Tissue-specific Analysis of Chromatin State Identifies Temporal Signatures of Enhancer Activity During Embryonic Development

Overview

Journal Nat Genet

Specialty Genetics

Date 2012 Jan 11

PMID 22231485

Citations 299

Authors

Stefan Bonn

Robert P Zinzen

Charles Girardot

E Hilary Gustafson

Alexis Perez-Gonzalez

Nicolas Delhomme

Yad Ghavi-Helm

Bartek Wilczynski

Andrew Riddell

Eileen E M Furlong

Affiliations

Soon will be listed here.

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.

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