title: Genome-wide analysis of the relationships between DNaseI HS, histone modifications and gene expression reveals distinct modes of chromatin domains.
abstract: To understand the molecular mechanisms that underlie global transcriptional regulation, it is essential to first identify all the transcriptional regulatory elements in the human genome. The advent of next-generation sequencing has provided a powerful platform for genome-wide analysis of different species and specific cell types; when combined with traditional techniques to identify regions of open chromatin [DNaseI hypersensitivity (DHS)] or specific binding locations of transcription factors [chromatin immunoprecipitation (ChIP)], and expression data from microarrays, we become uniquely poised to uncover the mysteries of the genome and its regulation. To this end, we have performed global meta-analysis of the relationship among data from DNaseI-seq, ChIP-seq and expression arrays, and found that specific correlations exist among regulatory elements and gene expression across different cell types. These correlations revealed four distinct modes of chromatin domain structure reflecting different functions: repressive, active, primed and bivalent. Furthermore, CCCTC-binding factor (CTCF) binding sites were identified based on these integrative data. Our findings uncovered a complex regulatory process involving by DNaseI HS sites and histone modifications, and suggest that these dynamic elements may be responsible for maintaining chromatin structure and integrity of the human genome. Our integrative approach provides an example by which data from diverse technology platforms may be integrated to provide more meaningful insights into global transcriptional regulation.
authors.affiliation: Beijing Institute of Radiation Medicine, Beijing 100850, China.
authors.forename: Wenjie
authors.initials: W
authors.lastname: Shu
authors.forename: Hebing
authors.initials: H
authors.lastname: Chen
authors.forename: Xiaochen
authors.initials: X
authors.lastname: Bo
authors.forename: Shengqi
authors.initials: S
authors.lastname: Wang
mesh_terms: D001665:Binding Sites; D000076246:CCCTC-Binding Factor; D002460:Cell Line; D002843:Chromatin / Q000737:chemistry*; D047369:Chromatin Immunoprecipitation; D003850:Deoxyribonuclease I; D015870:Gene Expression; D020869:Gene Expression Profiling; D015894:Genome, Human; D006657:Histones / Q000378:metabolism*; D006801:Humans; D012097:Repressor Proteins / Q000378:metabolism; D014157:Transcription Factors / Q000378:metabolism; D024363:Transcription Initiation Site
chemical_list: D000076246:CCCTC-Binding Factor; C000619697:CTCF protein, human; D002843:Chromatin; D006657:Histones; D012097:Repressor Proteins; D014157:Transcription Factors; D003850:Deoxyribonuclease I