High nucleosome occupancy is encoded at human regulatory sequences.
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.
Tillo
Desiree
D
Department of Molecular Genetics, University of Toronto, Toronto, Canada.
Kaplan
Noam
N
Moore
Irene K
IK
Fondufe-Mittendorf
Yvonne
Y
Gossett
Andrea J
AJ
Field
Yair
Y
Lieb
Jason D
JD
Widom
Jonathan
J
Segal
Eran
E
Hughes
Timothy R
TR
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*
D009707:Nucleosomes; D014157:Transcription Factors