Genome-wide nucleosome specificity and function of chromatin remodellers in ES cells

Abstract

SummaryATP-dependent chromatin remodellers allow access to DNA for transcription factors and the general transcription machinery, but whether mammalian chromatin remodellers1–3 target specific nucleosomes to regulate transcription is unclear. Here, we present genome-wide remodeller-nucleosome interaction profiles for 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 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 (TSSs) are nevertheless chromatinized with non-nucleosomal or subnucleosomal histone variants (H3.3 and H2A.Z) and modifications (H3K4me3 and H3K27ac). RNA polymerase (pol) II therefore navigates hundreds of bp of altered chromatin in the sense direction before encountering an MNase-resistant nucleosome at the 3′ end of the NFR. Transcriptome analysis upon remodeller depletion reveals reciprocal mechanisms of transcriptional regulation by remodellers. Whereas at active genes individual remodellers play 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.

Transcriptional Pause Sites Delineate Stable Nucleosome-Associated Premature Polyadenylation Suppressed by U1 snRNP

“…Among them, Chd1 have been linked with regulating the stalling of Pol II at promoter proximal nucleosomes (Skene et al, 2014). Using recently reported MNase digestion-coupled ChIP-seq datasets for various chromatin remodelers (de Dieuleveult et al, 2016), we investigated the relationship between PAS termination and chromatin remodeling. As previously reported (de Dieuleveult et al, 2016), most chromatin remodeling factors were enriched around the SNFR edges of genes with 2P clusters, aside from Chd2 being distributed across the gene body (Figures 5A and S6A).…”

“…Using recently reported MNase digestion-coupled ChIP-seq datasets for various chromatin remodelers (de Dieuleveult et al, 2016), we investigated the relationship between PAS termination and chromatin remodeling. As previously reported (de Dieuleveult et al, 2016), most chromatin remodeling factors were enriched around the SNFR edges of genes with 2P clusters, aside from Chd2 being distributed across the gene body (Figures 5A and S6A). Despite no major difference in MNase-seq signal between genes with or without 2P clusters, genes with 2P clusters were more strongly bound by several chromatin remodelers including Chd1, Chd2, and Chd9 (Figures 5A and S6B), suggesting that +1 stable nucleosomes associated with PAS termination are actively marked by several chromatin remodelers.…”

Regulation of nucleosome positioning by a CHD Type III chromatin remodeler and its relationship to developmental gene expression inDictyostelium

“…In mammalian stem cells, these complexes are likely to work in concert but act upon different aspects of transcription (de Dieuleveult et al 2016). If the combinatorial effect of these different spacing remodelers varies among genes, only a fraction of genes may be strongly sensitive to loss of chdC.…”

“…Nucleosome positioning in the metazoa is more intricate, involving many more remodeling complexes and an increased number of regulatory protein subunits. These remodeling complexes can associate with distinct genetic elements and genomic regions, interact with epigenetic regulators, and act with different functions to activate or repress gene regulation (Zhou et al 2002;Srinivasan et al 2008;Yang and Seto 2008;Dorighi and Tamkun 2013;Wu et al 2014;de Dieuleveult et al 2016). Although there is in vitro and in vivo evidence to show that chromatin remodeling complexes reposition nucleosomes throughout the genome, it remains unclear to what extent global changes in nucleosome positioning influence the regulation of gene expression (Kadoch and Crabtree 2015).…”

Kilobase Pair Chromatin Fiber Contacts Promoted by Living-System-Like DNA Linker Length Distributions and Nucleosome Depletion

“…60 Thus, the linker length values play a significant role in the flexibility and orientation of each chromatin loop, actively modulating kb range contacts, which are essential for gene identity, 15 gene activity 15,23 cell cycle stage, 69 and differentiation state. 70 …”