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Hisey JA, Radchenko EA, Mandel NH, McGinty R, Matos-Rodrigues G, Rastokina A, Masnovo C, Ceschi S, Hernandez A, Nussenzweig A, Mirkin S. Pathogenic CANVAS (AAGGG)n repeats stall DNA replication due to the formation of alternative DNA structures. Nucleic Acids Res 2024; 52:4361-4374. [PMID: 38381906 PMCID: PMC11077069 DOI: 10.1093/nar/gkae124] [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: 07/25/2023] [Revised: 02/06/2024] [Accepted: 02/08/2024] [Indexed: 02/23/2024] Open
Abstract
CANVAS is a recently characterized repeat expansion disease, most commonly caused by homozygous expansions of an intronic (A2G3)n repeat in the RFC1 gene. There are a multitude of repeat motifs found in the human population at this locus, some of which are pathogenic and others benign. In this study, we conducted structure-functional analyses of the pathogenic (A2G3)n and nonpathogenic (A4G)n repeats. We found that the pathogenic, but not the nonpathogenic, repeat presents a potent, orientation-dependent impediment to DNA polymerization in vitro. The pattern of the polymerization blockage is consistent with triplex or quadruplex formation in the presence of magnesium or potassium ions, respectively. Chemical probing of both repeats in vitro reveals triplex H-DNA formation by only the pathogenic repeat. Consistently, bioinformatic analysis of S1-END-seq data from human cell lines shows preferential H-DNA formation genome-wide by (A2G3)n motifs over (A4G)n motifs. Finally, the pathogenic, but not the nonpathogenic, repeat stalls replication fork progression in yeast and human cells. We hypothesize that the CANVAS-causing (A2G3)n repeat represents a challenge to genome stability by folding into alternative DNA structures that stall DNA replication.
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Affiliation(s)
- Julia A Hisey
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | | | | | - Ryan J McGinty
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA02115, USA
| | | | | | - Chiara Masnovo
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Silvia Ceschi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova 35131, Italy
| | | | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute NIH, Bethesda, MD20892, USA
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, MA 02155, USA
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2
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Ramachandran V, Mainan A, Roy S. Dynamic effects of the spine of hydrated magnesium on viral RNA pseudoknot structure. Phys Chem Chem Phys 2022; 24:24570-24581. [PMID: 36193826 DOI: 10.1039/d2cp01075e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
In the cellular environment, a viral RNA Pseudoknot (PK) structure is responsive to its prevailing ion atmosphere created by a mixture of monovalent and divalent cations. We investigate the influence of such a mixed-salt environment on RNA-PK structure at an atomic resolution through three sets of 1.5 μs explicit solvent molecular dynamics (MD) simulations and also by building a dynamic counterion-condensation (DCC) model at varying divalent Mg2+ concentrations. The DCC model includes explicit interaction of the ligand and adjacent chelated Mg2+ by extending the recently developed generalized Manning condensation model. Its implementation within an all-atom structure-based molecular dynamics framework bolsters its opportunity to explore large-length scale and long-timescale phenomena associated with complex RNA systems immersed in its dynamic ion environment. In the present case of RNA-PK, both explicit MD and DCC simulations reveal a spine of hydrated-Mg2+ to induce stem-I and stem-II closure where the minor groove between these stems is akin to breathing. Mg2+ mediated minor-groove narrowing is coupled with local base-flipping dynamics of a base triple and quadruple, changing the stem structure of such RNA. Contrary to the conversational view of the indispensable need for Mg2+ for the tertiary structure of RNA, the study warns about the plausible detrimental effect of specific Mg2+-phosphate interactions on the RNA-PK structure beyond a certain concentration of Mg2+.
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Affiliation(s)
- Vysakh Ramachandran
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India.
| | - Avijit Mainan
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India.
| | - Susmita Roy
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India.
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3
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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. Trinucleotide repeat expansions are the cause of several muscular- and neuro-degenerative diseases, and further expansions during intergenerational inheritance often leads to an earlier age-of-onset in the offspring. Some intergenerational expansions appear to occur during germ cell replication, but how those replication-associated expansions arise is incompletely understood. Because there are many replication barriers in genomes, including the structure-forming repeats themselves, we investigated whether a repeat placed after such a barrier had altered instability. We discovered that a restarted replication fork traversing a CAG repeat tract is highly error prone and repeat expansions and contractions are more prevalent in this case compared to normal replication. These results reveal a mechanism for replication-associated repeat instability relevant to disease-associated trinucleotide repeat expansions.
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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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4
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Whalen JM, Dhingra N, Wei L, Zhao X, Freudenreich CH. Relocation of Collapsed Forks to the Nuclear Pore Complex Depends on Sumoylation of DNA Repair Proteins and Permits Rad51 Association. Cell Rep 2021; 31:107635. [PMID: 32402281 DOI: 10.1016/j.celrep.2020.107635] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 01/07/2020] [Accepted: 04/21/2020] [Indexed: 10/24/2022] Open
Abstract
Expanded CAG repeats form stem-loop secondary structures that lead to fork stalling and collapse. Previous work has shown that these collapsed forks relocalize to nuclear pore complexes (NPCs) in late S phase in a manner dependent on replication, the nucleoporin Nup84, and the Slx5 protein, which prevents repeat fragility and instability. Here, we show that binding of the Smc5/6 complex to the collapsed fork triggers Mms21-dependent sumoylation of fork-associated DNA repair proteins, and that RPA, Rad52, and Rad59 are the key sumoylation targets that mediate relocation. The SUMO interacting motifs of Slx5 target collapsed forks to the NPC. Notably, Rad51 foci only co-localize with the repeat after it is anchored to the nuclear periphery and Rad51 exclusion from the early collapsed fork is dependent on RPA sumoylation. This pathway may provide a mechanism to constrain recombination at stalled or collapsed forks until it is required for fork restart.
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Affiliation(s)
- Jenna M Whalen
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Nalini Dhingra
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Lei Wei
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Xiaolan Zhao
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - 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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5
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Deshmukh AL, Porro A, Mohiuddin M, Lanni S, Panigrahi GB, Caron MC, Masson JY, Sartori AA, Pearson CE. FAN1, a DNA Repair Nuclease, as a Modifier of Repeat Expansion Disorders. J Huntingtons Dis 2021; 10:95-122. [PMID: 33579867 PMCID: PMC7990447 DOI: 10.3233/jhd-200448] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
FAN1 encodes a DNA repair nuclease. Genetic deficiencies, copy number variants, and single nucleotide variants of FAN1 have been linked to karyomegalic interstitial nephritis, 15q13.3 microdeletion/microduplication syndrome (autism, schizophrenia, and epilepsy), cancer, and most recently repeat expansion diseases. For seven CAG repeat expansion diseases (Huntington's disease (HD) and certain spinocerebellar ataxias), modification of age of onset is linked to variants of specific DNA repair proteins. FAN1 variants are the strongest modifiers. Non-coding disease-delaying FAN1 variants and coding disease-hastening variants (p.R507H and p.R377W) are known, where the former may lead to increased FAN1 levels and the latter have unknown effects upon FAN1 functions. Current thoughts are that ongoing repeat expansions in disease-vulnerable tissues, as individuals age, promote disease onset. Fan1 is required to suppress against high levels of ongoing somatic CAG and CGG repeat expansions in tissues of HD and FMR1 transgenic mice respectively, in addition to participating in DNA interstrand crosslink repair. FAN1 is also a modifier of autism, schizophrenia, and epilepsy. Coupled with the association of these diseases with repeat expansions, this suggests a common mechanism, by which FAN1 modifies repeat diseases. Yet how any of the FAN1 variants modify disease is unknown. Here, we review FAN1 variants, associated clinical effects, protein structure, and the enzyme's attributed functional roles. We highlight how variants may alter its activities in DNA damage response and/or repeat instability. A thorough awareness of the FAN1 gene and FAN1 protein functions will reveal if and how it may be targeted for clinical benefit.
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Affiliation(s)
- Amit L Deshmukh
- Program of Genetics & Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
| | - Antonio Porro
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Mohiuddin Mohiuddin
- Program of Genetics & Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
| | - Stella Lanni
- Program of Genetics & Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
| | - Gagan B Panigrahi
- Program of Genetics & Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
| | - Marie-Christine Caron
- Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, Quebec, Canada.,Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Québec City, Quebec, Canada
| | - Jean-Yves Masson
- Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, Quebec, Canada.,Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Québec City, Quebec, Canada
| | - Alessandro A Sartori
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Christopher E Pearson
- Program of Genetics & Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada.,University of Toronto, Program of Molecular Genetics, Toronto, Ontario, Canada
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6
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Alternative DNA Structures In Vivo: Molecular Evidence and Remaining Questions. Microbiol Mol Biol Rev 2020; 85:85/1/e00110-20. [PMID: 33361270 DOI: 10.1128/mmbr.00110-20] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Duplex DNA naturally folds into a right-handed double helix in physiological conditions. Some sequences of unusual base composition may nevertheless form alternative structures, as was shown for many repeated sequences in vitro However, evidence for the formation of noncanonical structures in living cells is difficult to gather. It mainly relies on genetic assays demonstrating their function in vivo or through genetic instability reflecting particular properties of such structures. Efforts were made to reveal their existence directly in a living cell, mainly by generating antibodies specific to secondary structures or using chemical ligands selected for their affinity to these structures. Among secondary structure-forming DNAs are G-quadruplexes, human fragile sites containing minisatellites, AT-rich regions, inverted repeats able to form cruciform structures, hairpin-forming CAG/CTG triplet repeats, and triple helices formed by homopurine-homopyrimidine GAA/TTC trinucleotide repeats. Many of these alternative structures are involved in human pathologies, such as neurological or developmental disorders, as in the case of trinucleotide repeats, or cancers triggered by translocations linked to fragile sites. This review will discuss and highlight evidence supporting the formation of alternative DNA structures in vivo and will emphasize the role of the mismatch repair machinery in binding mispaired DNA duplexes, triggering genetic instability.
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7
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Mosbach V, Viterbo D, Descorps-Declère S, Poggi L, Vaysse-Zinkhöfer W, Richard GF. Resection and repair of a Cas9 double-strand break at CTG trinucleotide repeats induces local and extensive chromosomal deletions. PLoS Genet 2020; 16:e1008924. [PMID: 32673314 PMCID: PMC7413560 DOI: 10.1371/journal.pgen.1008924] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 08/07/2020] [Accepted: 06/10/2020] [Indexed: 12/26/2022] Open
Abstract
Microsatellites are short tandem repeats, ubiquitous in all eukaryotes and represent ~2% of the human genome. Among them, trinucleotide repeats are responsible for more than two dozen neurological and developmental disorders. Targeting microsatellites with dedicated DNA endonucleases could become a viable option for patients affected with dramatic neurodegenerative disorders. Here, we used the Streptococcus pyogenes Cas9 to induce a double-strand break within the expanded CTG repeat involved in myotonic dystrophy type 1, integrated in a yeast chromosome. Repair of this double-strand break generated unexpected large chromosomal deletions around the repeat tract. These deletions depended on RAD50, RAD52, DNL4 and SAE2, and both non-homologous end-joining and single-strand annealing pathways were involved. Resection and repair of the double-strand break (DSB) were totally abolished in a rad50Δ strain, whereas they were impaired in a sae2Δ mutant, only on the DSB end containing most of the repeat tract. This observation demonstrates that Sae2 plays significant different roles in resecting a DSB end containing a repeated and structured sequence as compared to a non-repeated DSB end. In addition, we also discovered that gene conversion was less efficient when the DSB could be repaired using a homologous template, suggesting that the trinucleotide repeat may interfere with gene conversion too. Altogether, these data show that SpCas9 may not be the best choice when inducing a double-strand break at or near a microsatellite, especially in mammalian genomes that contain many more dispersed repeated elements than the yeast genome. With the discovery of highly specific DNA endonucleases such as TALEN and CRISPR-Cas systems, gene editing has become an attractive approach to address genetic disorders. Myotonic dystrophy type 1 (Steinert disease) is due to a large expansion of a CTG trinucleotide repeat in the DMPK gene. At the present time, despite numerous therapeutic attempts, this dramatic neurodegenerative disorder still has no cure. In the present work, we tried to use the Cas9 endonuclease to induce a double-strand break within the expanded CTG repeat of the DMPK gene integrated in the yeast genome. Surprisingly, this break induced chromosomal deletions around the repeat tract. These deletions were local and involved non-homologous joining of the two DNA ends, or more extensive involving homologous recombination between repeated elements upstream and downstream the break. Using yeast genetics, we investigated the genetic requirements for these deletions and found that the triplet repeat tract altered the capacity of the repair machinery to faithfully repair the double-strand break. These results have implications for future gene therapy approaches in human patients.
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Affiliation(s)
| | | | - Stéphane Descorps-Declère
- Institut Pasteur, CNRS, UMR3525, Paris, France
- Institut Pasteur, Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), Paris, France
| | - Lucie Poggi
- Institut Pasteur, CNRS, UMR3525, Paris, France
- Sorbonne Universités, Collège doctoral, Paris, France
| | - Wilhelm Vaysse-Zinkhöfer
- Institut Pasteur, CNRS, UMR3525, Paris, France
- Sorbonne Universités, Collège doctoral, Paris, France
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8
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The nuclear pore complex prevents sister chromatid recombination during replicative senescence. Nat Commun 2020; 11:160. [PMID: 31919430 PMCID: PMC6952416 DOI: 10.1038/s41467-019-13979-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 12/10/2019] [Indexed: 12/15/2022] Open
Abstract
The Nuclear Pore Complex (NPC) has emerged as an important hub for processing various types of DNA damage. Here, we uncover that fusing a DNA binding domain to the NPC basket protein Nup1 reduces telomere relocalization to nuclear pores early after telomerase inactivation. This Nup1 modification also impairs the relocalization to the NPC of expanded CAG/CTG triplet repeats. Strikingly, telomerase negative cells bypass senescence when expressing this Nup1 modification by maintaining a minimal telomere length compatible with proliferation through rampant unequal exchanges between sister chromatids. We further report that a Nup1 mutant lacking 36 C-terminal residues recapitulates the phenotypes of the Nup1-LexA fusion indicating a direct role of Nup1 in the relocation of stalled forks to NPCs and restriction of error-prone recombination between repeated sequences. Our results reveal a new mode of telomere maintenance that could shed light on how 20% of cancer cells are maintained without telomerase or ALT. The Nuclear Pore Complex has been linked to DNA damage processing. Here the authors reveal that the Nup1 C-terminus is critical for the relocalization of eroded telomeres to nuclear pores and that modification of Nup1 promotes sister chromatid recombination and unleashes a new telomere maintenance mechanism.
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9
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Polleys EJ, Freudenreich CH. Genetic Assays to Study Repeat Fragility in Saccharomyces cerevisiae. Methods Mol Biol 2020; 2056:83-101. [PMID: 31586342 DOI: 10.1007/978-1-4939-9784-8_5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Trinucleotide repeats are common in the human genome and can undergo changes in repeat number and cause length-dependent chromosome fragility. Expanded CAG repeats have been linked to over 14 human diseases and are considered hotspots for breakage and genomic rearrangement. Here we describe two Saccharomyces cerevisiae based assays that evaluate the rate of chromosome breakage that occurs within a repeat tract (fragility), with variations that allow the role of transcription to be evaluated. The first fragility assay utilizes end-loss and subsequent telomere addition as the main mode of repair of a yeast artificial chromosome (YAC). The second fragility assay relies on the fact that a chromosomal break stimulates recombination-mediated repair. A PCR-based assay can be used to evaluate instability of the repeat in the same conditions used to measure repeat fragility. These assays have contributed to understanding the genetic mechanisms that cause chromosome breaks and tract-length changes at unstable trinucleotide repeats.
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10
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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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11
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Gellon L, Kaushal S, Cebrián J, Lahiri M, Mirkin SM, Freudenreich CH. Mrc1 and Tof1 prevent fragility and instability at long CAG repeats by their fork stabilizing function. Nucleic Acids Res 2019; 47:794-805. [PMID: 30476303 PMCID: PMC6344861 DOI: 10.1093/nar/gky1195] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 11/13/2018] [Indexed: 12/14/2022] Open
Abstract
Fork stabilization at DNA impediments is key to maintaining replication fork integrity and preventing chromosome breaks. Mrc1 and Tof1 are two known stabilizers that travel with the replication fork. In addition to a structural role, Mrc1 has a DNA damage checkpoint function. Using a yeast model system, we analyzed the role of Mrc1 and Tof1 at expanded CAG repeats of medium and long lengths, which are known to stall replication forks and cause trinucleotide expansion diseases such as Huntington's disease and myotonic dystrophy. We demonstrate that the fork stabilizer but not the checkpoint activation function of Mrc1 is key for preventing DNA breakage and death of cells containing expanded CAG tracts. In contrast, both Mrc1 functions are important in preventing repeat length instability. Mrc1 has a general fork protector role that is evident at forks traversing both repetitive and non-repetitive DNA, though it becomes crucial at long CAG repeat lengths. In contrast, the role of Tof1 in preventing fork breakage is specific to long CAG tracts of 85 or more repeats. Our results indicate that long CAG repeats have a particular need for Tof1 and highlight the importance of fork stabilizers in maintaining fork integrity during replication of structure-forming repeats.
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Affiliation(s)
- Lionel Gellon
- Department of Biology, Tufts University, Suite 4700, 200 Boston Ave, Medford, MA 02155, USA
| | - Simran Kaushal
- Department of Biology, Tufts University, Suite 4700, 200 Boston Ave, Medford, MA 02155, USA
| | - Jorge Cebrián
- Department of Biology, Tufts University, Suite 4700, 200 Boston Ave, Medford, MA 02155, USA
| | - Mayurika Lahiri
- Department of Biology, Tufts University, Suite 4700, 200 Boston Ave, Medford, MA 02155, USA
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Suite 4700, 200 Boston Ave, Medford, MA 02155, USA
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12
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Wang Z, Wang Y, Liu T, Wang Y, Zhang W. Effects of the PIWI/MID domain of Argonaute protein on the association of miRNAi's seed base with the target. RNA (NEW YORK, N.Y.) 2019; 25:620-629. [PMID: 30770397 PMCID: PMC6467011 DOI: 10.1261/rna.069328.118] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 02/01/2019] [Indexed: 05/24/2023]
Abstract
The small interfering RNAs (siRNA) or microRNAs (miRNA) incorporated into the RNA-induced silencing complex with the Argonaute (Ago) protein associates with target mRNAs through base-pairing, which leads to the cleavage or knockdown of the target mRNA. The seed region of the s(m)iRNA is crucial for target recognition. In this work, a molecular dynamic simulation was utilized to study the thermodynamics and kinetic properties of the third seed base binding to the target in the presence of the PIWI/MID domain of Ago. The results showed that in the presence of the PIWI/MID domain, the entropy and enthalpy changes for the association of the seed base with the target were smaller than those in the absence of protein. The binding affinity was increased due to the reduced entropy penalty, which resulted from the preorganization of the seed base into the A-helix form. In the presence of the protein, the association barrier resulting from the unfavorable entropy loss and the dissociation barrier coming from the destruction of hydrogen bonding and base-stacking interactions were lower than those in the absence of the protein. These results indicate that the seed region is crucial for fast recognition and association with the correct target.
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Affiliation(s)
- Zhen Wang
- Department of Physics, Wuhan University, Wuhan, Hubei 430072, P.R. China
| | - Yanli Wang
- Department of Physics, Wuhan University, Wuhan, Hubei 430072, P.R. China
| | - Taigang Liu
- Department of Physics, Wuhan University, Wuhan, Hubei 430072, P.R. China
| | - Yujie Wang
- Department of Physics, Wuhan University, Wuhan, Hubei 430072, P.R. China
| | - Wenbing Zhang
- Department of Physics, Wuhan University, Wuhan, Hubei 430072, P.R. China
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Klein HL, Bačinskaja G, Che J, Cheblal A, Elango R, Epshtein A, Fitzgerald DM, Gómez-González B, Khan SR, Kumar S, Leland BA, Marie L, Mei Q, Miné-Hattab J, Piotrowska A, Polleys EJ, Putnam CD, Radchenko EA, Saada AA, Sakofsky CJ, Shim EY, Stracy M, Xia J, Yan Z, Yin Y, Aguilera A, Argueso JL, Freudenreich CH, Gasser SM, Gordenin DA, Haber JE, Ira G, Jinks-Robertson S, King MC, Kolodner RD, Kuzminov A, Lambert SAE, Lee SE, Miller KM, Mirkin SM, Petes TD, Rosenberg SM, Rothstein R, Symington LS, Zawadzki P, Kim N, Lisby M, Malkova A. Guidelines for DNA recombination and repair studies: Cellular assays of DNA repair pathways. MICROBIAL CELL (GRAZ, AUSTRIA) 2019; 6:1-64. [PMID: 30652105 PMCID: PMC6334234 DOI: 10.15698/mic2019.01.664] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 08/29/2018] [Accepted: 09/14/2018] [Indexed: 12/29/2022]
Abstract
Understanding the plasticity of genomes has been greatly aided by assays for recombination, repair and mutagenesis. These assays have been developed in microbial systems that provide the advantages of genetic and molecular reporters that can readily be manipulated. Cellular assays comprise genetic, molecular, and cytological reporters. The assays are powerful tools but each comes with its particular advantages and limitations. Here the most commonly used assays are reviewed, discussed, and presented as the guidelines for future studies.
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Affiliation(s)
- Hannah L. Klein
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Giedrė Bačinskaja
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Jun Che
- Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, USA
| | - Anais Cheblal
- Friedrich Miescher Institute for Biomedical Research (FMI), 4058 Basel, Switzerland
| | - Rajula Elango
- Department of Biology, University of Iowa, Iowa City, IA, USA
| | - Anastasiya Epshtein
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Devon M. Fitzgerald
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Belén Gómez-González
- Centro Andaluz de BIología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla, Seville, Spain
| | - Sharik R. Khan
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Sandeep Kumar
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Léa Marie
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, USA
| | - Qian Mei
- Systems, Synthetic and Physical Biology Graduate Program, Rice University, Houston, TX, USA
| | - Judith Miné-Hattab
- Institut Curie, PSL Research University, CNRS, UMR3664, F-75005 Paris, France
- Sorbonne Université, Institut Curie, CNRS, UMR3664, F-75005 Paris, France
| | - Alicja Piotrowska
- NanoBioMedical Centre, Faculty of Physics, Adam Mickiewicz University, Umultowska 85, 61-614 Poznan, Poland
| | | | - Christopher D. Putnam
- Ludwig Institute for Cancer Research, University of California School of Medicine, San Diego, La Jolla, CA, USA
- Department of Medicine, University of California School of Medicine, San Diego, La Jolla, CA, USA
| | | | - Anissia Ait Saada
- Institut Curie, PSL Research University, CNRS, UMR3348 F-91405, Orsay, France
- University Paris Sud, Paris-Saclay University, CNRS, UMR3348, F-91405, Orsay, France
| | - Cynthia J. Sakofsky
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - Eun Yong Shim
- Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, USA
| | - Mathew Stracy
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Jun Xia
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Zhenxin Yan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Yi Yin
- Department of Molecular Genetics and Microbiology and University Program in Genetics and Genomics, Duke University Medical Center, Durham, NC USA
| | - Andrés Aguilera
- Centro Andaluz de BIología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla, Seville, Spain
| | - Juan Lucas Argueso
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | - Catherine H. Freudenreich
- Department of Biology, Tufts University, Medford, MA USA
- Program in Genetics, Tufts University, Boston, MA, USA
| | - Susan M. Gasser
- Friedrich Miescher Institute for Biomedical Research (FMI), 4058 Basel, Switzerland
| | - Dmitry A. Gordenin
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - James E. Haber
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center Brandeis University, Waltham, MA, USA
| | - Grzegorz Ira
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Sue Jinks-Robertson
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC USA
| | | | - Richard D. Kolodner
- Ludwig Institute for Cancer Research, University of California School of Medicine, San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California School of Medicine, San Diego, La Jolla, CA, USA
- Moores-UCSD Cancer Center, University of California School of Medicine, San Diego, La Jolla, CA, USA
- Institute of Genomic Medicine, University of California School of Medicine, San Diego, La Jolla, CA, USA
| | - Andrei Kuzminov
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Sarah AE Lambert
- Institut Curie, PSL Research University, CNRS, UMR3348 F-91405, Orsay, France
- University Paris Sud, Paris-Saclay University, CNRS, UMR3348, F-91405, Orsay, France
| | - Sang Eun Lee
- Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, USA
| | - Kyle M. Miller
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | | | - Thomas D. Petes
- Department of Molecular Genetics and Microbiology and University Program in Genetics and Genomics, Duke University Medical Center, Durham, NC USA
| | - Susan M. Rosenberg
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Systems, Synthetic and Physical Biology Graduate Program, Rice University, Houston, TX, USA
| | - Rodney Rothstein
- Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Lorraine S. Symington
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, USA
| | - Pawel Zawadzki
- NanoBioMedical Centre, Faculty of Physics, Adam Mickiewicz University, Umultowska 85, 61-614 Poznan, Poland
| | - Nayun Kim
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Michael Lisby
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Anna Malkova
- Department of Biology, University of Iowa, Iowa City, IA, USA
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Krol K, Antoniuk-Majchrzak J, Skoneczny M, Sienko M, Jendrysek J, Rumienczyk I, Halas A, Kurlandzka A, Skoneczna A. Lack of G1/S control destabilizes the yeast genome via replication stress-induced DSBs and illegitimate recombination. J Cell Sci 2018; 131:jcs.226480. [PMID: 30463853 DOI: 10.1242/jcs.226480] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 11/05/2018] [Indexed: 12/13/2022] Open
Abstract
The protein Swi6 in Saccharomyces cerevisiae is a cofactor in two complexes that regulate the transcription of the genes controlling the G1/S transition. It also ensures proper oxidative and cell wall stress responses. Previously, we found that Swi6 was crucial for the survival of genotoxic stress. Here, we show that a lack of Swi6 causes replication stress leading to double-strand break (DSB) formation, inefficient DNA repair and DNA content alterations, resulting in high cell mortality. Comparative genome hybridization experiments revealed that there was a random genome rearrangement in swi6Δ cells, whereas in diploid swi6Δ/swi6Δ cells, chromosome V is duplicated. SWI4 and PAB1, which are located on chromosome V and are known multicopy suppressors of swi6Δ phenotypes, partially reverse swi6Δ genome instability when overexpressed. Another gene on chromosome V, RAD51, also supports swi6Δ survival, but at a high cost; Rad51-dependent illegitimate recombination in swi6Δ cells appears to connect DSBs, leading to genome rearrangement and preventing cell death.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Kamil Krol
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | | | - Marek Skoneczny
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Marzena Sienko
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Justyna Jendrysek
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Izabela Rumienczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Agnieszka Halas
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Anna Kurlandzka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Adrianna Skoneczna
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
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15
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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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16
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McGinty RJ, Mirkin SM. Cis- and Trans-Modifiers of Repeat Expansions: Blending Model Systems with Human Genetics. Trends Genet 2018; 34:448-465. [PMID: 29567336 PMCID: PMC5959756 DOI: 10.1016/j.tig.2018.02.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 02/15/2018] [Accepted: 02/19/2018] [Indexed: 12/30/2022]
Abstract
Over 30 hereditary diseases are caused by the expansion of microsatellite repeats. The length of the expandable repeat is the main hereditary determinant of these disorders. They are also affected by numerous genomic variants that are either nearby (cis) or physically separated from (trans) the repetitive locus, which we review here. These genetic variants have largely been elucidated in model systems using gene knockouts, while a few have been directly observed as single-nucleotide polymorphisms (SNPs) in patients. There is a notable disconnect between these two bodies of knowledge: knockouts poorly approximate the SNP-level variation in human populations that gives rise to medically relevant cis- and trans-modifiers, while the rarity of these diseases limits the statistical power of SNP-based analysis in humans. We propose that high-throughput SNP-based screening in model systems could become a useful approach to quickly identify and characterize modifiers of clinical relevance for patients.
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Affiliation(s)
- Ryan J McGinty
- 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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Lošdorfer Božič A, Micheletti C, Podgornik R, Tubiana L. Compactness of viral genomes: effect of disperse and localized random mutations. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:084006. [PMID: 29334364 PMCID: PMC7104904 DOI: 10.1088/1361-648x/aaa7b0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 12/29/2017] [Accepted: 01/15/2018] [Indexed: 06/07/2023]
Abstract
Genomes of single-stranded RNA viruses have evolved to optimize several concurrent properties. One of them is the architecture of their genomic folds, which must not only feature precise structural elements at specific positions, but also allow for overall spatial compactness. The latter was shown to be disrupted by random synonymous mutations, a disruption which can consequently negatively affect genome encapsidation. In this study, we use three mutation schemes with different degrees of locality to mutate the genomes of phage MS2 and Brome Mosaic virus in order to understand the observed sensitivity of the global compactness of their folds. We find that mutating local stretches of their genomes' sequence or structure is less disruptive to their compactness compared to inducing randomly-distributed mutations. Our findings are indicative of a mechanism for the conservation of compactness acting on a global scale of the genomes, and have several implications for understanding the interplay between local and global architecture of viral RNA genomes.
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Affiliation(s)
- Anže Lošdorfer Božič
- Department of Theoretical Physics, Jožef Stefan Institute, SI-1000 Ljubljana, Slovenia
| | | | - Rudolf Podgornik
- Department of Theoretical Physics, Jožef Stefan Institute, SI-1000 Ljubljana, Slovenia
- Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Luca Tubiana
- Faculty of Physics, University of Vienna, A-1090 Vienna, Austria
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18
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Abstract
Eukaryotic genomes contain many repetitive DNA sequences that exhibit size instability. Some repeat elements have the added complication of being able to form secondary structures, such as hairpin loops, slipped DNA, triplex DNA or G-quadruplexes. Especially when repeat sequences are long, these DNA structures can form a significant impediment to DNA replication and repair, leading to DNA nicks, gaps, and breaks. In turn, repair or replication fork restart attempts within the repeat DNA can lead to addition or removal of repeat elements, which can sometimes lead to disease. One important DNA repair mechanism to maintain genomic integrity is recombination. Though early studies dismissed recombination as a mechanism driving repeat expansion and instability, recent results indicate that mitotic recombination is a key pathway operating within repetitive DNA. The action is two-fold: first, it is an important mechanism to repair nicks, gaps, breaks, or stalled forks to prevent chromosome fragility and protect cell health; second, recombination can cause repeat expansions or contractions, which can be deleterious. In this review, we summarize recent developments that illuminate the role of recombination in maintaining genome stability at DNA repeats.
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