Homologous recombination as a mechanism to recognize repetitive DNA sequences in an RNAi pathway

Abstract

Quelling is an RNAi-related phenomenon that posttranscriptionally silences repetitive DNA and transposons in Neurospora. We previously identified a type of DNA damage-induced small RNA called qiRNA that originates from ribosomal DNA. To understand how small RNAs are generated from repetitive DNA, we carried out a genetic screen to identify genes required for qiRNA biogenesis. Factors directly involved in homologous recombination (HR) and chromatin remodeling factors required for HR are essential for qiRNA production. HR is also required for quelling, and quelling is also the result of DNA damage, indicating that quelling and qiRNA production share a common mechanism. Together, our results suggest that DNA damage-triggered HR-based recombination allows the RNAi pathway to recognize repetitive DNA to produce small RNA.

Histone H3K56 Acetylation Is Required for Quelling-induced Small RNA Production through Its Role in Homologous Recombination

“…Protein and RNA Analyses-Protein extraction, quantification, and Western blot analysis were performed as described previously (18,23). Nuclear protein extracts were prepared as described previously (24).…”

“…Chromatin Immunoprecipitation (ChIP)-ChIP experiment was performed as described previously (18). A double strand break (DSB) was induced by culture in liquid medium containing QA for 2 days.…”

“…Our recent study showed that both quelling and qiRNA production are caused by DNA damage/replication stress (18). DNA damage agent treatment can induce quelling-induced siRNA in the quelled strain.…”

“…However, the mechanistic details of this HRbased siRNA biogenesis pathway are not clear. A number of chromatin remodelers are also required for both HR and siRNA pathway in Neurospora (18), indicating that a favorable chromatin environment is essential for this siRNA biogenesis pathway (18).…”

“…We recently showed that homologous recombination (HR) pathway is required for quelling and qiRNA production. This lead to the proposal that HR serves a mechanism to recognize repetitive DNA and initiates aRNA transcription under DNA damage condition (18). However, the mechanistic details of this HRbased siRNA biogenesis pathway are not clear.…”