Small RNA-mediated genomic silencing promotes telomere stability in the absence of telomerase

Abstract

Small RNAs with homology to telomeres can map to heterochromatic segments of the C. elegans genome, although small RNAs with perfect homology to (TTAGGC)n telomere repeats are exceptionally rare. The heterochromatin mark H3K9me2 is enriched at C. elegans sub-telomeres, and we found that the HP1 protein HPL-2 that binds H3K9me2 promotes telomere stability in the absence of telomerase. Small RNA silencing can promote H3K9 methylation, and we found that telomere stability in the absence of telomerase required WAGO-1 and HRDE-1 Argonaute proteins that bind small RNAs as well as germ granule proteins MUT-7 and MUT-14 that promote small RNA biogenesis. Loss of HRDE-1, WAGO-1 or PPW-2 Argonautes or the germ granule protein MUT-16 resulted in depletion of subtelomeric small RNAs. Loss of telomerase induces biogenesis of subtelomeric small RNAs from 5 end of the telomeric lncRNA TERRA, whereas loss of both telomerase and small RNA-mediated genome silencing induces TERRA expression, telomere damage and accelerated sterility. We propose that small RNA-mediated heterochromatin formation and telomerase function redundantly to repress a form of telomeric DNA damage that is coupled to TERRA expression and subtelomeric small RNA biogenesis. Long read sequencing revealed few mutations at 5 ends of telomeres for most N2 wild type C. elegans strains. Despite abundant subtelomeric small RNAs, telomere repeats of TERRA strongly resisted RNA-dependent RNA polymerase activity, revealing an exceptional quality of telomere repeat RNA. Article summaryLoss of telomerase and either small RNA biogenesis factors or heterochromatin proteins resulted in rapid onset of telomere fusions. We identified Argonaute proteins that bind to subtelomeric small RNAs and promote telomere stability in the absence of telomerase. Telomeres are transcribed to create the non-coding RNA TERRA that is a composite of subtelomere sequence and telomere repeats. Although subtelomeric small RNAs were upregulated in the absence of telomerase, the telomere sequence of TERRA was completely resistant to small RNA biogenesis. Small RNAs and TERRA may interact to promote repair of damaged telomeres that cannot be healed by telomerase.