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Distinct properties of cell-type-specific and shared transcription factor binding sites.

Publication ,  Journal Article
Gertz, J; Savic, D; Varley, KE; Partridge, EC; Safi, A; Jain, P; Cooper, GM; Reddy, TE; Crawford, GE; Myers, RM
Published in: Mol Cell
October 10, 2013

Most human transcription factors bind a small subset of potential genomic sites and often use different subsets in different cell types. To identify mechanisms that govern cell-type-specific transcription factor binding, we used an integrative approach to study estrogen receptor α (ER). We found that ER exhibits two distinct modes of binding. Shared sites, bound in multiple cell types, are characterized by high-affinity estrogen response elements (EREs), inaccessible chromatin, and a lack of DNA methylation, while cell-specific sites are characterized by a lack of EREs, co-occurrence with other transcription factors, and cell-type-specific chromatin accessibility and DNA methylation. These observations enabled accurate quantitative models of ER binding that suggest tethering of ER to one-third of cell-specific sites. The distinct properties of cell-specific binding were also observed with glucocorticoid receptor and for ER in primary mouse tissues, representing an elegant genomic encoding scheme for generating cell-type-specific gene regulation.

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Published In

Mol Cell

DOI

EISSN

1097-4164

Publication Date

October 10, 2013

Volume

52

Issue

1

Start / End Page

25 / 36

Location

United States

Related Subject Headings

  • Transfection
  • Transcription Factors
  • Thermodynamics
  • Response Elements
  • Receptors, Glucocorticoid
  • RNA Interference
  • Promoter Regions, Genetic
  • Models, Biological
  • Mice
  • Humans
 

Citation

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Gertz, J., Savic, D., Varley, K. E., Partridge, E. C., Safi, A., Jain, P., … Myers, R. M. (2013). Distinct properties of cell-type-specific and shared transcription factor binding sites. Mol Cell, 52(1), 25–36. https://doi.org/10.1016/j.molcel.2013.08.037
Gertz, Jason, Daniel Savic, Katherine E. Varley, E Christopher Partridge, Alexias Safi, Preti Jain, Gregory M. Cooper, Timothy E. Reddy, Gregory E. Crawford, and Richard M. Myers. “Distinct properties of cell-type-specific and shared transcription factor binding sites.Mol Cell 52, no. 1 (October 10, 2013): 25–36. https://doi.org/10.1016/j.molcel.2013.08.037.
Gertz J, Savic D, Varley KE, Partridge EC, Safi A, Jain P, et al. Distinct properties of cell-type-specific and shared transcription factor binding sites. Mol Cell. 2013 Oct 10;52(1):25–36.
Gertz, Jason, et al. “Distinct properties of cell-type-specific and shared transcription factor binding sites.Mol Cell, vol. 52, no. 1, Oct. 2013, pp. 25–36. Pubmed, doi:10.1016/j.molcel.2013.08.037.
Gertz J, Savic D, Varley KE, Partridge EC, Safi A, Jain P, Cooper GM, Reddy TE, Crawford GE, Myers RM. Distinct properties of cell-type-specific and shared transcription factor binding sites. Mol Cell. 2013 Oct 10;52(1):25–36.
Journal cover image

Published In

Mol Cell

DOI

EISSN

1097-4164

Publication Date

October 10, 2013

Volume

52

Issue

1

Start / End Page

25 / 36

Location

United States

Related Subject Headings

  • Transfection
  • Transcription Factors
  • Thermodynamics
  • Response Elements
  • Receptors, Glucocorticoid
  • RNA Interference
  • Promoter Regions, Genetic
  • Models, Biological
  • Mice
  • Humans