title: High nucleosome occupancy is encoded at human regulatory sequences.
abstract: Active eukaryotic regulatory sites are characterized by open chromatin, and yeast promoters and transcription factor binding sites (TFBSs) typically have low intrinsic nucleosome occupancy. Here, we show that in contrast to yeast, DNA at human promoters, enhancers, and TFBSs generally encodes high intrinsic nucleosome occupancy. In most cases we examined, these elements also have high experimentally measured nucleosome occupancy in vivo. These regions typically have high G+C content, which correlates positively with intrinsic nucleosome occupancy, and are depleted for nucleosome-excluding poly-A sequences. We propose that high nucleosome preference is directly encoded at regulatory sequences in the human genome to restrict access to regulatory information that will ultimately be utilized in only a subset of differentiated cells.
authors.affiliation: Department of Molecular Genetics, University of Toronto, Toronto, Canada.
authors.forename: Desiree
authors.initials: D
authors.lastname: Tillo
authors.forename: Noam
authors.initials: N
authors.lastname: Kaplan
authors.forename: Irene K
authors.initials: IK
authors.lastname: Moore
authors.forename: Yvonne
authors.initials: Y
authors.lastname: Fondufe-Mittendorf
authors.forename: Andrea J
authors.initials: AJ
authors.lastname: Gossett
authors.forename: Yair
authors.initials: Y
authors.lastname: Field
authors.forename: Jason D
authors.initials: JD
authors.lastname: Lieb
authors.forename: Jonathan
authors.initials: J
authors.lastname: Widom
authors.forename: Eran
authors.initials: E
authors.lastname: Segal
authors.forename: Timothy R
authors.initials: TR
authors.lastname: Hughes
mesh_terms: D001482:Base Composition; D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D015496:CD4-Positive T-Lymphocytes / Q000166:cytology / Q000378:metabolism; D002478:Cells, Cultured; D018899:CpG Islands / Q000235:genetics; D004742:Enhancer Elements, Genetic / Q000235:genetics; D005347:Fibroblasts / Q000166:cytology / Q000378:metabolism; D006367:HeLa Cells; D006801:Humans; D019169:Jurkat Cells; D009707:Nucleosomes / Q000378:metabolism*; D011401:Promoter Regions, Genetic / Q000235:genetics; D011485:Protein Binding; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D009707:Nucleosomes; D014157:Transcription Factors