Genome-wide Nucleosome Specificity and Function of Chromatin Remodellers in ES Cells

Overview

Journal Nature

Specialty Science

Date 2016 Jan 28

PMID 26814966

Citations 123

Authors

Maud de Dieuleveult

Kuangyu Yen

Isabelle Hmitou

Arnaud Depaux

Faycal Boussouar

Daria Bou Dargham

Sylvie Jounier

Helene Humbertclaude

Florence Ribierre

Celine Baulard

Nina P Farrell

Bongsoo Park

Celine Keime

Lucie Carriere

Soizick Berlivet

Marta Gut

Ivo Gut

Michel Werner

Jean-Francois Deleuze

Robert Olaso

Jean-Christophe Aude

Sophie Chantalat

B Franklin Pugh

Matthieu Gerard

Affiliations

Soon will be listed here.

Abstract

ATP-dependent chromatin remodellers allow access to DNA for transcription factors and the general transcription machinery, but whether mammalian chromatin remodellers target specific nucleosomes to regulate transcription is unclear. Here we present genome-wide remodeller-nucleosome interaction profiles for the chromatin remodellers Chd1, Chd2, Chd4, Chd6, Chd8, Chd9, Brg1 and Ep400 in mouse embryonic stem (ES) cells. These remodellers bind one or both full nucleosomes that flank micrococcal nuclease (MNase)-defined nucleosome-free promoter regions (NFRs), where they separate divergent transcription. Surprisingly, large CpG-rich NFRs that extend downstream of annotated transcriptional start sites are nevertheless bound by non-nucleosomal or subnucleosomal histone variants (H3.3 and H2A.Z) and marked by H3K4me3 and H3K27ac modifications. RNA polymerase II therefore navigates hundreds of base pairs of altered chromatin in the sense direction before encountering an MNase-resistant nucleosome at the 3' end of the NFR. Transcriptome analysis after remodeller depletion reveals reciprocal mechanisms of transcriptional regulation by remodellers. Whereas at active genes individual remodellers have either positive or negative roles via altering nucleosome stability, at polycomb-enriched bivalent genes the same remodellers act in an opposite manner. These findings indicate that remodellers target specific nucleosomes at the edge of NFRs, where they regulate ES cell transcriptional programs.

Citing Articles

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