Disordered region of H3K9 methyltransferase Clr4 binds the nucleosome and contributes to its activity

Elias Akoury; Guoli Ma; Segolene Demolin; Cornelia Brönner; Manuel Zocco; Alexandre Cirilo; Nives Ivic; Mario Halic

doi:10.1093/nar/gkz480

Disordered region of H3K9 methyltransferase Clr4 binds the nucleosome and contributes to its activity

Nucleic Acids Res. 2019 Jul 26;47(13):6726-6736. doi: 10.1093/nar/gkz480.

Authors

Elias Akoury^{1

2

3}, Guoli Ma¹, Segolene Demolin¹, Cornelia Brönner¹, Manuel Zocco^{1

4}, Alexandre Cirilo¹, Nives Ivic^{1

5}, Mario Halic^{1

6}

Affiliations

¹ Department of Biochemistry, Gene Center, Ludwig-Maximilians-Universität LMU, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.
² Department of Chemistry, Faculty of Chemistry and Pharmacy, Ludwig-Maximilians-Universität LMU, Butenandtstrasse 5-13, 81377 Munich, Germany.
³ Department of Natural Sciences, Lebanese American University, Beirut 1102-2801, Lebanon.
⁴ Université Libre de Bruxelles, IRIBHM, Brussels B-1070, Belgium.
⁵ Department of Physical Chemistry, Rudjer Boskovic Institute, 10000 Zagreb, Croatia.
⁶ Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.

Abstract

Heterochromatin is a distinctive chromatin structure that is essential for chromosome segregation, genome stability and regulation of gene expression. H3K9 methylation (H3K9me), a hallmark of heterochromatin, is deposited by the Su(var)3-9 family of proteins; however, the mechanism by which H3K9 methyltransferases bind and methylate the nucleosome is poorly understood. In this work we determined the interaction of Clr4, the fission yeast H3K9 methyltransferase, with nucleosomes using nuclear magnetic resonance, biochemical and genetic assays. Our study shows that the Clr4 chromodomain binds the H3K9me3 tail and that both, the chromodomain and the disordered region connecting the chromodomain and the SET domain, bind the nucleosome core. We show that interaction of the disordered region with the nucleosome core is independent of H3K9me and contributes to H3K9me in vitro and in vivo. Moreover, we show that those interactions with the nucleosome core are contributing to de novo deposition of H3K9me and to establishment of heterochromatin.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Cell Cycle Proteins / chemistry
Cell Cycle Proteins / genetics
Cell Cycle Proteins / metabolism*
DNA, Fungal / metabolism*
Gene Deletion
Heterochromatin / metabolism*
Heterochromatin / ultrastructure
Histone Code*
Histone-Lysine N-Methyltransferase / chemistry
Histone-Lysine N-Methyltransferase / metabolism*
Methyltransferases / chemistry
Methyltransferases / genetics
Methyltransferases / metabolism*
Models, Molecular
Mutagenesis, Insertional
Mutation, Missense
Nucleic Acid Conformation
Nucleosomes / metabolism*
Protein Binding
Protein Conformation
Protein Domains
Protein Interaction Mapping
RNA, Fungal / metabolism
Recombinant Fusion Proteins / metabolism
Schizosaccharomyces / genetics*
Schizosaccharomyces / growth & development
Schizosaccharomyces pombe Proteins / chemistry
Schizosaccharomyces pombe Proteins / genetics
Schizosaccharomyces pombe Proteins / metabolism*

Substances

Cell Cycle Proteins
DNA, Fungal
Heterochromatin
Nucleosomes
RNA, Fungal
Recombinant Fusion Proteins
Schizosaccharomyces pombe Proteins
Methyltransferases
Histone-Lysine N-Methyltransferase
clr4 protein, S pombe

Grants and funding

R01 GM135599/GM/NIGMS NIH HHS/United States