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Series GSE156069 Query DataSets for GSE156069
Status Public on Feb 01, 2024
Title Clr4SUV39H1 ubiquitination and non-coding RNA mediate transcriptional silencing via heterochromatic phase transitions
Organism Schizosaccharomyces pombe
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Summary Transcriptional silencing by RNAi paradoxically relies on transcription, but how the transition from transcription to silencing is achieved has remained unclear. The Cryptic Loci Regulator complex (CLRC) in Schizosaccharomyces pombe is a cullin-ring E3 ligase required for silencing that is recruited by RNAi. We found that the E2 ubiquitin conjugating enzyme Ubc4 interacts with CLRC and mono-ubiquitinates the histone H3K9 methyltransferase Clr4SUV39H1, promoting the transition from co-transcriptional gene silencing (H3K9me2) to transcriptional gene silencing (H3K9me3). Ubiquitination of Clr4 occurs in an intrinsically disordered region (IDR), which undergoes robust liquid-liquid phase separation (LLPS), along with Swi6HP1 the effector of transcriptional gene silencing. Phase separation of Clr4 and Swi6 is exquisitely sensitive to non-coding RNA (ncRNA), which promotes dimerization, chromatin association, and di-, but not tri- methylation instead. Ubc4-CLRC also targets the transcriptional co-activator Bdf2BRD4, down-regulating centromeric transcription and small RNA production. The deubiquitinase Ubp3 counteracts both activities.
 
Overall design Enrichment of H3K9me2, H3K9me3, RNA Pol II, Flag-Clr4, Epe1-Flag and Bdf2-Flag by ChIP-seq. Enrichment of sRNA by sRNA-seq.
 
Contributor(s) Kim HS, Roche B, Martienssen RA
Citation(s)
  • Kim HS, Roche B, Bhattacharjee S, Todeschini L et al. Clr4(SUV39H1) ubiquitination and non-coding RNA mediate transcriptional silencing of heterochromatin via Swi6 phase separation. Nat Commun 2024 Oct 30;15(1):9384. PMID: 39477922
Submission date Aug 11, 2020
Last update date Dec 13, 2024
Contact name Hyun Soo Kim
E-mail(s) hskim@cshl.edu
Organization name Cold Spring Harbor Laboratory
Department Plant
Lab Martienssen
Street address 1 Bungtown Rd
City Cold Spring Harbor
State/province New York
ZIP/Postal code 11724
Country USA
 
Platforms (1)
GPL16192 Illumina MiSeq (Schizosaccharomyces pombe)
Samples (76)
GSM6409915 01-01_H3K9me2 ChIP-seq_WT
GSM6409917 01-02_H3K9me2 ChIP-seq_ubc4-1
GSM6409918 01-03_H3K9me2 ChIP-seq_cul4-1
Relations
BioProject PRJNA656575
SRA SRP277097

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

Supplementary file Size Download File type/resource
GSE156069_RAW.tar 79.1 Mb (http)(custom) TAR (of BEDGRAPH, BIGWIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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