Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0

The DDR complex facilitates the genome-wide association of RNA Polymerase V to promoters and evolutionarily young transposons


ABSTRACT: The plant-specific DNA-dependent RNA polymerase V (Pol V) evolved from Pol II to function in an RNA-directed DNA methylation pathway. Here, we have identified targets of Pol V in Arabidopsis thaliana on a genome-wide scale using ChIP-seq of NRPE1, the largest catalytic subunit of Pol V. We found that Pol V is enriched at promoters and evolutionarily recent transposons. This localization pattern is highly correlated with Pol V-dependent DNA methylation and small RNA accumulation. We also show that genome-wide association of Pol V with chromatin is dependent on all members of a putative chromatin-remodeling complex termed DDR. Our study presents the first genome-wide view of Pol V occupancy and sheds light on the mechanistic basis of Pol V localization. Furthermore, these findings suggest a role for Pol V and RNA-directed DNA methylation in genome surveillance and in responding to genome evolution. For wild type plants (ecotype Columbia) and nrpe1 mutants whole-genome small RNA (sRNA-seq) and bisulfite sequencing (BS-seq) was performed. In addition whole genome chromatin immunoprecipitation (ChIP-seq) was performed on wild type (ecotype Columbia) plants as a negative control with experimentals consiting of wild type plants carrying a C-terminally epitope tagged (2XFLAG) NRPE1, as well as the NRPE1-FLAG construct in drd1, dms3, and rdm1 mutant backgrounds.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Christopher Hale 

PROVIDER: E-GEOD-39247 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

altmetric image

Publications

DDR complex facilitates global association of RNA polymerase V to promoters and evolutionarily young transposons.

Zhong Xuehua X   Hale Christopher J CJ   Law Julie A JA   Johnson Lianna M LM   Feng Suhua S   Tu Andy A   Jacobsen Steven E SE  

Nature structural & molecular biology 20120805 9


The plant-specific DNA-dependent RNA polymerase V (Pol V) evolved from Pol II to function in an RNA-directed DNA methylation pathway. Here, we have identified targets of Pol V in Arabidopsis thaliana on a genome-wide scale using ChIP-seq of NRPE1, the largest catalytic subunit of Pol V. We found that Pol V is enriched at promoters and evolutionarily recent transposons. This localization pattern is highly correlated with Pol V-dependent DNA methylation and small RNA accumulation. We also show tha  ...[more]

Similar Datasets

2013-05-13 | E-GEOD-45368 | biostudies-arrayexpress
2015-02-01 | E-GEOD-61192 | biostudies-arrayexpress
2014-01-01 | E-GEOD-52041 | biostudies-arrayexpress
2012-08-07 | E-GEOD-38286 | biostudies-arrayexpress
2014-06-01 | E-GEOD-54677 | biostudies-arrayexpress
2013-11-01 | E-GEOD-49090 | biostudies-arrayexpress
2014-08-01 | E-GEOD-57963 | biostudies-arrayexpress
2012-05-02 | E-GEOD-37644 | biostudies-arrayexpress
2013-08-26 | E-GEOD-39405 | biostudies-arrayexpress
2014-06-06 | E-GEOD-58029 | biostudies-arrayexpress