Pioneer factor interactions and unmethylated CpG dinucleotides mark silent tissue-specific enhancers in embryonic stem cells

Jian Xu, Scott D. Pope, Ali R. Jazirehi, Joanne L. Attema, Peter Papathanasiou, Jason A. Watts, Kenneth S. Zaret, Irving L. Weissman, Stephen T. Smale

Research output: Contribution to journalArticle

88 Citations (Scopus)

Abstract

Recent studies have suggested that, in ES cells, inactive genes encoding early developmental regulators possess bivalent histone modification domains and are therefore poised for activation. However, bivalent domains were not observed at typical tissue-specific genes. Here, we show that windows of unmethylated CpG dinucleotides and putative pioneer factor interactions mark enhancers for at least some tissue-specific genes in ES cells. The unmethylated windows expand in cells that express the gene and contract, disappear, or remain unchanged in nonexpressing tissues. However, in ES cells, they do not always coincide with common histone modifications. Genomic footprinting and chromatin immunoprecipitation demonstrated that transcription factor binding underlies the unmethylated windows at enhancers for the Ptcra and Alb1 genes. After stable integration of premethylated Ptcra enhancer constructs into the ES cell genome, the unmethylated windows readily appeared. In contrast, the premethylated constructs remained fully methylated and silent after introduction into Ptcra-expressing thymocytes. These findings provide initial functional support for a model in which pioneer factor interactions in ES cells promote the assembly of a chromatin structure that is permissive for subsequent activation, and in which differentiated tissues lack the machinery required for gene activation when these ES cell marks are absent. The enhancer marks may therefore represent important features of the pluripotent state.

Original languageEnglish (US)
Pages (from-to)12377-12382
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume104
Issue number30
DOIs
StatePublished - Jul 24 2007

Fingerprint

Embryonic Stem Cells
Histone Code
Genes
Chromatin Assembly and Disassembly
Chromatin Immunoprecipitation
Thymocytes
Contracts
Transcriptional Activation
Transcription Factors
Genome

Keywords

  • Chromatin
  • Hematopoiesis

ASJC Scopus subject areas

  • Genetics
  • General

Cite this

Pioneer factor interactions and unmethylated CpG dinucleotides mark silent tissue-specific enhancers in embryonic stem cells. / Xu, Jian; Pope, Scott D.; Jazirehi, Ali R.; Attema, Joanne L.; Papathanasiou, Peter; Watts, Jason A.; Zaret, Kenneth S.; Weissman, Irving L.; Smale, Stephen T.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 104, No. 30, 24.07.2007, p. 12377-12382.

Research output: Contribution to journalArticle

Xu, Jian ; Pope, Scott D. ; Jazirehi, Ali R. ; Attema, Joanne L. ; Papathanasiou, Peter ; Watts, Jason A. ; Zaret, Kenneth S. ; Weissman, Irving L. ; Smale, Stephen T. / Pioneer factor interactions and unmethylated CpG dinucleotides mark silent tissue-specific enhancers in embryonic stem cells. In: Proceedings of the National Academy of Sciences of the United States of America. 2007 ; Vol. 104, No. 30. pp. 12377-12382.
@article{6e148490259e4cf0bf92cab382cbf32d,
title = "Pioneer factor interactions and unmethylated CpG dinucleotides mark silent tissue-specific enhancers in embryonic stem cells",
abstract = "Recent studies have suggested that, in ES cells, inactive genes encoding early developmental regulators possess bivalent histone modification domains and are therefore poised for activation. However, bivalent domains were not observed at typical tissue-specific genes. Here, we show that windows of unmethylated CpG dinucleotides and putative pioneer factor interactions mark enhancers for at least some tissue-specific genes in ES cells. The unmethylated windows expand in cells that express the gene and contract, disappear, or remain unchanged in nonexpressing tissues. However, in ES cells, they do not always coincide with common histone modifications. Genomic footprinting and chromatin immunoprecipitation demonstrated that transcription factor binding underlies the unmethylated windows at enhancers for the Ptcra and Alb1 genes. After stable integration of premethylated Ptcra enhancer constructs into the ES cell genome, the unmethylated windows readily appeared. In contrast, the premethylated constructs remained fully methylated and silent after introduction into Ptcra-expressing thymocytes. These findings provide initial functional support for a model in which pioneer factor interactions in ES cells promote the assembly of a chromatin structure that is permissive for subsequent activation, and in which differentiated tissues lack the machinery required for gene activation when these ES cell marks are absent. The enhancer marks may therefore represent important features of the pluripotent state.",
keywords = "Chromatin, Hematopoiesis",
author = "Jian Xu and Pope, {Scott D.} and Jazirehi, {Ali R.} and Attema, {Joanne L.} and Peter Papathanasiou and Watts, {Jason A.} and Zaret, {Kenneth S.} and Weissman, {Irving L.} and Smale, {Stephen T.}",
year = "2007",
month = "7",
day = "24",
doi = "10.1073/pnas.0704579104",
language = "English (US)",
volume = "104",
pages = "12377--12382",
journal = "Proceedings of the National Academy of Sciences of the United States of America",
issn = "0027-8424",
number = "30",

}

TY - JOUR

T1 - Pioneer factor interactions and unmethylated CpG dinucleotides mark silent tissue-specific enhancers in embryonic stem cells

AU - Xu, Jian

AU - Pope, Scott D.

AU - Jazirehi, Ali R.

AU - Attema, Joanne L.

AU - Papathanasiou, Peter

AU - Watts, Jason A.

AU - Zaret, Kenneth S.

AU - Weissman, Irving L.

AU - Smale, Stephen T.

PY - 2007/7/24

Y1 - 2007/7/24

N2 - Recent studies have suggested that, in ES cells, inactive genes encoding early developmental regulators possess bivalent histone modification domains and are therefore poised for activation. However, bivalent domains were not observed at typical tissue-specific genes. Here, we show that windows of unmethylated CpG dinucleotides and putative pioneer factor interactions mark enhancers for at least some tissue-specific genes in ES cells. The unmethylated windows expand in cells that express the gene and contract, disappear, or remain unchanged in nonexpressing tissues. However, in ES cells, they do not always coincide with common histone modifications. Genomic footprinting and chromatin immunoprecipitation demonstrated that transcription factor binding underlies the unmethylated windows at enhancers for the Ptcra and Alb1 genes. After stable integration of premethylated Ptcra enhancer constructs into the ES cell genome, the unmethylated windows readily appeared. In contrast, the premethylated constructs remained fully methylated and silent after introduction into Ptcra-expressing thymocytes. These findings provide initial functional support for a model in which pioneer factor interactions in ES cells promote the assembly of a chromatin structure that is permissive for subsequent activation, and in which differentiated tissues lack the machinery required for gene activation when these ES cell marks are absent. The enhancer marks may therefore represent important features of the pluripotent state.

AB - Recent studies have suggested that, in ES cells, inactive genes encoding early developmental regulators possess bivalent histone modification domains and are therefore poised for activation. However, bivalent domains were not observed at typical tissue-specific genes. Here, we show that windows of unmethylated CpG dinucleotides and putative pioneer factor interactions mark enhancers for at least some tissue-specific genes in ES cells. The unmethylated windows expand in cells that express the gene and contract, disappear, or remain unchanged in nonexpressing tissues. However, in ES cells, they do not always coincide with common histone modifications. Genomic footprinting and chromatin immunoprecipitation demonstrated that transcription factor binding underlies the unmethylated windows at enhancers for the Ptcra and Alb1 genes. After stable integration of premethylated Ptcra enhancer constructs into the ES cell genome, the unmethylated windows readily appeared. In contrast, the premethylated constructs remained fully methylated and silent after introduction into Ptcra-expressing thymocytes. These findings provide initial functional support for a model in which pioneer factor interactions in ES cells promote the assembly of a chromatin structure that is permissive for subsequent activation, and in which differentiated tissues lack the machinery required for gene activation when these ES cell marks are absent. The enhancer marks may therefore represent important features of the pluripotent state.

KW - Chromatin

KW - Hematopoiesis

UR - http://www.scopus.com/inward/record.url?scp=34547635650&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=34547635650&partnerID=8YFLogxK

U2 - 10.1073/pnas.0704579104

DO - 10.1073/pnas.0704579104

M3 - Article

VL - 104

SP - 12377

EP - 12382

JO - Proceedings of the National Academy of Sciences of the United States of America

JF - Proceedings of the National Academy of Sciences of the United States of America

SN - 0027-8424

IS - 30

ER -