singh
dc.format.extent vol. 18
dc.language.iso en en_US
dc.publisher SAGE Journals en_US
dc.subject ChIP en_US
dc.subject GC-richness en_US
dc.subject TSSs en_US
dc.subject POLR2A en_US
dc.title Distinct DNA sequence preference for histone occupancy in primary and transformed cells en_US
dc.type Article en_US
dc.relation.journal Cancer Informatics


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