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Series GSE86515 Query DataSets for GSE86515
Status Public on Jan 01, 2017
Title Decoupling the downstream effects of germline nuclear RNAi reveals that transcriptional repression and heritable RNAi are independent of the H3K9me3 response in C. elegans [RNA-seq]
Organism Caenorhabditis elegans
Experiment type Expression profiling by high throughput sequencing
Summary Germline nuclear RNAi in C. elegans is a transgenerational gene-silencing pathway that leads to the H3K9 trimethylation (H3K9me3) response and transcriptional repression of target genes. The H3K9me3 response induced either by exogenous dsRNA or endogenous siRNA (endo-siRNA) is highly specific to the target loci and transgenerationally heritable. Despite these features, the role of H3K9me3 in transcriptional repression and heritable gene silencing at native target genes has not been tested. To resolve this gap, we first determined that the combined activities of three H3K9 histone methyltransferases (HMTs), MET-2, SET-25, and SET-32, are responsible for virtually all of the detectable level of germline nuclear RNAi-dependent H3K9me3 at native genes, triggered either by exogenous dsRNA or endo-siRNAs. By performing RNA Polymerase II ChIP-seq and pre-mRNA-seq analyses, we found that the loss of the H3K9me3 response at germline nuclear RNAi targets in the met-2;set-25;set-32 mutant does not lead to any defect in transcriptional repression or heritable RNAi. Therefore, H3K9me3 is not required for exogenous dsRNA-induced heritable RNAi or the maintenance of endo siRNA-mediated transcriptional silencing in C. elegans germline. This study provides a unique paradigm in which transcriptional silencing and heterochromatin, triggered by the same upstream pathway, can be decoupled.
Overall design In this study we tested if RNAi-mediated H3K9me3 is required for the heritable RNAi and transcriptional silencing at native endogenous and exogenous RNAi targets. Using genetic approach we generated nearly completely deficient H3K9me3 worm strain (met-2;set-25;set-32). Using Pol II ChIP-seq, pre-mRNA-seq and mRNA-seq we validated transcriptional changes at the endogenous targets in the H3K9me3 deficient condition (met-2;set-25;set-32). We performed oma-1 dsRNA feeding and heritable RNAi experiment and using H3K9me3 ChIP-seq measured level of RNAi-triggered H3K9me3 contribution by set-32 or met-2;set-25 or met-2;set-25;set-32 HMTs at the oma-1 gene. Using oma-1 mRNA and pre-mRNA qRT-PCR we tested heritable RNAi effect at oma-1 genomic locus in these HMT mutants.
Contributor(s) Kalinava N, Ni JZ, Peterman K, Chen E, Gu SG
Citation(s) 28228846
NIH grant(s)
Grant ID Grant title Affiliation Name
R01 GM111752 RNA-mediated Chromatin Regulation and Epigenetic Inheritance in C. elegans RUTGERS, THE STATE UNIVERSITY OF NEW JERSEY Guoping Gu
Submission date Sep 07, 2016
Last update date May 15, 2019
Contact name Sam Guoping Gu
Organization name Rutgers University
Department Molecular Biology and Biochemistry
Street address 604 Allison Road
City Piscataway
State/province New Jersey
ZIP/Postal code 08854
Country USA
Platforms (1)
GPL13657 Illumina HiSeq 2000 (Caenorhabditis elegans)
Samples (5)
GSM2304889 mRNA-seq_WT_OP50
GSM2304919 mRNA-seq_set-32_OP50
GSM2304920 mRNA-seq_met-2set-25_OP50
This SubSeries is part of SuperSeries:
GSE86517 Decoupling the downstream effects of germline nuclear RNAi reveals that transcriptional repression and heritable RNAi are independent of the H3K9me3 response in C. elegans
BioProject PRJNA342126
SRA SRP087443

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Supplementary file Size Download File type/resource
GSE86515_mRNA_seq_all_genes_with_GRTS_GRH_Targets_all_perfectAligned_reads_rpkm.xlsx 1.2 Mb (ftp)(http) XLSX
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