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Series GSE141347

Query DataSets for GSE141347

Status

Public on May 01, 2020

Title

C. elegans nuclear RNAi factor SET-32 is an H3K23 methyltransferase and deposits the transgenerational heritable modification of H3K23me3

Organism

Caenorhabditis elegans

Experiment type

Genome binding/occupancy profiling by high throughput sequencing

Summary

Nuclear RNAi provides a highly tractable system to study RNA-mediated chromatin changes and epigenetic inheritance. Recent studies indicate that nuclear RNAi-mediated heterochromatin is highly complex in its regulation and function. The knowledge of histone modifications that are involved in nuclear RNAi and the corresponding histone modifying enzymes remains limited. In this study, we show that the heterochromatin mark H3K23me3 is induced by nuclear RNAi at both exogenous and endogenous targets in C. elegans. In addition, RNAi-induced H3K23me3 can be inherited for at least four generations. We also demonstrate that the histone methyltransferase SET-32, methylates H3K23 in vitro. Both set-32 and the germline nuclear RNAi Argonaute, hrde-1, are required for nuclear RNAi-induced H3K23me3 in vivo. Our data poise H3K23me3 as a chromatin modification involved in the nuclear RNAi pathway and provides the field with a new target for uncovering the role of heterochromatin in transgenerational epigenetic silencing.

Overall design

In this study we tested if H3K23me1/2/3 is induced by nuclear RNAi at both the exogenous and endogenous targets. We performed oma-1 dsRNA feeding and heritable RNAi experiments. We investigated the whole genome distribution of H3K23me3 and its overlap with H3K9me3. We tested its genetic requirements in the nuclear RNAi pathway and for three histone methyltransferases in vivo: MET-2, SET-25 and SET-32 by examining oma-1 and endogenous nuclear RNAi targets as well as whole genome changes in these mutants.

Contributor(s)

Schwartz-Orbach L, Zhang C, Sidoli S, Amin R, Kaur D, Zhebrun A, Ni J, Gu S

Citation(s)

Submission date

Dec 03, 2019

Last update date

Aug 24, 2020

Contact name

Sam Guoping Gu

E-mail(s)

ggu@dls.rutgers.edu

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)

Illumina HiSeq 2000 (Caenorhabditis elegans)

Samples (52)

More...

GSM4201581	WT GFP RNAi H3K23me1 ChIP-seq
GSM4201582	WT GFP RNAi H3K23me2 ChIP-seq
GSM4201583	WT GFP RNAi H3K23me3 ChIP-seq

GSM4201584	WT GFP RNAi H3K9me3 ChIP-seq
GSM4201585	WT GFP RNAi input
GSM4201586	WT H3K23me1 ChIP-seq
GSM4201587	WT H3K23me2 ChIP-seq
GSM4201588	WT H3K23me3 ChIP-seq
GSM4201589	WT H3K27me3 ChIP-seq
GSM4201590	WT H3K9me3 ChIP-seq
GSM4201591	WT input rep1
GSM4201592	WT input rep2
GSM4201593	WT input rep3
GSM4201594	oma-1 feeding, F0, H3K23me3 ChIP, WT
GSM4201595	post oma-1 feeding, OP50 feeding, F1 H3K23me3 ChIP, WT
GSM4201596	post oma-1 feeding, OP50 feeding, F2 H3K23me3 ChIP, WT
GSM4201597	post oma-1 feeding, OP50 feeding, F3 H3K23me3 ChIP, WT
GSM4201598	post oma-1 feeding, OP50 feeding, F4 H3K23me3 ChIP, WT
GSM4201599	oma-1 feeding, F0, H3K9me3 ChIP, WT
GSM4201600	post oma-1 feeding, OP50 feeding, F1 H3K9me3 ChIP, WT
GSM4201601	post oma-1 feeding, OP50 feeding, F2 H3K9me3 ChIP, WT
GSM4201602	post oma-1 feeding, OP50 feeding, F3 H3K9me3 ChIP, WT
GSM4201603	post oma-1 feeding, OP50 feeding, F4 H3K9me3 ChIP, WT
GSM4201604	WT oma-1 RNAi H3K23me1 ChIP-seq
GSM4201605	WT oma-1 RNAi H3K23me2 ChIP-seq
GSM4201606	WT oma-1 RNAi H3K23me3 ChIP-seq rep1
GSM4201607	WT oma-1 RNAi H3K23me3 ChIP-seq rep2
GSM4201608	WT oma-1 RNAi H3K9me3 ChIP-seq
GSM4201609	WT oma-1 RNAi input
GSM4201610	WT smg-1 RNAi H3K23me3 ChIP
GSM4201611	WT smg-1 RNAi H3K9me3 ChIP
GSM4201612	set-32 mutant no RNAi H3K23me3 ChIP
GSM4201613	set-32 mutant no RNAi H3K9me3 ChIP
GSM4201614	set-32 mutant no RNAi input
GSM4201615	set-32 oma-1 RNAi H3K23me3 ChIP rep1
GSM4201616	set-32 oma-1 RNAi H3K23me3 ChIP rep2
GSM4201617	set-32 oma-1 RNAi H3K9me3 ChIP
GSM4201618	met-2 set-25 no RNAi H3K23me3 ChIP
GSM4201619	met-2 set-25 no RNAi H3K9me3 ChIP rep1
GSM4201620	met-2 set-25 no RNAi H3K9me3 ChIP rep2
GSM4201621	met-2 set-25 no RNAi input
GSM4201622	met-2 set-25 oma-1 RNAi H3K23me3 ChIP rep1
GSM4201623	met-2 set-25 oma-1 RNAi H3K23me3 ChIP rep2
GSM4201624	hrde-1 no RNAi H3K23me3 ChIP rep1
GSM4201625	hrde-1 no RNAi H3K23me3 ChIP rep2
GSM4201626	hrde-1 no RNAi H3K9me3 ChIP
GSM4201627	hrde-1 no RNAi input
GSM4201628	hrde-1 oma-1 RNAi H3K9me3 ChIP rep1
GSM4201629	hrde-1 oma-1 RNAi H3K9me3 ChIP rep2
GSM4201630	glp-1 no RNAi H3K23me3 ChIP
GSM4201631	glp-1 no RNAi H3K9me3 ChIP
GSM4201632	glp-1 no RNAi input

Relations

BioProject

SRA

Download family	Format
SOFT formatted family file(s)	SOFT
MINiML formatted family file(s)	MINiML
Series Matrix File(s)	TXT

Supplementary file	Size	Download	File type/resource
GSE141347_NCBI_proccessed_data_GU_11012019_Normalized_cov1kb.txt.gz	9.4 Mb	(ftp)(http)	TXT
SRA Run Selector
Raw data are available in SRA
Processed data are available on Series record

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