The histone methyltransferase SDG8 mediates the epigenetic modification of light and carbon responsive genes in plants.
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.
Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA. yl54@nyu.edu.
Ying
Y
Li
Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA. indmuk@gmail.com.
Indrani
I
Mukherjee
Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA. karen.thum@gmail.com.
Karen E
KE
Thum
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, 11724, USA. tanurdziclab@gmail.com.|School of Biological Sciences, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia. tanurdziclab@gmail.com.
Milos
M
Tanurdzic
Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA. mkatari@nyu.edu.
Manpreet S
MS
Katari
Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA. obertello@dna.uba.ar.|Instituto de Ingeniería Genética y Biología Molecular (INGEBI-CONICET), Vuelta de Obligado 2490 Piso 2, Buenos Aires, C1428ADN, Argentina. obertello@dna.uba.ar.
Mariana
M
Obertello
Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA. me77@nyu.edu.
Molly B
MB
Edwards
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, 11724, USA. mccombie@cshl.edu.
W Richard
WR
McCombie
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, 11724, USA. martiens@cshl.edu.
Robert A
RA
Martienssen
Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA. gloria.coruzzi@nyu.edu.
Gloria M
GM
Coruzzi
D017360:Arabidopsis / Q000235:genetics* / Q000502:physiology / Q000528:radiation effects; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism*; D002244:Carbon / Q000378:metabolism*; D002874:Chromosome Mapping; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D017353:Gene Deletion; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D011495:Histone-Lysine N-Methyltransferase / Q000235:genetics / Q000378:metabolism*; D005810:Multigene Family; D015203:Reproducibility of Results
D029681:Arabidopsis Proteins; D002244:Carbon; D011495:Histone-Lysine N-Methyltransferase; C556085:LAZ2 protein, Arabidopsis