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PMID: 10077607 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.

Periodical distribution of transcription factor sites in promoter regions and connection with chromatin structure.

Proceedings of the National Academy of Sciences of the United States of America ·Vol. 96 ·No. 6 ·1999-03-16 ·Pages 2891-5

Ioshikhes I, Trifonov EN, Zhang MQ

Abstract

Nucleosomes regulate transcriptional initiation when positioned in the promoter area. This may require the transcription factor (TF) sites to be correlated with the nucleosome positions and phased on the nucleosome surface. If this is the case, one would expect a periodical distribution of TF sites in the vicinity of promoters, with the nucleosomal period of 10.1-10.5 bp. We examined the distributions of putative binding sites of 323 different TFs along 1, 057 sequences of the Eukaryotic Promoter Database (release 50) [Cavin Perier, R., Junier, T. & Bucher, P. (1998) Nucleic Acids Res. 26, 353-357] and of 218 TFs on 673 sequences of the Lead Exon Database of human promoter sequences. We obtained a statistically significant overrepresentation of TF sites distributed with the main period of 10.1-10.5 bp in the region -50 to +120 around the transcription start site and in few locations nearby. Correlation of the positioning of the TF sites with the nucleosomes is further reinforced by sequence-directed mapping of the nucleosomes, a method previously developed.

MeSH Terms
Animals Binding Sites/genetics Chromatin/genetics,ultrastructure Genome, Human Humans Promoter Regions, Genetic/genetics Transcription Factors/genetics Transcription, Genetic
Chemicals
Chromatin Transcription Factors
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Ioshikhes I
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
Trifonov E N
Zhang M Q
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Article Info
Journal
Proceedings of the National Academy of Sciences of the United States of America
Abbr.
Proc Natl Acad Sci U S A
ISSN
0027-8424
DOI
10.1073/pnas.96.6.2891
Published
1999-03-16
Pages
2891-5
Language
English
Region
United States
NLM ID
7505876
PMCID
PMC15865
Subset
IM
Grants
NHGRI NIH HHS · R01 HG001696 · United States
NHGRI NIH HHS · HG01696 · United States
External Links
PubMed source DOI: 10.1073/pnas.96.6.2891 PMC Full Text View journal details
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