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Series GSE18215 Query DataSets for GSE18215
Status Public on Oct 01, 2009
Title High throughput sequencing of mutants in the WAGO pathway
Organism Caenorhabditis elegans
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary Diverse naturally-occurring small RNA species interact with Argonaute proteins to mediate sequence-specific regulation in animals. In addition to micro-RNAs (miRNAs), which collectively regulate thousands of target mRNAs, other endogenous small RNA species include the Piwi-associated piRNAs that are important for fertility and a less well-characterized class of small RNAs often referred to simply as endo-siRNAs. Here we have utilized deep-sequencing technology and C. elegans genetics to explore the biogenesis and function of endo-siRNAs. We describe conditional alleles of the dicer-related helicase, drh-3, that implicate DRH-3 in both the response to foreign dsRNA as well as the RNA-dependent RNA Polymerase (RdRP)-dependent biogenesis of a diverse class of endogenous small RNAs, termed 22G-RNAs. We show that 22G-RNAs are abundantly expressed in the germline and maternally inherited and are the products of at least two distinct 22G-RNA systems. One system is dependent on worm-specific AGOs, including WAGO-1, which localizes to germline nuage-related structures termed P-granules. The WAGO 22G-RNA system silences transposons, pseudogenes and cryptic loci as well as a number of genes. Finally, we demonstrate that components of the nonsense-mediated decay pathway function in at least one of the multiple, distinct WAGO surveillance pathways. These findings broaden our understanding of the biogenesis and diversity of 22G-RNA species and suggest potential novel regulatory functions for these small RNAs.
Overall design 18 samples examined. Small RNA libraries generated from: C. elegans animals with mutations in the WAGO pathway and a WAGO-1 immunopercipitate.
Contributor(s) Gu W, Mello CC
Citation(s) 19800275, 29456136
Submission date Sep 22, 2009
Last update date Jul 26, 2019
Contact name Craig Mello
Organization name University of Massachusetts Medical School
Department Program in Molecular Medicine
Lab Craig Mello
Street address 368 Plantatoin Street, Suite AS5-2047
City Worcester
State/province MA
ZIP/Postal code 01605
Country USA
Platforms (1)
GPL9269 Illumina Genome Analyzer II (Caenorhabditis elegans)
Samples (18)
GSM455387 WT_CIPPNK_seq_s1
GSM455388 WT_CIPPNK_seq_s2
GSM455389 drh-3_CIPPNK_seq_s2
This SubSeries is part of SuperSeries:
GSE18231 WAGO pathway
SRA SRP001449
BioProject PRJNA123493

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

Supplementary file Size Download File type/resource
GSE18215_RAW.tar 770.3 Mb (http)(custom) TAR (of GFF, TAR)
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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