CTCF induces histone variant incorporation, erases the H3K27me3 histone mark and opens chromatin.

Oliver Weth,Rainer Renkawitz,Joerg Leers,Katharina Günther,Niels Galjart,Christine Paprotka,Manuel Baierl,Astrid Schulte

doi:10.1093/nar/gku937

Abstract

Insulators functionally separate active chromatin domains from inactive ones. The insulator factor, CTCF, has been found to bind to boundaries and to mediate insulator function. CTCF binding sites are depleted for the histone modification H3K27me3 and are enriched for the histone variant H3.3. In order to determine whether demethylation of H3K27me3 and H3.3 incorporation are a requirement for CTCF binding at domain boundaries or whether CTCF causes these changes, we made use of the LacI DNA binding domain to control CTCF binding by the Lac inducer IPTG. Here we show that, in contrast to the related factor CTCFL, the N-terminus plus zinc finger domain of CTCF is sufficient to open compact chromatin rapidly. This is preceded by incorporation of the histone variant H3.3, which thereby removes the H3K27me3 mark. This demonstrates the causal role for CTCF in generating the chromatin features found at insulators. Thereby, spreading of a histone modification from one domain through the insulator into the neighbouring domain is inhibited.

Highlights

On the 2D level the eukaryotic genome is structured into domains, which may serve several functions
These are located in active chromatin, which is flanked by a stretch of more than 20 kb marked by H3K27me3 (Supplementary Figure S1)
The genes distant from any H3K27me3 domain boundary (DUSP16, RPLPO, COX6A1 and Actin), while harbouring a CTCF site (CTS) in the vicinity of the promoter, did not respond to CTCF depletion, nor did the CTCF negative gene UBC. This suggests that depletion of CTCF from the boundary may result in a spreading of H3K27me3 into the active domain and thereby cause gene repression

Summary

Introduction

On the 2D level the eukaryotic genome is structured into domains, which may serve several functions. As a marker for a repressed domain the triple methylation of lysine of histone H3 (H3K27me3) is often found, which is a hallmark of Polycomb-repressed chromatin [2,3] The absence of such a mark and the presence of methylated H3K4 or acetylated H3K9 are indicative of an active domain. The characterization of the CTCF bound chromatin interactome has identified loop contacts associated with CTCF binding [11] These interacting CTCF boundaries showed a unique enrichment for H3K27me within the loops. A subset of these boundaries is bound by CTCF with a clear segregation of repressive and active chromatin marks at these regions

Methods

Results

Conclusion