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Series GSE261327

Query DataSets for GSE261327

Status

Public on Aug 21, 2024

Title

The RPD3L deacetylation complex is required for facultative heterochromatin repression in Neurospora crassa [ChIP-seq]

Organism

Neurospora crassa

Experiment type

Genome binding/occupancy profiling by high throughput sequencing

Summary

Repression of facultative heterochromatin is essential for developmental processes in numerous organisms. Methylation of histone H3 lysine 27 (H3K27) by Polycomb repressive complex 2 is a prominent feature of facultative heterochromatin in both fungi and higher eukaryotes. Although this methylation is frequently crucial for silencing, the detailed mechanism of repression remains poorly understood. We utilized a forward genetics approach to identify three previously uncharacterized genes required to maintain silencing at facultative heterochromatin genes in Neurospora crassa: sds3 (NCU01599), rlp1 (RPD3L protein 1; NCU09007) and rlp2 (RPD3L protein 2; NCU02898). We found that SDS3, RLP1, and RLP2 associate with N. crassa homologs of the Saccharomyces cerevisiae RPD3L complex and are required for repression of a subset of H3K27-methylated genes. Loss of these genes does not lead to loss of H3K27 methylation but increases acetylation of histone H3 lysine 14 at upregulated genes, and SDS3 binding levels are highest at genes derepressed upon loss of sds3, rlp1, and rlp2, implying that RPD3L-driven deacetylation is a previously undescribed factor required for silencing of facultative heterochromatin in N. crassa.

Overall design

To analyze levels of histone modifications in RPD3L and RPD3S mutants, we performed ChIP-seq in ∆sds3, ∆rlp1, ∆rlp2, ∆eaf-3, and strain N6279 treated with TSA with antibodies against H3K27me2me3, H3K9ac, and H3K14ac.

Contributor(s)

Mumford CC, Tanizawa H, Wiles ET, McNaught KJ, Jamieson K, Tsukamoto K, Selker EU

Citation(s)

Submission date

Mar 11, 2024

Last update date

Aug 22, 2024

Contact name

Hideki Tanizawa

E-mail(s)

[email protected]

Phone

011-706-5035

Organization name

Hokkaido University

Department

Institute for Genetic Medicine

Lab

Division of Genome Biology

Street address

Kita 15, Nishi 7, Kita-ku

City

Sapporo

State/province

Hokkaido

ZIP/Postal code

060-8615

Country

Japan

Platforms (3)

GPL20660	Illumina NextSeq 500 (Neurospora crassa)
GPL23150	Illumina HiSeq 4000 (Neurospora crassa)
GPL26551	Illumina NovaSeq 6000 (Neurospora crassa)

Samples (32)

More...

GSM8140585	ChIP-seq H3K27me2me3 WT strain: N3752
GSM8140586	ChIP-seq H3K27me2me3 WT strain: N3753
GSM8140587	ChIP-seq H3K27me2me3 ∆rlp2 (∆NCU02898) strain: N6706

GSM8140588	ChIP-seq H3K27me2me3 ∆rlp2 (∆NCU02898) strain: N6708
GSM8140589	ChIP-seq H3K27me2me3 ∆rlp1 (∆NCU09007) strain: N8185
GSM8140590	ChIP-seq H3K27me2me3 ∆rlp1 (∆NCU09007) strain: N8186
GSM8140591	ChIP-seq H3K27me2me3 ∆sds3 (∆NCU01599) strain: N8193
GSM8140592	ChIP-seq H3K27me2me3 ∆sds3 (∆NCU01599) strain: N8194
GSM8140593	ChIP-seq H3K9ac WT strain: N3752
GSM8140594	ChIP-seq H3K9ac WT strain: N3753
GSM8140595	ChIP-seq H3K9ac ∆rlp2 (∆NCU02898) strain: N6706
GSM8140596	ChIP-seq H3K9ac ∆rlp2 (∆NCU02898) strain: N6708
GSM8140597	ChIP-seq H3K9ac ∆rlp1 (∆NCU09007) strain: N8185
GSM8140598	ChIP-seq H3K9ac ∆rlp1 (∆NCU09007) strain: N8186
GSM8140599	ChIP-seq H3K9ac ∆sds3 (∆NCU01599) strain: N8193
GSM8140600	ChIP-seq H3K9ac ∆sds3 (∆NCU01599) strain: N8194
GSM8140601	ChIP-seq H3K14ac WT strain: N3752
GSM8140602	ChIP-seq H3K14ac WT strain: N3753
GSM8140603	ChIP-seq H3K14ac ∆rlp2 (∆NCU02898) strain: N6706
GSM8140604	ChIP-seq H3K14ac ∆rlp2 (∆NCU02898) strain: N6708
GSM8140605	ChIP-seq H3K14ac ∆rlp1 (∆NCU09007) strain: N8185
GSM8140606	ChIP-seq H3K14ac ∆rlp1 (∆NCU09007) strain: N8186
GSM8140607	ChIP-seq H3K14ac ∆sds3 (∆NCU01599) strain: N8193
GSM8140608	ChIP-seq H3K14ac ∆sds3 (∆NCU01599) strain: N8194
GSM8140609	ChIP-seq H3K9ac 0 ul TSA added; his-3; pNCU05173::hph; pNCU07152::nat-1 strain: N6279 biol rep 1
GSM8140610	ChIP-seq H3K9ac 0 ul TSA added; his-3; pNCU05173::hph; pNCU07152::nat-1 strain: N6279 biol rep 2
GSM8140611	ChIP-seq H3K9ac 5 ul TSA added; his-3; pNCU05173::hph; pNCU07152::nat-1 strain: N6279 biol rep 1
GSM8140612	ChIP-seq H3K9ac 5 ul TSA added; his-3; pNCU05173::hph; pNCU07152::nat-1 strain: N6279 biol rep 2
GSM8140613	ChIP-seq H3K14ac 0 ul TSA added; his-3; pNCU05173::hph; pNCU07152::nat-1 strain: N6279 biol rep 1
GSM8140614	ChIP-seq H3K14ac 0 ul TSA added; his-3; pNCU05173::hph; pNCU07152::nat-1 strain: N6279 biol rep 2
GSM8140615	ChIP-seq H3K14ac 5 ul TSA added; his-3; pNCU05173::hph; pNCU07152::nat-1 strain: N6279 biol rep 1
GSM8140616	ChIP-seq H3K14ac 5 ul TSA added; his-3; pNCU05173::hph; pNCU07152::nat-1 strain: N6279 biol rep 2

Relations

BioProject

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
GSE261327_RAW.tar	1.7 Gb	(http)(custom)	TAR (of BW)
SRA Run Selector
Raw data are available in SRA

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