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

Ioshikhes, I., Trifonov, E. N., Zhang, M. Q. (1999) Periodical distribution of transcription factor sites in promoter regions and connection with chromatin structure. Proceedings of the National Academy of Sciences, 96 (6). pp. 2891-5. ISSN 0027-8424 (Print)

URL: http://www.ncbi.nlm.nih.gov/pubmed/10077607
DOI: 10.1073/pnas.96.6.2891

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.

Item Type: Paper
Uncontrolled Keywords: Animals Binding Sites/genetics Chromatin/ genetics/ultrastructure Genome, Human Humans Promoter Regions (Genetics)/ genetics Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S. Transcription Factors/ genetics Transcription, Genetic
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > transcription
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > Chromatin dynamics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > nucleosome
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > transcription factor
CSHL Authors:
Communities: CSHL labs > Zhang lab
Depositing User: Kathleen Darby
Date Deposited: 30 Apr 2014 13:31
Last Modified: 30 Apr 2014 13:31
PMCID: PMC15865
Related URLs:
URI: http://repository.cshl.edu/id/eprint/29800

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