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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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RNAi triggered by specialized machinery silences developmental genes and retrotransposons

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

ORGANISM(S): Schizosaccharomyces pombe

SUBMITTER: Shiv Grewal

PROVIDER: E-GEOD-41643 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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RNAi triggered by specialized machinery silences developmental genes and retrotransposons.

Yamanaka Soichiro S Mehta Sameet S Reyes-Turcu Francisca E FE Zhuang Fanglei F Fuchs Ryan T RT Rong Yikang Y Robb Gregory B GB Grewal Shiv I S SI

Nature 20121114 7433

RNA interference (RNAi) is a conserved mechanism in which small interfering RNAs (siRNAs) guide the degradation of cognate RNAs, but also promote heterochromatin assembly at repetitive DNA elements such as centromeric repeats. However, the full extent of RNAi functions and its endogenous targets have not been explored. Here we show that, in the fission yeast Schizosaccharomyces pombe, RNAi and heterochromatin factors cooperate to silence diverse loci, including sexual differentiation genes, gene ...[more]

PMID: 23151475

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RNAi triggered by specialized machinery silences developmental genes and retrotransposons (RNA-Seq)

Project description:RNAi is a conserved mechanism in which small interfering RNAs (siRNAs) guide the degradation of cognate RNAs, but also promote heterochromatin assembly at repetitive DNA elements such as centromeric repeats. However, the full extent of RNAi functions and its endogenous targets have not been explored. Here we show that in the fission yeast Schizosaccharomyces pombe, RNAi and heterochromatin factors cooperate to silence diverse loci, including sexual differentiation genes, genes encoding transmembrane proteins, and retrotransposons that are also targeted by the exosome RNA degradation machinery. In the absence of the exosome, transcripts are processed preferentially by the RNAi machinery, revealing widespread occurrence of siRNA clusters and corresponding increase in heterochromatin modifications across large domains. We show that the generation of siRNAs and heterochromatin assembly by RNAi is triggered by a mechanism involving the canonical poly(A) polymerase Pla1 and an associated RNA surveillance factor Red1, which also activate the exosome. Remarkably, siRNA production and heterochromatin modifications at genes are regulated by environmental growth conditions, and by developmental signals that induce gene expression during sexual differentiation. Our analyses uncover interplay between RNAi and the exosome that is conserved in higher eukaryotes, and show that differentiation signals modulate RNAi silencing to regulate developmental genes. We sequenced 7 samples from Schizosaccharomyces pombe and 2 samples from Drosophila melanogaster.

2012-11-26 | E-GEOD-41634 | biostudies-arrayexpress

A conserved factor Dhp1/Rat1/Xrn2 triggers premature transcription termination and nucleates heterochromatin to promote gene silencing [sRNA-seq]

Project description:Co-transcriptional RNA processing and surveillance factors mediate heterochromatin formation in fission yeast. In addition to RNAi, RNA elimination machinery including MTREC (Mtl1-Red1 core) and the exosome are involved in facultative heterochromatin assembly, however, the exact mechanisms remain unclear. Here we show that RNA elimination factors cooperate with the conserved exoribonuclease Dhp1/Rat1/Xrn2, which couples pre-mRNA 3â-end processing to transcription termination, to promote premature termination and facultative heterochromatin formation at meiotic genes. Dhp1 also affects termination of transcripts at genes that are targets of RNAi-mediated heterochromatin assembly. Moreover, Dhp1 facilitates constitutive heterochromatin formation and silencing at centromeric and mating-type loci. Remarkably, we find that Dhp1 interacts with the Clr4/Suv39h methyltransferase complex and acts directly to nucleate heterochromatin. Our results uncover a novel role for 3â-end processing and termination machinery in gene silencing through premature termination and suggest that non-canonical termination by Dhp1 and RNA elimination factors is linked to heterochromatin assembly. These findings have important implications for understanding mechanisms of gene silencing in higher eukaryotes. Sequencing and analysis of small RNA in two S. pombe mutants

2016-01-05 | E-GEOD-74739 | biostudies-arrayexpress

Nascent elongating transcript sequencing (NET-seq) for Escherichia coli and Bacillus subtilis reveals a consensus pause sequence enriched at translation start sites.

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2014-05-05 | E-GEOD-56720 | biostudies-arrayexpress

Post-licensing specification of eukaryotic replication origins by facilitated Mcm2-7 sliding along DNA

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2016-01-07 | E-GEOD-69065 | biostudies-arrayexpress

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The genomes of the ancestral species of peanut - a remarkable case of living archaeology

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