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Series GSE62435 Query DataSets for GSE62435
Status Public on Mar 01, 2015
Title Global Functional Targets of the Histone Methyltransferase SDG8 Uncover a Role for Histone Modification in Energy Metabolism
Organism Arabidopsis thaliana
Experiment type Expression profiling by array
Summary Histone methylation modulates gene expression in response to external and internal cues. We uncovered a non-redundant role for the Arabidopsis histone methyltransferase, SDG8, which provides a unique opportunity to study the global function of a specific histone methyltransferase within in a multicellular organism. We previously used a promoter responsive to light and carbon in a positive genetic screen to identify an Arabidopsis carbon and light insensitive mutant cli186. In this study, we characterize the mutant cli186 as a complete deletion of a histone methyltransferase gene SDG8 (now renamed sdg8-5). To assess the global role of SDG8, we compared the global histone methylation patterns and the transcriptome of sdg8-5 to wild type (WT) in the context of a transient carbon and light treatment. We showed that the complete deletion of SDG8 in sdg8-5 is associated with a dramatic reduction of H3K36me3 towards the 3’ of the gene body, which correlates with significant reduction in gene expression. We uncovered 1,084 “high confidence” functional targets of SDG8 – affected in both H3K36me3 marks and gene expression – that are associated with specific biological processes including defense, photosynthesis, nutrient metabolism and energy metabolism. Importantly, 71% of these functional targets are responsive to carbon and/or light. Our model suggests that SDG8 functions to mark specific sets of genes with H3K36me3 in the gene body for active transcription, to tune genes involved in primary metabolism that are responsive to the energy level in the environment.
 
Overall design Wild type Arabidopisis and sdg8-5 plants were grown in hydroponics system for three weeks, then starved for carbonhydrate and light for 24 h. They were then treated with carbon and/or light or remained untreated as controls.Three biological replicates were collected, resulting in 24 samples (2 genotypes X 2 carbonhydrate treatmens X 2 light treatments X3 biological replicates).
 
Contributor(s) LI Y, Mukherjee I, Thum KE, Tanurdzic M, Katari MS, Obertello M, McCombie WR, Martienssen RA, Coruzzi GM
Citation(s) 25928034
Submission date Oct 16, 2014
Last update date Jun 12, 2017
Contact name Ying Li
Organization name New York University
Department Biology
Lab Coruzzi Lab
Street address 12 Waverly Place
City New York
State/province NY
ZIP/Postal code 10012
Country USA
 
Platforms (1)
GPL198 [ATH1-121501] Affymetrix Arabidopsis ATH1 Genome Array
Samples (24)
GSM1526966 WT_mC_mL_rep1
GSM1526967 WT_pC_mL_rep1
GSM1526968 WT_mC_pL_rep1
Relations
BioProject PRJNA264092

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE62435_RAW.tar 49.9 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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