Transcriptomics

Dataset Information

475

RNA-seq of coding RNA in frg1-2 mutant and wild-type strains of Arabidopsis


ABSTRACT: DNA methylation in Arabidopsis thaliana is maintained by at least four different enzymes: MET1, CMT3, DRM2, and CMT2. However, DNA methylation is established exclusively by the enzyme DRM2, which acts in the RNA-directed DNA methylation (RdDM) pathway. Some RdDM components belong to gene families and have partially redundant functions, such as DICER-LIKE 2, 3 and 4, and IDN2- LIKE 1 and 2. Traditional mutagenesis screens usually fail to detect genes if they are redundant, since the loss of one gene can be compensated by a related gene. In an effort to circumvent this issue, we utilized co-expression data to identify closely related genes that are co-regulated with genes in the RdDM pathway. Here we report the discovery of two redundant proteins, SNF2-RING-HELICASE-LIKE1 and 2 (FRG1 and 2) that are putative chromatin-related paralogous proteins. Analysis of genome–wide bisulfite sequencing shows that simultaneous mutations of FRG1 and 2 cause broad defects in methylation at RdDM targeted loci. We also show that FRG1 stably associates with Su(var)3-9-related SUVR2, a known RdDM component, in vivo. Combined, our results identify FRG1 and FRG2 as novel components of the RdDM machinery. mRNA profiles of 14 days old seedlings of Columbia 0 wild type and frg1-1 frg2-1 double mutants, 3 biological replicates each.

REANALYSED by: E-GEOD-62799

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Arabidopsis thaliana  

SUBMITTER: Steve E Jacobsen   Hume Stroud  Martin Groth 

PROVIDER: E-GEOD-62799 | ArrayExpress | 2014-11-25

SECONDARY ACCESSION(S): GSE62801SRP049368GSE62799PRJNA265182PRJNA265183

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

SNF2 chromatin remodeler-family proteins FRG1 and -2 are required for RNA-directed DNA methylation.

Groth Martin M   Stroud Hume H   Feng Suhua S   Greenberg Maxim V C MV   Vashisht Ajay A AA   Wohlschlegel James A JA   Jacobsen Steven E SE   Ausin Israel I  

Proceedings of the National Academy of Sciences of the United States of America 20141125 49


DNA methylation in Arabidopsis thaliana is maintained by at least four different enzymes: DNA methyltransferase1 (MET1), chromomethylase3 (CMT3), domains rearranged methyltransferase2 (DRM2), and chromomethylase2 (CMT2). However, DNA methylation is established exclusively by the enzyme DRM2, which acts in the RNA-directed DNA methylation (RdDM) pathway. Some RdDM components belong to gene families and have partially redundant functions, such as the endoribonucleases dicer-like 2, 3, and 4, and i  ...[more]

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