1
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Cadden G, Wilken S, Magennis S. A single CAA interrupt in a DNA three-way junction containing a CAG repeat hairpin results in parity-dependent trapping. Nucleic Acids Res 2024; 52:9317-9327. [PMID: 39041420 PMCID: PMC11347167 DOI: 10.1093/nar/gkae644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 07/04/2024] [Accepted: 07/14/2024] [Indexed: 07/24/2024] Open
Abstract
An increasing number of human disorders are attributed to genomic expansions of short tandem repeats (STRs). Secondary DNA structures formed by STRs are believed to play an important role in expansion, while the presence of nucleotide interruptions within the pure repeat sequence is known to delay the onset and progression of disease. We have used two single-molecule fluorescence techniques to analyse the structure and dynamics of DNA three-way junctions (3WJs) containing CAG repeat hairpin slipouts, with and without a single CAA interrupt. For a 3WJ with a (CAG)10 slipout, the CAA interrupt is preferentially located in the hairpin loop, and the branch migration dynamics are 4-fold slower than for the 3WJ with a pure (CAG)10, and 3-fold slower than a 3WJ with a pure (CAG)40 repeat. The (CAG)11 3WJ with CAA interrupt adopts a conformation that places the interrupt in or near the hairpin loop, with similar dynamics to the pure (CAG)10 and (CAG)11 3WJs. We have shown that changing a single nucleotide (G to A) in a pure repeat can have a large impact on 3WJ structure and dynamics, which may be important for the protective role of interrupts in repeat expansion diseases.
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Affiliation(s)
- Gillian M Cadden
- School of Chemistry, University of Glasgow, Joseph Black Building, University Avenue, Glasgow G12 8QQ, UK
| | - Svea J Wilken
- School of Chemistry, University of Glasgow, Joseph Black Building, University Avenue, Glasgow G12 8QQ, UK
| | - Steven W Magennis
- School of Chemistry, University of Glasgow, Joseph Black Building, University Avenue, Glasgow G12 8QQ, UK
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2
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Kojak N, Kuno J, Fittipaldi KE, Khan A, Wenger D, Glasser M, Donnianni RA, Tang Y, Zhang J, Huling K, Ally R, Mujica AO, Turner T, Magardino G, Huang PY, Kerk SY, Droguett G, Prissette M, Rojas J, Gomez T, Gagliardi A, Hunt C, Rabinowitz JS, Gong G, Poueymirou W, Chiao E, Zambrowicz B, Siao CJ, Kajimura D. Somatic and intergenerational G4C2 hexanucleotide repeat instability in a human C9orf72 knock-in mouse model. Nucleic Acids Res 2024; 52:5732-5755. [PMID: 38597682 PMCID: PMC11162798 DOI: 10.1093/nar/gkae250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 03/19/2024] [Accepted: 03/28/2024] [Indexed: 04/11/2024] Open
Abstract
Expansion of a G4C2 repeat in the C9orf72 gene is associated with familial Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal Dementia (FTD). To investigate the underlying mechanisms of repeat instability, which occurs both somatically and intergenerationally, we created a novel mouse model of familial ALS/FTD that harbors 96 copies of G4C2 repeats at a humanized C9orf72 locus. In mouse embryonic stem cells, we observed two modes of repeat expansion. First, we noted minor increases in repeat length per expansion event, which was dependent on a mismatch repair pathway protein Msh2. Second, we found major increases in repeat length per event when a DNA double- or single-strand break (DSB/SSB) was artificially introduced proximal to the repeats, and which was dependent on the homology-directed repair (HDR) pathway. In mice, the first mode primarily drove somatic repeat expansion. Major changes in repeat length, including expansion, were observed when SSB was introduced in one-cell embryos, or intergenerationally without DSB/SSB introduction if G4C2 repeats exceeded 400 copies, although spontaneous HDR-mediated expansion has yet to be identified. These findings provide a novel strategy to model repeat expansion in a non-human genome and offer insights into the mechanism behind C9orf72 G4C2 repeat instability.
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Affiliation(s)
- Nada Kojak
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - Junko Kuno
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | | | | | - David Wenger
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | | | | | - Yajun Tang
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - Jade Zhang
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - Katie Huling
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - Roxanne Ally
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | | | | | | | - Pei Yi Huang
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - Sze Yen Kerk
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | | | | | - Jose Rojas
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | | | | | | | | | - Guochun Gong
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | | | - Eric Chiao
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
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3
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Gadgil RY, Rider SD, Shrestha R, Alhawach V, Hitch D, Leffak M. Microsatellite break-induced replication generates highly mutagenized extrachromosomal circular DNAs. NAR Cancer 2024; 6:zcae027. [PMID: 38854437 PMCID: PMC11161834 DOI: 10.1093/narcan/zcae027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 05/17/2024] [Accepted: 05/24/2024] [Indexed: 06/11/2024] Open
Abstract
Extrachromosomal circular DNAs (eccDNAs) are produced from all regions of the eucaryotic genome. We used inverse PCR of non-B microsatellites capable of forming hairpin, triplex, quadruplex and AT-rich structures integrated at a common ectopic chromosomal site to show that these non-B DNAs generate highly mutagenized eccDNAs by replication-dependent mechanisms. Mutagenesis occurs within the non-B DNAs and extends several kilobases bidirectionally into flanking and nonallelic DNA. Each non-B DNA exhibits a different pattern of mutagenesis, while sister clones containing the same non-B DNA also display distinct patterns of recombination, microhomology-mediated template switching and base substitutions. Mutations include mismatches, short duplications, long nontemplated insertions, large deletions and template switches to sister chromatids and nonallelic chromosomes. Drug-induced replication stress or the depletion of DNA repair factors Rad51, the COPS2 signalosome subunit or POLη change the pattern of template switching and alter the eccDNA mutagenic profiles. We propose an asynchronous capture model based on break-induced replication from microsatellite-induced DNA double strand breaks to account for the generation and circularization of mutagenized eccDNAs and the appearance of genomic homologous recombination deficiency (HRD) scars. These results may help to explain the appearance of tumor eccDNAS and their roles in neoantigen production, oncogenesis and resistance to chemotherapy.
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Affiliation(s)
- Rujuta Yashodhan Gadgil
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH 45435, USA
| | - S Dean Rider
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH 45435, USA
| | - Resha Shrestha
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH 45435, USA
| | - Venicia Alhawach
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH 45435, USA
| | - David C Hitch
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH 45435, USA
| | - Michael Leffak
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH 45435, USA
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4
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Papp D, Hernandez LA, Mai TA, Haanen TJ, O’Donnell MA, Duran AT, Hernandez SM, Narvanto JE, Arguello B, Onwukwe MO, Mirkin SM, Kim JC. Massive contractions of myotonic dystrophy type 2-associated CCTG tetranucleotide repeats occur via double-strand break repair with distinct requirements for DNA helicases. G3 (BETHESDA, MD.) 2024; 14:jkad257. [PMID: 37950892 PMCID: PMC10849350 DOI: 10.1093/g3journal/jkad257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 07/06/2023] [Accepted: 10/19/2023] [Indexed: 11/13/2023]
Abstract
Myotonic dystrophy type 2 (DM2) is a genetic disease caused by expanded CCTG DNA repeats in the first intron of CNBP. The number of CCTG repeats in DM2 patients ranges from 75 to 11,000, yet little is known about the molecular mechanisms responsible for repeat expansions or contractions. We developed an experimental system in Saccharomyces cerevisiae that enables the selection of large-scale contractions of (CCTG)100 within the intron of a reporter gene and subsequent genetic analysis. Contractions exceeded 80 repeat units, causing the final repetitive tract to be well below the threshold for disease. We found that Rad51 and Rad52 are involved in these massive contractions, indicating a mechanism that uses homologous recombination. Srs2 helicase was shown previously to stabilize CTG, CAG, and CGG repeats. Loss of Srs2 did not significantly affect CCTG contraction rates in unperturbed conditions. In contrast, loss of the RecQ helicase Sgs1 resulted in a 6-fold decrease in contraction rate with specific evidence that helicase activity is required for large-scale contractions. Using a genetic assay to evaluate chromosome arm loss, we determined that CCTG and reverse complementary CAGG repeats elevate the rate of chromosomal fragility compared to a short-track control. Overall, our results demonstrate that the genetic control of CCTG repeat contractions is notably distinct among disease-causing microsatellite repeat sequences.
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Affiliation(s)
- David Papp
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Luis A Hernandez
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Theresa A Mai
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Terrance J Haanen
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Meghan A O’Donnell
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Ariel T Duran
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Sophia M Hernandez
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Jenni E Narvanto
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Berenice Arguello
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Marvin O Onwukwe
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Jane C Kim
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
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5
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Gadgil RY, Rider SD, Shrestha R, Alhawach V, Hitch DC, Leffak M. Microsatellite break-induced replication generates highly mutagenized extrachromosomal circular DNAs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.12.575055. [PMID: 38260482 PMCID: PMC10802558 DOI: 10.1101/2024.01.12.575055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Extrachromosomal circular DNAs (eccDNAs) are produced from all regions of the eucaryotic genome. In tumors, highly transcribed eccDNAs have been implicated in oncogenesis, neoantigen production and resistance to chemotherapy. Here we show that unstable microsatellites capable of forming hairpin, triplex, quadruplex and AT-rich structures generate eccDNAs when integrated at a common ectopic site in human cells. These non-B DNA prone microsatellites form eccDNAs by replication-dependent mechanisms. The microsatellite-based eccDNAs are highly mutagenized and display template switches to sister chromatids and to nonallelic chromosomal sites. High frequency mutagenesis occurs within the eccDNA microsatellites and extends bidirectionally for several kilobases into flanking DNA and nonallelic DNA. Mutations include mismatches, short duplications, longer nontemplated insertions and large deletions. Template switching leads to recurrent deletions and recombination domains within the eccDNAs. Template switching events are microhomology-mediated, but do not occur at all potential sites of complementarity. Each microsatellite exhibits a distinct pattern of recombination, microhomology choice and base substitution signature. Depletion of Rad51, the COPS2 signalosome subunit or POLη alter the eccDNA mutagenic profiles. We propose an asynchronous capture model based on break-induced replication from microsatellite-induced DNA breaks for the generation and circularization of mutagenized eccDNAs and genomic homologous recombination deficiency (HRD) scars.
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6
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Caldecott KW. Causes and consequences of DNA single-strand breaks. Trends Biochem Sci 2024; 49:68-78. [PMID: 38040599 DOI: 10.1016/j.tibs.2023.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/20/2023] [Accepted: 11/03/2023] [Indexed: 12/03/2023]
Abstract
DNA single-strand breaks (SSBs) are among the most common lesions arising in human cells, with tens to hundreds of thousands arising in each cell, each day. Cells have efficient mechanisms for the sensing and repair of these ubiquitous DNA lesions, but the failure of these processes to rapidly remove SSBs can lead to a variety of pathogenic outcomes. The threat posed by unrepaired SSBs is illustrated by the existence of at least six genetic diseases in which SSB repair (SSBR) is defective, all of which are characterised by neurodevelopmental and/or neurodegenerative pathology. Here, I review current understanding of how SSBs arise and impact on critical molecular processes, such as DNA replication and gene transcription, and their links to human disease.
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Affiliation(s)
- Keith W Caldecott
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK.
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7
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Rastokina A, Cebrián J, Mozafari N, Mandel NH, Smith CI, Lopes M, Zain R, Mirkin S. Large-scale expansions of Friedreich's ataxia GAA•TTC repeats in an experimental human system: role of DNA replication and prevention by LNA-DNA oligonucleotides and PNA oligomers. Nucleic Acids Res 2023; 51:8532-8549. [PMID: 37216608 PMCID: PMC10484681 DOI: 10.1093/nar/gkad441] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 05/02/2023] [Accepted: 05/20/2023] [Indexed: 05/24/2023] Open
Abstract
Friedreich's ataxia (FRDA) is caused by expansions of GAA•TTC repeats in the first intron of the human FXN gene that occur during both intergenerational transmissions and in somatic cells. Here we describe an experimental system to analyze large-scale repeat expansions in cultured human cells. It employs a shuttle plasmid that can replicate from the SV40 origin in human cells or be stably maintained in S. cerevisiae utilizing ARS4-CEN6. It also contains a selectable cassette allowing us to detect repeat expansions that accumulated in human cells upon plasmid transformation into yeast. We indeed observed massive expansions of GAA•TTC repeats, making it the first genetically tractable experimental system to study large-scale repeat expansions in human cells. Further, GAA•TTC repeats stall replication fork progression, while the frequency of repeat expansions appears to depend on proteins implicated in replication fork stalling, reversal, and restart. Locked nucleic acid (LNA)-DNA mixmer oligonucleotides and peptide nucleic acid (PNA) oligomers, which interfere with triplex formation at GAA•TTC repeats in vitro, prevented the expansion of these repeats in human cells. We hypothesize, therefore, that triplex formation by GAA•TTC repeats stall replication fork progression, ultimately leading to repeat expansions during replication fork restart.
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Affiliation(s)
| | - Jorge Cebrián
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Negin Mozafari
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-171 77 Stockholm, Sweden
| | | | - C I Edvard Smith
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-171 77 Stockholm, Sweden
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, Zurich 8057, Switzerland
| | - Rula Zain
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-171 77 Stockholm, Sweden
- Center for Rare Diseases, Karolinska University Hospital, SE-17176 Stockholm, Sweden
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, MA 02155, USA
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8
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Ahmed-Seghir S, Jalan M, Grimsley HE, Sharma A, Twayana S, Kosiyatrakul ST, Thompson C, Schildkraut CL, Powell SN. A local ATR-dependent checkpoint pathway is activated by a site-specific replication fork block in human cells. eLife 2023; 12:RP87357. [PMID: 37647215 PMCID: PMC10468204 DOI: 10.7554/elife.87357] [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] [Indexed: 09/01/2023] Open
Abstract
When replication forks encounter DNA lesions that cause polymerase stalling, a checkpoint pathway is activated. The ATR-dependent intra-S checkpoint pathway mediates detection and processing of sites of replication fork stalling to maintain genomic integrity. Several factors involved in the global checkpoint pathway have been identified, but the response to a single replication fork barrier (RFB) is poorly understood. We utilized the Escherichia coli-based Tus-Ter system in human MCF7 cells and showed that the Tus protein binding to TerB sequences creates an efficient site-specific RFB. The single fork RFB was sufficient to activate a local, but not global, ATR-dependent checkpoint response that leads to phosphorylation and accumulation of DNA damage sensor protein γH2AX, confined locally to within a kilobase of the site of stalling. These data support a model of local management of fork stalling, which allows global replication at sites other than the RFB to continue to progress without delay.
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Affiliation(s)
- Sana Ahmed-Seghir
- Department of Radiation Oncology and the Molecular Biology Program, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Manisha Jalan
- Department of Radiation Oncology and the Molecular Biology Program, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Helen E Grimsley
- Department of Radiation Oncology and the Molecular Biology Program, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Aman Sharma
- Department of Radiation Oncology and the Molecular Biology Program, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Shyam Twayana
- Department of Cell Biology, Albert Einstein College of MedicineNew YorkUnited States
| | | | - Christopher Thompson
- Department of Radiation Oncology and the Molecular Biology Program, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Carl L Schildkraut
- Department of Cell Biology, Albert Einstein College of MedicineNew YorkUnited States
| | - Simon N Powell
- Department of Radiation Oncology and the Molecular Biology Program, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
- Molecular Biology Program, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
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9
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Papp D, Hernandez LA, Mai TA, Haanen TJ, O’Donnell MA, Duran AT, Hernandez SM, Narvanto JE, Arguello B, Onwukwe MO, Kolar K, Mirkin SM, Kim JC. Massive contractions of Myotonic Dystrophy Type 2-associated CCTG tetranucleotide repeats occur via double strand break repair with distinct requirements for helicases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.06.548036. [PMID: 37461657 PMCID: PMC10350092 DOI: 10.1101/2023.07.06.548036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
Myotonic Dystrophy Type 2 (DM2) is a genetic disease caused by expanded CCTG DNA repeats in the first intron of CNBP. The number of CCTG repeats in DM2 patients ranges from 75-11,000, yet little is known about the molecular mechanisms responsible for repeat expansions or contractions. We developed an experimental system in Saccharomyces cerevisiae that enables selection of large-scale contractions of (CCTG)100 within the intron of a reporter gene and subsequent genetic analysis. Contractions exceeded 80 repeat units, causing the final repetitive tract to be well below the threshold for disease. We found that Rad51 and Rad52 are required for these massive contractions, indicating a mechanism that involves homologous recombination. Srs2 helicase was shown previously to stabilize CTG, CAG, and CGG repeats. Loss of Srs2 did not significantly affect CCTG contraction rates in unperturbed conditions. In contrast, loss of the RecQ helicase Sgs1 resulted in a 6-fold decrease in contraction rate with specific evidence that helicase activity is required for large-scale contractions. Using a genetic assay to evaluate chromosome arm loss, we determined that CCTG and reverse complementary CAGG repeats elevate the rate of chromosomal fragility compared to a low-repeat control. Overall, our results demonstrate that the genetic control of CCTG repeat contractions is notably distinct among disease-causing microsatellite repeat sequences.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Kara Kolar
- Department of Biology, Tufts University, Medford, MA 02155
| | | | - Jane C. Kim
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078
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10
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Ahmed-Seghir S, Jalan M, Grimsley HE, Sharma A, Twayana S, Kosiyatrakul ST, Thompson C, Schildkraut CL, Powell SN. A local ATR-dependent checkpoint pathway is activated by a site-specific replication fork block in human cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.26.534293. [PMID: 36993263 PMCID: PMC10055377 DOI: 10.1101/2023.03.26.534293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
When replication forks encounter DNA lesions that cause polymerase stalling a checkpoint pathway is activated. The ATR-dependent intra-S checkpoint pathway mediates detection and processing of sites of replication fork stalling to maintain genomic integrity. Several factors involved in the global checkpoint pathway have been identified, but the response to a single replication fork barrier (RFB) is poorly understood. We utilized the E.coli -based Tus- Ter system in human MCF7 cells and showed that the Tus protein binding to TerB sequences creates an efficient site-specific RFB. The single fork RFB was sufficient to activate a local, but not global, ATR-dependent checkpoint response that leads to phosphorylation and accumulation of DNA damage sensor protein γH2AX, confined locally to within a kilobase of the site of stalling. These data support a model of local management of fork stalling, which allows global replication at sites other than the RFB to continue to progress without delay.
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11
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Polleys EJ, Del Priore I, Haber JE, Freudenreich CH. Structure-forming CAG/CTG repeats interfere with gap repair to cause repeat expansions and chromosome breaks. Nat Commun 2023; 14:2469. [PMID: 37120647 PMCID: PMC10148874 DOI: 10.1038/s41467-023-37901-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 04/04/2023] [Indexed: 05/01/2023] Open
Abstract
Expanded CAG/CTG repeats are sites of DNA damage, leading to repeat length changes. Homologous recombination (HR) is one cause of repeat instability and we hypothesized that gap filling was a driver of repeat instability during HR. To test this, we developed an assay such that resection and ssDNA gap fill-in would occur across a (CAG)70 or (CTG)70 repeat tract. When the ssDNA template was a CTG sequence, there were increased repeat contractions and a fragile site was created leading to large-scale deletions. When the CTG sequence was on the resected strand, resection was inhibited, resulting in repeat expansions. Increased nucleolytic processing by deletion of Rad9, the ortholog of 53BP1, rescued repeat instability and chromosome breakage. Loss of Rad51 increased contractions implicating a protective role for Rad51 on ssDNA. Together, our work implicates structure-forming repeats as an impediment to resection and gap-filling which can lead to mutations and large-scale deletions.
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Affiliation(s)
- Erica J Polleys
- Department of Biology, Tufts University, Medford, MA, 02155, USA.
| | | | - James E Haber
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA, 02454, USA
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12
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Li J, Wan L, Wang Y, Chen Y, Lee HK, Lam SL, Guo P. Solution Nuclear Magnetic Resonance Structures of ATTTT and ATTTC Pentanucleotide Repeats Associated with SCA37 and FAMEs. ACS Chem Neurosci 2023; 14:289-299. [PMID: 36580663 DOI: 10.1021/acschemneuro.2c00593] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Expansions of ATTTT and ATTTC pentanucleotide repeats in the human genome are recently found to be associated with at least seven neurodegenerative diseases, including spinocerebellar ataxia type 37 (SCA37) and familial adult myoclonic epilepsy (FAME) types 1, 2, 3, 4, 6, and 7. The formation of non-B DNA structures during some biological processes is thought as a causative factor for repeat expansions. Yet, the structural basis for these pyrimidine-rich ATTTT and ATTTC repeat expansions remains elusive. In this study, we investigated the solution structures of ATTTT and ATTTC repeats using nuclear magnetic resonance spectroscopy. Here, we reveal that ATTTT and ATTTC repeats can form a highly compact minidumbbell structure at the 5'-end using their first two repeats. The high-resolution structure of two ATTTT repeats was determined, showing a regular TTTTA pentaloop and a quasi TTTT/A pentaloop. Furthermore, the minidumbbell structure could escape from proofreading by the Klenow fragment of DNA polymerase I when it was located at five or more base pairs away from the priming site, leading to a small-scale repeat expansion. Results of this work improve our understanding of ATTTT and ATTTC repeat expansions in SCA37 and FAMEs, and provide high-resolution structural information for rational drug design.
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Affiliation(s)
- Jinxia Li
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong 999077, China
| | - Liqi Wan
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong 999077, China
| | - Yang Wang
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC) Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China.,School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Yawen Chen
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Hung Kay Lee
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong 999077, China
| | - Sik Lok Lam
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong 999077, China
| | - Pei Guo
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC) Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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13
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Heterogeneous migration routes of DNA triplet repeat slip-outs. BIOPHYSICAL REPORTS 2022; 2:None. [PMID: 36299495 PMCID: PMC9586884 DOI: 10.1016/j.bpr.2022.100070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/08/2022] [Indexed: 12/02/2022]
Abstract
It is unclear how the length of a repetitive DNA tract determines the onset and progression of repeat expansion diseases, but the dynamics of secondary DNA structures formed by repeat sequences are believed to play an important role. It was recently shown that three-way DNA junctions containing slip-out hairpins of CAG or CTG repeats and contiguous triplet repeats in the adjacent duplex displayed single-molecule FRET (smFRET) dynamics that were ascribed to both local conformational motions and longer-range branch migration. Here we explore these so-called "mobile" slip-out structures through a detailed kinetic analysis of smFRET trajectories and coarse-grained modeling. Despite the apparent structural simplicity, with six FRET states resolvable, most smFRET states displayed biexponential dwell-time distributions, attributed to structural heterogeneity and overlapping FRET states. Coarse-grained modeling for a (GAC)10 repeat slip-out included trajectories that corresponded to a complete round of branch migration; the structured free energy landscape between slippage events supports the dynamical complexity observed by smFRET. A hairpin slip-out with 40 CAG repeats, which is above the repeat length required for disease in several triplet repeat disorders, displayed smFRET dwell times that were on average double those of 3WJs with 10 repeats. The rate of secondary-structure rearrangement via branch migration, relative to particular DNA processing pathways, may be an important factor in the expansion of triplet repeat expansion diseases.
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14
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Guo P, Han D. Targeting Pathogenic DNA and RNA Repeats: A Conceptual Therapeutic Way for Repeat Expansion Diseases. Chemistry 2022; 28:e202201749. [PMID: 35727679 DOI: 10.1002/chem.202201749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Indexed: 11/06/2022]
Abstract
Expansions of short tandem repeats (STRs) in the human genome cause nearly 50 neurodegenerative diseases, which are mostly inheritable, nonpreventable and incurable, posing as a huge threat to human health. Non-B DNAs formed by STRs are thought to be structural intermediates that can cause repeat expansions. The subsequent transcripts harboring expanded RNA repeats can further induce cellular toxicity through forming specific structures. Direct targeting of these pathogenic DNA and RNA repeats has emerged as a new potential therapeutic strategy to cure repeat expansion diseases. In this conceptual review, we first introduce the roles of DNA and RNA structures in the genetic instabilities and pathomechanisms of repeat expansion diseases, then describe structural features of DNA and RNA repeats with a focus on the tertiary structures determined by X-ray crystallography and solution nuclear magnetic resonance spectroscopy, and finally discuss recent progress and perspectives of developing chemical tools that target pathogenic DNA and RNA repeats for curing repeat expansion diseases.
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Affiliation(s)
- Pei Guo
- The Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital), Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, P. R. China
| | - Da Han
- The Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital), Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, P. R. China.,Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
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15
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Radchenko EA, Aksenova AY, Volkov KV, Shishkin AA, Pavlov YI, Mirkin SM. Partners in crime: Tbf1 and Vid22 promote expansions of long human telomeric repeats at an interstitial chromosome position in yeast. PNAS NEXUS 2022; 1:pgac080. [PMID: 35832866 PMCID: PMC9272169 DOI: 10.1093/pnasnexus/pgac080] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 06/01/2022] [Indexed: 02/05/2023]
Abstract
In humans, telomeric repeats (TTAGGG)n are known to be present at internal chromosomal sites. These interstitial telomeric sequences (ITSs) are an important source of genomic instability, including repeat length polymorphism, but the molecular mechanisms responsible for this instability remain to be understood. Here, we studied the mechanisms responsible for expansions of human telomeric (Htel) repeats that were artificially inserted inside a yeast chromosome. We found that Htel repeats in an interstitial chromosome position are prone to expansions. The propensity of Htel repeats to expand depends on the presence of a complex of two yeast proteins: Tbf1 and Vid22. These two proteins are physically bound to an interstitial Htel repeat, and together they slow replication fork progression through it. We propose that slow progression of the replication fork through the protein complex formed by the Tbf1 and Vid22 partners at the Htel repeat cause DNA strand slippage, ultimately resulting in repeat expansions.
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Affiliation(s)
| | | | - Kirill V Volkov
- Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, 199034, Russia
| | | | - Youri I Pavlov
- Eppley Institute for Research In Cancer and Allied Diseases, Omaha, NE 68198, USA
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16
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Malone EG, Thompson MD, Byrd AK. Role and Regulation of Pif1 Family Helicases at the Replication Fork. Int J Mol Sci 2022; 23:ijms23073736. [PMID: 35409096 PMCID: PMC8998199 DOI: 10.3390/ijms23073736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 02/04/2023] Open
Abstract
Pif1 helicases are a multifunctional family of DNA helicases that are important for many aspects of genomic stability in the nucleus and mitochondria. Pif1 helicases are conserved from bacteria to humans. Pif1 helicases play multiple roles at the replication fork, including promoting replication through many barriers such as G-quadruplex DNA, the rDNA replication fork barrier, tRNA genes, and R-loops. Pif1 helicases also regulate telomerase and promote replication termination, Okazaki fragment maturation, and break-induced replication. This review highlights many of the roles and regulations of Pif1 at the replication fork that promote cellular health and viability.
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Affiliation(s)
- Emory G. Malone
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (E.G.M.); (M.D.T.)
| | - Matthew D. Thompson
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (E.G.M.); (M.D.T.)
| | - Alicia K. Byrd
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (E.G.M.); (M.D.T.)
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- Correspondence: ; Tel.: +1-501-526-6488
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17
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Yi J, Wan L, Liu Y, Lam SL, Chan HYE, Han D, Guo P. NMR solution structures of d(GGCCTG)n repeats associated with spinocerebellar ataxia type 36. Int J Biol Macromol 2022; 201:607-615. [DOI: 10.1016/j.ijbiomac.2022.01.097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 01/11/2022] [Accepted: 01/13/2022] [Indexed: 01/03/2023]
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18
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Kim D, Lee J, Cho CH, Kim EJ, Bhattacharya D, Yoon HS. Group II intron and repeat-rich red algal mitochondrial genomes demonstrate the dynamic recent history of autocatalytic RNAs. BMC Biol 2022; 20:2. [PMID: 34996446 PMCID: PMC8742464 DOI: 10.1186/s12915-021-01200-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 11/29/2021] [Indexed: 11/10/2022] Open
Abstract
Background Group II introns are mobile genetic elements that can insert at specific target sequences, however, their origins are often challenging to reconstruct because of rapid sequence decay following invasion and spread into different sites. To advance understanding of group II intron spread, we studied the intron-rich mitochondrial genome (mitogenome) in the unicellular red alga, Porphyridium. Results Analysis of mitogenomes in three closely related species in this genus revealed they were 3–6-fold larger in size (56–132 kbp) than in other red algae, that have genomes of size 21–43 kbp. This discrepancy is explained by two factors, group II intron invasion and expansion of repeated sequences in large intergenic regions. Phylogenetic analysis demonstrates that many mitogenome group II intron families are specific to Porphyridium, whereas others are closely related to sequences in fungi and in the red alga-derived plastids of stramenopiles. Network analysis of intron-encoded proteins (IEPs) shows a clear link between plastid and mitochondrial IEPs in distantly related species, with both groups associated with prokaryotic sequences. Conclusion Our analysis of group II introns in Porphyridium mitogenomes demonstrates the dynamic nature of group II intron evolution, strongly supports the lateral movement of group II introns among diverse eukaryotes, and reveals their ability to proliferate, once integrated in mitochondrial DNA. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01200-3.
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Affiliation(s)
- Dongseok Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, South Korea
| | - JunMo Lee
- Department of Oceanography, Kyungpook National University, Daegu, 41566, South Korea
| | - Chung Hyun Cho
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, South Korea
| | - Eun Jeung Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, South Korea
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, South Korea.
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19
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Hayward BE, Usdin K. Mechanisms of Genome Instability in the Fragile X-Related Disorders. Genes (Basel) 2021; 12:genes12101633. [PMID: 34681027 PMCID: PMC8536109 DOI: 10.3390/genes12101633] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/12/2021] [Accepted: 10/14/2021] [Indexed: 12/17/2022] Open
Abstract
The Fragile X-related disorders (FXDs), which include the intellectual disability fragile X syndrome (FXS), are disorders caused by expansion of a CGG-repeat tract in the 5′ UTR of the X-linked FMR1 gene. These disorders are named for FRAXA, the folate-sensitive fragile site that localizes with the CGG-repeat in individuals with FXS. Two pathological FMR1 allele size classes are distinguished. Premutation (PM) alleles have 54–200 repeats and confer the risk of fragile X-associated tremor/ataxia syndrome (FXTAS) and fragile X-associated primary ovarian insufficiency (FXPOI). PM alleles are prone to both somatic and germline expansion, with female PM carriers being at risk of having a child with >200+ repeats. Inheritance of such full mutation (FM) alleles causes FXS. Contractions of PM and FM alleles can also occur. As a result, many carriers are mosaic for different sized alleles, with the clinical presentation depending on the proportions of these alleles in affected tissues. Furthermore, it has become apparent that the chromosomal fragility of FXS individuals reflects an underlying problem that can lead to chromosomal numerical and structural abnormalities. Thus, large numbers of CGG-repeats in the FMR1 gene predisposes individuals to multiple forms of genome instability. This review will discuss our current understanding of these processes.
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20
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Spivakovsky-Gonzalez E, Polleys EJ, Masnovo C, Cebrian J, Molina-Vargas AM, Freudenreich CH, Mirkin SM. Rad9-mediated checkpoint activation is responsible for elevated expansions of GAA repeats in CST-deficient yeast. Genetics 2021; 219:6343461. [PMID: 34849883 DOI: 10.1093/genetics/iyab125] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 07/26/2021] [Indexed: 11/13/2022] Open
Abstract
Large-scale expansion of (GAA)n repeats in the first intron of the FXN gene is responsible for the severe neurodegenerative disease, Friedreich's ataxia in humans. We have previously conducted an unbiased genetic screen for GAA repeat instability in a yeast experimental system. The majority of genes that came from this screen encoded the components of DNA replication machinery, strongly implying that replication irregularities are at the heart of GAA repeat expansions. This screen, however, also produced two unexpected hits: members of the CST complex, CDC13 and TEN1 genes, which are required for telomere maintenance. To understand how the CST complex could affect intra-chromosomal GAA repeats, we studied the well-characterized temperature-sensitive cdc13-1 mutation and its effects on GAA repeat instability in yeast. We found that in-line with the screen results, this mutation leads to ∼10-fold increase in the rate of large-scale expansions of the (GAA)100 repeat at semi-permissive temperature. Unexpectedly, the hyper-expansion phenotype of the cdc13-1 mutant largely depends on activation of the G2/M checkpoint, as deletions of individual genes RAD9, MEC1, RAD53, and EXO1 belonging to this pathway rescued the increased GAA expansions. Furthermore, the hyper-expansion phenotype of the cdc13-1 mutant depended on the subunit of DNA polymerase δ, Pol32. We hypothesize, therefore, that increased repeat expansions in the cdc13-1 mutant happen during post-replicative repair of nicks or small gaps within repetitive tracts during the G2 phase of the cell cycle upon activation of the G2/M checkpoint.
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Affiliation(s)
| | - Erica J Polleys
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Chiara Masnovo
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Jorge Cebrian
- Department of Biology, Tufts University, Medford, MA 02155, USA.,Department of Pharmacology and Toxicology, School of Medicine, Universidad Complutense de Madrid, Instituto de Investigación Sanitaria Gregorio Marañón, CIBERCV, Madrid 28040, Spain
| | - Adrian M Molina-Vargas
- Department of Biology, Tufts University, Medford, MA 02155, USA.,Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | | | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, MA 02155, USA
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21
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Gold MA, Whalen JM, Freon K, Hong Z, Iraqui I, Lambert SAE, Freudenreich CH. Restarted replication forks are error-prone and cause CAG repeat expansions and contractions. PLoS Genet 2021; 17:e1009863. [PMID: 34673780 PMCID: PMC8562783 DOI: 10.1371/journal.pgen.1009863] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 11/02/2021] [Accepted: 10/06/2021] [Indexed: 12/16/2022] Open
Abstract
Disease-associated trinucleotide repeats form secondary DNA structures that interfere with replication and repair. Replication has been implicated as a mechanism that can cause repeat expansions and contractions. However, because structure-forming repeats are also replication barriers, it has been unclear whether the instability occurs due to slippage during normal replication progression through the repeat, slippage or misalignment at a replication stall caused by the repeat, or during subsequent replication of the repeat by a restarted fork that has altered properties. In this study, we have specifically addressed the fidelity of a restarted fork as it replicates through a CAG/CTG repeat tract and its effect on repeat instability. To do this, we used a well-characterized site-specific replication fork barrier (RFB) system in fission yeast that creates an inducible and highly efficient stall that is known to restart by recombination-dependent replication (RDR), in combination with long CAG repeat tracts inserted at various distances and orientations with respect to the RFB. We find that replication by the restarted fork exhibits low fidelity through repeat sequences placed 2-7 kb from the RFB, exhibiting elevated levels of Rad52- and Rad8ScRad5/HsHLTF-dependent instability. CAG expansions and contractions are not elevated to the same degree when the tract is just in front or behind the barrier, suggesting that the long-traveling Polδ-Polδ restarted fork, rather than fork reversal or initial D-loop synthesis through the repeat during stalling and restart, is the greatest source of repeat instability. The switch in replication direction that occurs due to replication from a converging fork while the stalled fork is held at the barrier is also a significant contributor to the repeat instability profile. Our results shed light on a long-standing question of how fork stalling and RDR contribute to expansions and contractions of structure-forming trinucleotide repeats, and reveal that tolerance to replication stress by fork restart comes at the cost of increased instability of repetitive sequences.
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Affiliation(s)
- Michaela A. Gold
- Department of Biology, Tufts University, Medford, Massachusetts, United States of America
| | - Jenna M. Whalen
- Department of Biology, Tufts University, Medford, Massachusetts, United States of America
| | - Karine Freon
- Institut Curie, Université PSL, Orsay, France
- Université Paris-Saclay, Orsay, France
| | - Zixin Hong
- Department of Biology, Tufts University, Medford, Massachusetts, United States of America
| | - Ismail Iraqui
- Institut Curie, Université PSL, Orsay, France
- Université Paris-Saclay, Orsay, France
| | - Sarah A. E. Lambert
- Institut Curie, Université PSL, Orsay, France
- Université Paris-Saclay, Orsay, France
- Equipes Labélisées Ligue Nationale Contre Le Cancer, Orsay, France
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22
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Lokanga RA, Kumari D, Usdin K. Common Threads: Aphidicolin-Inducible and Folate-Sensitive Fragile Sites in the Human Genome. Front Genet 2021; 12:708860. [PMID: 34567068 PMCID: PMC8456018 DOI: 10.3389/fgene.2021.708860] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/28/2021] [Indexed: 11/13/2022] Open
Abstract
The human genome has many chromosomal regions that are fragile, demonstrating chromatin breaks, gaps, or constrictions on exposure to replication stress. Common fragile sites (CFSs) are found widely distributed in the population, with the largest subset of these sites being induced by aphidicolin (APH). Other fragile sites are only found in a subset of the population. One group of these so-called rare fragile sites (RFSs) is induced by folate stress. APH-inducible CFSs are generally located in large transcriptionally active genes that are A + T rich and often enriched for tracts of AT-dinucleotide repeats. In contrast, all the folate-sensitive sites mapped to date consist of transcriptionally silenced CGG microsatellites. Thus, all the folate-sensitive fragile sites may have a very similar molecular basis that differs in key ways from that of the APH CFSs. The folate-sensitive FSs include FRAXA that is associated with Fragile X syndrome (FXS), the most common heritable form of intellectual disability. Both CFSs and RFSs can cause chromosomal abnormalities. Recent work suggests that both APH-inducible fragile sites and FRAXA undergo Mitotic DNA synthesis (MiDAS) when exposed to APH or folate stress, respectively. Interestingly, blocking MiDAS in both cases prevents chromosome fragility but increases the risk of chromosome mis-segregation. MiDAS of both APH-inducible and FRAXA involves conservative DNA replication and POLD3, an accessory subunit of the replicative polymerase Pol δ that is essential for break-induced replication (BIR). Thus, MiDAS is thought to proceed via some form of BIR-like process. This review will discuss the recent work that highlights the similarities and differences between these two groups of fragile sites and the growing evidence for the presence of many more novel fragile sites in the human genome.
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Affiliation(s)
| | - Daman Kumari
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Karen Usdin
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
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23
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Stewart JA, Hillegass MB, Oberlitner JH, Younkin EM, Wasserman BF, Casper AM. Noncanonical outcomes of break-induced replication produce complex, extremely long-tract gene conversion events in yeast. G3 (BETHESDA, MD.) 2021; 11:jkab245. [PMID: 34568913 PMCID: PMC8473981 DOI: 10.1093/g3journal/jkab245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 07/06/2021] [Indexed: 11/18/2022]
Abstract
Long-tract gene conversions (LTGC) can result from the repair of collapsed replication forks, and several mechanisms have been proposed to explain how the repair process produces this outcome. We studied LTGC events produced from repair collapsed forks at yeast fragile site FS2. Our analysis included chromosome sizing by contour-clamped homogeneous electric field electrophoresis, next-generation whole-genome sequencing, and Sanger sequencing across repair event junctions. We compared the sequence and structure of LTGC events in our cells to the expected qualities of LTGC events generated by proposed mechanisms. Our evidence indicates that some LTGC events arise from half-crossover during BIR, some LTGC events arise from gap repair, and some LTGC events can be explained by either gap repair or "late" template switch during BIR. Also based on our data, we propose that models of collapsed replication forks be revised to show not a one-end double-strand break (DSB), but rather a two-end DSB in which the ends are separated in time and subject to gap repair.
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Affiliation(s)
- Joseph A Stewart
- Department of Environmental & Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | | | - Joseph H Oberlitner
- Department of Biology, Interdisciplinary Graduate Program in Genetics, The University of Iowa, Iowa City, IA 52242, USA
| | - Ellen M Younkin
- Department of Biology, Eastern Michigan University, Ypsilanti, MI 48197, USA
| | - Beth F Wasserman
- Department of Biology, Eastern Michigan University, Ypsilanti, MI 48197, USA
| | - Anne M Casper
- Department of Biology, Eastern Michigan University, Ypsilanti, MI 48197, USA
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24
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Wu X, Malkova A. Break-induced replication mechanisms in yeast and mammals. Curr Opin Genet Dev 2021; 71:163-170. [PMID: 34481360 DOI: 10.1016/j.gde.2021.08.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/17/2021] [Accepted: 08/05/2021] [Indexed: 11/26/2022]
Abstract
Break-induced replication (BIR) is a pathway specialized in repair of double-strand DNA breaks with only one end capable of invading homologous template that can arise following replication collapse, telomere erosion or DNA cutting by site-specific endonucleases. For a long time, yeast remained the only model system to study BIR. Studies in yeast demonstrated that BIR represents an unusual mode of DNA synthesis that is driven by a migrating bubble and leads to conservative inheritance of newly synthesized DNA. This unusual type of DNA synthesis leads to high levels of mutations and chromosome rearrangements. Recently, multiple examples of BIR were uncovered in mammalian cells that allowed the comparison of BIR between organisms. It appeared initially that BIR in mammalian cells is predominantly independent of RAD51, and therefore different from BIR that is predominantly Rad51-dependent in yeast. However, a series of systematic studies utilizing site-specific DNA breaks for BIR initiation in mammalian reporters led to the discovery of highly efficient RAD51-dependent BIR, allowing side-by side comparison with BIR in yeast which is the focus of this review.
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Affiliation(s)
- Xiaohua Wu
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, United States.
| | - Anna Malkova
- Department of Biology, University of Iowa, Iowa City, IA 52242, United States.
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25
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Polleys EJ, Freudenreich CH. Homologous recombination within repetitive DNA. Curr Opin Genet Dev 2021; 71:143-153. [PMID: 34464817 DOI: 10.1016/j.gde.2021.08.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 08/06/2021] [Accepted: 08/12/2021] [Indexed: 12/16/2022]
Abstract
Many microsatellite DNA sequences are able to form non-B form DNA secondary structures, such as hairpin loops, cruciforms, triplex DNA or G-quadruplexes. These DNA structures can form a significant impediment to DNA replication and repair, leading to DNA nicks, gaps, and breaks, which can be repaired by homologous recombination (HR). Recent work understanding HR at structure-forming repeats has focused on genetic requirements for replication fork restart, break induced replication (BIR) at broken forks, recombination during and after relocalization of breaks or stalled forks to the nuclear periphery, and how repair pathway choice and kinetics are navigated in the presence of a repeat tract. In this review, we summarize recent developments that illuminate the role of recombination in repairing DNA damage or causing tract length changes within repetitive DNA and its role in maintaining genome stability.
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Affiliation(s)
- Erica J Polleys
- Department of Biology, Tufts University, Medford MA 02155, United States
| | - Catherine H Freudenreich
- Department of Biology, Tufts University, Medford MA 02155, United States; Program in Genetics, Tufts University, Boston MA 02111, United States.
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26
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Al-Zain AM, Symington LS. The dark side of homology-directed repair. DNA Repair (Amst) 2021; 106:103181. [PMID: 34311272 DOI: 10.1016/j.dnarep.2021.103181] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/16/2021] [Accepted: 07/16/2021] [Indexed: 10/20/2022]
Abstract
DNA double strand breaks (DSB) are cytotoxic lesions that can lead to genome rearrangements and genomic instability, which are hallmarks of cancer. The two main DSB repair pathways are non-homologous end joining and homologous recombination (HR). While HR is generally highly accurate, it has the potential for rearrangements that occur directly or through intermediates generated during the repair process. Whole genome sequencing of cancers has revealed numerous types of structural rearrangement signatures that are often indicative of repair mediated by sequence homology. However, it can be challenging to delineate repair mechanisms from sequence analysis of rearrangement end products from cancer genomes, or even model systems, because the same rearrangements can be generated by different pathways. Here, we review homology-directed repair pathways and their consequences. Exploring those pathways can lead to a greater understanding of rearrangements that occur in cancer cells.
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Affiliation(s)
- Amr M Al-Zain
- Program in Biological Sciences, Columbia University, New York, NY, 10027, United States; Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, 10032, United States
| | - Lorraine S Symington
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, 10032, United States; Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY, 10032, United States.
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27
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Replication-independent instability of Friedreich's ataxia GAA repeats during chronological aging. Proc Natl Acad Sci U S A 2021; 118:2013080118. [PMID: 33495349 PMCID: PMC7865128 DOI: 10.1073/pnas.2013080118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The inheritance of long (GAA)n repeats in the frataxin gene causes the debilitating neurodegenerative disease Friedreich’s ataxia. Subsequent expansions of these repeats throughout a patient’s lifetime in the affected tissues, like the nervous system, may contribute to disease onset. We developed an experimental model to characterize the mechanisms of repeat instability in nondividing cells to better understand how mutations can occur as cells age chronologically. We show that repeats can expand in nondividing cells. Notably, however, large deletions are the major type of repeat-mediated genome instability in nondividing cells, implicating the loss of important genetic material with aging in the progression of Friedreich’s ataxia. Nearly 50 hereditary diseases result from the inheritance of abnormally long repetitive DNA microsatellites. While it was originally believed that the size of inherited repeats is the key factor in disease development, it has become clear that somatic instability of these repeats throughout an individual’s lifetime strongly contributes to disease onset and progression. Importantly, somatic instability is commonly observed in terminally differentiated, postmitotic cells, such as neurons. To unravel the mechanisms of repeat instability in nondividing cells, we created an experimental system to analyze the mutability of Friedreich’s ataxia (GAA)n repeats during chronological aging of quiescent Saccharomyces cerevisiae. Unexpectedly, we found that the predominant repeat-mediated mutation in nondividing cells is large-scale deletions encompassing parts, or the entirety, of the repeat and adjacent regions. These deletions are caused by breakage at the repeat mediated by mismatch repair (MMR) complexes MutSβ and MutLα and DNA endonuclease Rad1, followed by end-resection by Exo1 and repair of the resulting double-strand breaks (DSBs) via nonhomologous end joining. We also observed repeat-mediated gene conversions as a result of DSB repair via ectopic homologous recombination during chronological aging. Repeat expansions accrue during chronological aging as well—particularly in the absence of MMR-induced DSBs. These expansions depend on the processivity of DNA polymerase δ while being counteracted by Exo1 and MutSβ, implicating nick repair. Altogether, these findings show that the mechanisms and types of (GAA)n repeat instability differ dramatically between dividing and nondividing cells, suggesting that distinct repeat-mediated mutations in terminally differentiated somatic cells might influence Friedreich’s ataxia pathogenesis.
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Altered replication stress response due to CARD14 mutations promotes recombination-induced revertant mosaicism. Am J Hum Genet 2021; 108:1026-1039. [PMID: 34004138 DOI: 10.1016/j.ajhg.2021.04.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 04/22/2021] [Indexed: 01/07/2023] Open
Abstract
Revertant mosaicism, or "natural gene therapy," refers to the spontaneous in vivo reversion of an inherited mutation in a somatic cell. Only approximately 50 human genetic disorders exhibit revertant mosaicism, implicating a distinctive role played by mutant proteins in somatic correction of a pathogenic germline mutation. However, the process by which mutant proteins induce somatic genetic reversion in these diseases remains unknown. Here we show that heterozygous pathogenic CARD14 mutations causing autoinflammatory skin diseases, including psoriasis and pityriasis rubra pilaris, are repaired mainly via homologous recombination. Rather than altering the DNA damage response to exogenous stimuli, such as X-irradiation or etoposide treatment, mutant CARD14 increased DNA double-strand breaks under conditions of replication stress. Furthermore, mutant CARD14 suppressed new origin firings without promoting crossover events in the replication stress state. Together, these results suggest that mutant CARD14 alters the replication stress response and preferentially drives break-induced replication (BIR), which is generally suppressed in eukaryotes. Our results highlight the involvement of BIR in reversion events, thus revealing a previously undescribed role of BIR that could potentially be exploited to develop therapeutics for currently intractable genetic diseases.
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29
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Kockler ZW, Osia B, Lee R, Musmaker K, Malkova A. Repair of DNA Breaks by Break-Induced Replication. Annu Rev Biochem 2021; 90:165-191. [PMID: 33792375 DOI: 10.1146/annurev-biochem-081420-095551] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Double-strand DNA breaks (DSBs) are the most lethal type of DNA damage, making DSB repair critical for cell survival. However, some DSB repair pathways are mutagenic and promote genome rearrangements, leading to genome destabilization. One such pathway is break-induced replication (BIR), which repairs primarily one-ended DSBs, similar to those formed by collapsed replication forks or telomere erosion. BIR is initiated by the invasion of a broken DNA end into a homologous template, synthesizes new DNA within the context of a migrating bubble, and is associated with conservative inheritance of new genetic material. This mode of synthesis is responsible for a high level of genetic instability associated with BIR. Eukaryotic BIR was initially investigated in yeast, but now it is also actively studied in mammalian systems. Additionally, a significant breakthrough has been made regarding the role of microhomology-mediated BIR in the formation of complex genomic rearrangements that underly various human pathologies.
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Affiliation(s)
- Z W Kockler
- Department of Biology, University of Iowa, Iowa City, Iowa 52242, USA;
| | - B Osia
- Department of Biology, University of Iowa, Iowa City, Iowa 52242, USA;
| | - R Lee
- Department of Biology, University of Iowa, Iowa City, Iowa 52242, USA;
| | - K Musmaker
- Department of Biology, University of Iowa, Iowa City, Iowa 52242, USA;
| | - A Malkova
- Department of Biology, University of Iowa, Iowa City, Iowa 52242, USA;
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30
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Young SJ, West SC. Coordinated roles of SLX4 and MutSβ in DNA repair and the maintenance of genome stability. Crit Rev Biochem Mol Biol 2021; 56:157-177. [PMID: 33596761 PMCID: PMC7610648 DOI: 10.1080/10409238.2021.1881433] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 01/06/2021] [Accepted: 01/22/2021] [Indexed: 12/14/2022]
Abstract
SLX4 provides a molecular scaffold for the assembly of multiple protein complexes required for the maintenance of genome stability. It is involved in the repair of DNA crosslinks, the resolution of recombination intermediates, the response to replication stress and the maintenance of telomere length. To carry out these diverse functions, SLX4 interacts with three structure-selective endonucleases, MUS81-EME1, SLX1 and XPF-ERCC1, as well as the telomere binding proteins TRF2, RTEL1 and SLX4IP. Recently, SLX4 was shown to interact with MutSβ, a heterodimeric protein involved in DNA mismatch repair, trinucleotide repeat instability, crosslink repair and recombination. Importantly, MutSβ promotes the pathogenic expansion of CAG/CTG trinucleotide repeats, which is causative of myotonic dystrophy and Huntington's disease. The colocalization and specific interaction of MutSβ with SLX4, together with their apparently overlapping functions, are suggestive of a common role in reactions that promote DNA maintenance and genome stability. This review will focus on the role of SLX4 in DNA repair, the interplay between MutSβ and SLX4, and detail how they cooperate to promote recombinational repair and DNA crosslink repair. Furthermore, we speculate that MutSβ and SLX4 may provide an alternative cellular mechanism that modulates trinucleotide instability.
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Affiliation(s)
- Sarah J Young
- DNA Recombination and Repair Laboratory, The Francis Crick Institute, London, UK
| | - Stephen C West
- DNA Recombination and Repair Laboratory, The Francis Crick Institute, London, UK
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31
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Li S, Wang H, Jehi S, Li J, Liu S, Wang Z, Truong L, Chiba T, Wang Z, Wu X. PIF1 helicase promotes break-induced replication in mammalian cells. EMBO J 2021; 40:e104509. [PMID: 33470420 PMCID: PMC8047440 DOI: 10.15252/embj.2020104509] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 12/01/2020] [Accepted: 12/10/2020] [Indexed: 12/20/2022] Open
Abstract
Break‐induced replication (BIR) is a specialized homologous‐recombination pathway for DNA double‐strand break (DSB) repair, which often induces genome instability. In this study, we establish EGFP‐based recombination reporters to systematically study BIR in mammalian cells and demonstrate an important role of human PIF1 helicase in promoting BIR. We show that at endonuclease cleavage sites, PIF1‐dependent BIR is used for homology‐initiated recombination requiring long track DNA synthesis, but not short track gene conversion (STGC). We also show that structure formation‐prone AT‐rich DNA sequences derived from common fragile sites (CFS‐ATs) induce BIR upon replication stress and oncogenic stress, and PCNA‐dependent loading of PIF1 onto collapsed/broken forks is critical for BIR activation. At broken replication forks, even STGC‐mediated repair of double‐ended DSBs depends on POLD3 and PIF1, revealing an unexpected mechanism of BIR activation upon replication stress that differs from the conventional BIR activation model requiring DSB end sensing at endonuclease‐generated breaks. Furthermore, loss of PIF1 is synthetically lethal with loss of FANCM, which is involved in protecting CFS‐ATs. The breast cancer‐associated PIF1 mutant L319P is defective in BIR, suggesting a direct link of BIR to oncogenic processes.
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Affiliation(s)
- Shibo Li
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Hailong Wang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Sanaa Jehi
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Jun Li
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Shuo Liu
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Zi Wang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA.,Biomedical Gerontology Laboratory, Department of Health Science and Social Welfare, School of Human Sciences, Waseda University, Tokorozawa, Japan
| | - Lan Truong
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Takuya Chiba
- Biomedical Gerontology Laboratory, Department of Health Science and Social Welfare, School of Human Sciences, Waseda University, Tokorozawa, Japan
| | - Zefeng Wang
- CAS Key Laboratory of Computational Biology, University of Chinese Academy of Sciences, Shanghai Institute of Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiaohua Wu
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
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32
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Stivison EA, Young KJ, Symington LS. Interstitial telomere sequences disrupt break-induced replication and drive formation of ectopic telomeres. Nucleic Acids Res 2021; 48:12697-12710. [PMID: 33264397 PMCID: PMC7736798 DOI: 10.1093/nar/gkaa1081] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 10/20/2020] [Accepted: 10/22/2020] [Indexed: 01/18/2023] Open
Abstract
Break-induced replication (BIR) is a mechanism used to heal one-ended DNA double-strand breaks, such as those formed at collapsed replication forks or eroded telomeres. Instead of utilizing a canonical replication fork, BIR is driven by a migrating D-loop and is associated with a high frequency of mutagenesis. Here we show that when BIR encounters an interstitial telomere sequence (ITS), the machinery frequently terminates, resulting in the formation of an ectopic telomere. The primary mechanism to convert the ITS to a functional telomere is by telomerase-catalyzed addition of telomeric repeats with homology-directed repair serving as a back-up mechanism. Termination of BIR and creation of an ectopic telomere is promoted by Mph1/FANCM helicase, which has the capacity to disassemble D-loops. Other sequences that have the potential to seed new telomeres but lack the unique features of a natural telomere sequence, do not terminate BIR at a significant frequency in wild-type cells. However, these sequences can form ectopic telomeres if BIR is made less processive. Our results support a model in which features of the ITS itself, such as the propensity to form secondary structures and telomeric protein binding, pose a challenge to BIR and increase the vulnerability of the D-loop to dissociation by helicases, thereby promoting ectopic telomere formation.
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Affiliation(s)
- Elizabeth A Stivison
- Program in Nutritional and Metabolic Biology, Columbia University Irving Medical Center, New York, NY 10032, USA.,Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Kati J Young
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Lorraine S Symington
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA.,Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
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33
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Conformational and migrational dynamics of slipped-strand DNA three-way junctions containing trinucleotide repeats. Nat Commun 2021; 12:204. [PMID: 33420051 PMCID: PMC7794359 DOI: 10.1038/s41467-020-20426-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 11/30/2020] [Indexed: 12/18/2022] Open
Abstract
Expansions of CAG/CTG trinucleotide repeats in DNA are the cause of at least 17 degenerative human disorders, including Huntington’s Disease. Repeat instability is thought to occur via the formation of intrastrand hairpins during replication, repair, recombination, and transcription though relatively little is known about their structure and dynamics. We use single-molecule Förster resonance energy transfer to study DNA three-way junctions (3WJs) containing slip-outs composed of CAG or CTG repeats. 3WJs that only have repeats in the slip-out show two-state behavior, which we attribute to conformational flexibility at the 3WJ branchpoint. When the triplet repeats extend into the adjacent duplex, additional dynamics are observed, which we assign to interconversion of positional isomers. We propose a branchpoint migration model that involves conformational rearrangement, strand exchange, and bulge-loop movement. This migration has implications for how repeat slip-outs are processed by the cellular machinery, disease progression, and their development as drug targets. DNA three-way junctions are branched structures formed during replication, repair, and recombination, and are involved in models of repeat expansion. Here the authors use single-molecule Förster resonance energy transfer to reveal the dynamics of DNA three-way junctions containing slip-outs composed of CAG or CTG repeats.
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34
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Brown RE, Freudenreich CH. Structure-forming repeats and their impact on genome stability. Curr Opin Genet Dev 2020; 67:41-51. [PMID: 33279816 DOI: 10.1016/j.gde.2020.10.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 10/22/2020] [Accepted: 10/24/2020] [Indexed: 12/12/2022]
Abstract
Repetitive sequences throughout the genome are a major source of endogenous DNA damage, due to the propensity of many of them to form alternative non-B DNA structures that can interfere with replication, transcription, and DNA repair. These repetitive sequences are prone to breakage (fragility) and instability (changes in repeat number). Repeat fragility and expansions are linked to several diseases, including many cancers and neurodegenerative diseases, hence the importance of understanding the mechanisms that cause genome instability and contribute to these diseases. This review focuses on recent findings of mechanisms causing repeat fragility and instability, new associations between repeat expansions and genetic diseases, and potential therapeutic options to target repeat expansions.
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Affiliation(s)
- Rebecca E Brown
- Program in Genetics, Tufts University Graduate School of Biomedical Sciences, Boston, MA 02111, USA
| | - Catherine H Freudenreich
- Department of Biology, Tufts University, Medford, MA 02155, USA; Program in Genetics, Tufts University Graduate School of Biomedical Sciences, Boston, MA 02111, USA.
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35
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Deshpande M, Romanski PA, Rosenwaks Z, Gerhardt J. Gynecological Cancers Caused by Deficient Mismatch Repair and Microsatellite Instability. Cancers (Basel) 2020; 12:E3319. [PMID: 33182707 PMCID: PMC7697596 DOI: 10.3390/cancers12113319] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/30/2020] [Accepted: 11/07/2020] [Indexed: 01/05/2023] Open
Abstract
Mutations in mismatch repair genes leading to mismatch repair (MMR) deficiency (dMMR) and microsatellite instability (MSI) have been implicated in multiple types of gynecologic malignancies. Endometrial carcinoma represents the largest group, with approximately 30% of these cancers caused by dMMR/MSI. Thus, testing for dMMR is now routine for endometrial cancer. Somatic mutations leading to dMMR account for approximately 90% of these cancers. However, in 5-10% of cases, MMR protein deficiency is due to a germline mutation in the mismatch repair genes MLH1, MSH2, MSH6, PMS2, or EPCAM. These germline mutations, known as Lynch syndrome, are associated with an increased risk of both endometrial and ovarian cancer, in addition to colorectal, gastric, urinary tract, and brain malignancies. So far, gynecological cancers with dMMR/MSI are not well characterized and markers for detection of MSI in gynecological cancers are not well defined. In addition, currently advanced endometrial cancers have a poor prognosis and are treated without regard to MSI status. Elucidation of the mechanism causing dMMR/MSI gynecological cancers would aid in diagnosis and therapeutic intervention. Recently, a new immunotherapy was approved for the treatment of solid tumors with MSI that have recurred or progressed after failing traditional treatment strategies. In this review, we summarize the MMR defects and MSI observed in gynecological cancers, their prognostic value, and advances in therapeutic strategies to treat these cancers.
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Affiliation(s)
- Madhura Deshpande
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY 10021, USA; (M.D.); (P.A.R.); (Z.R.)
| | - Phillip A. Romanski
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY 10021, USA; (M.D.); (P.A.R.); (Z.R.)
| | - Zev Rosenwaks
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY 10021, USA; (M.D.); (P.A.R.); (Z.R.)
| | - Jeannine Gerhardt
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY 10021, USA; (M.D.); (P.A.R.); (Z.R.)
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY 10021, USA
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36
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Gadgil RY, Romer EJ, Goodman CC, Rider SD, Damewood FJ, Barthelemy JR, Shin-Ya K, Hanenberg H, Leffak M. Replication stress at microsatellites causes DNA double-strand breaks and break-induced replication. J Biol Chem 2020; 295:15378-15397. [PMID: 32873711 DOI: 10.1074/jbc.ra120.013495] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 08/23/2020] [Indexed: 12/12/2022] Open
Abstract
Short tandemly repeated DNA sequences, termed microsatellites, are abundant in the human genome. These microsatellites exhibit length instability and susceptibility to DNA double-strand breaks (DSBs) due to their tendency to form stable non-B DNA structures. Replication-dependent microsatellite DSBs are linked to genome instability signatures in human developmental diseases and cancers. To probe the causes and consequences of microsatellite DSBs, we designed a dual-fluorescence reporter system to detect DSBs at expanded (CTG/CAG) n and polypurine/polypyrimidine (Pu/Py) mirror repeat structures alongside the c-myc replication origin integrated at a single ectopic chromosomal site. Restriction cleavage near the (CTG/CAG)100 microsatellite leads to homology-directed single-strand annealing between flanking AluY elements and reporter gene deletion that can be detected by flow cytometry. However, in the absence of restriction cleavage, endogenous and exogenous replication stressors induce DSBs at the (CTG/CAG)100 and Pu/Py microsatellites. DSBs map to a narrow region at the downstream edge of the (CTG)100 lagging-strand template. (CTG/CAG) n chromosome fragility is repeat length-dependent, whereas instability at the (Pu/Py) microsatellites depends on replication polarity. Strikingly, restriction-generated DSBs and replication-dependent DSBs are not repaired by the same mechanism. Knockdown of DNA damage response proteins increases (Rad18, polymerase (Pol) η, Pol κ) or decreases (Mus81) the sensitivity of the (CTG/CAG)100 microsatellites to replication stress. Replication stress and DSBs at the ectopic (CTG/CAG)100 microsatellite lead to break-induced replication and high-frequency mutagenesis at a flanking thymidine kinase gene. Our results show that non-B structure-prone microsatellites are susceptible to replication-dependent DSBs that cause genome instability.
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Affiliation(s)
- Rujuta Yashodhan Gadgil
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA
| | - Eric J Romer
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA
| | - Caitlin C Goodman
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA
| | - S Dean Rider
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA
| | - French J Damewood
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA
| | - Joanna R Barthelemy
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA
| | - Kazuo Shin-Ya
- Biomedical Information Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Helmut Hanenberg
- Department of Otorhinolaryngology and Head/Neck Surgery, Heinrich Heine University, Düsseldorf, Germany; Department of Pediatrics III, University Children's Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Michael Leffak
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA.
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37
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Xu P, Pan F, Roland C, Sagui C, Weninger K. Dynamics of strand slippage in DNA hairpins formed by CAG repeats: roles of sequence parity and trinucleotide interrupts. Nucleic Acids Res 2020; 48:2232-2245. [PMID: 31974547 PMCID: PMC7049705 DOI: 10.1093/nar/gkaa036] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 12/11/2019] [Accepted: 01/15/2020] [Indexed: 01/08/2023] Open
Abstract
DNA trinucleotide repeats (TRs) can exhibit dynamic expansions by integer numbers of trinucleotides that lead to neurodegenerative disorders. Strand slipped hairpins during DNA replication, repair and/or recombination may contribute to TR expansion. Here, we combine single-molecule FRET experiments and molecular dynamics studies to elucidate slipping dynamics and conformations of (CAG)n TR hairpins. We directly resolve slipping by predominantly two CAG units. The slipping kinetics depends on the even/odd repeat parity. The populated states suggest greater stability for 5′-AGCA-3′ tetraloops, compared with alternative 5′-CAG-3′ triloops. To accommodate the tetraloop, even(odd)-numbered repeats have an even(odd) number of hanging bases in the hairpin stem. In particular, a paired-end tetraloop (no hanging TR) is stable in (CAG)n = even, but such situation cannot occur in (CAG)n = odd, where the hairpin is “frustrated’’ and slips back and forth between states with one TR hanging at the 5′ or 3′ end. Trinucleotide interrupts in the repeating CAG pattern associated with altered disease phenotypes select for specific conformers with favorable loop sequences. Molecular dynamics provide atomic-level insight into the loop configurations. Reducing strand slipping in TR hairpins by sequence interruptions at the loop suggests disease-associated variations impact expansion mechanisms at the level of slipped hairpins.
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Affiliation(s)
- Pengning Xu
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
| | - Feng Pan
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
| | - Christopher Roland
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
| | - Celeste Sagui
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
| | - Keith Weninger
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
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38
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Khristich AN, Mirkin SM. On the wrong DNA track: Molecular mechanisms of repeat-mediated genome instability. J Biol Chem 2020; 295:4134-4170. [PMID: 32060097 PMCID: PMC7105313 DOI: 10.1074/jbc.rev119.007678] [Citation(s) in RCA: 155] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Expansions of simple tandem repeats are responsible for almost 50 human diseases, the majority of which are severe, degenerative, and not currently treatable or preventable. In this review, we first describe the molecular mechanisms of repeat-induced toxicity, which is the connecting link between repeat expansions and pathology. We then survey alternative DNA structures that are formed by expandable repeats and review the evidence that formation of these structures is at the core of repeat instability. Next, we describe the consequences of the presence of long structure-forming repeats at the molecular level: somatic and intergenerational instability, fragility, and repeat-induced mutagenesis. We discuss the reasons for gender bias in intergenerational repeat instability and the tissue specificity of somatic repeat instability. We also review the known pathways in which DNA replication, transcription, DNA repair, and chromatin state interact and thereby promote repeat instability. We then discuss possible reasons for the persistence of disease-causing DNA repeats in the genome. We describe evidence suggesting that these repeats are a payoff for the advantages of having abundant simple-sequence repeats for eukaryotic genome function and evolvability. Finally, we discuss two unresolved fundamental questions: (i) why does repeat behavior differ between model systems and human pedigrees, and (ii) can we use current knowledge on repeat instability mechanisms to cure repeat expansion diseases?
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Affiliation(s)
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, Massachusetts 02155.
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39
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RAD52: Viral Friend or Foe? Cancers (Basel) 2020; 12:cancers12020399. [PMID: 32046320 PMCID: PMC7072633 DOI: 10.3390/cancers12020399] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/06/2020] [Accepted: 02/06/2020] [Indexed: 02/06/2023] Open
Abstract
Mammalian Radiation Sensitive 52 (RAD52) is a gene whose scientific reputation has recently seen a strong resurgence. In the past decade, RAD52, which was thought to be dispensable for most DNA repair and recombination reactions in mammals, has been shown to be important for a bevy of DNA metabolic pathways. One of these processes is termed break-induced replication (BIR), a mechanism that can be used to re-start broken replication forks and to elongate the ends of chromosomes in telomerase-negative cells. Viruses have historically evolved a myriad of mechanisms in which they either conscript cellular factors or, more frequently, inactivate them as a means to enable their own replication and survival. Recent data suggests that Adeno-Associated Virus (AAV) may replicate its DNA in a BIR-like fashion and/or utilize RAD52 to facilitate viral transduction and, as such, likely conscripts/requires the host RAD52 protein to promote its perpetuation.
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40
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Viterbo D, Richard GF. Quantifying Replication Fork Progression at CTG Repeats by 2D Gel Electrophoresis. Methods Mol Biol 2020; 2056:69-81. [PMID: 31586341 DOI: 10.1007/978-1-4939-9784-8_4] [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] [Indexed: 06/10/2023]
Abstract
Physical separation of branched DNA from linear molecules is based on the difference of mobility of linear versus branched DNA during two-dimensional agarose gel electrophoresis. Structured DNA migrates as slower species when compared to linear DNA of similar molecular weight. Metabolic processes such as S phase replication or double strand-break repair may generate branched DNA molecules. Trinucleotide repeats are naturally prone to form secondary structures that can modify their migration through an agarose gel matrix. These structures may also interfere in vivo with replication, by slowing down replication-fork progression, transiently stalling forks, possibly leading to secondary structure such as Holliday junctions or hemicatenanes. Alternatively, reversed replication forks may occur following fork stalling, disrupting replication dynamics and modifying DNA migration on agarose gel. So although two-dimensional agarose gel electrophoresis theoretically allows to resolve a mixture of structured DNA molecules and quantify them by radioactive hybridization, its practical application to trinucleotide repeats faces some serious technical challenges.
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Affiliation(s)
- David Viterbo
- Department Genomes & Genetics, Institut Pasteur, CNRS, UMR3525, Paris, France.
| | - Guy-Franck Richard
- Department Genomes & Genetics, Institut Pasteur, CNRS, UMR3525, Paris, France
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41
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Defects in the GINS complex increase the instability of repetitive sequences via a recombination-dependent mechanism. PLoS Genet 2019; 15:e1008494. [PMID: 31815930 PMCID: PMC6922473 DOI: 10.1371/journal.pgen.1008494] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 12/19/2019] [Accepted: 10/25/2019] [Indexed: 12/16/2022] Open
Abstract
Faithful replication and repair of DNA lesions ensure genome maintenance. During replication in eukaryotic cells, DNA is unwound by the CMG helicase complex, which is composed of three major components: the Cdc45 protein, Mcm2-7, and the GINS complex. The CMG in complex with DNA polymerase epsilon (CMG-E) participates in the establishment and progression of the replisome. Impaired functioning of the CMG-E was shown to induce genomic instability and promote the development of various diseases. Therefore, CMG-E components play important roles as caretakers of the genome. In Saccharomyces cerevisiae, the GINS complex is composed of the Psf1, Psf2, Psf3, and Sld5 essential subunits. The Psf1-1 mutant form fails to interact with Psf3, resulting in impaired replisome assembly and chromosome replication. Here, we show increased instability of repeat tracts (mononucleotide, dinucleotide, trinucleotide and longer) in yeast psf1-1 mutants. To identify the mechanisms underlying this effect, we analyzed repeated sequence instability using derivatives of psf1-1 strains lacking genes involved in translesion synthesis, recombination, or mismatch repair. Among these derivatives, deletion of RAD52, RAD51, MMS2, POL32, or PIF1 significantly decreased DNA repeat instability. These results, together with the observed increased amounts of single-stranded DNA regions and Rfa1 foci suggest that recombinational mechanisms make important contributions to repeat tract instability in psf1-1 cells. We propose that defective functioning of the CMG-E complex in psf1-1 cells impairs the progression of DNA replication what increases the contribution of repair mechanisms such as template switch and break-induced replication. These processes require sequence homology search which in case of a repeated DNA tract may result in misalignment leading to its expansion or contraction. Processes that ensure genome stability are crucial for all organisms to avoid mutations and decrease the risk of diseases. The coordinated activity of mechanisms underlying the maintenance of high-fidelity DNA duplication and repair is critical to deal with the malfunction of replication forks or DNA damage. Repeated sequences in DNA are particularly prone to instability; these sequences undergo expansions or contractions, leading in humans to various neurological, neurodegenerative, and neuromuscular disorders. A mutant form of one of the noncatalytic subunits of active DNA helicase complex impairs DNA replication. Here, we show that this form also significantly increases the instability of mononucleotide, dinucleotide, trinucleotide and longer repeat tracts. Our results suggest that in cells that harbor a mutated variant of the helicase complex, continuation of DNA replication is facilitated by recombination processes, and this mechanism can be highly mutagenic during repair synthesis through repetitive regions, especially regions that form secondary structures. Our results indicate that proper functioning of the DNA helicase complex is crucial for maintenance of the stability of repeated DNA sequences, especially in the context of recently described disorders in which mutations or deregulation of the human homologs of genes encoding DNA helicase subunits were observed.
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42
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House NC, Polleys EJ, Quasem I, De la Rosa Mejia M, Joyce CE, Takacsi-Nagy O, Krebs JE, Fuchs SM, Freudenreich CH. Distinct roles for S. cerevisiae H2A copies in recombination and repeat stability, with a role for H2A.1 threonine 126. eLife 2019; 8:53362. [PMID: 31804179 PMCID: PMC6927750 DOI: 10.7554/elife.53362] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 11/26/2019] [Indexed: 01/14/2023] Open
Abstract
CAG/CTG trinuncleotide repeats are fragile sequences that when expanded form DNA secondary structures and cause human disease. We evaluated CAG/CTG repeat stability and repair outcomes in histone H2 mutants in S. cerevisiae. Although the two copies of H2A are nearly identical in amino acid sequence, CAG repeat stability depends on H2A copy 1 (H2A.1) but not copy 2 (H2A.2). H2A.1 promotes high-fidelity homologous recombination, sister chromatid recombination (SCR), and break-induced replication whereas H2A.2 does not share these functions. Both decreased SCR and the increase in CAG expansions were due to the unique Thr126 residue in H2A.1 and hta1Δ or hta1-T126A mutants were epistatic to deletion of the Polδ subunit Pol32, suggesting a role for H2A.1 in D-loop extension. We conclude that H2A.1 plays a greater repair-specific role compared to H2A.2 and may be a first step towards evolution of a repair-specific function for H2AX compared to H2A in mammalian cells.
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Affiliation(s)
- Nealia Cm House
- Department of Biology, Tufts University, Medford, United States
| | - Erica J Polleys
- Department of Biology, Tufts University, Medford, United States
| | | | | | - Cailin E Joyce
- Department of Biology, Tufts University, Medford, United States
| | | | - Jocelyn E Krebs
- Department of Biological Sciences, University of Alaska Anchorage, Anchorage, United States
| | - Stephen M Fuchs
- Department of Biology, Tufts University, Medford, United States
| | - Catherine H Freudenreich
- Department of Biology, Tufts University, Medford, United States.,Program in Genetics, Graduate School of Biomedical Sciences, Tufts University, Boston, United States
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43
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Ni CW, Wei YJ, Shen YI, Lee IR. Long-Range Hairpin Slippage Reconfiguration Dynamics in Trinucleotide Repeat Sequences. J Phys Chem Lett 2019; 10:3985-3990. [PMID: 31241956 DOI: 10.1021/acs.jpclett.9b01524] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Trinucleotide repeat (TNR) sequences, which are responsible for several neurodegenerative genetic diseases, fold into hairpins that interfere with the protein machinery in replication or repair, thus leading to dynamic mutation -abnormal expansions of the genome. Despite their high thermodynamic stability, these hairpins can undergo configurational rearrangements, which may be crucial for continuous dynamic mutation. Here, we used CTG repeats as a model system to study their structural dynamics at the single-molecule level. A unique dynamic two-state configuration interchange was discovered over a wide range of odd-numbered CTG repeat sequences. Employing repeat-number-dependent kinetic analysis, we proposed a bulge translocation model, which is driven by the local instability and can be extended reasonably to longer (pathologically relevant) hairpins, implying the potential role in error accumulation in repeat expansion.
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Affiliation(s)
- Cheng-Wei Ni
- Department of Chemistry , National Taiwan Normal University , Taipei 11677 , Taiwan
| | - Yu-Jie Wei
- Department of Chemistry , National Taiwan Normal University , Taipei 11677 , Taiwan
| | - Yang-I Shen
- Department of Chemistry , National Taiwan Normal University , Taipei 11677 , Taiwan
| | - I-Ren Lee
- Department of Chemistry , National Taiwan Normal University , Taipei 11677 , Taiwan
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44
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Neil AJ, Liang MU, Khristich AN, Shah KA, Mirkin SM. RNA-DNA hybrids promote the expansion of Friedreich's ataxia (GAA)n repeats via break-induced replication. Nucleic Acids Res 2019; 46:3487-3497. [PMID: 29447396 PMCID: PMC5909440 DOI: 10.1093/nar/gky099] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 02/05/2018] [Indexed: 12/21/2022] Open
Abstract
Expansion of simple DNA repeats is responsible for numerous hereditary diseases in humans. The role of DNA replication, repair and transcription in the expansion process has been well documented. Here we analyzed, in a yeast experimental system, the role of RNA–DNA hybrids in genetic instability of long (GAA)n repeats, which cause Friedreich’s ataxia. Knocking out both yeast RNase H enzymes, which counteract the formation of RNA–DNA hybrids, increased (GAA)n repeat expansion and contraction rates when the repetitive sequence was transcribed. Unexpectedly, we observed a similar increase in repeat instability in RNase H-deficient cells when we either changed the direction of transcription-replication collisions, or flipped the repeat sequence such that the (UUC)n run occurred in the transcript. The increase in repeat expansions in RNase H-deficient strains was dependent on Rad52 and Pol32 proteins, suggesting that break-induced replication (BIR) is responsible for this effect. We conclude that expansions of (GAA)n repeats are induced by the formation of RNA–DNA hybrids that trigger BIR. Since this stimulation is independent of which strand of the repeat (homopurine or homopyrimidine) is in the RNA transcript, we hypothesize that triplex H-DNA structures stabilized by an RNA–DNA hybrid (H-loops), rather than conventional R-loops, could be responsible.
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Affiliation(s)
- Alexander J Neil
- Department of Biology, Tufts University, Medford, MA 02155, USA.,Genetics Program, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, MA 02111, USA
| | - Miranda U Liang
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | | | - Kartik A Shah
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, MA 02155, USA
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45
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Bhandari J, Karg T, Golic KG. Homolog-Dependent Repair Following Dicentric Chromosome Breakage in Drosophila melanogaster. Genetics 2019; 212:615-630. [PMID: 31053594 PMCID: PMC6614899 DOI: 10.1534/genetics.119.302247] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 04/29/2019] [Indexed: 12/11/2022] Open
Abstract
Double-strand DNA breaks are repaired by one of several mechanisms that rejoin two broken ends. However, cells are challenged when asked to repair a single broken end and respond by: (1) inducing programmed cell death; (2) healing the broken end by constructing a new telomere; (3) adapting to the broken end and resuming the mitotic cycle without repair; and (4) using information from the sister chromatid or homologous chromosome to restore a normal chromosome terminus. During one form of homolog-dependent repair in yeast, termed break-induced replication (BIR), a template chromosome can be copied for hundreds of kilobases. BIR efficiency depends on Pif1 helicase and Pol32, a nonessential subunit of DNA polymerase δ. To date, there is little evidence that BIR can be used for extensive chromosome repair in higher eukaryotes. We report that a dicentric chromosome broken in mitosis in the male germline of Drosophila melanogaster is usually repaired by healing, but can also be repaired in a homolog-dependent fashion, restoring at least 1.3 Mb of terminal sequence information. This mode of repair is significantly reduced in pif1 and pol32 mutants. Formally, the repaired chromosomes are recombinants. However, the absence of reciprocal recombinants and the dependence on Pif1 and Pol32 strongly support the hypothesis that BIR is the mechanism for restoration of the chromosome terminus. In contrast to yeast, pif1 mutants in Drosophila exhibit a reduced rate of chromosome healing, likely owing to fundamental differences in telomeres between these organisms.
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Affiliation(s)
- Jayaram Bhandari
- School of Biological Sciences, University of Utah, Salt Lake City, Utah 84112
| | - Travis Karg
- School of Biological Sciences, University of Utah, Salt Lake City, Utah 84112
| | - Kent G Golic
- School of Biological Sciences, University of Utah, Salt Lake City, Utah 84112
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46
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Minina JM, Karamysheva TV, Rubtsov NB, Zhdanova NS. Replication timing of large Sorex granarius (Soricidae, Eulipotyphla) telomeres. PROTOPLASMA 2018; 255:1477-1486. [PMID: 29627866 DOI: 10.1007/s00709-018-1244-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 03/19/2018] [Indexed: 06/08/2023]
Abstract
Previously, we described the unique feature of telomeric regions in Iberian shrew Sorex granarius: its telomeres have two ranges of size, very small (3.8 kb of telomeric repeats on average) and very large discontinuous telomeres (213 kb) interrupted with 18S rDNA. In this study, we have demonstrated extraordinary replication pattern of S. granarius large telomeres that have not been shown before in other studied mammal. Using the ReD-FISH procedure, we observed prolonged, through S period, large telomere replication. Furthermore, revealed ReD-FISH asymmetric signals were probably caused by partial replication of telomeres within an hour of 5-bromodeoxyuridine treatment due to the large size and special organization. We also found that in contrast to the telomeric halo from primary fibroblasts of bovine, mink, and common shrew, telomere halo of S. granarius consists of multiple loops bundled together, some of which contain rDNA. Here, we suggested several replicons firing possibly stochastic in each large telomere. Finally, we performed the TIF assay to reveal DNA damage responses at the telomeres, and along with TIF in nuclei, we found large bodies of telomeric DNA and ɤ-H2AX in the cytoplasm and on the surface of fibroblasts. We discuss the possibility of additional origin activation together with recombination-dependent replication pathways, mainly homologous recombination including BIR for replication fork stagnation overcoming and further S. granarius large telomere replication.
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Affiliation(s)
- Julia M Minina
- The Federal Research Center Institute of Cytology and Genetics of SB RAS, Lavrentjeva av. 10, 630090, Novosibirsk, Russia.
| | - Tatjana V Karamysheva
- The Federal Research Center Institute of Cytology and Genetics of SB RAS, Lavrentjeva av. 10, 630090, Novosibirsk, Russia
| | - Nicolaj B Rubtsov
- The Federal Research Center Institute of Cytology and Genetics of SB RAS, Lavrentjeva av. 10, 630090, Novosibirsk, Russia
| | - Natalia S Zhdanova
- The Federal Research Center Institute of Cytology and Genetics of SB RAS, Lavrentjeva av. 10, 630090, Novosibirsk, Russia
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47
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Freudenreich CH. R-loops: targets for nuclease cleavage and repeat instability. Curr Genet 2018; 64:789-794. [PMID: 29327083 PMCID: PMC6039234 DOI: 10.1007/s00294-018-0806-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 01/03/2018] [Accepted: 01/08/2018] [Indexed: 01/09/2023]
Abstract
R-loops form when transcribed RNA remains bound to its DNA template to form a stable RNA:DNA hybrid. Stable R-loops form when the RNA is purine-rich, and are further stabilized by DNA secondary structures on the non-template strand. Interestingly, many expandable and disease-causing repeat sequences form stable R-loops, and R-loops can contribute to repeat instability. Repeat expansions are responsible for multiple neurodegenerative diseases, including Huntington's disease, myotonic dystrophy, and several types of ataxias. Recently, it was found that R-loops at an expanded CAG/CTG repeat tract cause DNA breaks as well as repeat instability (Su and Freudenreich, Proc Natl Acad Sci USA 114, E8392-E8401, 2017). Two factors were identified as causing R-loop-dependent breaks at CAG/CTG tracts: deamination of cytosines and the MutLγ (Mlh1-Mlh3) endonuclease, defining two new mechanisms for how R-loops can generate DNA breaks (Su and Freudenreich, Proc Natl Acad Sci USA 114, E8392-E8401, 2017). Following R-loop-dependent nicking, base excision repair resulted in repeat instability. These results have implications for human repeat expansion diseases and provide a paradigm for how RNA:DNA hybrids can cause genome instability at structure-forming DNA sequences. This perspective summarizes mechanisms of R-loop-induced fragility at G-rich repeats and new links between DNA breaks and repeat instability.
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Affiliation(s)
- Catherine H Freudenreich
- Department of Biology, Tufts University, Medford, MA, 02155, USA.
- Program in Genetics, Tufts University, Boston, MA, 02111, USA.
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48
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49
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Mechanisms of genetic instability caused by (CGG) n repeats in an experimental mammalian system. Nat Struct Mol Biol 2018; 25:669-676. [PMID: 30061600 PMCID: PMC6082162 DOI: 10.1038/s41594-018-0094-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 06/19/2018] [Indexed: 12/17/2022]
Abstract
We describe a new experimental system to study genome instability caused by fragile X (CGG)n repeats in mammalian cells. It is based on a selectable cassette carrying the HyTK gene under the control of the FMR1 promoter with (CGG)n repeats in its 5′-UTR, which was integrated into the unique RL5 site in murine erythroid leukemia cells. Carrier-size (CGG)n repeats dramatically elevate the frequency of the reporter’s inactivation making cells ganciclovir-resistant. These resistant clones have a unique mutational signature: a change in the repeat length concurrent with mutagenesis in the reporter gene. Inactivation of genes implicated in break-induced replication including POLD3, POLD4, RAD52, RAD51 and SMARCAL1, reduced the frequency of ganciclovir-resistant clones to the baseline level that was observed in the absence of (CGG)n repeats. We propose that replication fork collapse at carrier-size (CGG)n repeats can trigger break-induced replication, which result in simultaneous repeat length changes and mutagenesis at a distance.
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50
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Trinucleotide repeat instability during double-strand break repair: from mechanisms to gene therapy. Curr Genet 2018; 65:17-28. [DOI: 10.1007/s00294-018-0865-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 06/25/2018] [Accepted: 07/01/2018] [Indexed: 12/26/2022]
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