Yeast Sen1 Helicase Protects the Genome from Transcription-Associated Instability

Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
Molecular cell (Impact Factor: 14.02). 01/2011; 41(1):21-32. DOI: 10.1016/j.molcel.2010.12.007
Source: PubMed


Sen1 of S. cerevisiae is a known component of the NRD complex implicated in transcription termination of nonpolyadenylated as well as some polyadenylated RNA polymerase II transcripts. We now show that Sen1 helicase possesses a wider function by restricting the occurrence of RNA:DNA hybrids that may naturally form during transcription, when nascent RNA hybridizes to DNA prior to its packaging into RNA protein complexes. These hybrids displace the nontranscribed strand and create R loop structures. Loss of Sen1 results in transient R loop accumulation and so elicits transcription-associated recombination. SEN1 genetically interacts with DNA repair genes, suggesting that R loop resolution requires proteins involved in homologous recombination. Based on these findings, we propose that R loop formation is a frequent event during transcription and a key function of Sen1 is to prevent their accumulation and associated genome instability.

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    • "Importantly, TAR is highly elevated when RNA processing is perturbed and R-loops accumulate, or when R-loop removal mechanisms are disabled. The RNA component of R-loops can be removed by the Sen1 RNA-DNA helicase (Mischo et al. 2011) or degraded by ribonuclease (RNase) H1 or RNase H2 (reviewed in Cerritelli and Crouch 2009), which are generally considered to be functionally redundant. "
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    ABSTRACT: Two types of RNA:DNA associations can lead to genome instability: the formation of R-loops during transcription and the incorporation of ribonucleotide monophosphates (rNMPs) into DNA during replication. Both ribonuclease (RNase) H1 and RNase H2 degrade the RNA component of R-loops, whereas only RNase H2 can remove one or a few rNMPs from DNA. We performed high-resolution mapping of mitotic recombination events throughout the yeast genome in diploid strains of Saccharomyces cerevisiae lacking RNase H1 (rnh1Δ), RNase H2 (rnh201Δ), or both RNase H1 and RNase H2 (rnh1Δ rnh201Δ). We found little effect on recombination in the rnh1Δ strain, but elevated recombination in both the rnh201Δ and the double-mutant strains; levels of recombination in the double mutant were about 50% higher than in the rnh201 single-mutant strain. An rnh201Δ mutant that additionally contained a mutation that reduces rNMP incorporation by DNA polymerase ε (pol2-M644L) had a level of instability similar to that observed in the presence of wild-type Polε. This result suggests that the elevated recombination observed in the absence of only RNase H2 is primarily a consequence of R loops rather than misincorporated rNMPs.
    Preview · Article · Sep 2015 · Genetics
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    • " helicase structurally related to Senataxin , prevent DNA damages caused by RNA : DNA hybrids accu - mulation , suggesting that this function has been evolution - arily conserved ( Yuce and West , 2013 ; Sollier et al . , 2014 ) . Another suggested distinct role of Sen1 / Senataxin is to pro - mote transcription termination by removing R - loops ( Mischo et al . , 2011 ; Skourti - Stathaki et al . , 2011 ) . It is therefore possi - ble that specific termination factors are engaged at fork passage to inhibit transcription . The above scenario is also consistent with the finding that the exosome , a multi - protein complex that degrades aberrant RNA molecules and is involved in tran - scription terminat"
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    ABSTRACT: DNA replication and transcription are vital cellular processes during which the genetic information is copied into complementary DNA and RNA molecules. Highly complex machineries required for DNA and RNA synthesis compete for the same DNA template, therefore being on a collision course. Unscheduled replication-transcription clashes alter the gene transcription program and generate replication stress, reducing fork speed. Molecular pathways and mechanisms that minimize the conflict between replication and transcription have been extensively characterized in prokaryotic cells and recently identified also in eukaryotes. A pathological outcome of replication-transcription collisions is the formation of stable RNA:DNA hybrids in molecular structures called R-loops. Growing evidence suggests that R-loop accumulation promotes both genetic and epigenetic instability, thus severely affecting genome functionality. In the present review, we summarize the current knowledge related to replication and transcription conflicts in eukaryotes, their consequences on genome instability and the pathways involved in their resolution. These findings are relevant to clarify the molecular basis of cancer and neurodegenerative diseases.
    Full-text · Article · Apr 2015 · Frontiers in Genetics
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    • "Disruption of the Setx gene in mice leads to a defect in spermatogenesis , caused by failure of meiotic recombination (Becherel et al., 2013). Sen1, the SETX yeast homolog, was shown to contribute to the processing of various RNA species and to the distribution of RNA polymerase II (RNAPII) across the genome (Mischo et al., 2011; Steinmetz et al., 2006; Ursic et al., 1997). This probably occurs via its direct interaction with RNAPII and certain RNA processing factors (Suraweera et al., 2009). "
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    ABSTRACT: The mechanisms contributing to transcription-associated genomic instability are both complex and incompletely understood. Although R-loops are normal transcriptional intermediates, they are also associated with genomic instability. Here, we show that BRCA1 is recruited to R-loops that form normally over a subset of transcription termination regions. There it mediates the recruitment of a specific, physiological binding partner, senataxin (SETX). Disruption of this complex led to R-loop-driven DNA damage at those loci as reflected by adjacent γ-H2AX accumulation and ssDNA breaks within the untranscribed strand of relevant R-loop structures. Genome-wide analysis revealed widespread BRCA1 binding enrichment at R-loop-rich termination regions (TRs) of actively transcribed genes. Strikingly, within some of these genes in BRCA1 null breast tumors, there are specific insertion/deletion mutations located close to R-loop-mediated BRCA1 binding sites within TRs. Thus, BRCA1/SETX complexes support a DNA repair mechanism that addresses R-loop-based DNA damage at transcriptional pause sites. Copyright © 2015 Elsevier Inc. All rights reserved.
    Full-text · Article · Feb 2015 · Molecular Cell
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