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Title: The SUVR2 associated proteins FRINGE1 and 2 are required for RdDM in Arabidopsis [Bisulfite-seq]      
dateReleased:
11-25-2014
description:
DNA methylation in Arabidopsis thaliana is maintained by at least four different enzymes MET1, CMT3, DRM2 and CMT2. However, new methylation patterns are established exclusively by the enzyme DRM2, which acts within a pathway termed RNA-directed DNA methylation (RdDM). Some RdDM components belong to gene families and have partially redundant functions (i.e. DICER LIKE 2, 3 and 4 and IDN2 PARALOG 1 and 2). Traditional screens, which usually affect single genes, usually fail to detect genes if they are redundant, since the loss of one gene is compensated by a related gene. In an effort to circumvent this caveat, we utilized co-expression data to identify closely related genes that are co-regulated with genes in the RdDM pathway. We report the discovery of two redundant proteins, SNF2-RING-HELICASE1 and 2 (FRINGE1 and 2) that are putative chromatin-related paralogous proteins. Analysis of genome–wide bisulfite sequencing shows that simultaneous mutations of FRINGE1 and 2 cause broad defects in methylation at RdDM targeted loci. We also show that FRINGE1 stably associates with Su(var)3-9-related SUVR2, a known RdDM component, in vivo. Combined our results identify FRINGE1 and FRINGE2 as novel components of the RdDM machinery. One fringe 1/2 sample analyzed.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-59959
refinement:
raw
alternateIdentifiers:
59959
keywords:
functional genomics
dateModified:
11-29-2014
availability:
available
types:
gene expression
name:
Arabidopsis thaliana
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-59959/E-GEOD-59959.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-59959/E-GEOD-59959.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59959
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress

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