Constitutive nucleosome depletion and ordered factor assembly at the GRP78 promoter revealed by single molecule footprinting

Einav Nili Gal-Yam, Shinwu Jeong, Amos Tanay, Gerda Egger, Amy S. Lee, Peter A. Jones

Research output: Contribution to journalArticle

53 Citations (Scopus)

Abstract

Chromatin organization and transcriptional regulation are interrelated processes. A shortcoming of current experimental approaches to these complex events is the lack of methods that can capture the activation process on single promoters. We have recently described a method that combines methyltransferase M.SssI treatment of intact nuclei and bisulfite sequencing allowing the representation of replicas of single promoters in terms of protected and unprotected footprint modules. Here we combine this method with computational analysis to study single molecule dynamics of transcriptional activation in the stress inducible GRP78 promoter. We show that a 350-base pair region upstream of the transcription initiation site is constitutively depleted of nucleosomes, regardless of the induction state of the promoter, providing one of the first examples for such a promoter in mammals. The 350-base pair nucleosome-free region can be dissected into modules, identifying transcription factor binding sites and their combinatorial organization during endoplasmic reticulum stress. The interaction of the transcriptional machinery with the GRP78 core promoter is highly organized, represented by six major combinatorial states. We show that the TATA box is frequently occupied in the noninduced state, that stress induction results in sequential loading of the endoplasmic reticulum stress response elements, and that a substantial portion of these elements is no longer occupied following recruitment of factors to the transcription initiation site. Studying the positioning of nucleosomes and transcription factors at the single promoter level provides a powerful tool to gain novel insights into the transcriptional process in eukaryotes.

Original languageEnglish (US)
Pages (from-to)1451-1463
Number of pages13
JournalPLoS genetics
Volume2
Issue number9
DOIs
StatePublished - Oct 10 2006

Fingerprint

nucleosomes
Nucleosomes
Endoplasmic Reticulum Stress
Transcription Initiation Site
promoter regions
Base Pairing
Transcription Factors
TATA Box
Methyltransferases
Response Elements
eukaryote
Eukaryota
footprint
machinery
Transcriptional Activation
positioning
Chromatin
Mammals
endoplasmic reticulum
mammal

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics
  • Genetics(clinical)
  • Cancer Research

Cite this

Constitutive nucleosome depletion and ordered factor assembly at the GRP78 promoter revealed by single molecule footprinting. / Gal-Yam, Einav Nili; Jeong, Shinwu; Tanay, Amos; Egger, Gerda; Lee, Amy S.; Jones, Peter A.

In: PLoS genetics, Vol. 2, No. 9, 10.10.2006, p. 1451-1463.

Research output: Contribution to journalArticle

Gal-Yam, Einav Nili ; Jeong, Shinwu ; Tanay, Amos ; Egger, Gerda ; Lee, Amy S. ; Jones, Peter A. / Constitutive nucleosome depletion and ordered factor assembly at the GRP78 promoter revealed by single molecule footprinting. In: PLoS genetics. 2006 ; Vol. 2, No. 9. pp. 1451-1463.
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