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Clr4/Suv39 and RNA quality control factors cooperate to trigger RNAi and suppress antisense RNA

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Schizosaccharomyces pombe

PROVIDER: GSE26999 | GEO | 2011/04/12

SECONDARY ACCESSION(S): PRJNA135901

REPOSITORIES: GEO

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Clr4/Suv39 and RNA quality control factors cooperate to trigger RNAi and suppress antisense RNA.

Project description:Pervasive transcription of eukaryotic genomes generates a plethora of noncoding RNAs. In fission yeast, the heterochromatin factor Clr4/Suv39 methyltransferase facilitates RNA interference (RNAi)-mediated processing of centromeric transcripts into small interfering RNAs (siRNAs). Clr4 also mediates degradation of antisense RNAs at euchromatic loci, but the underlying mechanism has remained elusive. We show that Clr4 and the RNAi effector RITS (RNA-induced transcriptional silencing) interact with Mlo3, a protein related to mRNA quality control and export factors. Loss of Clr4 impairs RITS interaction with Mlo3, which is required for centromeric siRNA production and antisense suppression. Mlo3 also interacts with the RNA surveillance factor TRAMP, which suppresses antisense RNAs targeted by Clr4 and RNAi. These findings link Clr4 to RNA quality control machinery and suggest a pathway for processing potentially deleterious RNAs through the coordinated actions of RNAi and other RNA processing activities.

| S-EPMC6309853 | biostudies-literature

Clr4/Suv39 and RNA quality control factors cooperate to trigger RNAi and suppress antisense RNA

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2011-04-12 | E-GEOD-26999 | biostudies-arrayexpress

Clr4/Suv39 and RNA quality control factors cooperate to trigger RNAi and suppress antisense RNA (ChIP)

Project description:Occupancy profiling of Mlo3 in wild type and clr4∆ fission yeast Schizosaccharomyces pombe Agilent 60mer array was used to analyze DNA recovered by immunoprecipitation of Mlo3-Flag from asynchronous culture of fission yeast.

2011-04-12 | E-GEOD-26997 | biostudies-arrayexpress

Clr4/Suv39 and RNA quality control factors cooperate to trigger RNAi and suppress antisense RNA (expression)

Project description:Expression profile of Schizosaccharomyces pombe genome in ?mlo3, mlo3-A, mlo3-A?h2a.z, ?cid14?h2a.z and mlo3-A?cid14 cells. Expression profile of mutant cells compared to wild-type cells. Agilent 60mer oligonucleotide custom array containing probes spanning large portion of chromosome 2 at 50bp resolution was used to profile expression levels in mutant cells and to compare them to levels in wild-type cells.

2011-04-12 | E-GEOD-26995 | biostudies-arrayexpress

Clr4/Suv39 and RNA quality control factors cooperate to trigger RNAi and suppress antisense RNA (ChIP)

Project description:Occupancy profiling of Mlo3 in wild type and clr4∆ fission yeast Schizosaccharomyces pombe

2011-04-12 | GSE26997 | GEO

Clr4/Suv39 and RNA quality control factors cooperate to trigger RNAi and suppress antisense RNA (expression)

Project description:Expression profile of Schizosaccharomyces pombe genome in ∆mlo3, mlo3-A, mlo3-A∆h2a.z, ∆cid14∆h2a.z and mlo3-A∆cid14 cells. Expression profile of mutant cells compared to wild-type cells.

2011-04-12 | GSE26995 | GEO

RNA quality control factors nucleate Clr4/SUV39H and trigger constitutive heterochromatin assembly

Project description:In eukaryotes, the Suv39 family of proteins tri-methylate lysine 9 of histone H3 (H3K9me) to form constitutive heterochromatin. However, how Suv39 proteins are nucleated at heterochromatin is not fully described. In the fission yeast, current models posit that Argonaute1-associated small RNAs (sRNAs) nucleate the sole H3K9 methyltransferase, Clr4/SUV39H, to centromeres. Here, we show that in the absence of all sRNAs and H3K9me, the Mtl1 and Red1 core (MTREC)/PAXT complex nucleates Clr4/SUV39H at a heterochromatic long noncoding RNA (lncRNA) at which the two H3K9 deacetylases, Sir2 and Clr3, also accumulate by distinct mechanisms. Iterative cycles of H3K9 deacetylation and methylation spread Clr4/SUV39H from the nucleation center in an sRNA-independent manner, generating a basal H3K9me state. This is acted upon by the RNAi machinery to augment and amplify the Clr4/H3K9me signal at centromeres to establish heterochromatin. Overall, our data reveal that lncRNAs and RNA quality control factors can nucleate heterochromatin and function as epigenetic silencers in eukaryotes.

2024-05-16 | PXD039519 | Pride

RNA quality control factors nucleate Clr4/SUV39H and trigger constitutive heterochromatin assembly

Project description:RNA surveillance (MTREC) and degradation (exosome) complexes nucleate Clr4/SUV39H at a heterochromatic long noncoding RNA, at which the two deacetylases, Sir2 and Clr3, also amass by distinct mechanisms. Iterative cycles of H3K9 deacetylation and methylation spread Clr4 from the nucleation center which with the help from RNAi establish heterochromatin. (this is like the abstract for the paper) To identify nuclear Sir2-interacting proteins, a protocol was adopted by which frozen intact nuclei suitable for biochemical purifications were released by low pressure, semi-automated cryogrinding of frozen yeast pellets after which the nuclei were isolated by differential centrifugation. From these nuclear extracts, FLAG-tagged Sir2 was purified and analyzed by nanoscale micro-capillary tandem mass spectrometry.

2024-02-25 | MSV000094160 | MassIVE

Histone H2A.Z cooperates with RNAi and heterochromatin factors to suppress antisense RNAs.

Project description:Eukaryotic transcriptomes are characterized by widespread transcription of noncoding and antisense RNAs, which is linked to key chromosomal processes, such as chromatin remodelling, gene regulation and heterochromatin assembly. However, these transcripts can be deleterious, and their accumulation is suppressed by several mechanisms including degradation by the nuclear exosome. The mechanisms by which cells differentiate coding RNAs from transcripts targeted for degradation are not clear. Here we show that the variant histone H2A.Z, which is loaded preferentially at the 5' ends of genes by the Swr1 complex containing a JmjC domain protein, mediates suppression of antisense transcripts in the fission yeast Schizosaccharomyces pombe genome. H2A.Z is partially redundant in this regard with the Clr4 (known as SUV39H in mammals)-containing heterochromatin silencing complex that is also distributed at euchromatic loci, and with RNA interference component Argonaute (Ago1). Loss of Clr4 or Ago1 alone has little effect on antisense transcript levels, but cells lacking either of these factors and H2A.Z show markedly increased levels of antisense RNAs that are normally degraded by the exosome. These analyses suggest that as well as performing other functions, H2A.Z is a component of a genome indexing mechanism that cooperates with heterochromatin and RNAi factors to suppress read-through antisense transcripts.

| S-EPMC2746258 | biostudies-literature

Histone H2A.Z cooperates with RNAi and heterochromatin factors to suppress antisense RNAs

Project description:Expression profile of mutant cells compared to wild-type cells: Expression profile of Schizosaccharomyces pombe genome in ∆pht1, ∆ago1, ∆clr4, rik1, ∆pht1rik1, ∆pht1∆ago1 and ∆pht1∆clr4 cells. Expression profile of Schizosaccharomyces pombe genome in ∆rrp6, ∆cid14, ∆swi6, ∆swr1, ∆set1, ∆pht1∆swi6 and ∆pht1∆set1 cells. Expression profile of Schizosaccharomyces pombe genome in ∆alp13, ∆cph1, ∆set2, clr6-1 and ∆cph1∆pht1 cells. Occupancy profiling: Occupancy profiling of RNA polymerase II, histone variant H2A.Z and ClrC subunit Rik1 in fission yeast Schizosaccharomyces pombe Occupancy profiling of histone variant H2A.Z in ∆msc1 cells.

2009-08-25 | GSE17271 | GEO

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