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Series GSE201234 Query DataSets for GSE201234
Status Public on Feb 17, 2023
Title AGO4 slicer activity reveals the passenger strand function of plant 23 nt siRNAs and the post-slicing retention of target RNAs mediating RNA-directed DNA methylation [WGBS]
Organism Arabidopsis thaliana
Experiment type Methylation profiling by high throughput sequencing
Summary In plants, transcriptional silencing by RNA-directed DNA methylation (RdDM) is mediated by ARGONAUTE 4 (AGO4) and 24 nt short-interfering RNAs (siRNAs) that are generated in parallel with 23 nt RNAs of unknown function. We show that 23 nt RNAs serve as the passenger strands of 23/24 nt duplexes loaded into AGO4. The 24 nt siRNAs then guide AGO4 slicing of the passenger strands, generating 11 and 12 nt cleavage products. Unexpectedly, we find that the 12 nt products remain associated with the guide strand-AGO4 complexes. Long noncoding RNAs generated at RdDM loci are similarly sliced and retained by AGO4. These results suggest a model in which RNA POLYMERASE V transcripts at target loci are sliced repeatedly as transcription elongation proceeds, sequentially releasing AGO4-siRNA-scaffold RNA complexes that independently recruit the RdDM machinery. Consistent with this hypothesis, plant lines expressing wild-type versus slicing-defective AGO4 show quantitative variation in cytosine methylation and siRNA levels within RdDM loci.
 
Overall design Whole-genome bisulfite sequencing of wild-type Arabidopsis thaliana ecotype/strain Wassilewskija, ago4-4 null-mutant plants, and ago4-4 plants that stably express transgenes expressing either wild-type or slicing-defective AGO4.
 
Contributor(s) Wang F, Huang H, Pikaard C
Citation(s) 36746605
Submission date Apr 21, 2022
Last update date Feb 18, 2023
Contact name Craig S. Pikaard
E-mail(s) cpikaard@indiana.edu
Organization name Howard Hughes Medical Institute, Indiana University
Department Department of Biology and Department of Molecular and Cellular Biochemistry
Street address 915 E. Third Street
City Bloomington
State/province Indiana
ZIP/Postal code 47405
Country USA
 
Platforms (1)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
Samples (8)
GSM6053234 WGBS, ago4-4, biol rep 1
GSM6053235 WGBS, ago4-4, biol rep 2
GSM6053236 WGBS, ago4-4/AGO4-D742A, biol rep 1
This SubSeries is part of SuperSeries:
GSE201235 Enzymatic reactions of AGO4 in RNA-directed DNA methylation: siRNA duplex loading, passenger strand elimination, target RNA slicing, and sliced target retention
Relations
BioProject PRJNA830474

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
GSE201234_RAW.tar 2.1 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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