Dataset Information


Characterization of small RNA-generating regions targeted by RNA polymerase V in Arabidopsis

ABSTRACT: In plants, heterochromatin is maintained by a small RNA-based gene silencing mechanism known as RNA-directed DNA methylation (RdDM). RdDM requires the non-redundant functions of two plant-specific DNA-dependent RNA polymerases (Pol) Pol IV and Pol V. Pol IV plays a major role in siRNA biogenesis, while Pol V may recruit DNA methylation machinery to target endogenous loci for silencing. Although small RNA-generating regions which are dependent on both Pol IV and Pol V have been identified previously, the genomic loci targeted Pol V for siRNA accumulation and silencing have not been described extensively. To characterize the Pol V-dependent, heterochromatic siRNA-generating regions in the Arabidopsis genome, we deeply sequenced the small RNA populations of wild-type and Pol V mutant plants. Furthermore, we characterized the siRNA-generating regions which were dependent on RdDM effectors and examined their dependency on Pol V. Small RNA libraries were generated and deeply sequenced from mutant alleles dms4-1, drd1-1, dms3-1, and rdm1-4, along with their control library (“Wt(T+S)”) which has been described previously (Kanno et al. 2004 Current Biology). More than 2,000 small RNA-generating loci were identified which were greatly suppressed in Pol V mutants. Overall design: The Pol V-dependent, heterochromatic siRNA-generating regions were characterized in the Arabidopsis genome by deep sequencing the small RNA populations of wild-type and Pol V mutant plants. Deep SBS sequencing was used for small RNA profiling of immature inflorescence tissues from RNA polymerase V and RdDM mutants.

INSTRUMENT(S): Illumina Genome Analyzer IIx (Arabidopsis thaliana)

ORGANISM(S): Arabidopsis thaliana  

SUBMITTER: Blake C. Meyers  

PROVIDER: GSE36424 | GEO | 2012-06-11



Similar Datasets

2012-06-11 | E-GEOD-36424 | ArrayExpress
2013-06-03 | E-GEOD-44209 | ArrayExpress
2014-11-11 | E-GEOD-57215 | ArrayExpress
2014-08-05 | E-GEOD-47852 | ArrayExpress
| GSE99691 | GEO
| GSE99693 | GEO
| GSE99692 | GEO
| GSE99689 | GEO
2013-05-30 | E-GEOD-47453 | ArrayExpress
2013-05-13 | E-GEOD-45368 | ArrayExpress