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Németh E, Szüts D. The mutagenic consequences of defective DNA repair. DNA Repair (Amst) 2024; 139:103694. [PMID: 38788323 DOI: 10.1016/j.dnarep.2024.103694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/10/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024]
Abstract
Multiple separate repair mechanisms safeguard the genome against various types of DNA damage, and their failure can increase the rate of spontaneous mutagenesis. The malfunction of distinct repair mechanisms leads to genomic instability through different mutagenic processes. For example, defective mismatch repair causes high base substitution rates and microsatellite instability, whereas homologous recombination deficiency is characteristically associated with deletions and chromosome instability. This review presents a comprehensive collection of all mutagenic phenotypes associated with the loss of each DNA repair mechanism, drawing on data from a variety of model organisms and mutagenesis assays, and placing greatest emphasis on systematic analyses of human cancer datasets. We describe the latest theories on the mechanism of each mutagenic process, often explained by reliance on an alternative repair pathway or the error-prone replication of unrepaired, damaged DNA. Aided by the concept of mutational signatures, the genomic phenotypes can be used in cancer diagnosis to identify defective DNA repair pathways.
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Affiliation(s)
- Eszter Németh
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - Dávid Szüts
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary.
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Lay MA, Thompson VF, Adelakun AD, Schwartz JC. Ewing Sarcoma Related protein 1 recognizes R-loops by binding DNA forks. Biopolymers 2024; 115:e23576. [PMID: 38511874 PMCID: PMC11127786 DOI: 10.1002/bip.23576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 03/07/2024] [Accepted: 03/08/2024] [Indexed: 03/22/2024]
Abstract
EWSR1 (Ewing Sarcoma Related protein 1) is an RNA binding protein that is ubiquitously expressed across cell lines and involved in multiple parts of RNA processing, such as transcription, splicing, and mRNA transport. EWSR1 has also been implicated in cellular mechanisms to control formation of R-loops, a three-stranded nucleic acid structure consisting of a DNA:RNA hybrid and a displaced single-stranded DNA strand. Unscheduled R-loops result in genomic and transcription stress. Loss of function of EWSR1 functions commonly found in Ewing Sarcoma correlates with high abundance of R-loops. In this study, we investigated the mechanism for EWSR1 to recognize an R-loop structure specifically. Using electrophoretic mobility shift assays (EMSA), we detected the high affinity binding of EWSR1 to substrates representing components found in R-loops. EWSR1 specificity could be isolated to the DNA fork region, which transitions between double- and single-stranded DNA. Our data suggests that the Zinc-finger domain (ZnF) with flanking arginine and glycine rich (RGG) domains provide high affinity binding, while the RNA recognition motif (RRM) with its RGG domains offer improved specificity. This model offers a rational for EWSR1 specificity to encompass a wide range in contexts due to the DNA forks always found with R-loops.
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Affiliation(s)
- Michelle A Lay
- Department of Pharmacology, University of Arizona, Tucson, Arizona, USA
- University of Arizona Cancer Center, University of Arizona, Tucson, Arizona, USA
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, USA
| | - Valery F Thompson
- Department of Pharmacology, University of Arizona, Tucson, Arizona, USA
- University of Arizona Cancer Center, University of Arizona, Tucson, Arizona, USA
| | - Ajibola D Adelakun
- Department of Pharmacology, University of Arizona, Tucson, Arizona, USA
- University of Arizona Cancer Center, University of Arizona, Tucson, Arizona, USA
- Department of Pharmaceutical Sciences, University of Arizona, Tucson, Arizona, USA
| | - Jacob C Schwartz
- Department of Pharmacology, University of Arizona, Tucson, Arizona, USA
- University of Arizona Cancer Center, University of Arizona, Tucson, Arizona, USA
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Bandau S, Alvarez V, Jiang H, Graff S, Sundaramoorthy R, Gierlinski M, Toman M, Owen-Hughes T, Sidoli S, Lamond A, Alabert C. RNA polymerase II promotes the organization of chromatin following DNA replication. EMBO Rep 2024; 25:1387-1414. [PMID: 38347224 PMCID: PMC10933433 DOI: 10.1038/s44319-024-00085-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 01/17/2024] [Accepted: 01/23/2024] [Indexed: 02/18/2024] Open
Abstract
Understanding how chromatin organisation is duplicated on the two daughter strands is a central question in epigenetics. In mammals, following the passage of the replisome, nucleosomes lose their defined positioning and transcription contributes to their re-organisation. However, whether transcription plays a greater role in the organization of chromatin following DNA replication remains unclear. Here we analysed protein re-association with newly replicated DNA upon inhibition of transcription using iPOND coupled to quantitative mass spectrometry. We show that nucleosome assembly and the re-establishment of most histone modifications are uncoupled from transcription. However, RNAPII acts to promote the re-association of hundreds of proteins with newly replicated chromatin via pathways that are not observed in steady-state chromatin. These include ATP-dependent remodellers, transcription factors and histone methyltransferases. We also identify a set of DNA repair factors that may handle transcription-replication conflicts during normal transcription in human non-transformed cells. Our study reveals that transcription plays a greater role in the organization of chromatin post-replication than previously anticipated.
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Affiliation(s)
- Susanne Bandau
- MCDB, School of Life Sciences, University of Dundee, DD15EH, Dundee, UK
| | - Vanesa Alvarez
- MCDB, School of Life Sciences, University of Dundee, DD15EH, Dundee, UK
| | - Hao Jiang
- Laboratory of Quantitative Proteomics, MCDB, School of Life Sciences, University of Dundee, DD15EH, Dundee, UK
| | - Sarah Graff
- Department of Biochemistry at the Albert Einstein College of Medicine, New York, NY, USA
| | | | - Marek Gierlinski
- Data Analysis Group, Division of Computational Biology, School of Life Sciences, University of Dundee, Dow Street, DD1 5EH, Dundee, UK
| | - Matt Toman
- Laboratory of Chromatin Structure and Function, MCDB, School of Life Sciences, University of Dundee, DD15EH, Dundee, UK
| | - Tom Owen-Hughes
- Laboratory of Chromatin Structure and Function, MCDB, School of Life Sciences, University of Dundee, DD15EH, Dundee, UK
| | - Simone Sidoli
- Department of Biochemistry at the Albert Einstein College of Medicine, New York, NY, USA
| | - Angus Lamond
- Laboratory of Quantitative Proteomics, MCDB, School of Life Sciences, University of Dundee, DD15EH, Dundee, UK
| | - Constance Alabert
- MCDB, School of Life Sciences, University of Dundee, DD15EH, Dundee, UK.
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Lay MA, Thompson VF, Adelakun AD, Schwartz JC. Ewing Sarcoma Related protein 1 recognizes R-loops by binding DNA forks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.20.576463. [PMID: 38293191 PMCID: PMC10827230 DOI: 10.1101/2024.01.20.576463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
EWSR1 (Ewing Sarcoma Related protein 1) is an RNA binding protein that is ubiquitously expressed across cell lines and involved in multiple parts of RNA processing, such as transcription, splicing, and mRNA transport. EWSR1 has also been implicated in cellular mechanisms to control formation of R-loops, a three-stranded nucleic acid structure consisting of a DNA:RNA hybrid and a displaced single-stranded DNA strand. Unscheduled R-loops result in genomic and transcription stress. Loss of function of EWSR1 functions commonly found in Ewing Sarcoma correlates with high abundance of R-loops. In this study, we investigated the mechanism for EWSR1 to recognize an R-loop structure specifically. Using electrophoretic mobility shift assays (EMSA), we detected the high affinity binding of EWSR1 to substrates representing components found in R-loops. EWSR1 specificity could be isolated to the DNA fork region, which transitions between double- and single-stranded DNA. Our data suggests that the Zinc-finger domain (ZnF) with flanking arginine and glycine rich (RGG) domains provide high affinity binding, while the RNA recognition motif (RRM) with its RGG domains offer improved specificity. This model offers a rational for EWSR1 specificity to encompass a wide range in contexts due to the DNA forks always found with R-loops.
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Affiliation(s)
- Michelle A Lay
- Department of Pharmacology, University of Arizona, Tucson, AZ 85724, USA
- University of Arizona Cancer Center, Tucson, AZ 85724, USA
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85724, USA
| | - Valery F Thompson
- Department of Pharmacology, University of Arizona, Tucson, AZ 85724, USA
- University of Arizona Cancer Center, Tucson, AZ 85724, USA
| | - Ajibola D Adelakun
- Department of Pharmacology, University of Arizona, Tucson, AZ 85724, USA
- University of Arizona Cancer Center, Tucson, AZ 85724, USA
- Department of Pharmaceutical Sciences, University of Arizona, Tucson, AZ 85724, USA
| | - Jacob C Schwartz
- Department of Pharmacology, University of Arizona, Tucson, AZ 85724, USA
- University of Arizona Cancer Center, Tucson, AZ 85724, USA
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Thakur BL, Kusi NA, Mosavarpour S, Zhu R, Redon CE, Fu H, Dhall A, Pongor LS, Sebastian R, Indig FE, Aladjem MI. SIRT1 Prevents R-Loops during Chronological Aging by Modulating DNA Replication at rDNA Loci. Cells 2023; 12:2630. [PMID: 37998365 PMCID: PMC10669956 DOI: 10.3390/cells12222630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 11/25/2023] Open
Abstract
In metazoans, the largest sirtuin, SIRT1, is a nuclear protein implicated in epigenetic modifications, circadian signaling, DNA recombination, replication, and repair. Our previous studies have demonstrated that SIRT1 binds replication origins and inhibits replication initiation from a group of potential initiation sites (dormant origins). We studied the effects of aging and SIRT1 activity on replication origin usage and the incidence of transcription-replication collisions (creating R-loop structures) in adult human cells obtained at different time points during chronological aging and in cancer cells. In primary, untransformed cells, SIRT1 activity declined and the prevalence of R-loops rose with chronological aging. Both the reduction in SIRT1 activity and the increased abundance of R-loops were also observed during the passage of primary cells in culture. All cells, regardless of donor age or transformation status, reacted to the short-term, acute chemical inhibition of SIRT1 with the activation of excessive replication initiation events coincident with an increased prevalence of R-loops. However, cancer cells activated dormant replication origins, genome-wide, during long-term proliferation with mutated or depleted SIRT1, whereas, in primary cells, the aging-associated SIRT1-mediated activation of dormant origins was restricted to rDNA loci. These observations suggest that chronological aging and the associated decline in SIRT1 activity relax the regulatory networks that protect cells against excess replication and that the mechanisms protecting from replication-transcription collisions at the rDNA loci manifest as differentially enhanced sensitivities to SIRT1 decline and chronological aging.
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Affiliation(s)
- Bhushan L. Thakur
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (B.L.T.); (N.A.K.); (S.M.); (R.Z.); (C.E.R.); (H.F.); (A.D.); (L.S.P.); (R.S.)
| | - Nana A. Kusi
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (B.L.T.); (N.A.K.); (S.M.); (R.Z.); (C.E.R.); (H.F.); (A.D.); (L.S.P.); (R.S.)
| | - Sara Mosavarpour
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (B.L.T.); (N.A.K.); (S.M.); (R.Z.); (C.E.R.); (H.F.); (A.D.); (L.S.P.); (R.S.)
| | - Roger Zhu
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (B.L.T.); (N.A.K.); (S.M.); (R.Z.); (C.E.R.); (H.F.); (A.D.); (L.S.P.); (R.S.)
| | - Christophe E. Redon
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (B.L.T.); (N.A.K.); (S.M.); (R.Z.); (C.E.R.); (H.F.); (A.D.); (L.S.P.); (R.S.)
| | - Haiqing Fu
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (B.L.T.); (N.A.K.); (S.M.); (R.Z.); (C.E.R.); (H.F.); (A.D.); (L.S.P.); (R.S.)
| | - Anjali Dhall
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (B.L.T.); (N.A.K.); (S.M.); (R.Z.); (C.E.R.); (H.F.); (A.D.); (L.S.P.); (R.S.)
| | - Lorinc S. Pongor
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (B.L.T.); (N.A.K.); (S.M.); (R.Z.); (C.E.R.); (H.F.); (A.D.); (L.S.P.); (R.S.)
| | - Robin Sebastian
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (B.L.T.); (N.A.K.); (S.M.); (R.Z.); (C.E.R.); (H.F.); (A.D.); (L.S.P.); (R.S.)
| | - Fred E. Indig
- Confocal Imaging Facility, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA;
| | - Mirit I. Aladjem
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (B.L.T.); (N.A.K.); (S.M.); (R.Z.); (C.E.R.); (H.F.); (A.D.); (L.S.P.); (R.S.)
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