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Series GSE93358 Query DataSets for GSE93358
Status Public on Feb 25, 2017
Title Functional analysis of the Arabidopsis thaliana Pol V largest subunit, NRPE1, carboxy-terminal domain by whole genome bisulfite sequencing
Organism Arabidopsis thaliana
Experiment type Methylation profiling by high throughput sequencing
Summary RNA Polymerase V transcription recruits siRNA-Argonaute protein complexes to chromatin, thereby specifying sites of RNA-directed DNA methylation (RdDM) and transcriptional gene silencing in plants. The Pol V largest subunit, NRPE1, has an extensive carboxyl-terminal domain (CTD) that is dispensable for catalytic activity in vitro, yet essential in vivo. A CTD subdomain, DeCL, named for its similarity to a chloroplast protein, DEFECTIVE CHLOROPLASTS AND LEAVES, is required for Pol V function at virtually all loci, similar to mutants defective for Pol V recruitment. Deletions removing three other CTD subdomains affect overlapping subsets of loci, similar to mutants lacking proteins that bind Pol V or its transcripts. A yeast two-hybrid screen for CTD-interactors identified the 3-prime -> 5-prime exoribonuclease, RRP6L1 as an interactor with the DeCL subdomain and the adjacent QS subdomain, named for its numerous glutamine-serine (QS) repeats. These RRP6L1-binding subdomains immediately follow the Argonaute-binding subdomain. Experimental evidence indicates that RRP6L1 trims the 3-prime ends of Pol V transcripts sliced by ARGONAUTE 4 (AGO4), suggesting a model whereby the adjacent CTD subdomains enable the spatial and temporal coordination of AGO4 and RRP6L1 RNA processing activities.
Overall design NRPE1 constructs with targeted carboxy-terminal domain deletions were assessed for their ability to complement nrpe1-11 mutants. Controls include Col-0 wild-type plants, nrpe1-11 mutant plants, and nrpe1-11 mutants expressing a full length NRPE1 transgene.
Contributor(s) Wendte JM, Pikaard CS
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Submission date Jan 10, 2017
Last update date May 15, 2019
Contact name Jered Wendte
Organization name Indiana University
Street address 915 E. 3rd Street
City Bloomington
State/province IN
ZIP/Postal code 47405
Country USA
Platforms (1)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
Samples (26)
GSM2451991 Col-0 rep1
GSM2451992 Col-0 rep2
GSM2451993 nrpe1-11 rep1
This SubSeries is part of SuperSeries:
GSE93360 Functional analysis of the RNA polymerase V CTD
BioProject PRJNA360690
SRA SRP096354

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE93358_RAW.tar 2.9 Gb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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