Comment[ArrayExpressAccession]	E-GEOD-39405
MAGE-TAB Version	1.1		
Public Release Date	2013-08-26
Investigation Title	The SET-domain protein SUVR5 mediates H3K9me2 deposition and silencing at stimulus response genes in a DNA methylation independent manner		
Comment[Submitted Name]	The SET-domain protein SUVR5 mediates H3K9me2 deposition and silencing at stimulus response genes in a DNA methylation independent manner
Experiment Description	In eukaryotic cells, environmental and developmental signals alter chromatin structure and modulate gene expression. Heterochromatin constitutes the transcriptionally inactive state of the genome and in plants and mammals is generally characterized by DNA methylation and histone modifications such as histone H3 lysine 9 (H3K9) methylation. In Arabidopsis thaliana DNA methylation and H3K9 methylation are usually colocated and set up a mutually self reinforcing and stable state. Here, in contrast, we found that SUVR5, a plant Su(var)3-9 homolog with a SET histone methyltransferase domain, mediates H3K9me2 deposition and regulates gene expression in a DNA-methylation-independent manner. SUVR5 binds DNA through its zinc fingers and represses  the expression of a subset of stimulus response genes. This represents a novel mechanism for plants to regulate their chromatin and transcriptional state, which may allow for the adaptability and modulation necessary to rapidly respond to extracellular cues. Investigation of gene expression profiles of suvr5-1, ldl1 ldl2 and suvr5 ldl1 ldl2 mutants.		
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl	
Person Last Name	Stroud	Jacobsen	
Person First Name	Hume	Steve	
Person Email	geo@ncbi.nlm.nih.gov		
Person Affiliation	University of California, Los Angeles		
Person Address	University of California, Los Angeles, 4045 Terasaki Life Sciences Building, Los Angeles, CA, USA		
Person Roles	submitter		
Protocol Name	P-GSE39405-3	P-GSE39405-2	P-GSE39405-1
Protocol Description	mRNA-Seq reads were first trimmed to 50mers and mapped with Bowtie (Langmead, et al. 2009 Genome Biol.) to TAIR8 chr1..5, allowing up to 2 mismatches and retaining only uniquely-mapping reads. Genome_build: TAIR8 Supplementary_files_format_and_content: Processed files indicate the coordinates of uniquely mapped reads. Column 1 is chromosome. Column 2 is the genomic strand (+/-). Column 3 is the genomic coordinate.	Leaves from wild type Col-0, suvr5-1, ldl1-2 ldl2 and suvr5-1 ldl1-2 ldl2 3 week-old plants were used for RNA extraction using Trizol (Invitrogen) following the manufacturer instructions. 10 mg of total RNA was treated with DNaseI (Roche), and cleaned up with RNeasy columns (Qiagen). Poly(A) was purified using the Dynabeads mRNA Purification Kit (Invitrogen) and used to generate the mRNA-seq libraries following the manufacturer’s instructions (Illumina).	All plants were grown under long day conditions.
Protocol Type	normalization data transformation protocol	nucleic acid library construction protocol	growth protocol
Experimental Factor Name	GENETIC VARIANT		
Experimental Factor Type	genetic variant		
Publication Title	The SET-domain protein SUVR5 mediates H3K9me2 deposition and silencing at stimulus response genes in a DNA methylation-independent manner.		
Publication Author List	Caro E, Stroud H, Greenberg MV, Bernatavichute YV, Feng S, Groth M, Vashisht AA, Wohlschlegel J, Jacobsen SE		
PubMed ID	23071452		
Publication DOI	10.1371/journal.pgen.1002995		
Comment[SecondaryAccession]	GSE39405		
Comment[GEOReleaseDate]	2013-08-26		
Comment[ArrayExpressSubmissionDate]	2012-07-16		
Comment[GEOLastUpdateDate]	2013-08-30		
Comment[AEExperimentType]	RNA-seq of coding RNA		
Comment[SecondaryAccession]	SRP014426		
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR522012-SRR522015		
SDRF File	E-GEOD-39405.sdrf.txt