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Positional specificity of different transcription factor classes within enhancers.

Gene expression is controlled by sequence-specific transcription factors (TFs), which bind to regulatory sequences in DNA. TF binding occurs in nucleosome-depleted regions of DNA (NDRs), which generally encompass regions with lengths similar to those protected by nucleosomes. However, less is known... Full description

Journal Title: Proceedings of the National Academy of Sciences of the United States of America July 24, 2018, Vol.115(30), pp.E7222-E7230
Main Author: Grossman, Sharon R
Other Authors: Engreitz, Jesse , Ray, John P , Nguyen, Tung H , Hacohen, Nir , Lander, Eric S
Format: Electronic Article Electronic Article
Language: English
Subjects:
ID: E-ISSN: 1091-6490 ; DOI: 10.1073/pnas.1804663115
Link: http://search.proquest.com/docview/2067885825/?pq-origsite=primo
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title: Positional specificity of different transcription factor classes within enhancers.
format: Article
creator:
  • Grossman, Sharon R
  • Engreitz, Jesse
  • Ray, John P
  • Nguyen, Tung H
  • Hacohen, Nir
  • Lander, Eric S
subjects:
  • Gene Expression Regulation–Physiology
  • Humans–Physiology
  • Jurkat Cells–Genetics
  • Response Elements–Metabolism
  • Transcription Factors–Metabolism
  • U937 Cells–Metabolism
  • Transcription Factors
  • Chromatin Structure
  • Gene Regulation
  • Genomics
  • Transcription Factor Binding
ispartof: Proceedings of the National Academy of Sciences of the United States of America, July 24, 2018, Vol.115(30), pp.E7222-E7230
description: Gene expression is controlled by sequence-specific transcription factors (TFs), which bind to regulatory sequences in DNA. TF binding occurs in nucleosome-depleted regions of DNA (NDRs), which generally encompass regions with lengths similar to those protected by nucleosomes. However, less is known about where within these regions specific TFs tend to be found. Here, we characterize the positional bias of inferred binding sites for 103 TFs within ~500,000 NDRs across 47 cell types. We find that distinct classes of TFs display different binding preferences: Some tend to have binding sites toward the edges, some toward the center, and some at other positions within the NDR. These patterns are highly consistent across cell types, suggesting that they may reflect TF-specific intrinsic structural or functional characteristics. In particular, TF classes with binding sites at NDR edges are enriched for those known to interact with histones and chromatin remodelers, whereas TFs with central enrichment interact with other TFs and cofactors such as p300. Our results suggest distinct regiospecific binding patterns and functions of TF classes within enhancers. transcription factor binding | gene regulation | genomics | chromatin structure
language: eng
source:
identifier: E-ISSN: 1091-6490 ; DOI: 10.1073/pnas.1804663115
fulltext: fulltext
issn:
  • 10916490
  • 1091-6490
url: Link


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titlePositional specificity of different transcription factor classes within enhancers.
creatorGrossman, Sharon R ; Engreitz, Jesse ; Ray, John P ; Nguyen, Tung H ; Hacohen, Nir ; Lander, Eric S
contributorGrossman, Sharon R (correspondence author) ; Grossman, Sharon R (record owner)
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identifierE-ISSN: 1091-6490 ; DOI: 10.1073/pnas.1804663115
subjectGene Expression Regulation–Physiology ; Humans–Physiology ; Jurkat Cells–Genetics ; Response Elements–Metabolism ; Transcription Factors–Metabolism ; U937 Cells–Metabolism ; Transcription Factors ; Chromatin Structure ; Gene Regulation ; Genomics ; Transcription Factor Binding
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descriptionGene expression is controlled by sequence-specific transcription factors (TFs), which bind to regulatory sequences in DNA. TF binding occurs in nucleosome-depleted regions of DNA (NDRs), which generally encompass regions with lengths similar to those protected by nucleosomes. However, less is known about where within these regions specific TFs tend to be found. Here, we characterize the positional bias of inferred binding sites for 103 TFs within ~500,000 NDRs across 47 cell types. We find that distinct classes of TFs display different binding preferences: Some tend to have binding sites toward the edges, some toward the center, and some at other positions within the NDR. These patterns are highly consistent across cell types, suggesting that they may reflect TF-specific intrinsic structural or functional characteristics. In particular, TF classes with binding sites at NDR edges are enriched for those known to interact with histones and chromatin remodelers, whereas TFs with central enrichment interact with other TFs and cofactors such as p300. Our results suggest distinct regiospecific binding patterns and functions of TF classes within enhancers. transcription factor binding | gene regulation | genomics | chromatin structure
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