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The RNA-induced transcriptional silencing complex is targeted to chromatin exclusively via base-pairing interactions with nascent transcripts

ABSTRACT: Small RNAs are implicated in chromatin modification and transcriptional gene silencing across the eukaryotic kingdom. Although well understood, fundamental mechanistic aspects of RNA-mediated chromatin regulation have remained obscure. It has not been possible to unambiguously distinguish whether small RNA loaded Argonaute proteins target the nascent transcript or the underlying DNA sequence. Here, we demonstrate that transcription of the target locus is indispensable for the formation of heterochromatin in fission yeast. Yet, high transcriptional activity opposes RNA-directed chromatin silencing. We further find that pre-mRNA splicing is compatible with RNA-directed heterochromatin formation. Small RNAs complementary to promoter distal introns trigger the formation of stable heterochromatin irrespective of pre-mRNA splicing. However, targeting a functional intron close to the 5’ end of a transcript results in a bistable chromatin state. Together, our results disprove siRNA-DNA base-pairing and provide mechanistic insights that will inform the experimental design of small RNA-directed chromatin silencing studies in multicellular organisms.

ORGANISM(S): Schizosaccharomyces pombe

PROVIDER: GSE87672 | GEO | 2017/02/13

SECONDARY ACCESSION(S): PRJNA345512

REPOSITORIES: GEO

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A nuclear RNA export factor variant licenses piRNA-guided heterochromatin formation

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2019-06-12 | PXD011201 | Pride

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RNA expression profiling for Paf1 complex mutant strains [miRNA]

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Project description:Nuclear Argonaute proteins, guided by their bound small RNAs, orchestrate heterochromatin formation at transposon insertions and repetitive genomic loci. The molecular mechanisms that, besides recruiting heterochromatin effector proteins, are required for this silencing process are poorly understood. Here, we show that the SFiNX complex, the central silencing mediator downstream of nuclear Piwi-piRNA complexes in Drosophila, enables co-transcriptional silencing via the formation of molecular condensates. Condensate formation is stimulated by nucleic acid binding and requires SFiNX to form a homodimer. The dynein light chain dLC8, a highly conserved dimerization hub protein, mediates homo-dimerization of SFiNX. Point mutations preventing dLC8-mediated SFiNX dimerization result in transposon de-repression and sterility. dLC8’s function can be bypassed with a heterologous dimerization domain, suggesting that dimerization is a constitutive rather than a regulated feature of SFiNX. We propose that nucleic-acid stimulated condensate formation enables co-transcriptional silencing through the retention of the target RNA at chromatin, thereby allowing effector proteins to establish heterochromatin at the target locus.

2021-02-12 | PXD022010 | Pride

Mediator directs co-transcriptional heterochromatin assembly by RNAi-dependent and -independent pathways.

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Panoramix SUMOylation at chromatin recruits the heterochromatin machinery to piRNA target loci [CUT&RUN]

2021-08-22 | GSE173235 | GEO

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2021-08-22 | GSE173222 | GEO

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