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Kumari D, Lokanga RA, McCann C, Ried T, Usdin K. The fragile X locus is prone to spontaneous DNA damage that is preferentially repaired by nonhomologous end-joining to preserve genome integrity. iScience 2024; 27:108814. [PMID: 38303711 PMCID: PMC10831274 DOI: 10.1016/j.isci.2024.108814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/26/2023] [Accepted: 01/02/2024] [Indexed: 02/03/2024] Open
Abstract
A long CGG-repeat tract in the FMR1 gene induces the epigenetic silencing that causes fragile X syndrome (FXS). Epigenetic changes include H4K20 trimethylation, a heterochromatic modification frequently implicated in transcriptional silencing. Here, we report that treatment with A-196, an inhibitor of SUV420H1/H2, the enzymes responsible for H4K20 di-/trimethylation, does not affect FMR1 transcription, but does result in increased chromosomal duplications. Increased duplications were also seen in FXS cells treated with SCR7, an inhibitor of Lig4, a ligase essential for NHEJ. Our study suggests that the fragile X (FX) locus is prone to spontaneous DNA damage that is normally repaired by NHEJ. We suggest that heterochromatinization of the FX allele may be triggered, at least in part, in response to this DNA damage.
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Affiliation(s)
- Daman Kumari
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rachel Adihe Lokanga
- Section of Cancer Genomics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Cai McCann
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Thomas Ried
- Section of Cancer Genomics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Karen Usdin
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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2
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Yousuf A, Ahmed N, Qurashi A. Non-canonical DNA/RNA structures associated with the pathogenesis of Fragile X-associated tremor/ataxia syndrome and Fragile X syndrome. Front Genet 2022; 13:866021. [PMID: 36110216 PMCID: PMC9468596 DOI: 10.3389/fgene.2022.866021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 07/22/2022] [Indexed: 11/13/2022] Open
Abstract
Fragile X-associated tremor/ataxia syndrome (FXTAS) and fragile X syndrome (FXS) are primary examples of fragile X-related disorders (FXDs) caused by abnormal expansion of CGG repeats above a certain threshold in the 5′-untranslated region of the fragile X mental retardation (FMR1) gene. Both diseases have distinct clinical manifestations and molecular pathogenesis. FXTAS is a late-adult-onset neurodegenerative disorder caused by a premutation (PM) allele (CGG expansion of 55–200 repeats), resulting in FMR1 gene hyperexpression. On the other hand, FXS is a neurodevelopmental disorder that results from a full mutation (FM) allele (CGG expansions of ≥200 repeats) leading to heterochromatization and transcriptional silencing of the FMR1 gene. The main challenge is to determine how CGG repeat expansion affects the fundamentally distinct nature of FMR1 expression in FM and PM ranges. Abnormal CGG repeat expansions form a variety of non-canonical DNA and RNA structures that can disrupt various cellular processes and cause distinct effects in PM and FM alleles. Here, we review these structures and how they are related to underlying mutations and disease pathology in FXS and FXTAS. Finally, as new CGG expansions within the genome have been identified, it will be interesting to determine their implications in disease pathology and treatment.
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3
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Selectively recognizing extrahelical conformations of DNA trinucleotide repeats by a hydroxylated porphyrin ligand. Anal Chim Acta 2022; 1190:339265. [PMID: 34857129 DOI: 10.1016/j.aca.2021.339265] [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: 06/22/2021] [Revised: 10/06/2021] [Accepted: 11/08/2021] [Indexed: 11/24/2022]
Abstract
Trinucleotide repeats (TRs) with abnormal lengths and atypical folding are implicated in various neurodegenerative diseases. The least stable cytosine-cytosine (C-C) mismatches in TRs when structuring into homoduplexes/hairpins have more chance in certain sequence contexts to preferentially adopt an extrahelical (E-motif) conformation with respect to those in polarity-inverted intrahelical counterparts. Herein, we designed a trihydroxyphenyl porphyrin ligand (POH3) to meet the challenge towards resolving the E-motif conformation. POH3 exhibited a specific 2:1 binding with DNAs adopting the E-motif cytosine conformation, independent of the TRs length. The trihydroxyl pattern was very crucial to gain the E-motif selectivity over the polarity-inverted counterparts via the complementary hydrogen bonding that occurred in the minor groove. Our work first elucidates the rationale in designing ligands to selectively resolve the E-motif nucleotides within TRs.
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4
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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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Zhao X, Usdin K. (Dys)function Follows Form: Nucleic Acid Structure, Repeat Expansion, and Disease Pathology in FMR1 Disorders. Int J Mol Sci 2021; 22:ijms22179167. [PMID: 34502075 PMCID: PMC8431139 DOI: 10.3390/ijms22179167] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/17/2021] [Accepted: 08/18/2021] [Indexed: 12/26/2022] Open
Abstract
Fragile X-related disorders (FXDs), also known as FMR1 disorders, are examples of repeat expansion diseases (REDs), clinical conditions that arise from an increase in the number of repeats in a disease-specific microsatellite. In the case of FXDs, the repeat unit is CGG/CCG and the repeat tract is located in the 5' UTR of the X-linked FMR1 gene. Expansion can result in neurodegeneration, ovarian dysfunction, or intellectual disability depending on the number of repeats in the expanded allele. A growing body of evidence suggests that the mutational mechanisms responsible for many REDs share several common features. It is also increasingly apparent that in some of these diseases the pathologic consequences of expansion may arise in similar ways. It has long been known that many of the disease-associated repeats form unusual DNA and RNA structures. This review will focus on what is known about these structures, the proteins with which they interact, and how they may be related to the causative mutation and disease pathology in the FMR1 disorders.
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Affiliation(s)
- Xiaonan Zhao
- Correspondence: (X.Z.); (K.U.); Tel.: +1-301-451-6322 (X.Z.); +1-301-496-2189 (K.U.)
| | - Karen Usdin
- Correspondence: (X.Z.); (K.U.); Tel.: +1-301-451-6322 (X.Z.); +1-301-496-2189 (K.U.)
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6
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Ajjugal Y, Kolimi N, Rathinavelan T. Secondary structural choice of DNA and RNA associated with CGG/CCG trinucleotide repeat expansion rationalizes the RNA misprocessing in FXTAS. Sci Rep 2021; 11:8163. [PMID: 33854084 PMCID: PMC8046799 DOI: 10.1038/s41598-021-87097-y] [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: 10/03/2020] [Accepted: 03/22/2021] [Indexed: 11/09/2022] Open
Abstract
CGG tandem repeat expansion in the 5'-untranslated region of the fragile X mental retardation-1 (FMR1) gene leads to unusual nucleic acid conformations, hence causing genetic instabilities. We show that the number of G…G (in CGG repeat) or C…C (in CCG repeat) mismatches (other than A…T, T…A, C…G and G…C canonical base pairs) dictates the secondary structural choice of the sense and antisense strands of the FMR1 gene and their corresponding transcripts in fragile X-associated tremor/ataxia syndrome (FXTAS). The circular dichroism (CD) spectra and electrophoretic mobility shift assay (EMSA) reveal that CGG DNA (sense strand of the FMR1 gene) and its transcript favor a quadruplex structure. CD, EMSA and molecular dynamics (MD) simulations also show that more than four C…C mismatches cannot be accommodated in the RNA duplex consisting of the CCG repeat (antisense transcript); instead, it favors an i-motif conformational intermediate. Such a preference for unusual secondary structures provides a convincing justification for the RNA foci formation due to the sequestration of RNA-binding proteins to the bidirectional transcripts and the repeat-associated non-AUG translation that are observed in FXTAS. The results presented here also suggest that small molecule modulators that can destabilize FMR1 CGG DNA and RNA quadruplex structures could be promising candidates for treating FXTAS.
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Affiliation(s)
- Yogeeshwar Ajjugal
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana State, 502285, India
| | - Narendar Kolimi
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana State, 502285, India
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7
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Pan F, Zhang Y, Man VH, Roland C, Sagui C. E-motif formed by extrahelical cytosine bases in DNA homoduplexes of trinucleotide and hexanucleotide repeats. Nucleic Acids Res 2019; 46:942-955. [PMID: 29190385 PMCID: PMC5778509 DOI: 10.1093/nar/gkx1186] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Accepted: 11/13/2017] [Indexed: 12/01/2022] Open
Abstract
Atypical DNA secondary structures play an important role in expandable trinucleotide repeat (TR) and hexanucleotide repeat (HR) diseases. The cytosine mismatches in C-rich homoduplexes and hairpin stems are weakly bonded; experiments show that for certain sequences these may flip out of the helix core, forming an unusual structure termed an ‘e-motif’. We have performed molecular dynamics simulations of C-rich TR and HR DNA homoduplexes in order to characterize the conformations, stability and dynamics of formation of the e-motif, where the mismatched cytosines symmetrically flip out in the minor groove, pointing their base moieties towards the 5′-direction in each strand. TRs have two non-equivalent reading frames, (GCC)n and (CCG)n; while HRs have three: (CCCGGC)n, (CGGCCC)n, (CCCCGG)n. We define three types of pseudo basepair steps related to the mismatches and show that the e-motif is only stable in (GCC)n and (CCCGGC)n homoduplexes due to the favorable stacking of pseudo GpC steps (whose nature depends on whether TRs or HRs are involved) and the formation of hydrogen bonds between the mismatched cytosine at position i and the cytosine (TRs) or guanine (HRs) at position i − 2 along the same strand. We also characterize the extended e-motif, where all mismatched cytosines are extruded, their extra-helical stacking additionally stabilizing the homoduplexes.
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Affiliation(s)
- Feng Pan
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
| | - Yuan Zhang
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
| | - Viet Hoang Man
- 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
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8
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Repeat Instability in the Fragile X-Related Disorders: Lessons from a Mouse Model. Brain Sci 2019; 9:brainsci9030052. [PMID: 30832215 PMCID: PMC6468611 DOI: 10.3390/brainsci9030052] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 02/21/2019] [Accepted: 02/27/2019] [Indexed: 12/21/2022] Open
Abstract
The fragile X-related disorders (FXDs) are a group of clinical conditions that result primarily from an unusual mutation, the expansion of a CGG-repeat tract in exon 1 of the FMR1 gene. Mouse models are proving useful for understanding many aspects of disease pathology in these disorders. There is also reason to think that such models may be useful for understanding the molecular basis of the unusual mutation responsible for these disorders. This review will discuss what has been learnt to date about mechanisms of repeat instability from a knock-in FXD mouse model and what the implications of these findings may be for humans carrying expansion-prone FMR1 alleles.
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9
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Abu Diab M, Eiges R. The Contribution of Pluripotent Stem Cell (PSC)-Based Models to the Study of Fragile X Syndrome (FXS). Brain Sci 2019; 9:brainsci9020042. [PMID: 30769941 PMCID: PMC6406836 DOI: 10.3390/brainsci9020042] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 02/11/2019] [Accepted: 02/13/2019] [Indexed: 02/06/2023] Open
Abstract
Fragile X syndrome (FXS) is the most common heritable form of cognitive impairment. It results from a deficiency in the fragile X mental retardation protein (FMRP) due to a CGG repeat expansion in the 5′-UTR of the X-linked FMR1 gene. When CGGs expand beyond 200 copies, they lead to epigenetic gene silencing of the gene. In addition, the greater the allele size, the more likely it will become unstable and exhibit mosaicism for expansion size between and within tissues in affected individuals. The timing and mechanisms of FMR1 epigenetic gene silencing and repeat instability are far from being understood given the lack of appropriate cellular and animal models that can fully recapitulate the molecular features characteristic of the disease pathogenesis in humans. This review summarizes the data collected to date from mutant human embryonic stem cells, induced pluripotent stem cells, and hybrid fusions, and discusses their contribution to the investigation of FXS, their key limitations, and future prospects.
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Affiliation(s)
- Manar Abu Diab
- Stem Cell Research Laboratory, Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem 91031, Israel.
- School of Medicine, Hebrew University of Jerusalem, Jerusalem 9112102, Israel.
| | - Rachel Eiges
- Stem Cell Research Laboratory, Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem 91031, Israel.
- School of Medicine, Hebrew University of Jerusalem, Jerusalem 9112102, Israel.
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10
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Kumari D, Gazy I, Usdin K. Pharmacological Reactivation of the Silenced FMR1 Gene as a Targeted Therapeutic Approach for Fragile X Syndrome. Brain Sci 2019; 9:brainsci9020039. [PMID: 30759772 PMCID: PMC6406686 DOI: 10.3390/brainsci9020039] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 02/07/2019] [Accepted: 02/08/2019] [Indexed: 12/22/2022] Open
Abstract
More than ~200 CGG repeats in the 5′ untranslated region of the FMR1 gene results in transcriptional silencing and the absence of the FMR1 encoded protein, FMRP. FMRP is an RNA-binding protein that regulates the transport and translation of a variety of brain mRNAs in an activity-dependent manner. The loss of FMRP causes dysregulation of many neuronal pathways and results in an intellectual disability disorder, fragile X syndrome (FXS). Currently, there is no effective treatment for FXS. In this review, we discuss reactivation of the FMR1 gene as a potential approach for FXS treatment with an emphasis on the use of small molecules to inhibit the pathways important for gene silencing.
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Affiliation(s)
- Daman Kumari
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Inbal Gazy
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Karen Usdin
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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11
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Gazy I, Hayward B, Potapova S, Zhao X, Usdin K. Double-strand break repair plays a role in repeat instability in a fragile X mouse model. DNA Repair (Amst) 2018; 74:63-69. [PMID: 30606610 DOI: 10.1016/j.dnarep.2018.12.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 12/19/2018] [Accepted: 12/20/2018] [Indexed: 11/28/2022]
Abstract
Expansion of a CGG-repeat tract in the 5' UTR of FMR1 is responsible for the Fragile X-related disorders (FXDs), FXTAS, FXPOI and FXS. Previous work in a mouse model of these disorders has implicated proteins in the base excision and the mismatch repair (MMR) pathways in the expansion mechanism. However, the precise role of these factors in this process is not well understood. The essential role of MutLγ, a complex that plays a minor role in MMR but that is essential for resolving Holliday junctions during meiosis, raises the possibility that expansions proceed via a Holliday junction-like intermediate that is processed to generate a double-strand break (DSB). We show here in an FXD mouse model that LIG4, a ligase essential for non-homologous end-joining (NHEJ), a form of DSB repair (DSBR), protects against expansions. However, a mutation in MRE11, a nuclease that is important for several other DSBR pathways including homologous recombination (HR), has no effect on the extent of expansion. Our results suggest that the expansion pathway competes with NHEJ for the processing of a DSB intermediate. Thus, expansion likely proceeds via an NHEJ-independent DSBR pathway that may also be HR-independent.
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Affiliation(s)
- Inbal Gazy
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, United States
| | - Bruce Hayward
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, United States
| | - Svetlana Potapova
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, United States
| | - Xiaonan Zhao
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, United States
| | - Karen Usdin
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, United States.
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12
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Kingsland A, Maibaum L. DNA Base Pair Mismatches Induce Structural Changes and Alter the Free-Energy Landscape of Base Flip. J Phys Chem B 2018; 122:12251-12259. [DOI: 10.1021/acs.jpcb.8b06007] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Addie Kingsland
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Lutz Maibaum
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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13
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Pan F, Man VH, Roland C, Sagui C. Structure and Dynamics of DNA and RNA Double Helices Obtained from the CCG and GGC Trinucleotide Repeats. J Phys Chem B 2018; 122:4491-4512. [PMID: 29617130 DOI: 10.1021/acs.jpcb.8b01658] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Expansions of both GGC and CCG sequences lead to a number of expandable, trinucleotide repeat (TR) neurodegenerative diseases. Understanding of these diseases involves, among other things, the structural characterization of the atypical DNA and RNA secondary structures. We have performed molecular dynamics simulations of (GCC) n and (GGC) n homoduplexes in order to characterize their conformations, stability, and dynamics. Each TR has two reading frames, which results in eight nonequivalent RNA/DNA homoduplexes, characterized by CpG or GpC steps between the Watson-Crick base pairs. Free energy maps for the eight homoduplexes indicate that the C-mismatches prefer anti-anti conformations, while G-mismatches prefer anti-syn conformations. Comparison between three modifications of the DNA AMBER force field shows good agreement for the mismatch free energy maps. The mismatches in DNA-GCC (but not CCG) are extrahelical, forming an extended e-motif. The mismatched duplexes exhibit characteristic sequence-dependent step twist, with strong variations in the G-rich sequences and the e-motif. The distribution of Na+ is highly localized around the mismatches, especially G-mismatches. In the e-motif, there is strong Na+ binding by two G(N7) atoms belonging to the pseudo GpC step created when cytosines are extruded and by extrahelical cytosines. Finally, we used a novel technique based on fast melting by means of an infrared laser pulse to classify the relative stability of the different DNA-CCG and -GGC homoduplexes.
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Affiliation(s)
- Feng Pan
- Department of Physics , North Carolina State University , Raleigh , North Carolina 27695-8202 , United States
| | - Viet Hoang Man
- Department of Physics , North Carolina State University , Raleigh , North Carolina 27695-8202 , United States
| | - Christopher Roland
- Department of Physics , North Carolina State University , Raleigh , North Carolina 27695-8202 , United States
| | - Celeste Sagui
- Department of Physics , North Carolina State University , Raleigh , North Carolina 27695-8202 , United States
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14
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Singh A, Kukreti S. Homoduplex to i-motif structural switch exhibited by a cytosine rich strand of the MYH7 heavy chain β gene promoter at physiological pH. RSC Adv 2018; 8:34202-34214. [PMID: 35548637 PMCID: PMC9087296 DOI: 10.1039/c8ra05179h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Accepted: 09/09/2018] [Indexed: 11/21/2022] Open
Abstract
Genomic locations such as promoter, exon, intron, telomeric and non-telomeric regions are rich in GC-rich sequences with the potential to form G- and C-tetraplexes on both strands independently. Herein, we employed biophysical and biochemical methods to study a 34-mer C-rich DNA sequence of the myosin heavy chain β gene (MYH7β) promoter, namely HM34C for humans and the rabbit counterpart, RM34C, which differs from HM34C at three positions (three bases). Circular dichroism (CD), UV-thermal denaturation and native gel electrophoresis studies demonstrated that both the C-rich promoter segments form C-tetraplex (i-motif) structures. The CD studies revealed that HM34C forms the i-motif structure at acidic pH (5.2) in the presence of 0.1 M NaCl but remains unstructured at physiological pH. Interestingly, RM34C can form the stable i-motif structure in acidic as well as physiological pH. A shift in the positive peak from 280 nm to 275 nm with the increase in temperature from 4 °C to 30 °C was observed in temperature-dependent CD studies. UV-melting studies showed a biphasic transition for RM34C, indicating the existence of two structural species at neutral pH. In view of these findings we suggest that at physiological pH, the RM34C sequence exists in equilibrium between two structural motifs, i.e. the i-motif and homoduplex structure. This study may add to the understanding of the i-motif/homoduplex in equilibrium in physiological environments. Genomic locations such as promoter, exon, intron, telomeric and non-telomeric regions are rich in GC-rich sequences with the potential to form G- and C-tetraplexes on both strands independently.![]()
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Affiliation(s)
- Anju Singh
- Nucleic Acids Research Lab
- Department of Chemistry
- University of Delhi
- Delhi-110007
- India
| | - Shrikant Kukreti
- Nucleic Acids Research Lab
- Department of Chemistry
- University of Delhi
- Delhi-110007
- India
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15
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Hayward BE, Kumari D, Usdin K. Recent advances in assays for the fragile X-related disorders. Hum Genet 2017; 136:1313-1327. [PMID: 28866801 DOI: 10.1007/s00439-017-1840-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 08/24/2017] [Indexed: 12/17/2022]
Abstract
The fragile X-related disorders are a group of three clinical conditions resulting from the instability of a CGG-repeat tract at the 5' end of the FMR1 transcript. Fragile X-associated tremor/ataxia syndrome (FXTAS) and fragile X-associated primary ovarian insufficiency (FXPOI) are disorders seen in carriers of FMR1 alleles with 55-200 repeats. Female carriers of these premutation (PM) alleles are also at risk of having a child who has an FMR1 allele with >200 repeats. Most of these full mutation (FM) alleles are epigenetically silenced resulting in a deficit of the FMR1 gene product, FMRP. This results in fragile X Syndrome (FXS), the most common heritable cause of intellectual disability and autism. The diagnosis and study of these disorders is challenging, in part because the detection of alleles with large repeat numbers has, until recently, been either time-consuming or unreliable. This problem is compounded by the mosaicism for repeat length and/or DNA methylation that is frequently seen in PM and FM carriers. Furthermore, since AGG interruptions in the repeat tract affect the risk that a FM allele will be maternally transmitted, the ability to accurately detect these interruptions in female PM carriers is an additional challenge that must be met. This review will discuss some of the pros and cons of some recently described assays for these disorders, including those that detect FMRP levels directly, as well as emerging technologies that promise to improve the diagnosis of these conditions and to be useful in both basic and translational research settings.
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Affiliation(s)
- Bruce E Hayward
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, Building 8, Room 2A19, National Institutes of Health, 8 Center Drive MSC 0830, Bethesda, MD, 20892, USA
| | - Daman Kumari
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, Building 8, Room 2A19, National Institutes of Health, 8 Center Drive MSC 0830, Bethesda, MD, 20892, USA
| | - Karen Usdin
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, Building 8, Room 2A19, National Institutes of Health, 8 Center Drive MSC 0830, Bethesda, MD, 20892, USA.
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Mor-Shaked H, Eiges R. Modeling Fragile X Syndrome Using Human Pluripotent Stem Cells. Genes (Basel) 2016; 7:genes7100077. [PMID: 27690107 PMCID: PMC5083916 DOI: 10.3390/genes7100077] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 09/02/2016] [Accepted: 09/12/2016] [Indexed: 02/06/2023] Open
Abstract
Fragile X syndrome (FXS) is the most common heritable form of cognitive impairment. It results from a loss-of-function mutation by a CGG repeat expansion at the 5′ untranslated region of the X-linked fragile X mental retardation 1 (FMR1) gene. Expansion of the CGG repeats beyond 200 copies results in protein deficiency by leading to aberrant methylation of the FMR1 promoter and the switch from active to repressive histone modifications. Additionally, the CGGs become increasingly unstable, resulting in high degree of variation in expansion size between and within tissues of affected individuals. It is still unclear how the FMR1 protein (FMRP) deficiency leads to disease pathology in neurons. Nor do we know the mechanisms by which the CGG expansion results in aberrant DNA methylation, or becomes unstable in somatic cells of patients, at least in part due to the lack of appropriate animal or cellular models. This review summarizes the current contribution of pluripotent stem cells, mutant human embryonic stem cells, and patient-derived induced pluripotent stem cells to disease modeling of FXS for basic and applied research, including the development of new therapeutic approaches.
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Affiliation(s)
- Hagar Mor-Shaked
- Stem Cell Research Laboratory, Medical Genetics Institute, Shaare Zedek Medical Center Affiliated with the Hebrew University School of Medicine, Jerusalem 91031, Israel.
| | - Rachel Eiges
- Stem Cell Research Laboratory, Medical Genetics Institute, Shaare Zedek Medical Center Affiliated with the Hebrew University School of Medicine, Jerusalem 91031, Israel.
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Ups and Downs: Mechanisms of Repeat Instability in the Fragile X-Related Disorders. Genes (Basel) 2016; 7:genes7090070. [PMID: 27657135 PMCID: PMC5042400 DOI: 10.3390/genes7090070] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 08/30/2016] [Accepted: 09/13/2016] [Indexed: 02/06/2023] Open
Abstract
The Fragile X-related disorders (FXDs) are a group of clinical conditions resulting from the expansion of a CGG/CCG-repeat tract in exon 1 of the Fragile X mental retardation 1 (FMR1) gene. While expansions of the repeat tract predominate, contractions are also seen with the net result being that individuals can show extensive repeat length heterogeneity in different tissues. The mechanisms responsible for expansion and contraction are still not well understood. This review will discuss what is known about these processes and current evidence that supports a model in which expansion arises from the interaction of components of the base excision repair, mismatch repair and transcription coupled repair pathways.
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A MutSβ-Dependent Contribution of MutSα to Repeat Expansions in Fragile X Premutation Mice? PLoS Genet 2016; 12:e1006190. [PMID: 27427765 PMCID: PMC4948851 DOI: 10.1371/journal.pgen.1006190] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 06/22/2016] [Indexed: 12/11/2022] Open
Abstract
The fragile X-related disorders result from expansion of a CGG/CCG microsatellite in the 5’ UTR of the FMR1 gene. We have previously demonstrated that the MSH2/MSH3 complex, MutSβ, that is important for mismatch repair, is essential for almost all expansions in a mouse model of these disorders. Here we show that the MSH2/MSH6 complex, MutSα also contributes to the production of both germ line and somatic expansions as evidenced by the reduction in the number of expansions observed in Msh6-/- mice. This effect is not mediated via an indirect effect of the loss of MSH6 on the level of MSH3. However, since MutSβ is required for 98% of germ line expansions and almost all somatic ones, MutSα is apparently not able to efficiently substitute for MutSβ in the expansion process. Using purified human proteins we demonstrate that MutSα, like MutSβ, binds to substrates with loop-outs of the repeats and increases the thermal stability of the structures that they form. We also show that MutSα facilitates binding of MutSβ to these loop-outs. These data suggest possible models for the contribution of MutSα to repeat expansion. In addition, we show that unlike MutSβ, MutSα may also act to protect against repeat contractions in the Fmr1 gene. The repeat expansion diseases are a group of human genetic disorders that are caused by expansion of a specific microsatellite in a single affected gene. How this expansion occurs is unknown, but previous work in various models for different diseases in the group, including the fragile X-related disorders (FXDs), has implicated the mismatch repair complex MutSβ in the process. With the exception of somatic expansion in Friedreich ataxia, MutSα has not been reported to contribute to generation of expansions in other disease models. Here we show that MutSα does in fact play a role in both germ line and somatic expansions in a mouse model of the FXDs since the expansion frequency is significantly reduced in Msh6-/- mice. However, since we have previously shown that loss of MutSβ eliminates almost all expansions, MutSα is apparently not able to fully substitute for MutSβ in the expansion process. We also show here that MutSα increases the stability of the structures formed by the fragile X repeats that are thought to be the substrates for expansion and promotes binding of MutSβ to the repeats. This, together with our genetic data, suggests possible models for how MutSα and MutSβ, could co-operate to generate repeat expansions in the FXDs.
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Zhao XN, Usdin K. The transcription-coupled repair protein ERCC6/CSB also protects against repeat expansion in a mouse model of the fragile X premutation. Hum Mutat 2015; 36:482-7. [PMID: 25726753 DOI: 10.1002/humu.22777] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 02/20/2015] [Indexed: 12/31/2022]
Abstract
The fragile X-related disorders (FXDs) are members of the group of diseases known as the repeat expansion diseases. The FXDs result from expansion of an unstable CGG/CCG repeat tract in the 5' UTR of the FMR1 gene. Contractions are also seen, albeit at lower frequency. We have previously shown that ERCC6/CSB plays an auxiliary role in promoting germ line and somatic expansions in a mouse model of the FXDs. However, work in model systems of other repeat expansion diseases has suggested that CSB may protect against expansions by promoting contractions. Since FXD mice normally have such a high expansion frequency, it is possible that such a protective effect would have been masked. We thus examined the effect of the loss of CSB in an Msh2(+/-) background where the germ line expansion frequency is reduced and in an Msh2(-/-) background where expansions do not occur, but contractions do. Our data show that in addition to promoting repeat expansion, CSB does in fact protect the genome from germ line expansions in the FXD mouse model. However, it likely does so not by promoting contractions but by promoting an error-free process that preserves the parental allele.
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Affiliation(s)
- Xiao-Nan Zhao
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
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20
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Kumari D, Hayward B, Nakamura AJ, Bonner WM, Usdin K. Evidence for chromosome fragility at the frataxin locus in Friedreich ataxia. Mutat Res 2015; 781:14-21. [PMID: 26379101 PMCID: PMC4631761 DOI: 10.1016/j.mrfmmm.2015.08.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 08/14/2015] [Accepted: 08/27/2015] [Indexed: 11/18/2022]
Abstract
Friedreich ataxia (FRDA) is a member of the Repeat Expansion Diseases, a group of genetic conditions resulting from an increase/expansion in the size of a specific tandem array. FRDA results from expansion of a GAA/TTC-tract in the first intron of the frataxin gene (FXN). The disease-associated tandem repeats all form secondary structures that are thought to contribute to the propensity of the repeat to expand. The subset of these diseases that result from a CGG/CCG-repeat expansion, such as Fragile X syndrome, also express a folate-sensitive fragile site coincident with the repeat on the affected chromosome. This chromosome fragility involves the generation of chromosome/chromatid gaps or breaks, or the high frequency loss of one or both copies of the affected gene when cells are grown under folate stress or as we showed previously, in the presence of an inhibitor of the ATM checkpoint kinase. Whether Repeat Expansion Disease loci containing different repeats form similar fragile sites was not known. We show here that the region of chromosome 9 that contains the FXN locus is intrinsically prone to breakage in vivo even in control cells. However, like FXS alleles, FRDA alleles show significantly elevated levels of chromosome abnormalities in the presence of an ATM inhibitor, consistent with the formation of a fragile site.
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Affiliation(s)
- Daman Kumari
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bruce Hayward
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Asako J Nakamura
- Laboratory of Molecular Pharmacology, CCR, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - William M Bonner
- Laboratory of Molecular Pharmacology, CCR, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Karen Usdin
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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21
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Zhao XN, Kumari D, Gupta S, Wu D, Evanitsky M, Yang W, Usdin K. Mutsβ generates both expansions and contractions in a mouse model of the Fragile X-associated disorders. Hum Mol Genet 2015; 24:7087-96. [PMID: 26420841 DOI: 10.1093/hmg/ddv408] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 09/22/2015] [Indexed: 11/13/2022] Open
Abstract
Fragile X-associated disorders are Repeat Expansion Diseases that result from expansion of a CGG/CCG-repeat in the FMR1 gene. Contractions of the repeat tract also occur, albeit at lower frequency. However, these contractions can potentially modulate disease symptoms or generate an allele with repeat numbers in the normal range. Little is known about the expansion mechanism and even less about contractions. We have previously demonstrated that the mismatch repair (MMR) protein MSH2 is required for expansions in a mouse model of these disorders. Here, we show that MSH3, the MSH2-binding partner in the MutSβ complex, is required for 98% of germ line expansions and all somatic expansions in this model. In addition, we provide evidence for two different contraction mechanisms that operate in the mouse model, a MutSβ-independent one that generates small contractions and a MutSβ-dependent one that generates larger ones. We also show that MutSβ complexes formed with the repeats have altered kinetics of ATP hydrolysis relative to complexes with bona fide MMR substrates and that MutSβ increases the stability of the CCG-hairpins at physiological temperatures. These data may have important implications for our understanding of the mechanism(s) of repeat instability and for the role of MMR proteins in this process.
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Affiliation(s)
- Xiao-Nan Zhao
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology
| | - Daman Kumari
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology
| | - Shikha Gupta
- Section on Structure and Mechanisms of DNA repair, replication and recombination, Laboratory of Molecular Biology and
| | - Di Wu
- Section on Physical Biochemistry, Laboratory of Biochemistry and Genetics, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0830, USA
| | - Maya Evanitsky
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology
| | - Wei Yang
- Section on Structure and Mechanisms of DNA repair, replication and recombination, Laboratory of Molecular Biology and
| | - Karen Usdin
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology,
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22
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Le HP, Masuda Y, Tsurimoto T, Maki S, Katayama T, Furukohri A, Maki H. Short CCG repeat in huntingtin gene is an obstacle for replicative DNA polymerases, potentially hampering progression of replication fork. Genes Cells 2015; 20:817-33. [PMID: 26271349 DOI: 10.1111/gtc.12275] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 06/22/2015] [Indexed: 01/02/2023]
Abstract
Trinucleotide repeats (TNRs) are highly unstable in genomes, and their expansions are linked to human disorders. DNA replication is reported to be involved in TNR instability, but the current models are insufficient in explaining TNR expansion is induced during replication. Here, we investigated replication fork progression across huntingtin (HTT)-gene-derived fragments using an Escherichia coli oriC plasmid DNA replication system. We found most of the forks to travel smoothly across the HTT fragments even when the fragments had a pathological length of CAG/CTG repeats (approximately 120 repeats). A little fork stalling in the fragments was observed, but it occurred within a short 3'-flanking region downstream of the repeats. This region contains another short TNR, (CCG/CGG)7 , and the sense strand containing CCG repeats appeared to impede the replicative DNA polymerase Pol III. Examining the behavior of the human leading and lagging replicative polymerases Pol epsilon (hPolε) and Pol delta (hPolδ) on this sequence, we found hPolδ replicating DNA across the CCG repeats but hPolε stalling at the CCG repeats even if the secondary structure is eliminated by a single-stranded binding protein. These findings offer insights into the distinct behavior of leading and lagging polymerases at CCG/CGG repeats, which may be important for understanding the process of replication arrest and genome instability at the HTT gene.
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Affiliation(s)
- Hang Phuong Le
- Division of Systems Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, 630-0192, Nara, Japan
| | - Yuji Masuda
- Department of Genome Dynamics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, 464-8601, Japan.,Department of Toxicogenomics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Toshiki Tsurimoto
- Department of Biology, School of Sciences, Kyushu University, Fukuoka, 812-8581, Japan
| | - Satoko Maki
- Division of Systems Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, 630-0192, Nara, Japan
| | - Tsutomu Katayama
- Department of Molecular Biology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Asako Furukohri
- Division of Systems Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, 630-0192, Nara, Japan
| | - Hisaji Maki
- Division of Systems Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, 630-0192, Nara, Japan
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Lokanga RA, Senejani AG, Sweasy JB, Usdin K. Heterozygosity for a hypomorphic Polβ mutation reduces the expansion frequency in a mouse model of the Fragile X-related disorders. PLoS Genet 2015; 11:e1005181. [PMID: 25886163 PMCID: PMC4401650 DOI: 10.1371/journal.pgen.1005181] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 03/27/2015] [Indexed: 11/19/2022] Open
Abstract
The Fragile X-related disorders (FXDs) are members of the Repeat Expansion Diseases, a group of human genetic conditions resulting from expansion of a specific tandem repeat. The FXDs result from expansion of a CGG/CCG repeat tract in the 5’ UTR of the FMR1 gene. While expansion in a FXD mouse model is known to require some mismatch repair (MMR) proteins, our previous work and work in mouse models of another Repeat Expansion Disease show that early events in the base excision repair (BER) pathway play a role in the expansion process. One model for repeat expansion proposes that a non-canonical MMR process makes use of the nicks generated early in BER to load the MMR machinery that then generates expansions. However, we show here that heterozygosity for a Y265C mutation in Polβ, a key polymerase in the BER pathway, is enough to significantly reduce both the number of expansions seen in paternal gametes and the extent of somatic expansion in some tissues of the FXD mouse. These data suggest that events in the BER pathway downstream of the generation of nicks are also important for repeat expansion. Somewhat surprisingly, while the number of expansions is smaller, the average size of the residual expansions is larger than that seen in WT animals. This may have interesting implications for the mechanism by which BER generates expansions. Unstable microsatellites are responsible for a number of debilitating human diseases known as the Repeat Expansion Diseases. The unstable microsatellites, which consist of tandem arrays of short repeat units, are prone to increase in length (expand) on intergenerational transmission and during the lifetime of the individual. Unlike the typical microsatellite instability seen in disorders like Lynch syndrome that arise from mutations in mismatch repair (MMR) genes, expansions of these microsatellites are abolished when MMR is lost. However, how MMR, which normally protects the genome against microsatellite instability, actually promotes microsatellite expansions in these diseases is unknown. There is evidence to suggest that a second DNA repair process, base excision repair (BER), may be involved, but whether the nicks generated early in the BER-process are subverted by an MMR-dependent pathway that generates expansions or whether some MMR proteins contribute to a BER-based expansion process is unclear. Here we show that a mutation that reduces the activity of Polβ, an essential BER enzyme, also reduces the expansion frequency. Since Polβ is essential for key events in BER downstream of the generation of nicks, our data favor a model in which expansions occur via a BER-dependent pathway in which MMR participates.
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Affiliation(s)
- Rachel Adihe Lokanga
- Section on Gene Structure and Disease, Laboratory of Cell and molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- Department of Biochemistry, University of Cape Town Medical School, Cape Town, South Africa
| | - Alireza Ghodsi Senejani
- Departments of Therapeutic Radiology and Human Genetics, Yale University, School of Medicine, New Haven, Connecticut, United States of America
| | - Joann Balazs Sweasy
- Departments of Therapeutic Radiology and Human Genetics, Yale University, School of Medicine, New Haven, Connecticut, United States of America
| | - Karen Usdin
- Section on Gene Structure and Disease, Laboratory of Cell and molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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24
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Ng KS, Lam SL. NMR proton chemical shift prediction of C·C mismatches in B-DNA. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 252:87-93. [PMID: 25681800 DOI: 10.1016/j.jmr.2015.01.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 01/09/2015] [Accepted: 01/11/2015] [Indexed: 05/15/2023]
Abstract
Accurate prediction of DNA chemical shifts facilitates resonance assignment and allows recognition of different conformational features. Based on the nearest neighbor model and base pair replacement approach, we have determined a set of triplet chemical shift values and correction factors for predicting the proton chemical shifts of B-DNA containing an internal C·C mismatch. Our results provide a reliable chemical shift prediction with an accuracy of 0.07 ppm for non-labile protons and 0.09 ppm for labile protons. In addition, we have also shown that the correction factors for C·C mismatches can be used interchangeably with those for T·T mismatches. As a result, we have generalized a set of correction factors for predicting the flanking residue chemical shifts of pyrimidine·pyrimidine mismatches.
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Affiliation(s)
- Kui Sang Ng
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
| | - Sik Lok Lam
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
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25
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Usdin K, House NCM, Freudenreich CH. Repeat instability during DNA repair: Insights from model systems. Crit Rev Biochem Mol Biol 2015; 50:142-67. [PMID: 25608779 DOI: 10.3109/10409238.2014.999192] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The expansion of repeated sequences is the cause of over 30 inherited genetic diseases, including Huntington disease, myotonic dystrophy (types 1 and 2), fragile X syndrome, many spinocerebellar ataxias, and some cases of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Repeat expansions are dynamic, and disease inheritance and progression are influenced by the size and the rate of expansion. Thus, an understanding of the various cellular mechanisms that cooperate to control or promote repeat expansions is of interest to human health. In addition, the study of repeat expansion and contraction mechanisms has provided insight into how repair pathways operate in the context of structure-forming DNA, as well as insights into non-canonical roles for repair proteins. Here we review the mechanisms of repeat instability, with a special emphasis on the knowledge gained from the various model systems that have been developed to study this topic. We cover the repair pathways and proteins that operate to maintain genome stability, or in some cases cause instability, and the cross-talk and interactions between them.
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Affiliation(s)
- Karen Usdin
- Laboratory of Cell and Molecular Biology, NIDDK, NIH , Bethesda, MD , USA
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26
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Mata G, Luedtke NW. Fluorescent Probe for Proton-Coupled DNA Folding Revealing Slow Exchange of i-Motif and Duplex Structures. J Am Chem Soc 2015; 137:699-707. [DOI: 10.1021/ja508741u] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Guillaume Mata
- Department of Chemistry, University of Zürich, Winterthurerstrasse
190, CH-8057 Zürich, Switzerland
| | - Nathan W. Luedtke
- Department of Chemistry, University of Zürich, Winterthurerstrasse
190, CH-8057 Zürich, Switzerland
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27
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Lokanga RA, Zhao XN, Usdin K. The mismatch repair protein MSH2 is rate limiting for repeat expansion in a fragile X premutation mouse model. Hum Mutat 2014; 35:129-36. [PMID: 24130133 DOI: 10.1002/humu.22464] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 10/03/2013] [Indexed: 11/06/2022]
Abstract
Fragile X-associated tremor and ataxia syndrome, Fragile X-associated primary ovarian insufficiency, and Fragile X syndrome are Repeat Expansion Diseases caused by expansion of a CGG•CCG-repeat microsatellite in the 5 UTR of the FMR1 gene. To help understand the expansion mechanism responsible for these disorders, we have crossed mice containing∼147 CGG•CCG repeats in the endogenous murine Fmr1 gene with mice containing a null mutation in the gene encoding the mismatch repair protein MSH2. MSH2 mutations are associated with elevated levels of generalized microsatellite instability. However, we show here for the first time that in the FX mouse model, all maternally and paternally transmitted expansions require Msh2. Even the loss of one Msh2 allele reduced the intergenerational expansion frequency significantly. Msh2 is also required for all somatic expansions and loss of even one functional Msh2 allele reduced the extent of somatic expansion in some organs. Tissues with lower levels of MSH2 were more sensitive to the loss of a single Msh2 allele. This suggests that MSH2 is rate limiting for expansion in this mouse model and that MSH2 levels may be a key factor that accounts for tissue-specific differences in expansion risk.
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28
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Usdin K, Hayward BE, Kumari D, Lokanga RA, Sciascia N, Zhao XN. Repeat-mediated genetic and epigenetic changes at the FMR1 locus in the Fragile X-related disorders. Front Genet 2014; 5:226. [PMID: 25101111 PMCID: PMC4101883 DOI: 10.3389/fgene.2014.00226] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 06/29/2014] [Indexed: 01/01/2023] Open
Abstract
The Fragile X-related disorders are a group of genetic conditions that include the neurodegenerative disorder, Fragile X-associated tremor/ataxia syndrome (FXTAS), the fertility disorder, Fragile X-associated primary ovarian insufficiency (FXPOI) and the intellectual disability, Fragile X syndrome (FXS). The pathology in all these diseases is related to the number of CGG/CCG-repeats in the 5′ UTR of the Fragile X mental retardation 1 (FMR1) gene. The repeats are prone to continuous expansion and the increase in repeat number has paradoxical effects on gene expression increasing transcription on mid-sized alleles and decreasing it on longer ones. In some cases the repeats can simultaneously both increase FMR1 mRNA production and decrease the levels of the FMR1 gene product, Fragile X mental retardation 1 protein (FMRP). Since FXTAS and FXPOI result from the deleterious consequences of the expression of elevated levels of FMR1 mRNA and FXS is caused by an FMRP deficiency, the clinical picture is turning out to be more complex than once appreciated. Added complications result from the fact that increasing repeat numbers make the alleles somatically unstable. Thus many individuals have a complex mixture of different sized alleles in different cells. Furthermore, it has become apparent that the eponymous fragile site, once thought to be no more than a useful diagnostic criterion, may have clinical consequences for females who inherit chromosomes that express this site. This review will cover what is currently known about the mechanisms responsible for repeat instability, for the repeat-mediated epigenetic changes that affect expression of the FMR1 gene, and for chromosome fragility. It will also touch on what current and future options are for ameliorating some of these effects.
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Affiliation(s)
- Karen Usdin
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda MD, USA
| | - Bruce E Hayward
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda MD, USA
| | - Daman Kumari
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda MD, USA
| | - Rachel A Lokanga
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda MD, USA
| | - Nicholas Sciascia
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda MD, USA
| | - Xiao-Nan Zhao
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda MD, USA
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29
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Yudkin D, Hayward BE, Aladjem MI, Kumari D, Usdin K. Chromosome fragility and the abnormal replication of the FMR1 locus in fragile X syndrome. Hum Mol Genet 2014; 23:2940-2952. [PMID: 24419320 PMCID: PMC9109252 DOI: 10.1093/hmg/ddu006] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 12/24/2013] [Accepted: 01/08/2014] [Indexed: 08/04/2023] Open
Abstract
Fragile X Syndrome (FXS) is a learning disability seen in individuals who have >200 CGG•CCG repeats in the 5' untranslated region of the X-linked FMR1 gene. Such alleles are associated with a fragile site, FRAXA, a gap or constriction in the chromosome that is coincident with the repeat and is induced by folate stress or thymidylate synthase inhibitors like fluorodeoxyuridine (FdU). The molecular basis of the chromosome fragility is unknown. Previous work has suggested that the stable intrastrand structures formed by the repeat may be responsible, perhaps via their ability to block DNA synthesis. We have examined the replication dynamics of normal and FXS cells with and without FdU. We show here that an intrinsic problem with DNA replication exists in the FMR1 gene of individuals with FXS even in the absence of FdU. Our data suggest a model for chromosome fragility in FXS in which the repeat impairs replication from an origin of replication (ORI) immediately adjacent to the repeat. The fact that the replication problem occurs even in the absence of FdU suggests that this phenomenon may have in vivo consequences, including perhaps accounting for the loss of the X chromosome containing the fragile site that causes Turner syndrome (45, X0) in female carriers of such alleles. Our data on FRAXA may also be germane for the other FdU-inducible fragile sites in humans, that we show here share many common features with FRAXA.
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Affiliation(s)
- Dmitry Yudkin
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology,
National Institute of Diabetes, Digestive and Kidney Diseases, and
- Department of Genomic Diversity and Evolution, Institute of Molecular and
Cellular Biology SB RAS, Novosibirsk 630090,
Russia
| | - Bruce E. Hayward
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology,
National Institute of Diabetes, Digestive and Kidney Diseases, and
| | - Mirit I. Aladjem
- DNA Replication Group, Laboratory of Molecular Pharmacology, Center for Cancer
Research, National Cancer Institute, National Institutes of
Health, Bethesda, MD 20892, USA
and
| | - Daman Kumari
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology,
National Institute of Diabetes, Digestive and Kidney Diseases, and
| | - Karen Usdin
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology,
National Institute of Diabetes, Digestive and Kidney Diseases, and
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Chromatin changes in the development and pathology of the Fragile X-associated disorders and Friedreich ataxia. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1819:802-10. [PMID: 22245581 DOI: 10.1016/j.bbagrm.2011.12.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Revised: 12/22/2011] [Accepted: 12/26/2011] [Indexed: 01/11/2023]
Abstract
The Fragile X-associated disorders (FXDs) and Friedreich ataxia (FRDA) are genetic conditions resulting from expansion of a trinucleotide repeat in a region of the affected gene that is transcribed but not translated. In the case of the FXDs, pathology results from expansion of CGG•CCG-repeat tract in the 5' UTR of the FMR1 gene, while pathology in FRDA results from expansion of a GAA•TTC-repeat in intron 1 of the FXN gene. Expansion occurs during gametogenesis or early embryogenesis by a mechanism that is not well understood. Associated Expansion then produces disease pathology in various ways that are not completely understood either. In the case of the FXDs, alleles with 55-200 repeats express higher than normal levels of a transcript that is thought to be toxic, while alleles with >200 repeats are silenced. In addition, alleles with >200 repeats are associated with a cytogenetic abnormality known as a fragile site, which is apparent as a constriction or gap in the chromatin that is seen when cells are grown in presence of inhibitors of thymidylate synthase. FRDA alleles show a deficit of the FXN transcript. This review will address the role of repeat-mediated chromatin changes in these aspects of FXD and FRDA disease pathology. This article is part of a Special Issue entitled: Chromatin in time and space.
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Rojsitthisak P, Jongaroonngamsang N, Romero RM, Haworth IS. HPLC-UV, MALDI-TOF-MS and ESI-MS/MS analysis of the mechlorethamine DNA crosslink at a cytosine-cytosine mismatch pair. PLoS One 2011; 6:e20745. [PMID: 21673963 PMCID: PMC3108972 DOI: 10.1371/journal.pone.0020745] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Accepted: 05/12/2011] [Indexed: 01/19/2023] Open
Abstract
Background Mechlorethamine [ClCH2CH2N(CH3)CH2CH2Cl], a nitrogen mustard alkylating agent, has been proven to form a DNA interstrand crosslink at a cytosine-cytosine (C-C) mismatch pair using gel electrophoresis. However, the atomic connectivity of this unusual crosslink is unknown. Methodology/Principal Findings HPLC-UV, MALDI-TOF-MS, and ESI-MS/MS were used to determine the atomic connectivity of the DNA C-C crosslink formed by mechlorethamine, MALDI-TOF-MS of the HPLC-purified reaction product of mechlorethamine with the DNA duplex d[CTCACACCGTGGTTC]•d[GAACCACCGTGTGAG] (underlined bases are a C-C mismatch pair) indicated formation of an interstrand crosslink at m/z 9222.088 [M−2H+Na]+. Following enzymatic digestion of the crosslinked duplex by snake venom phosphodiesterase and calf intestinal phosphatase, ESI-MS/MS indicated the presence of dC-mech-dC [mech = CH2CH2N(CH3)CH2CH2] at m/z 269.2 [M]2+ (expected m/z 269.6, exact mass 539.27) and its hydrolytic product dC-mech-OH at m/z 329.6 [M]+ (expected m/z 329.2). Fragmentation of dC-mech-dC gave product ions at m/z 294.3 and 236.9 [M]+, which are both due to loss of the 4-amino group of cytosine (as ammonia), in addition to dC and dC+HN(CH3)CH = CH2, respectively. The presence of m/z 269.2 [M]2+ and loss of ammonia exclude crosslink formation at cytosine N4 or O2 and indicate crosslinking through cytosine N3 with formation of two quaternary ammonium ions. Conclusions Our results provide an important addition to the literature, as the first example of the use of HPLC and MS for analysis of a DNA adduct at the N3 position of cytosine.
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Affiliation(s)
- Pornchai Rojsitthisak
- Department of Food and Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand.
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32
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Furniss S, Grover N. Thermodynamic examination of the pyrophosphate sensor helix in the thiamine pyrophosphate riboswitch. RNA (NEW YORK, N.Y.) 2011; 17:710-717. [PMID: 21367973 PMCID: PMC3062181 DOI: 10.1261/rna.2263211] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2010] [Accepted: 01/17/2011] [Indexed: 05/30/2023]
Abstract
Riboswitches are functional mRNA that control gene expression. Thiamine pyrophosphate (TPP) binds to thi-box riboswitch RNA and allosterically inhibits genes that code for proteins involved in the biosynthesis and transport of thiamine. Thiamine binding to the pyrimidine sensor helix and pyrophosphate binding to the pyrophosphate sensor helix cause changes in RNA conformation that regulate gene expression. Here we examine the thermodynamic properties of the internal loop of the pyrophosphate binding domain by comparing the wild-type construct (RNA WT) with six modified 2 x 2 bulged RNA and one 2 x 2 bulged DNA. The wild-type construct retains five conserved bases of the pyrophosphate sensor domain, two of which are in the 2 x 2 bulge (C65 and G66). The RNA WT construct was among the most stable (ΔG°₃₇ = -7.7 kcal/mol) in 1 M KCl at pH 7.5. Breaking the A•G mismatch of the bulge decreases the stability of the construct ~0.5-1 kcal/mol, but does not affect magnesium binding to the RNA WT. Guanine at position 48 is important for RNA-Mg²+ interactions of the TPP-binding riboswitch at pH 7.5. In the presence of 9.5 mM magnesium at pH 5.5, the bulged RNA constructs gained an average of 1.1 kcal/mol relative to 1 M salt. Formation of a single A+•C mismatch base pair contributes about 0.5 kcal/mol at pH 5.5, whereas two tandem A+•C mismatch base pairs together contribute about 2 kcal/mol.
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Affiliation(s)
- Stephanie Furniss
- Department of Chemistry and Biochemistry, the Colorado College, Colorado Springs, Colorado 80903, USA
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Zhou J, Wei C, Jia G, Wang X, Feng Z, Li C. Formation of i-motif structure at neutral and slightly alkaline pH. MOLECULAR BIOSYSTEMS 2009; 6:580-6. [PMID: 20174686 DOI: 10.1039/b919600e] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
It is well known that oligonucleotides containing tracts cytosines can form i-motif structures under acidic conditions (pH < 7). However, whether i-motif can be formed under normal physiological cellular conditions (pH 7.0-7.5) is yet no conclusive proof. In the present work, using circular dichroism (CD), UV absorption spectroscopies and native polyacrylamide gel electrophoresis (PAGE), we provided the compelling evidence for the formation of i-motif structures by four cytosine clusters, [C(3)TA(2)](3)C(3) (HT), [C(4)G](3)C(4)TA (RET), C(2)T(3)C(2)T(4)C(2)T(3)C(2) (CTC) and GC(2)GC(3)A(4)C(6)G (Rb), at neutral and slightly alkaline pH at 4 degrees C. Furthermore, for HT, we also supplied the evidence for the formation of i-motif structure by fluorescence resonance energy transfer (FRET) and investigated its folding kinetics. The formation time constants obtained by CD and fluorescence experiments are 214 and 493 s, respectively, indicating that HT can slowly form i-motif structure at pH 7.0 and 4 degrees C. This work implies that i-motif structures may possible form in vivo.
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Affiliation(s)
- Jun Zhou
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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Richard GF, Kerrest A, Dujon B. Comparative genomics and molecular dynamics of DNA repeats in eukaryotes. Microbiol Mol Biol Rev 2008; 72:686-727. [PMID: 19052325 PMCID: PMC2593564 DOI: 10.1128/mmbr.00011-08] [Citation(s) in RCA: 323] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Repeated elements can be widely abundant in eukaryotic genomes, composing more than 50% of the human genome, for example. It is possible to classify repeated sequences into two large families, "tandem repeats" and "dispersed repeats." Each of these two families can be itself divided into subfamilies. Dispersed repeats contain transposons, tRNA genes, and gene paralogues, whereas tandem repeats contain gene tandems, ribosomal DNA repeat arrays, and satellite DNA, itself subdivided into satellites, minisatellites, and microsatellites. Remarkably, the molecular mechanisms that create and propagate dispersed and tandem repeats are specific to each class and usually do not overlap. In the present review, we have chosen in the first section to describe the nature and distribution of dispersed and tandem repeats in eukaryotic genomes in the light of complete (or nearly complete) available genome sequences. In the second part, we focus on the molecular mechanisms responsible for the fast evolution of two specific classes of tandem repeats: minisatellites and microsatellites. Given that a growing number of human neurological disorders involve the expansion of a particular class of microsatellites, called trinucleotide repeats, a large part of the recent experimental work on microsatellites has focused on these particular repeats, and thus we also review the current knowledge in this area. Finally, we propose a unified definition for mini- and microsatellites that takes into account their biological properties and try to point out new directions that should be explored in a near future on our road to understanding the genetics of repeated sequences.
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Affiliation(s)
- Guy-Franck Richard
- Institut Pasteur, Unité de Génétique Moléculaire des Levures, CNRS, URA2171, Université Pierre et Marie Curie, UFR927, 25 rue du Dr. Roux, F-75015, Paris, France.
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35
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Abstract
Accurate and complete replication of the genome in every cell division is a prerequisite of genomic stability. Thus, both prokaryotic and eukaryotic replication forks are extremely precise and robust molecular machines that have evolved to be up to the task. However, it has recently become clear that the replication fork is more of a hurdler than a runner: it must overcome various obstacles present on its way. Such obstacles can be called natural impediments to DNA replication, as opposed to external and genetic factors. Natural impediments to DNA replication are particular DNA binding proteins, unusual secondary structures in DNA, and transcription complexes that occasionally (in eukaryotes) or constantly (in prokaryotes) operate on replicating templates. This review describes the mechanisms and consequences of replication stalling at various natural impediments, with an emphasis on the role of replication stalling in genomic instability.
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Affiliation(s)
- Ekaterina V. Mirkin
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Chicago, Illinois 60607
| | - Sergei M. Mirkin
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Chicago, Illinois 60607
- Corresponding author. Present address: Department of Biology, Tufts University, Medford, MA 02155. Phone: (617) 627-4794. Fax: (617) 627-3805. E-mail:
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37
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Gray SJ, Gerhardt J, Doerfler W, Small LE, Fanning E. An origin of DNA replication in the promoter region of the human fragile X mental retardation (FMR1) gene. Mol Cell Biol 2006; 27:426-37. [PMID: 17101793 PMCID: PMC1800797 DOI: 10.1128/mcb.01382-06] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Fragile X syndrome, the most common form of inherited mental retardation in males, arises when the normally stable 5 to 50 CGG repeats in the 5' untranslated region of the fragile X mental retardation protein 1 (FMR1) gene expand to over 200, leading to DNA methylation and silencing of the FMR1 promoter. Although the events that trigger local CGG expansion remain unknown, the stability of trinucleotide repeat tracts is affected by their position relative to an origin of DNA replication in model systems. Origins of DNA replication in the FMR1 locus have not yet been described. Here, we report an origin of replication adjacent to the FMR1 promoter and CGG repeats that was identified by scanning a 35-kb region. Prereplication proteins Orc3p and Mcm4p bind to chromatin in the FMR1 initiation region in vivo. The position of the FMR1 origin relative to the CGG repeats is consistent with a role in repeat maintenance. The FMR1 origin is active in transformed cell lines, fibroblasts from healthy individuals, fibroblasts from patients with fragile X syndrome, and fetal cells as early as 8 weeks old. The potential role of the FMR1 origin in CGG tract instability is discussed.
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Affiliation(s)
- Steven J Gray
- Department of Biological Sciences and Vanderbilt-Ingram Cancer Center, , Vanderbilt University, Nashville, TN 37235-1634, USA
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Zemánek M, Kypr J, Vorlícková M. Conformational properties of DNA containing (CCA)n and (TGG)n trinucleotide repeats. Int J Biol Macromol 2005; 36:23-32. [PMID: 15896838 DOI: 10.1016/j.ijbiomac.2005.03.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2004] [Revised: 03/11/2005] [Accepted: 03/11/2005] [Indexed: 10/25/2022]
Abstract
We have used CD spectroscopy, polyacrylamide gel electrophoresis, and UV absorption spectroscopy to study conformational properties of DNA fragments containing (CCA)n and (TGG)n repeats, which are the most length-polymorphic microsatellite sequences of the human genome. The (CCA)n fragments are random single strands at neutral and alkaline pH but they fold into intramolecular intercalated cytosine tetraplexes at mildly acid pH values. More acid values stabilize intermolecular tetraplex formation. The behavior of (TGG)n repeats is more complex. They form hairpins or antiparallel homoduplexes in low salt solutions which, however, are transformed into parallel-stranded guanine tetraplexes at physiological KCl concentrations. Their molecularity depends on the repeat number: (TGG)4 associates into an octameric complex, (TGG)8 forms tetramolecular complexes. (TGG)n with odd repeat numbers (5, 7, and 9) generate bimolecular and tetramolecular tetraplexes. The only (TGG)7 folds into an intramolecular tetraplex at low KCl concentrations, which is antiparallel-stranded. Moreover, the (TGG)(n) fragments provide various mutually slipped conformers whose population increases with salt concentration and with the increasing repeat number. However, the self-structures of both strands disappear in the presence of the complementary strand because both (TGG)n and (CCA)n prefer to associate into the classical heteroduplex. We suppose that the extreme conformational variability of the DNA strands stands behind the length polymorphism which the (CCA)n/(TGG)n repeats exhibit in the human genome.
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Affiliation(s)
- Michal Zemánek
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic
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Lenzmeier BA, Freudenreich CH. Trinucleotide repeat instability: a hairpin curve at the crossroads of replication, recombination, and repair. Cytogenet Genome Res 2003; 100:7-24. [PMID: 14526162 DOI: 10.1159/000072836] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2002] [Accepted: 01/06/2003] [Indexed: 11/19/2022] Open
Abstract
The trinucleotide repeats that expand to cause human disease form hairpin structures in vitro that are proposed to be the major source of their genetic instability in vivo. If a replication fork is a train speeding along a track of double-stranded DNA, the trinucleotide repeats are a hairpin curve in the track. Experiments have demonstrated that the train can become derailed at the hairpin curve, resulting in significant damage to the track. Repair of the track often results in contractions and expansions of track length. In this review we introduce the in vitro evidence for why CTG/CAG and CCG/CGG repeats are inherently unstable and discuss how experiments in model organisms have implicated the replication, recombination and repair machinery as contributors to trinucleotide repeat instability in vivo.
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Affiliation(s)
- B A Lenzmeier
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
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40
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Greene E, Handa V, Kumari D, Usdin K. Transcription defects induced by repeat expansion: fragile X syndrome, FRAXE mental retardation, progressive myoclonus epilepsy type 1, and Friedreich ataxia. Cytogenet Genome Res 2003; 100:65-76. [PMID: 14526165 DOI: 10.1159/000072839] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2002] [Accepted: 02/06/2003] [Indexed: 11/19/2022] Open
Abstract
Fragile X mental retardation syndrome, FRAXE mental retardation, Progressive myoclonus epilepsy Type I, and Friedreich ataxia are members of a larger group of genetic disorders known as the Repeat Expansion Diseases. Unlike other members of this group, these four disorders all result from a primary defect in the initiation or elongation of transcription. In this review, we discuss current models for the relationship between the expanded repeat and the disease symptoms.
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Affiliation(s)
- E Greene
- Section on Genomic Structure and Function, Laboratory of Molecular and Cellular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0830, USA
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Völker J, Makube N, Plum GE, Klump HH, Breslauer KJ. Conformational energetics of stable and metastable states formed by DNA triplet repeat oligonucleotides: implications for triplet expansion diseases. Proc Natl Acad Sci U S A 2002; 99:14700-5. [PMID: 12417759 PMCID: PMC137482 DOI: 10.1073/pnas.222519799] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have embedded the hexameric triplet repeats (CAG)(6) and (CTG)(6) between two (GC)(3) domains to produce two 30-mer hairpins with the sequences d[(GC)(3)(CAG)(6)(GC)(3)] and d[(GC)(3)(CTG)(6)(GC)(3)]. This construct reduces the conformational space available to these repetitive DNA sequences. We find that the (CAG)(6) and (CTG)(6) repeats form stable, ordered, single-stranded structures. These structures are stabilized at 62 degrees C by an average enthalpy per base of 1.38 kcal.mol(-1) for the CAG triplet and 2.87 kcal.mol(-1) for the CTG triplet, while being entropically destabilized by 3.50 cal.K(-1).mol(-1) for the CAG triplet and 7.6 cal.K(-1).mol(-1) for the CTG triplet. Remarkably, these values correspond, respectively, to 1/3 (for CAG) and 2/3 (for CTG) of the enthalpy and entropy per base values associated with Watson-Crick base pairs. We show that the presence of the loop structure kinetically inhibits duplex formation from the two complementary 30-mer hairpins, even though the duplex is the thermodynamically more stable state. Duplex formation, however, does occur at elevated temperatures. We propose that this thermally induced formation of a more stable duplex results from thermal disruption of the single-stranded order, thereby allowing the complementary domains to associate (perhaps via "kissing hairpins"). Our melting profiles show that, once duplex formation has occurred, the hairpin intermediate state cannot be reformed, consistent with our interpretation of kinetically trapped hairpin structures. The duplex formed by the two complementary oligonucleotides does not have any unusual optical or thermodynamic properties. By contrast, the very stable structures formed by the individual single-stranded triplet repeat sequences are thermally and thermodynamically unusual. We discuss this stable, triplet repeat, single-stranded structure and its interconversion with duplex in terms of triplet expansion diseases.
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Affiliation(s)
- J Völker
- Department of Chemistry and Chemical Biology, Rutgers, State University of New Jersey, 610 Taylor Road, Piscataway 08854, USA
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42
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Fojtík P, Vorlícková M. The fragile X chromosome (GCC) repeat folds into a DNA tetraplex at neutral pH. Nucleic Acids Res 2001; 29:4684-90. [PMID: 11713318 PMCID: PMC92515 DOI: 10.1093/nar/29.22.4684] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
UV absorption and CD spectroscopy, along with polyacrylamide gel electrophoresis, were used to study conformational properties of DNA fragments containing the trinucleotide repeat (GCC)(n) (n = 4, 8 or 16), whose expansion is correlated with the fragile X chromosome syndrome. We have found that the conformational spectrum of the (GCC)(n) strand is wider than has been shown so far. (GCC)(n) strands adopt the hairpin described in the literature under a wide range of salt concentrations, but only at alkaline (>7.5) pH values. However, at neutral and slightly acid pH (GCC)(4) and (GCC)(8) strands homodimerize. Our data suggest that the homodimer is a bimolecular tetraplex formed by two parallel-oriented hairpins held together by hemi-protonated intermolecular C.C(+) pairs. The (GCC)(16) strand forms the same tetraplex intramolecularly. We further show that below pH 5 (GCC)(n) strands generate intercalated cytosine tetraplexes, whose molecularity depends on DNA strand length. They are tetramolecular with (GCC)(4), bimolecular with (GCC)(8) and monomolecular with (GCC)(16). i-Tetraplex formation is a complex and slow process. The neutral tetraplex, on the other hand, arises with fast kinetics under physiological conditions. Thus it is a conformational alternative of the (GCC)(n) strand duplex with a complementary (GGC)(n) strand.
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Affiliation(s)
- P Fojtík
- Academy of Sciences of the Czech Republic, Institute of Biophysics, Královopolská 135, CZ-61265 Brno, Czech Republic
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43
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Rojsitthisak P, Romero RM, Haworth IS. Extrahelical cytosine bases in DNA duplexes containing d[GCC](n).d[GCC](n) repeats: detection by a mechlorethamine crosslinking reaction. Nucleic Acids Res 2001; 29:4716-23. [PMID: 11713322 PMCID: PMC92524 DOI: 10.1093/nar/29.22.4716] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The cytosine-cytosine (C-C) pair is one of the least stable DNA mismatch pairs. The bases of the C-C mismatch are only weakly hydrogen bonded, and previous work has shown that, in certain sequence contexts, they can become unstacked from the core helix, and adopt an 'extrahelical' location. Here, using DNA duplexes with d[GCC](n).d[GCC](n) fragments containing C-C mismatches in a 1,4 bp relationship, we show that cytosine bases of different formal mismatch pairs can be crosslinked by mechlorethamine. For example, in the duplex d[CTCTCGCCGCCGCCGTATC].d[GATACGCCGCCGCCGAGAG], where underlined cytosine bases are present as the formal C-C mismatch pairs C(7)-C(32), C(10)-C(29) and C(13)-C(26), we show that two mechlorethamine crosslinks form between C(13) and C(29) and between C(10) and C(32), in addition to crosslinks at C(7)-C(32), C(10)-C(29) and C(13)-C(26) (we have reported previously the crosslinking of formal C-C pairs by mechlorethamine). We interpret the formation of the C(13)-C(29) and C(10)-C(32) crosslinks as evidence of an extrahelical location of the crosslinkable cytosines. Such extrahelical cytosine bases have been observed previously for a single C-C mismatch pair (in the so-called E-motif conformation). In the E-motif, the extrahelical cytosines are folded back towards the 5'-end of the duplex, consistent with our crosslinking data, and also consistent with the absence of C(7)-C(29) and C(10)-C(26) crosslinks in the current work. Hence, our data provide evidence for an extended E-motif DNA (eE-DNA) conformation in short d[GCC](n).d[GCC](n) repeat fragments, and raise the possibility that such structures might occur in much longer d[GCC](n).d[GCC](n) repeat tracts.
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Affiliation(s)
- P Rojsitthisak
- Department of Pharmaceutical Sciences, University of Southern California, 1985 Zonal Avenue, Los Angeles, CA 90089-9121, USA
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Pataskar SS, Dash D, Brahmachari SK. Progressive myoclonus epilepsy [EPM1] repeat d(CCCCGCCCCGCG)n forms folded hairpin structures at physiological pH. J Biomol Struct Dyn 2001; 19:293-305. [PMID: 11697734 DOI: 10.1080/07391102.2001.10506740] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The secondary structure of DNA has been shown to be an important component in the mechanism of expansion of the trinucleotide repeats that are associated with many neurodegenerative disorders. Recently, expansion of a dodecamer repeat, (CCCCGCCCCGCG)n upstream of cystatin B gene has been shown to be the most common mutation associated with Progressive Myoclonus Epilepsy (EPM1) of Unverricht-Lundborg type. We have investigated structure of oligonucleotides containing one, two and three copies of the EPM1 repeat sequences at physiological pH. CD spectra and anomalous faster gel electrophoretic mobilty indicates formation of intramolecularly folded structures that are formed independent of concentration. Hydroxylamine probing allowed us to identify the C residues that are involved in C.G base pairing. P1 nuclease studies elucidated the presence of unpaired regions in the folded back structures. UV melting studies show biphasic melting curves for the oligonucleotides containing two and three EPM1 repeats. Our data suggests multiple hairpin structures for two and three repeat containing oligonucleotides. In this paper we show that oligonucleotides containing EPM1 repeat adopt secondary structures that may facilitate strand slippage thereby causing the expansion.
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Affiliation(s)
- S S Pataskar
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore
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45
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Kovtun IV, Goellner G, McMurray CT. Structural features of trinucleotide repeats associated with DNA expansion. Biochem Cell Biol 2001. [DOI: 10.1139/o01-101] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The mechanism of DNA expansion is not well understood. Recent evidence from genetic, in vivo, and in vitro studies has suggested a link between the formation of alternative DNA secondary structures by trinucleotide repeat tracts and their propensity to undergo expansion. This review will focus on structural features and the mechanism of expansion relevant to human disease.Key words: expansion, hairpin, trinucleotide repeat, polymerase slippage, recombination, repair.
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46
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Gearheart L, Caswell KK, Murphy CJ. Recognition of hypermethylated triplet repeats in vitro by cationic nanoparticles. JOURNAL OF BIOMEDICAL OPTICS 2001; 6:111-115. [PMID: 11375719 DOI: 10.1117/1.1344189] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2000] [Accepted: 09/13/2000] [Indexed: 05/23/2023]
Abstract
Genomic DNA contains many higher-order structural deviations from the Watson-Crick global average. The massive expansion and hypermethylation of the duplex triplet repeat (CCG)(n)(CGG)(n) has characteristic higher-order structures that are associated with the fragile X syndrome. We have used luminescent mineral nanoparticles of protein-sized cadmium sulfide in optical assays to detect anomalous DNA structures. The photoluminescence of these particles is sensitive to the presence and nature of adsorbates. We previously found that our nanoparticles bind the fragile X repeat well but do not bind to normal double-helical DNA. In this study, we have determined that these particles are also able to detect the hypermethylated forms of these triplet repeats. Therefore, these nanoparticles may form the basis for future optical assays of higher-order DNA structures, especially those associated with human disease.
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Affiliation(s)
- L Gearheart
- University of South Carolina, Department of Chemistry and Biochemistry, 631 Sumter Street, Columbia, South Carolina 29208, USA
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47
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Mariappan SV, Silks LA, Bradbury EM, Gupta G. Fragile X DNA triplet repeats, (GCC)n, form hairpins with single hydrogen-bonded cytosine.cytosine mispairs at the CpG sites: isotope-edited nuclear magnetic resonance spectroscopy on (GCC)n with selective 15N4-labeled cytosine bases. J Mol Biol 2001; 283:111-20. [PMID: 9761677 DOI: 10.1006/jmbi.1998.1990] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Here, we provide a direct proof that the formation of hairpins by (GCC)n at the 5'-UTR of the FMR-1 gene offers a mechanism for CpG hypermethylation associated with the fragile X syndrome. For this, we have performed hetero-nuclear (15N-1H) magnetic resonance spectroscopy to probe the structure of the CpG sites in the (GCC)n hairpins that are 15N-labeled at the amino (N4) groups of specific cytosine bases. Analyses of chemical shift, pH-induced chemical exchange, and NOE pattern of the (15N-labeled) amino protons of cytosine bases reveal that the cytosine bases at the CpG sites are intrahelical and well-stacked with the neighboring G.C base-pairs in the stem of these hairpins and probably form single hydrogen-bonded C.C mispairs. Measurements of pH-dependent 1H line-width also demonstrate that the C.C mispairs are more susceptible to open-closure than the G.C base-pairs. Thus, the Cs at the CpG sites of the (GCC)n hairpin are "flipped out" more easily to the activated state than those in the corresponding Watson-Crick duplex, (GCC)n. (GGC)n and this makes the hairpin a better target for methylation by the human methyltransferase, the enzyme that methylates the Cs at the CpG sites.
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Affiliation(s)
- S V Mariappan
- Theoretical Biology and Biophysics, Los alamos National Laboratory, Los Alamos, NM 87545, USA
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48
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Saha T, Usdin K. Tetraplex formation by the progressive myoclonus epilepsy type-1 repeat: implications for instability in the repeat expansion diseases. FEBS Lett 2001; 491:184-7. [PMID: 11240124 DOI: 10.1016/s0014-5793(01)02190-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The repeat expansion diseases are a group of genetic disorders resulting from an increase in size or expansion of a specific array of tandem repeats. It has been suggested that DNA secondary structures are responsible for this expansion. If this is so, we would expect that all unstable repeats should form such structures. We show here that the unstable repeat that causes progressive myoclonus epilepsy type-1 (EPM1), like the repeats associated with other diseases in this category, forms a variety of secondary structures. However, EPM1 is unique in that tetraplexes are the only structures likely to form in long unpaired repeat tracts under physiological conditions.
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Affiliation(s)
- T Saha
- Section on Genomic Structure and Function, Laboratory of Molecular and Cellular Biology, National Institute of Diabetes and Kidney Diseases, Building 8, Room 202, National Institutes of Health, 8 CENTER DR MSC 0830, Bethesda, MD 20892-0830, USA
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49
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Romero RM, Rojsitthisak P, Haworth IS. DNA Interstrand Crosslink Formation by Mechlorethamine at a Cytosine–Cytosine Mismatch Pair: Kinetics and Sequence Dependence. Arch Biochem Biophys 2001; 386:143-53. [PMID: 11368336 DOI: 10.1006/abbi.2000.2198] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Expansion of the triplet repeat DNA sequence d[CGG]n.d[CCG]n is a characteristic of Fragile X syndrome, a human neurodegenerative disease. Stable intrastrand conformations formed by both d[CGG]n and d[CCG]n, and involving G-G and C-C mismatch pairs, respectively, are believed to be of importance in the development of the disease. We have shown previously that C-C mismatch pairs can be crosslinked covalently by mechlorethamine, a nitrogen mustard alkylating agent, and hence this reaction may be of value as a probe for conformers of d[CCG]n. To characterize the mechlorethamine C-C crosslink reaction further, here we report the kinetics and sequence dependence of formation of the crosslink species, using a series of model duplexes. The rate of reaction depends on the base sequence proximal to the C-C mismatch pair. Hence, in 19mer duplexes containing a central d[M4M3M2M1Cn1n2n3n4].d[N4N3N2N1Cm1m2m3m4] sequence, where M-m and N-n are complementary base pairs, the amount of crosslink increased with increasing G-C content of the eight base pairs neighboring the C-C mismatch and with the proximity of the G-C pairs to the C-C mismatch. Molecular dynamics simulations of the solvated duplexes provided an explanation of these data. Hence, for a C-C pair flanked by G-C base pairs the mismatched cytosine bases remain stacked within the duplex, but for a C-C pair flanked by A-T base pairs, the simulations suggested local opening of the duplex around the C-C pair, making it a less effective target for mechlorethamine.
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Affiliation(s)
- R M Romero
- Department of Pharmaceutical Sciences, University of Southern California, Los Angeles 90089-9121, USA
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50
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Richard GF, Goellner GM, McMurray CT, Haber JE. Recombination-induced CAG trinucleotide repeat expansions in yeast involve the MRE11-RAD50-XRS2 complex. EMBO J 2000; 19:2381-90. [PMID: 10811629 PMCID: PMC384364 DOI: 10.1093/emboj/19.10.2381] [Citation(s) in RCA: 113] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Recombination induced by double-strand breaks (DSBs) in yeast leads to a higher proportion of expansions to contractions than does replication-associated tract length changes. Expansions are apparently dependent on the property of the repeat array to form hairpins, since DSB repair of a CAA(87) repeat induces only contractions of the repeat sequence. DSB-repair efficiency is reduced by 40% when DNA synthesis must traverse a CAG(98) array, as compared with a CAA(87) array. These data indicate that repair- associated DNA synthesis is inhibited by secondary structures formed by CAG(98) and that these structures promote repeat expansions during DSB repair. Overexpression of Mre11p or Rad50p suppresses the inhibition of DSB repair by CAG(98) and significantly increases the average size of expansions found at the recipient locus. Both effects are dependent on the integrity of the Mre11p-Rad50p-Xrs2p complex. The Mre11 complex thus appears to be directly involved in removing CAG or CTG hairpins that arise frequently during DNA synthesis accompanying gene conversion of these trinucleotide repeats.
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Affiliation(s)
- G F Richard
- Rosenstiel Center and Department of Biology, MS029, Brandeis University, Waltham, MA 02454-9110, USA
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