RNAi triggered by specialized machinery silences developmental genes and retrotransposons

Abstract

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 repeats1,2. 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 siRNA clusters and corresponding increase in heterochromatin modifications across large domains containing genes and retrotransposons. 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 these target loci 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.

Conserved factor Dhp1/Rat1/Xrn2 triggers premature transcription termination and nucleates heterochromatin to promote gene silencing

“…MTREC along with associated RNA-processing factors also has been implicated in RNAi-dependent assembly of heterochromatin domains on developmental genes and retrotransposons (10,11). To determine whether Dhp1 cooperates with MTREC to assemble RNAi-dependent HOODs, we introduced dhp1-2 into a strain carrying rrp6Δ that allows detection of HOODs under standard growth conditions (10).…”

“…In particular, RNAi machinery is believed to function in the assembly of major constitutive heterochromatin domains coating centromeres, telomeres, and the mating type (mat) locus (7)(8)(9). RNAi-dependent mechanisms also assemble dynamically regulated facultative heterochromatin domains, hereafter referred to as "HOODs", at discrete sites across the genome, including at developmental genes and retrotransposons (10). HOOD assembly is triggered by the specialized nuclear RNA processing and surveillance complex Mtl1-Red1 core (MTREC) and/or associated mRNA 3′-end processing activities, including the canonical poly (A) polymerase Pla1 and the poly(A)-binding protein Pab2, to direct transcripts into RNA degradation pathways and target heterochromatin assembly (10,11).…”

“…HOOD assembly is triggered by the specialized nuclear RNA processing and surveillance complex Mtl1-Red1 core (MTREC) and/or associated mRNA 3′-end processing activities, including the canonical poly (A) polymerase Pla1 and the poly(A)-binding protein Pab2, to direct transcripts into RNA degradation pathways and target heterochromatin assembly (10,11). Notably, HOODs are detected under certain growth conditions or when the 3′-to-5′ exoribonuclease subunit Rrp6 of the nuclear exosome is compromised (10,12).…”

Untimely expression of gametogenic genes in vegetative cells causes uniparental disomy

“…Independently of heterochromatin assembly, RNAi silences meiotic genes during vegetative growth 10,11 . The untimely expression of gametogenic genes, which has been found to occur in tumors in humans 12,13 and to induce tumorigenesis in Drosophila 14 , might be linked to aneuploidy observed in cancer cells.…”

“…The YTH-family protein Mmi1 promotes degradation of meiotic gene transcripts by RNAi and the nuclear exosome 10,11,15–18 . Comparing the expression profiles of cells lacking RNAi components or Mmi1 revealed that a majority of the meiotic genes that were upregulated in ago1 ∆ or dcr1 ∆ RNAi mutants (85 out of 152) were also upregulated in mmi1 ∆ (Fig.…”