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  • The EMBO Journal advance online publication 15 October 2009; doi:10.1038/emboj.2009.301

Histone H1 binding is inhibited by histone variant H3.3

Ulrich Braunschweig1, Greg J Hogan1,2, Ludo Pagie1 and Bas van Steensel1

  1. Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands

Correspondence to:

Bas van Steensel, Division of Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands. Tel.: +31 20 512 2040; Fax: +31 20 669 1383; E-mail: b.v.steensel@nki.nl

2Present address: Department of Biochemistry, Beckman Center, Stanford School of Medicine, Stanford, CA 94305, USA

Received 6 July 2009; Accepted 7 September 2009

Linker histones are involved in the formation of higher-order chromatin structure and the regulation of specific genes, yet it remains unclear what their principal binding determinants are. We generated a genome-wide high-resolution binding map for linker histone H1 in Drosophila cells, using DamID. H1 binds at similar levels across much of the genome, both in classic euchromatin and heterochromatin. Strikingly, there are pronounced dips of low H1 occupancy around transcription start sites for active genes and at many distant cis-regulatory sites. H1 dips are not due to lack of nucleosomes; rather, all regions with low binding of H1 show enrichment of the histone variant H3.3. Knockdown of H3.3 causes H1 levels to increase at these sites, with a concomitant increase in nucleosome repeat length. These changes are independent of transcriptional changes. Our results show that the H3.3 protein counteracts association of H1, providing a mechanism to keep diverse genomic sites in an open chromatin conformation.

  • Keywords:

    • chromatin,
    • DamID,
    • H1,
    • H3.3,
    • nucleosome spacing