A Novel Epigenetic Silencing Pathway Involving the Highly Conserved 5’-3’ Exoribonuclease Dhp1/Rat1/Xrn2 in Schizosaccharomyces pombe

Abstract

Epigenetic gene silencing plays a critical role in regulating gene expression and contributes to organismal development and cell fate acquisition in eukaryotes. In fission yeast, Schizosaccharomyces pombe, heterochromatin-associated gene silencing is known to be mediated by RNA processing pathways including RNA interference (RNAi) and a 3’-5’ exoribonuclease complex, the exosome. Here, we report a new RNA-processing pathway that contributes to epigenetic gene silencing and assembly of heterochromatin mediated by 5’-3’ exoribonuclease Dhp1/Rat1/Xrn2. Dhp1 mutation causes defective gene silencing both at peri-centromeric regions and at the silent mating type locus. Intriguingly, mutation in either of the two well-characterized Dhp1-interacting proteins, the Din1 pyrophosphohydrolase or the Rhn1 transcription termination factor, does not result in silencing defects at the main heterochromatic regions. We demonstrate that Dhp1 interacts with heterochromatic factors and is essential in the sequential steps of establishing silencing in a manner independent of both RNAi and the exosome. Genomic and genetic analyses suggest that Dhp1 is involved in post-transcriptional silencing of repetitive regions through its RNA processing activity. The results describe the unexpected role of Dhp1/Rat1/Xrn2 in chromatin-based silencing and elucidate how various RNA-processing pathways, acting together or independently, contribute to epigenetic regulation of the eukaryotic genome.

Iron homeostasis regulates facultative heterochromatin assembly in adaptive genome control

“…RNA elimination factors cooperate with the conserved exoribonuclease Dhp1 (Xrn2 in higher eukaryotes) that, in addition to promoting transcription termination, recruits Clr4 to assemble heterochromatin 35,36 . We tested whether the formation of heterochromatin islands detected at 18°C requires Dhp1.…”

“…However, we find that RNAi is dispensable for both facultative heterochromatin assembly and gene regulation at 18°C. Instead, this process requires RNA elimination machinery and Dhp1/Xrn2, a RNAPII termination factor linked to heterochromatin modifications 35,36,48 . Clr4 might recruit silencing effectors by methylating H3K9, as it does at constitutive heterochromatic loci 44 .…”

Defective XRN3‐mediated transcription termination in Arabidopsis affects the expression of protein‐coding genes

“…Only Xrn2 dominant negative catalytic mutation causes widespread termination defects for mRNA‐coding genes (Banerjee et al ., ; Brannan et al ., ; Fong et al ., ; Nojima et al ., ). Co‐transcriptional removal of RNAs by the Rat1 homologs Dhp1 and Xrn2 was implicated in heterochromatin formation in Schizosaccharomyces pombe and in the protection of genome integrity in human cells, respectively (Chalamcharla et al ., ; Morales et al ., ; Tucker et al ., ). On the other hand, studies in Caenorhabditis elegans and human cells show that biogenesis of both coding and non‐coding transcripts from polycistronic units may be regulated by Xrn2 activity, probably through Pol II transcription termination of upstream genes (Miki et al ., ; Wu et al ., ).…”

An RNA Degradation Complex Required for Spreading and Epigenetic Inheritance of Heterochromatin

“…pombe, Dhp1 has previously been shown to promote transcription termination within heterochromatin and a dhp1 mutation impairs the silencing of some heterochromatic reporter genes, although how heterochromatic RNAs become substrates for Dhp1 had remained unknown (Chalamcharla et al, 2015, Tucker et al, 2016. We hypothesized that the rixosome is specifically recruited to heterochromatin to initiate the degradation of heterochromatic RNAs, by channeling them through the 5'-3' and 3'-5' exonucleases Dhp1 and Dis3/Rrp6, respectively.…”