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Genome Biol. 2015 Apr 19;16:79. doi: 10.1186/s13059-015-0640-2.

The histone methyltransferase SDG8 mediates the epigenetic modification of light and carbon responsive genes in plants.

Author information

1
Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA. yl54@nyu.edu.
2
Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA. indmuk@gmail.com.
3
Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA. karen.thum@gmail.com.
4
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, 11724, USA. tanurdziclab@gmail.com.
5
School of Biological Sciences, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia. tanurdziclab@gmail.com.
6
Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA. mkatari@nyu.edu.
7
Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA. obertello@dna.uba.ar.
8
Instituto de Ingeniería Genética y Biología Molecular (INGEBI-CONICET), Vuelta de Obligado 2490 Piso 2, Buenos Aires, C1428ADN, Argentina. obertello@dna.uba.ar.
9
Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA. me77@nyu.edu.
10
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, 11724, USA. mccombie@cshl.edu.
11
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, 11724, USA. martiens@cshl.edu.
12
Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA. gloria.coruzzi@nyu.edu.

Abstract

BACKGROUND:

Histone methylation modifies the epigenetic state of target genes to regulate gene expression in the context of developmental and environmental changes. Previously, we used a positive genetic screen to identify an Arabidopsis mutant, cli186, which was impaired in carbon and light signaling. Here, we report a deletion of the Arabidopsis histone methyltransferase SDG8 in this mutant (renamed sdg8-5), which provides a unique opportunity to study the global function of a specific histone methyltransferase within a multicellular organism.

RESULTS:

To assess the specific role of SDG8, we examine how the global histone methylation patterns and transcriptome were altered in the sdg8-5 deletion mutant compared to wild type, within the context of transient light and carbon treatments. Our results reveal that the sdg8 deletion is associated with a significant reduction of H3K36me3, preferentially towards the 3' end of the gene body, accompanied by a reduction in gene expression. We uncover 728 direct targets of SDG8 that have altered methylation in the sdg8-5 mutant and are also bound by SDG8. As a group, this set of SDG8 targets is enriched in specific biological processes including defense, photosynthesis, nutrient metabolism and energy metabolism. Importantly, 64% of these SDG8 targets are responsive to light and/or carbon signals.

CONCLUSIONS:

The histone methyltransferase SDG8 functions to regulate the H3K36 methylation of histones associated with gene bodies in Arabidopsis. The H3K36me3 mark in turn is associated with high-level expression of a specific set of light and/or carbon responsive genes involved in photosynthesis, metabolism and energy production.

PMID:
25928034
PMCID:
PMC4464704
DOI:
10.1186/s13059-015-0640-2
[Indexed for MEDLINE]
Free PMC Article

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