Resection is responsible for loss of transcription around a double-strand break in Saccharomyces cerevisiae

Manfrini, Nicola; Clerici, Michela; Wéry, Maxime; Colombo, Chiara Vittoria; Descrimes, Marc; Morillon, Antonin; Fagagna, Fabrizio d’Adda di; Longhese, Maria Pia

doi:10.7554/elife.08942

Cited by 26 publications

(19 citation statements)

References 44 publications

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“…This conclusion highlights the differences between different biological systems since DDR kinases ATM and ATR are dispensable for transcriptional repression in yeast , while they play key roles in mammals, as described above. Several observations seem to exclude a key role for resection in DSB‐dependent transcriptional silencing in mammals.…”

Section: Dna‐end Resection: a Physical Trigger For Transcriptional Simentioning

confidence: 67%

“…More recently, Manfrini et al . extended this observation by showing that such decrease was not restricted to the MAT locus: DSBs at three distinct sites reduced both the steady‐state RNA levels of genes flanking the breaks and RNAPII occupancy, in a manner inversely proportional to the distance from the break. Of note, when resection was impaired by inactivating the key nucleases MRX (Mre11‐Rad50‐Xrs2) complex and the exonuclease 1 (Exo1), both transcription and RNAPII binding were restored to an extent depending on the severity of the resection defect.…”

Section: Dna‐end Resection: a Physical Trigger For Transcriptional Simentioning

confidence: 78%

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Express or repress? The transcriptional dilemma of damaged chromatin

et al. 2017

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The fine modulation of transcriptional activity around DNA lesions is essential to carefully regulate the crosstalk between the activation of the DNA damage response, DNA repair and transcription, particularly when the lesion occurs next to actively transcribed genes. Recently, several studies have been carried out to investigate how DNA lesions impact on local transcription, but the emerging model remains incomplete. Transcription of genes around damaged DNA is actively downregulated by the DNA damage response through different mechanisms, which appear specific to the chromatin context, the type of DNA damage or its complexity. Intriguingly, emerging evidence also indicates that transcription of noncoding RNAs (ncRNAs) is induced at sites of DNA damage, producing small ncRNAs that are, in turn, required for a full DNA damage response activation. We discuss here these recent findings, highlighting the major unresolved questions in the field, and propose ways to reconcile these apparently contradictory observations.

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Section: Dna‐end Resection: a Physical Trigger For Transcriptional Simentioning

confidence: 67%

Section: Dna‐end Resection: a Physical Trigger For Transcriptional Simentioning

confidence: 78%

Express or repress? The transcriptional dilemma of damaged chromatin

et al. 2017

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“…Thus, AddAB-dependent processing of DSB ends could affect the transcription of genes flanking a break site, as shown recently in yeast [54]. To test this possibility in Caulobacter , we performed RNA-seq on swarmer cells subjected to a single DSB.…”

Section: Resultsmentioning

confidence: 95%

Global analysis of double-strand break processing reveals in vivo properties of the helicase-nuclease complex AddAB

Badrinarayanan

Spille

et al. 2017

PLoS Genet

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In bacteria, double-strand break (DSB) repair via homologous recombination is thought to be initiated through the bi-directional degradation and resection of DNA ends by a helicasenuclease complex such as AddAB. The activity of AddAB has been well-studied in vitro, with translocation speeds between 400-2000 bp/s on linear DNA suggesting that a large section of DNA around a break site is processed for repair. However, the translocation rate and activity of AddAB in vivo is not known, and how AddAB is regulated to prevent excessive DNA degradation around a break site is unclear. To examine the functions and mechanistic regulation of AddAB inside bacterial cells, we developed a next-generation sequencingbased approach to assay DNA processing after a site-specific DSB was introduced on the chromosome of Caulobacter crescentus. Using this assay we determined the in vivo rates of DSB processing by AddAB and found that putative chi sites attenuate processing in a RecA-dependent manner. This RecA-mediated regulation of AddAB prevents the excessive loss of DNA around a break site, limiting the effects of DSB processing on transcription. In sum, our results, taken together with prior studies, support a mechanism for regulating AddAB that couples two key events of DSB repair-the attenuation of DNA-end processing and the initiation of homology search by RecA-thereby helping to ensure that genomic integrity is maintained during DSB repair. Author summaryDouble-strand breaks (DSBs) are a threat to genome integrity and are faithfully repaired via homologous recombination. The initial processing of DSB ends that prepares them for recombination has been well-studied in vitro, but is less well characterized in vivo. We describe a deep sequencing-based assay for assessing the early steps of DSB processing in bacterial cells by the helicase-nuclease complex AddAB. We find that a combination of chi site recognition and RecA loading is required to attenuate AddAB activity. In the PLOS Genetics | https://doi.org/10.1371/journal.pgen

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“…Because fork progression is reduced at both DAFCs, collapsed forks and unrepaired DSBs likely accumulate 5-10 kb from the chorion genes. Several studies have found that DSB generation leads to a decrease in local transcription, and a recent study in yeast found that a single unrepaired DSB reduces transcription up to 10 kb away on either side of the break site (31). We therefore propose that the absence of MMEJ repair leads to an accumulation of DSBs, inhibiting both fork progression and transcription at certain DAFCs.…”

Section: Discussionmentioning

confidence: 92%

Multiple mechanisms contribute to double-strand break repair at rereplication forks in Drosophila follicle cells

Alexander

Beagan

Orr‐Weaver

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Rereplication generates double-strand breaks (DSBs) at sites of fork collisions and causes genomic damage, including repeat instability and chromosomal aberrations. However, the primary mechanism used to repair rereplication DSBs varies across different experimental systems. In Drosophila follicle cells, developmentally regulated rereplication is used to amplify six genomic regions, two of which contain genes encoding eggshell proteins. We have exploited this system to test the roles of several DSB repair pathways during rereplication, using fork progression as a readout for DSB repair efficiency. Here we show that a null mutation in the microhomology-mediated end-joining (MMEJ) component, polymerase θ/mutagen-sensitive 308 (mus308), exhibits a sporadic thin eggshell phenotype and reduced chorion gene expression. Unlike other thin eggshell mutants, mus308 displays normal origin firing but reduced fork progression at two regions of rereplication. We also find that MMEJ compensates for loss of nonhomologous end joining to repair rereplication DSBs in a site-specific manner. Conversely, we show that fork progression is enhanced in the absence of both Drosophila Rad51 homologs, spindle-A and spindle-B, revealing homologous recombination is active and actually impairs fork movement during follicle cell rereplication. These results demonstrate that several DSB repair pathways are used during rereplication in the follicle cells and their contribution to productive fork progression is influenced by genomic position and repair pathway competition. Furthermore, our findings illustrate that specific rereplication DSB repair pathways can have major effects on cellular physiology, dependent upon genomic context. oogenesis | break-induced replication | DNA repair | NHEJ | fork collision

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Resection is responsible for loss of transcription around a double-strand break in Saccharomyces cerevisiae

Cited by 26 publications

References 44 publications

Express or repress? The transcriptional dilemma of damaged chromatin

Express or repress? The transcriptional dilemma of damaged chromatin

Global analysis of double-strand break processing reveals in vivo properties of the helicase-nuclease complex AddAB

Multiple mechanisms contribute to double-strand break repair at rereplication forks in Drosophila follicle cells

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