Histone H3 lysine 36 methylation affects temperature-induced alternative splicing and flowering in plants

Abstract

Background

Global warming severely affects flowering time and reproductive success of plants. Alternative splicing of pre-messenger RNA (mRNA) is an important mechanism underlying ambient temperature-controlled responses in plants, yet its regulation is poorly understood. An increase in temperature promotes changes in plant morphology as well as the transition from the vegetative to the reproductive phase in Arabidopsis thaliana via changes in splicing of key regulatory genes. Here we investigate whether a particular histone modification affects ambient temperature-induced alternative splicing and flowering time.

Results

We use a genome-wide approach and perform RNA-sequencing (RNA-seq) analyses and histone H3 lysine 36 tri-methylation (H3K36me3) chromatin immunoprecipitation sequencing (ChIP-seq) in plants exposed to different ambient temperatures. Analysis and comparison of these datasets reveal that temperature-induced differentially spliced genes are enriched in H3K36me3. Moreover, we find that reduction of H3K36me3 deposition causes alteration in temperature-induced alternative splicing. We also show that plants with mutations in H3K36me3 writers, eraser, or readers have altered high ambient temperature-induced flowering.

Conclusions

Our results show a key role for the histone mark H3K36me3 in splicing regulation and plant plasticity to fluctuating ambient temperature. Our findings open new perspectives for the breeding of crops that can better cope with environmental changes due to climate change.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-017-1235-x) contains supplementary material, which is available to authorized users.

Contributors

R. G. H. Immink: [e-mail]

Journal

Journal ID (nlm-ta): Genome Biol

Journal ID (iso-abbrev): Genome Biol

Title: Genome Biology

Publisher: BioMed Central (London )

ISSN (Print): 1474-7596

ISSN (Electronic): 1474-760X

Publication date (Electronic): 1 June 2017

Publication date PMC-release: 1 June 2017

Publication date Collection: 2017

Volume: 18

Affiliations

[1 ]ISNI 0000 0001 0791 5666, GRID grid.4818.5, Laboratory of Molecular Biology, , Wageningen University and Research, ; 6708 PB Wageningen, The Netherlands

[2 ]ISNI 0000 0001 0791 5666, GRID grid.4818.5, , Bioscience, Wageningen University and Research, ; 6708 PB Wageningen, The Netherlands

[3 ]ISNI 0000 0001 0791 5666, GRID grid.4818.5, Laboratory of Bioinformatics, , Wageningen University and Research, ; 6708 PB Wageningen, The Netherlands

[4 ]ISNI 0000 0001 0660 6765, GRID grid.419498.9, , Max Planck Institute for Plant Breeding Research, ; 50829 Köln, Germany

Article

Publisher ID: 1235

DOI: 10.1186/s13059-017-1235-x

PMC ID: 5452352

Copyright statement: © The Author(s). 2017

License:

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

Funding

Funded by: nwo

Award ID: the NWO grant (849.13.005) for the project ERACAPS13.012, FLOWPLAST

Categories

Subject: Research

Custom metadata

issue-copyright-statement © The Author(s) 2017