Histone variants shape chromatin states in Arabidopsis

Author:

Jamge Bhagyshree12,Lorković Zdravko J1,Axelsson Elin1ORCID,Osakabe Akihisa134,Shukla Vikas12ORCID,Yelagandula Ramesh15ORCID,Akimcheva Svetlana1,Kuehn Annika Luisa1,Berger Frédéric1ORCID

Affiliation:

1. Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter

2. Vienna BioCenter

3. Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-ku

4. PRESTO, Japan Science and Technology Agency, Honcho

5. Institute of Molecular Biotechnology, IMBA, Dr. Bohr-Gasse 3

Abstract

How different intrinsic sequence variations and regulatory modifications of histones combine in nucleosomes remain unclear. To test the importance of histone variants in the organization of chromatin we investigated how histone variants and histone modifications assemble in the Arabidopsis thaliana genome. We showed that a limited number of chromatin states divide euchromatin and heterochromatin into several subdomains. We found that histone variants are as significant as histone modifications in determining the composition of chromatin states. Particularly strong associations were observed between H2A variants and specific combinations of histone modifications. To study the role of H2A variants in organizing chromatin states we determined the role of the chromatin remodeler DECREASED IN DNA METHYLATION (DDM1) in the organization of chromatin states. We showed that the loss of DDM1 prevented the exchange of the histone variant H2A.Z to H2A.W in constitutive heterochromatin, resulting in significant effects on the definition and distribution of chromatin states in and outside of constitutive heterochromatin. We thus propose that dynamic exchanges of histone variants control the organization of histone modifications into chromatin states, acting as molecular landmarks.

Funder

Austrian Science Fund

Japan Society for the Promotion of Science

Japan Science and Technology Agency

Austrian Academy of Sciences

Publisher

eLife Sciences Publications, Ltd

Subject

General Immunology and Microbiology,General Biochemistry, Genetics and Molecular Biology,General Medicine,General Neuroscience

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