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Series GSE133618 Query DataSets for GSE133618
Status Public on Feb 24, 2020
Title Arabidopsis RNA Polymerase IV generates 21-22 nucleotide small RNAs that can participate in RNA-directed DNA methylation and may regulate genes
Organism Arabidopsis thaliana
Experiment type Other
Non-coding RNA profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary Canonically, Arabidopsis RNA Polymerase IV (Pol IV) is known to produce heterochromatic small RNAs (typically 23-24 nucleotide in length) that maintain silencing of transposable elements (TEs). In contrast, when TEs are transcriptionally activated and produce Pol II transcripts, these transcripts are degraded into 21-22 nt small RNAs (sRNAs) known to participate in post transcriptional gene silencing. Recently, it was reported that Pol IV can also produce 21-22 nt sRNAs in pollen. We investigated the mechanism of Pol IV dependent 21-22 nt sRNAs and show that this mechanism is not specific to pollen. Additionally, we show that these 21-22 nt sRNAs can participate in RNA-directed DNA methylation, are incorporated into ARGONAUTE 1 (AGO1) and may guide AGO1 to cleave genic mRNAs to regulate their expression.
 
Overall design Examination of total small RNA accumulation in wild-type Columbia and eight mutants.
AGO1 protein was immunoprecipitated and small RNAs incorporated in AGO1 was sequenced in wild-type Columbia and pol IV mutant.
Whole genome methylC-seq was performed for two mutants.
 
Contributor(s) Panda K, McCue AD, Slotkin RK
Citation(s) 32075560
Submission date Jul 01, 2019
Last update date Feb 24, 2020
Contact name R. Keith Slotkin
E-mail(s) kslotkin@danforthcenter.org
Organization name Donald Danforth Plant Science Center
Street address 975 North Warson Road
City St. Louis
State/province Missouri
ZIP/Postal code 63132
Country USA
 
Platforms (3)
GPL17639 Illumina HiSeq 2500 (Arabidopsis thaliana)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
GPL21785 Illumina HiSeq 4000 (Arabidopsis thaliana)
Samples (19)
GSM3913299 wt Col sRNA - replicate D
GSM3913300 dcl1 sRNA
GSM3913301 dcl2/dcl4 sRNA
Relations
BioProject PRJNA552049
SRA SRP212697

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Supplementary file Size Download File type/resource
GSE133618_RAW.tar 437.7 Mb (http)(custom) TAR (of TSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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