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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Available from: Andrés Aguilera, Oct 13, 2015
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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.
    Frontiers in Genetics 04/2015; 6. DOI:10.3389/fgene.2015.00166
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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.
    Molecular Cell 02/2015; 57(4):636-647. DOI:10.1016/j.molcel.2015.01.011 · 14.02 Impact Factor
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    • "We were particularly interested in one of these factors, Aquarius (AQR), a protein which is part of a subfamily of proteins possessing a conserved DEAxQ-like domain with putative RNA/ DNA helicase activity (Fairman-Williams et al., 2010; Hirose et al., 2006). Interestingly, this subfamily includes Senataxin (SETX), which is thought to promote efficient transcriptional termination by resolving R-loops formed at specific loci (Skourti-Stathaki et al., 2011), and its yeast ortholog, Sen1, which prevents R-loop-mediated genome instability (Alzu et al., 2012; Mischo et al., 2011). Knockdown of AQR robustly induced the DNA damage response (DDR), as evidenced by the phosphorylation of histone variant H2AX (termed gH2AX), a marker of DNA damage (see Figures S1A–S1C) (Paulsen et al., 2009). "
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    ABSTRACT: R-loops, consisting of an RNA-DNA hybrid and displaced single-stranded DNA, are physiological structures that regulate various cellular processes occurring on chromatin. Intriguingly, changes in R-loop dynamics have also been associated with DNA damage accumulation and genome instability; however, the mechanisms underlying R-loop-induced DNA damage remain unknown. Here we demonstrate in human cells that R-loops induced by the absence of diverse RNA processing factors, including the RNA/DNA helicases Aquarius (AQR) and Senataxin (SETX), or by the inhibition of topoisomerase I, are actively processed into DNA double-strand breaks (DSBs) by the nucleotide excision repair endonucleases XPF and XPG. Surprisingly, DSB formation requires the transcription-coupled nucleotide excision repair (TC-NER) factor Cockayne syndrome group B (CSB), but not the global genome repair protein XPC. These findings reveal an unexpected and potentially deleterious role for TC-NER factors in driving R-loop-induced DNA damage and genome instability. Copyright © 2014 Elsevier Inc. All rights reserved.
    Molecular cell 11/2014; 56(6). DOI:10.1016/j.molcel.2014.10.020 · 14.02 Impact Factor
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