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| Status |
Public on Nov 25, 2014 |
| Title |
The SUVR2 associated proteins FRINGE1 and 2 are required for RdDM in Arabidopsis [Bisulfite-seq] |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Methylation profiling by high throughput sequencing
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| Summary |
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.
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| Overall design |
One fringe 1/2 sample analyzed.
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| Contributor(s) |
Stroud H |
| Citation(s) |
25425661 |
| Submission date |
Jul 31, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Hume Stroud |
| Organization name |
UT Southwestern
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| Street address |
5323 Harry Hines Blvd
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| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390 |
| Country |
USA |
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| Platforms (1) |
| GPL13222 |
Illumina HiSeq 2000 (Arabidopsis thaliana) |
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| Samples (1) |
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| This SubSeries is part of SuperSeries: |
| GSE62801 |
The SNF2 and RING domain proteins FRG1 and 2 are required for RNA-directed DNA methylation in Arabidopsis |
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| Relations |
| BioProject |
PRJNA257191 |
| SRA |
SRP045137 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE59959_RAW.tar |
123.3 Mb |
(http)(custom) |
TAR (of WIG) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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