A Role for Small RNAs in DNA Double-Strand Break Repair

Abstract

Eukaryotes have evolved complex mechanisms to repair DNA double-strand breaks (DSBs) through coordinated actions of protein sensors, transducers, and effectors. Here we show that ∼21-nucleotide small RNAs are produced from the sequences in the vicinity of DSB sites in Arabidopsis and in human cells. We refer to these as diRNAs for DSB-induced small RNAs. In Arabidopsis, the biogenesis of diRNAs requires the PI3 kinase ATR, RNA polymerase IV (Pol IV), and Dicer-like proteins. Mutations in these proteins as well as in Pol V cause significant reduction in DSB repair efficiency. In Arabidopsis, diRNAs are recruited by Argonaute 2 (AGO2) to mediate DSB repair. Knock down of Dicer or Ago2 in human cells reduces DSB repair. Our findings reveal a conserved function for small RNAs in the DSB repair pathway. We propose that diRNAs may function as guide molecules directing chromatin modifications or the recruitment of protein complexes to DSB sites to facilitate repair.

mRNA Decay of Most Arabidopsis miRNA Targets Requires Slicer Activity of AGO1

“…Alternatively, phenotypic differences could be related to functions of AGO1 other than miRNA target repression. Indeed, the implication of AGO proteins in several pathways such as nonsense-mediated mRNA decay (Choe et al, 2010), alternative splicing (AmeyarZazoua et al, 2012;Yang et al, 2012b;Taliaferro et al, 2013;Alló et al, 2014), DNA double-strand break repair (Michalik et al, 2012;Wei et al, 2012), nucleosome occupancy at transcription start sites (Carissimi et al, 2015), and quality control of mRNAs encoding proteins entering the secretory pathway (Karamyshev et al, 2014) has been proposed during the last years. If that is the case, the conditional slicer-deficient alleles might be a valuable tool to investigate novel functions of plant AGO1 by decoupling these from target regulation.…”

RNAi in Plants: An Argonaute-Centered View

“…The predominant sRNA species include microRNAs (miRNAs) generated by DCL1 Kurihara and Watanabe, 2004;Qi et al, 2005), trans-acting small interfering RNAs (ta-siRNAs) processed by DCL4 (Peragine et al, 2004;Vazquez et al, 2004;Gasciolli et al, 2005;Xie et al, 2005), and heterochromatic siRNAs (hc-siRNAs) produced by DCL3 (Xie et al, 2004;Qi et al, 2005;Henderson et al, 2006). Additional types of sRNAs including natural antisense siRNAs (Borsani et al, 2005), long siRNAs , long miRNAs (lmiRNAs) (Wu et al, 2010), double-strand-break (DSB)-induced sRNAs (diRNAs) (Wei et al, 2012), and DCL-independent siRNA (sidRNAs) (Ye et al, 2016) have also been discovered. While miRNAs, ta-siRNAs, and natsiRNAs mediate posttranscriptional gene silencing (PTGS), hc-siRNAs, lmiRNAs, and sidRNAs direct DNA methylation thus inducing transcriptional gene silencing (TGS).…”

DROSHA associates to DNA damage sites and is required for DNA repair

“…On the contrary, they induce the synthesis of non coding transcripts, which can be further processed into smaller RNA by components of the RNA interference machinery and together play a supportive role in DDR signaling (Francia et al, 2012), (Wei et al, 2012), (Michalik et al, 2012), . We recently reported that RNAPII is recruited to DSBs in a MRN-dependent manner, where it synthesizes dilncRNAs from and towards DNA ends.…”

“…Interestingly, DROSHA inactivation by siRNA prevents telomere fusions. Other groups have reported an involvement of sequence-specific DICER dependent ncRNA in DNA repair by HR (Gao et al, 2014), (Wei et al, 2012) and knockdown of DICER or DROSHA significantly reduced accumulation of two major HR factors, Rad51 and BRCA1 to DSBs (Wang and Goldstein, 2016).…”