Preferential Repair of DNA Double-strand Break at the Active Gene in Vivo

Chaurasia, Priyasri; Sen, Rwik; Pandita, Tej K.; Bhaumik, Sukesh R.

doi:10.1074/jbc.m112.364661

Cited by 23 publications

(14 citation statements)

References 62 publications

(77 reference statements)

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“…Strain PWY002 with the galactose-inducible HO gene integrated at the ADE3 locus was constructed by transforming the linearized plasmid pYIPade3HO (kindly provided by Dr Virginia Zakian) into PWY001, following the procedures described in ( 15 ). The yeast strain PWY81 containing the HO cut site (HOcs) at the genomic ADH1 gene was constructed by transforming into strain JCY004 with DNA fragments PCR amplified from the HOcs-13Myc-KanMX cassette at the 3′ end of the ADH1 gene using genomic DNA extracted from strain PCY23 (a kind gift from Dr Sukesh R. Bhaumik) as PCR template ( 16 ). The positive transformants were selected on G418 plates, and screened for clones that contain HOcs inserted at the 3′ end of the ADH1 gene.…”

Section: Methodsmentioning

confidence: 99%

Proteomic identification of histone post-translational modifications and proteins enriched at a DNA double-strand break

Wang¹,

Byrum²,

Fowler³

et al. 2017

Nucleic Acids Research

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Here, we use ChAP-MS (chromatin affinity purification with mass spectrometry), for the affinity purification of a sequence-specific single-copy endogenous chromosomal locus containing a DNA double-strand break (DSB). We found multiple new histone post-translational modifications enriched on chromatin bearing a DSB from budding yeast. One of these, methylation of histone H3 on lysine 125, has not previously been reported. Among over 100 novel proteins enriched at a DSB were the phosphatase Sit4, the RNA pol II degradation factor Def1, the mRNA export protein Yra1 and the HECT E3 ligase Tom1. Each of these proteins was required for resistance to radiomimetics, and many were required for resistance to heat, which we show here to cause a defect in DSB repair in yeast. Yra1 and Def1 were required for DSB repair per se, while Sit4 was required for rapid inactivation of the DNA damage checkpoint after DSB repair. Thus, our unbiased proteomics approach has led to the unexpected discovery of novel roles for these and other proteins in the DNA damage response.

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Section: Methodsmentioning

confidence: 99%

Proteomic identification of histone post-translational modifications and proteins enriched at a DNA double-strand break

Wang¹,

Byrum²,

Fowler³

et al. 2017

Nucleic Acids Research

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“…Replication-born DSBs are preferentially repaired by homologous recombination using the intact sister chromatid as a template (Kadyk and Hartwell 1992;Johnson and Jasin 2000;González-Barrera et al 2003) but can also be repaired by homologous recombination with ectopic homologous sequences leading to chromosomal rearrangements (Pardo et al 2009). Some studies suggest that transcription channels DSB repair pathway choice toward homologous recombination (Chaurasia et al 2012;Aymard et al 2014) and an increasing amount of reports support that transcription definitely influences DSB repair (Aguilera and Gómez-González 2017;Marnef et al 2017). This is a phenomenon that we need to explore further, as it may have an important impact on transcription-associated genetic instability.…”

Section: Fork Protection and Replication Resumptionmentioning

confidence: 99%

Transcription-mediated replication hindrance: a major driver of genome instability

2019

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Genome replication involves dealing with obstacles that can result from DNA damage but also from chromatin alterations, topological stress, tightly bound proteins or non-B DNA structures such as R loops. Experimental evidence reveals that an engaged transcription machinery at the DNA can either enhance such obstacles or be an obstacle itself. Thus, transcription can become a potentially hazardous process promoting localized replication fork hindrance and stress, which would ultimately cause genome instability, a hallmark of cancer cells. Understanding the causes behind transcription–replication conflicts as well as how the cell resolves them to sustain genome integrity is the aim of this review.

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“…Furthermore, this recruitment is dependent on the presence of transcript RNA [42]. Not only are DSB repair proteins recruited to sites of DSBs in actively transcribed genes, but actively transcribed genes are repaired at a faster rate [43]. Following these recent findings, it is conceivable that transcript RNA may be playing a role in DSB repair at actively transcribed genes.…”

Section: Rna On the Frontlines Of Dna Damagementioning

confidence: 99%

DNA repair by RNA: Templated, or not templated, that is the question

2016

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Cells are continuously exposed to both endogenous and exogenous sources of genomic stress. To maintain chromosome stability, a variety of mechanisms have evolved to cope with the multitude of genetic abnormalities that can arise over the life of a cell. Still, failures to repair these lesions are the driving force of cancers and other degenerative disorders. DNA double-strand breaks (DSBs) are among the most toxic genetic lesions, inhibiting cell ability to replicate, and are sites of mutations and chromosomal rearrangements. DSB repair is known to proceed via two major mechanisms: homologous recombination (HR) and non-homologous end joining (NHEJ). HR reliance on the exchange of genetic information between two identical or nearly identical DNA molecules offers increased accuracy. While the preferred substrate for HR in mitotic cells is the sister chromatid, this is limited to the S and G2 phases of the cell cycle. However, abundant amounts of homologous genetic substrate may exist throughout the cell cycle in the form of RNA. Considered an uncommon occurrence, the direct transfer of information from RNA to DNA is thought to be limited to special circumstances. Studies have shown that RNA molecules reverse transcribed into cDNA can be incorporated into DNA at DSB sites via a non-templated mechanism by NHEJ or a templated mechanism by HR. In addition, synthetic RNA molecules can directly template the repair of DSBs in yeast and human cells via an HR mechanism. New work suggests that even endogenous transcript RNA can serve as a homologous template to repair a DSB in chromosomal DNA. In this perspective, we will review and discuss the recent advancements in DSB repair by RNA via non-templated and templated mechanisms. We will provide current findings, models and future challenges investigating RNA and its role in DSB repair.

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Preferential Repair of DNA Double-strand Break at the Active Gene in Vivo

Cited by 23 publications

References 62 publications

Proteomic identification of histone post-translational modifications and proteins enriched at a DNA double-strand break

Proteomic identification of histone post-translational modifications and proteins enriched at a DNA double-strand break

Transcription-mediated replication hindrance: a major driver of genome instability

DNA repair by RNA: Templated, or not templated, that is the question

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