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Series GSE64600 Query DataSets for GSE64600
Status Public on Feb 09, 2017
Title SUVH1, a histone methyltransferase, is required for the expression of genes targeted by DNA methylation
Organism Arabidopsis thaliana
Experiment type Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary Transposons and repeats are found throughout the genomes of all organisms. To prevent the harmful effects of these elements, repressive marks such as DNA methylation and H3K9me2 have evolved to control transposon activity and ultimately maintain genome integrity. However, how silencing mechanisms are themselves regulated to avoid stochastic silencing of genes remains unclear. Here, negative regulators of silencing were identified using a forward-genetic screen on a reporter line that harbors a LUCIFERASE (LUC) gene driven by a double 35S promoter. SUVH1, a SU(VAR)3-9 homolog, was isolated as a factor promoting the expression of the LUC gene. Treatment with a cytosine methylation inhibitor compromised the effect of the identified suvh1 mutation, indicating that SUVH1 is dispensable for LUC expression in the absence of DNA methylation. However, the suvh1 mutation did not alter DNA methylation levels at the LUC region or on a genome-wide scale; thus, SUVH1 may function downstream of DNA methylation. Histone methylation analysis revealed that suvh1 led to decreased H3K4me3 levels; in contrast, H3K9me2 levels remained unchanged. Moreover, the characterization of endogenous genes indicated that SUVH1 functions at genes with repressive marks in the promoter region. Taken together, these findings shed light on the regulatory network acting at genes with various epigenetic marks.
 
Overall design The BS-seq and mRNA-seq were performed on the reporter line YJ and the mutant YJ suvh1 to assess the effect on DNA methylation and transcriptome caused by suvh1 mutation
 
Contributor(s) Li S, Chen X
Citation(s) 26400170
Submission date Dec 31, 2014
Last update date May 15, 2019
Contact name shaofang Li
Organization name Beijing Academy of Agriculture and Forestry Science
Department Beijing Vegetable Research Center
Street address No 50, ZhanghuaLu, HAIDIAN
City Beijing
State/province Beijing
ZIP/Postal code 100097
Country China
 
Platforms (1)
GPL13222 Illumina HiSeq 2000 (Arabidopsis thaliana)
Samples (6)
GSM1575304 YJ Bsseq rep1
GSM1575305 YJ Bsseq rep2
GSM1575306 YJ suvh1 Bsseq rep1
Relations
BioProject PRJNA271395
SRA SRP051641

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Supplementary file Size Download File type/resource
GSE64600_RAW.tar 890.3 Mb (http)(custom) TAR (of WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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