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PMID: 22231485 Published · epublish English Journal Article Research Support, Non-U.S. Gov't

Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development.

Nature genetics ·Vol. 44 ·No. 2 ·2012-01-08 ·Pages 148-56

Bonn S, Zinzen RP, Girardot C, Gustafson EH, Perez-Gonzalez A, Delhomme N, Ghavi-Helm Y, Wilczyński B, Riddell A, Furlong EE

Abstract

Chromatin modifications are associated with many aspects of gene expression, yet their role in cellular transitions during development remains elusive. Here, we use a new approach to obtain cell type-specific information on chromatin state and RNA polymerase II (Pol II) occupancy within the multicellular Drosophila melanogaster embryo. We directly assessed the relationship between chromatin modifications and the spatio-temporal activity of enhancers. Rather than having a unique chromatin state, active developmental enhancers show heterogeneous histone modifications and Pol II occupancy. Despite this complexity, combined chromatin signatures and Pol II presence are sufficient to predict enhancer activity de novo. Pol II recruitment is highly predictive of the timing of enhancer activity and seems dependent on the timing and location of transcription factor binding. Chromatin modifications typically demarcate large regulatory regions encompassing multiple enhancers, whereas local changes in nucleosome positioning and Pol II occupancy delineate single active enhancers. This cell type-specific view identifies dynamic enhancer usage, an essential step in deciphering developmental networks.

MeSH Terms
Animals Chromatin/metabolism Chromatin Immunoprecipitation Drosophila melanogaster/embryology,genetics,metabolism Embryonic Development/genetics Enhancer Elements, Genetic Gene Expression Regulation, Developmental Histones/metabolism RNA Polymerase II/metabolism Transcription Factors/metabolism
Chemicals
Chromatin Histones Transcription Factors RNA Polymerase II
Authors & Affiliations
10 authors, click to expand affiliations / ORCID
Bonn Stefan
Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
Zinzen Robert P
Girardot Charles
Gustafson E Hilary
Perez-Gonzalez Alexis
Delhomme Nicolas
Ghavi-Helm Yad
Wilczyński Bartek
Riddell Andrew
Furlong Eileen E M
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Article Info
Journal
Nature genetics
Abbr.
Nat Genet
ISSN
1546-1718
DOI
10.1038/ng.1064
Published
2012-01-08
Epub
2012-00-08
Pages
148-56
Language
English
Region
United States
NLM ID
9216904
Subset
IM
External Links
PubMed source DOI: 10.1038/ng.1064 View journal details
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