1
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Brand CL, Oliver GT, Farkas IZ, Buszczak M, Levine MT. Recurrent Duplication and Diversification of a Vital DNA Repair Gene Family Across Drosophila. Mol Biol Evol 2024; 41:msae113. [PMID: 38865490 PMCID: PMC11210505 DOI: 10.1093/molbev/msae113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 05/30/2024] [Accepted: 06/04/2024] [Indexed: 06/14/2024] Open
Abstract
Maintaining genome integrity is vital for organismal survival and reproduction. Essential, broadly conserved DNA repair pathways actively preserve genome integrity. However, many DNA repair proteins evolve adaptively. Ecological forces like UV exposure are classically cited drivers of DNA repair evolution. Intrinsic forces like repetitive DNA, which also imperil genome integrity, have received less attention. We recently reported that a Drosophila melanogaster-specific DNA satellite array triggered species-specific, adaptive evolution of a DNA repair protein called Spartan/MH. The Spartan family of proteases cleave hazardous, covalent crosslinks that form between DNA and proteins ("DNA-protein crosslink repair"). Appreciating that DNA satellites are both ubiquitous and universally fast-evolving, we hypothesized that satellite DNA turnover spurs adaptive evolution of DNA-protein crosslink repair beyond a single gene and beyond the D. melanogaster lineage. This hypothesis predicts pervasive Spartan gene family diversification across Drosophila species. To study the evolutionary history of the Drosophila Spartan gene family, we conducted population genetic, molecular evolution, phylogenomic, and tissue-specific expression analyses. We uncovered widespread signals of positive selection across multiple Spartan family genes and across multiple evolutionary timescales. We also detected recurrent Spartan family gene duplication, divergence, and gene loss. Finally, we found that ovary-enriched parent genes consistently birthed functionally diverged, testis-enriched daughter genes. To account for Spartan family diversification, we introduce a novel mechanistic model of antagonistic coevolution that links DNA satellite evolution and adaptive regulation of Spartan protease activity. This framework promises to accelerate our understanding of how DNA repeats drive recurrent evolutionary innovation to preserve genome integrity.
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Affiliation(s)
- Cara L Brand
- Department of Biology and Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Genevieve T Oliver
- Department of Biology and Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Isabella Z Farkas
- Department of Biology and Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael Buszczak
- Department of Molecular Biology and Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Mia T Levine
- Department of Biology and Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
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Wade KJ, Suseno R, Kizer K, Williams J, Boquett J, Caillier S, Pollock NR, Renschen A, Santaniello A, Oksenberg JR, Norman PJ, Augusto DG, Hollenbach JA. MHConstructor: A high-throughput, haplotype-informed solution to the MHC assembly challenge. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.20.595060. [PMID: 38826378 PMCID: PMC11142050 DOI: 10.1101/2024.05.20.595060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
The extremely high levels of genetic polymorphism within the human major histocompatibility complex (MHC) limit the usefulness of reference-based alignment methods for sequence assembly. We incorporate a short read de novo assembly algorithm into a workflow for novel application to the MHC. MHConstructor is a containerized pipeline designed for high-throughput, haplotype-informed, reproducible assembly of both whole genome sequencing and target-capture short read data in large, population cohorts. To-date, no other self-contained tool exists for the generation of de novo MHC assemblies from short read data. MHConstructor facilitates wide-spread access to high quality, alignment-free MHC sequence analysis.
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Affiliation(s)
- Kristen J. Wade
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Rayo Suseno
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Kerry Kizer
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Jacqueline Williams
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Juliano Boquett
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Stacy Caillier
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Nicholas R. Pollock
- Department of Biomedical Informatics, Anschutz Medical Campus, University of Colorado, Aurora, Colorado, USA
- Department of Immunology and Microbiology, Anschutz Medical Campus, University of Colorado, Aurora, Colorado, USA
| | - Adam Renschen
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Adam Santaniello
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Jorge R. Oksenberg
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Paul J. Norman
- Department of Biomedical Informatics, Anschutz Medical Campus, University of Colorado, Aurora, Colorado, USA
- Department of Immunology and Microbiology, Anschutz Medical Campus, University of Colorado, Aurora, Colorado, USA
| | - Danillo G. Augusto
- Department of Biological Sciences, University of North Carolina Charlotte, Charlotte, NC, United States
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Jill A. Hollenbach
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, United States
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3
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Barreto-Galvez A, Niljikar M, Gagliardi J, Zhang R, Kumar V, Juruwala A, Pradeep A, Shaikh A, Tiwari P, Sharma K, Gerhardt J, Cao J, Kataoka K, Durbin A, Qi J, Ye BH, Madireddy A. Acetyl transferase EP300 deficiency leads to chronic replication stress mediated by defective fork protection at stalled replication forks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.29.538781. [PMID: 37163075 PMCID: PMC10168362 DOI: 10.1101/2023.04.29.538781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Mutations in the epigenetic regulator and global transcriptional activator, E1A binding protein (EP300), is being increasingly reported in aggressive hematological malignancies including adult T-cell leukemia/lymphoma (ATLL). However, the mechanistic contribution of EP300 dysregulation to cancer initiation and progression are currently unknown. Independent inhibition of EP300 in human cells results in the differential expression of genes involved in regulating the cell cycle, DNA replication and DNA damage response. Nevertheless, specific function played by EP300 in DNA replication initiation, progression and replication fork integrity has not been studied. Here, using ATLL cells as a model to study EP300 deficiency and an p300-selective PROTAC degrader, degrader as a pharmacologic tool, we reveal that EP300-mutated cells display prolonged cell cycle kinetics, due to pronounced dysregulations in DNA replication dynamics leading to persistent genomic instability. Aberrant DNA replication in EP300-mutated cells is characterized by elevated replication origin firing due to increased replisome pausing genome-wide. We demonstrate that EP300 deficiency results in nucleolytic degradation of nascently synthesized DNA at stalled forks due to a prominent defect in fork stabilization and protection. This in turn results in the accumulation of single stranded DNA gaps at collapsed replication forks, in EP300-deficient cells. Inhibition of Mre11 nuclease rescues the ssDNA accumulation indicating a dysregulation in downstream mechanisms that restrain nuclease activity at stalled forks. Importantly, we find that the absence of EP300 results in decreased expression of BRCA2 protein expression and a dependency on POLD3-mediated error-prone replication restart mechanisms. The overall S-phase abnormalities observed lead to under-replicated DNA in G2/M that instigates mitotic DNA synthesis. This in turn is associated with mitotic segregation defects characterized by elevated micronuclei formation, accumulation of cytosolic DNA and transmission of unrepaired inherited DNA lesions in the subsequent G1-phase in EP300-deficient cells. We demonstrate that the DNA replication dynamics of EP300-mutated cells ATLL cells recapitulate features of BRCA-deficient cancers. Altogether these results suggest that mutations in EP300 cause chronic DNA replication stress and defective replication fork restart results in persistent genomic instability that underlie aggressive chemo-resistant tumorigenesis in humans.
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4
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Stamidis N, Żylicz JJ. RNA-mediated heterochromatin formation at repetitive elements in mammals. EMBO J 2023; 42:e111717. [PMID: 36847618 PMCID: PMC10106986 DOI: 10.15252/embj.2022111717] [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: 05/20/2022] [Revised: 12/12/2022] [Accepted: 02/07/2023] [Indexed: 03/01/2023] Open
Abstract
The failure to repress transcription of repetitive genomic elements can lead to catastrophic genome instability and is associated with various human diseases. As such, multiple parallel mechanisms cooperate to ensure repression and heterochromatinization of these elements, especially during germline development and early embryogenesis. A vital question in the field is how specificity in establishing heterochromatin at repetitive elements is achieved. Apart from trans-acting protein factors, recent evidence points to a role of different RNA species in targeting repressive histone marks and DNA methylation to these sites in mammals. Here, we review recent discoveries on this topic and predominantly focus on the role of RNA methylation, piRNAs, and other localized satellite RNAs.
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Affiliation(s)
- Nikolaos Stamidis
- Novo Nordisk Foundation Center for Stem Cell Medicine, reNEW, University of Copenhagen, Copenhagen, Denmark
| | - Jan Jakub Żylicz
- Novo Nordisk Foundation Center for Stem Cell Medicine, reNEW, University of Copenhagen, Copenhagen, Denmark
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5
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Behboudi R, Nouri-Baygi M, Naghibzadeh M. RPTRF: A rapid perfect tandem repeat finder tool for DNA sequences. Biosystems 2023; 226:104869. [PMID: 36858110 DOI: 10.1016/j.biosystems.2023.104869] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 01/23/2023] [Accepted: 02/23/2023] [Indexed: 03/02/2023]
Abstract
The sequencing of eukaryotic genomes has shown that tandem repeats are abundant in their sequences. In addition to affecting some cellular processes, tandem repeats in the genome may be associated with specific diseases and have been the key to resolving criminal cases. Any tool developed for detecting tandem repeats must be accurate, fast, and useable in thousands of laboratories worldwide, including those with not very advanced computing capabilities. The proposed method, the Rapid Perfect Tandem Repeat Finder (RPTRF), minimizes the need for excess character comparison processing by indexing the input file and significantly helps to accelerate and prepare the output without artifacts by using an interval tree in the filtering section. The experiments demonstrated that the RPTRF is very fast in discovering all perfect tandem repeats of all categories of any genomic sequences. Although the detection of imperfect TRs is not the focus of the RPTRF, comparisons show that it even outperforms some other tools (in five selected gold standards) designed explicitly for this purpose. The implemented tool and how to use it are available on GitHub.
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Affiliation(s)
- Reza Behboudi
- Department of Computer Engineering, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mostafa Nouri-Baygi
- Department of Computer Engineering, Ferdowsi University of Mashhad, Mashhad, Iran.
| | - Mahmoud Naghibzadeh
- Department of Computer Engineering, Ferdowsi University of Mashhad, Mashhad, Iran
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6
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Thada V, Greenberg RA. Unpaved roads: How the DNA damage response navigates endogenous genotoxins. DNA Repair (Amst) 2022; 118:103383. [PMID: 35939975 PMCID: PMC9703833 DOI: 10.1016/j.dnarep.2022.103383] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 07/28/2022] [Accepted: 07/28/2022] [Indexed: 02/03/2023]
Abstract
Accurate DNA repair is essential for cellular and organismal homeostasis, and DNA repair defects result in genetic diseases and cancer predisposition. Several environmental factors, such as ultraviolet light, damage DNA, but many other molecules with DNA damaging potential are byproducts of normal cellular processes. In this review, we highlight some of the prominent sources of endogenous DNA damage as well as their mechanisms of repair, with a special focus on repair by the homologous recombination and Fanconi anemia pathways. We also discuss how modulating DNA damage caused by endogenous factors may augment current approaches used to treat BRCA-deficient cancers. Finally, we describe how synthetic lethal interactions may be exploited to exacerbate DNA repair deficiencies and cause selective toxicity in additional types of cancers.
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7
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Alvarez S, da Silva Almeida AC, Albero R, Biswas M, Barreto-Galvez A, Gunning TS, Shaikh A, Aparicio T, Wendorff A, Piovan E, Van Vlierberghe P, Gygi S, Gautier J, Madireddy A, A Ferrando A. Functional mapping of PHF6 complexes in chromatin remodeling, replication dynamics, and DNA repair. Blood 2022; 139:3418-3429. [PMID: 35338774 PMCID: PMC9185155 DOI: 10.1182/blood.2021014103] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 02/27/2022] [Indexed: 01/05/2023] Open
Abstract
The Plant Homeodomain 6 gene (PHF6) encodes a nucleolar and chromatin-associated leukemia tumor suppressor with proposed roles in transcription regulation. However, specific molecular mechanisms controlled by PHF6 remain rudimentarily understood. Here we show that PHF6 engages multiple nucleosome remodeling protein complexes, including nucleosome remodeling and deacetylase, SWI/SNF and ISWI factors, the replication machinery and DNA repair proteins. Moreover, after DNA damage, PHF6 localizes to sites of DNA injury, and its loss impairs the resolution of DNA breaks, with consequent accumulation of single- and double-strand DNA lesions. Native chromatin immunoprecipitation sequencing analyses show that PHF6 specifically associates with difficult-to-replicate heterochromatin at satellite DNA regions enriched in histone H3 lysine 9 trimethyl marks, and single-molecule locus-specific analyses identify PHF6 as an important regulator of genomic stability at fragile sites. These results extend our understanding of the molecular mechanisms controlling hematopoietic stem cell homeostasis and leukemia transformation by placing PHF6 at the crossroads of chromatin remodeling, replicative fork dynamics, and DNA repair.
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Affiliation(s)
- Silvia Alvarez
- Institute for Cancer Genetics, Columbia University, New York, NY
| | | | - Robert Albero
- Institute for Cancer Genetics, Columbia University, New York, NY
| | - Mayukh Biswas
- Institute for Cancer Genetics, Columbia University, New York, NY
| | | | - Thomas S Gunning
- Institute for Cancer Genetics, Columbia University, New York, NY
| | - Anam Shaikh
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ
| | - Tomas Aparicio
- Institute for Cancer Genetics, Columbia University, New York, NY
| | | | - Erich Piovan
- UOC Immunologia e Diagnostica Molecolare Oncologica, Istituto Oncologico Veneto-Istituto Di Ricovero e Cura a Carattere Scientifico (IRCCS), Padova, Italy
- Dipartimento di Scienze Chirurgiche, Oncologiche e Gastroenterologiche, Sezione di Oncologia, Università di Padova, Padova, Italy
| | - Pieter Van Vlierberghe
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Steven Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA
| | - Jean Gautier
- Institute for Cancer Genetics, Columbia University, New York, NY
- Department of Genetics and Development, College of Physicians and Surgeons, and
| | | | - Adolfo A Ferrando
- Institute for Cancer Genetics, Columbia University, New York, NY
- Department of Systems Biology, Columbia University, New York, NY; and
- Department of Pediatrics and
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
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8
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Saayman X, Esashi F. Breaking the paradigm: early insights from mammalian DNA breakomes. FEBS J 2022; 289:2409-2428. [PMID: 33792193 PMCID: PMC9451923 DOI: 10.1111/febs.15849] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 03/04/2021] [Accepted: 03/29/2021] [Indexed: 12/13/2022]
Abstract
DNA double-strand breaks (DSBs) can result from both exogenous and endogenous sources and are potentially toxic lesions to the human genome. If improperly repaired, DSBs can threaten genome integrity and contribute to premature ageing, neurodegenerative disorders and carcinogenesis. Through decades of work on genome stability, it has become evident that certain regions of the genome are inherently more prone to breakage than others, known as genome instability hotspots. Recent advancements in sequencing-based technologies now enable the profiling of genome-wide distributions of DSBs, also known as breakomes, to systematically map these instability hotspots. Here, we review the application of these technologies and their implications for our current understanding of the genomic regions most likely to drive genome instability. These breakomes ultimately highlight both new and established breakage hotspots including actively transcribed regions, loop boundaries and early-replicating regions of the genome. Further, these breakomes challenge the paradigm that DNA breakage primarily occurs in hard-to-replicate regions. With these advancements, we begin to gain insights into the biological mechanisms both invoking and protecting against genome instability.
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Affiliation(s)
- Xanita Saayman
- Sir William Dunn School of Pathology, University of Oxford, UK
| | - Fumiko Esashi
- Sir William Dunn School of Pathology, University of Oxford, UK
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9
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Zhao H, Ji Q, Wu Z, Wang S, Ren J, Yan K, Wang Z, Hu J, Chu Q, Hu H, Cai Y, Wang Q, Huang D, Ji Z, Li J, Belmonte JCI, Song M, Zhang W, Qu J, Liu GH. Destabilizing heterochromatin by APOE mediates senescence. NATURE AGING 2022; 2:303-316. [PMID: 35368774 DOI: 10.1038/s43587-022-00186-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 02/01/2022] [Indexed: 04/30/2023]
Abstract
Apolipoprotein E (APOE) is a component of lipoprotein particles that function in the homeostasis of cholesterol and other lipids. Although APOE is genetically associated with human longevity and Alzheimer's disease, its mechanistic role in aging is largely unknown. Here, we used human genetic, stress-induced and physiological cellular aging models to explore APOE-driven processes in stem cell homeostasis and aging. We report that in aged human mesenchymal progenitor cells (MPCs), APOE accumulation is a driver for cellular senescence. By contrast, CRISPR-Cas9-mediated deletion of APOE endows human MPCs with resistance to cellular senescence. Mechanistically, we discovered that APOE functions as a destabilizer for heterochromatin. Specifically, increased APOE leads to the degradation of nuclear lamina proteins and a heterochromatin-associated protein KRAB-associated protein 1 via the autophagy-lysosomal pathway, thereby disrupting heterochromatin and causing senescence. Altogether, our findings uncover a role of APOE as an epigenetic mediator of senescence and provide potential targets to ameliorate aging-related diseases.
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Affiliation(s)
- Hongkai Zhao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Science and Technology of China, Hefei, China
| | - Qianzhao Ji
- University of the Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Zeming Wu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Si Wang
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital, Capital Medical University, Beijing, China
- Chongqing Renji Hospital, University of the Chinese Academy of Sciences, Chongqing, China
| | - Jie Ren
- University of the Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- Chinese Academy of Sciences Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- China National Center for Bioinformation, Beijing, China
| | - Kaowen Yan
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Zehua Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Jianli Hu
- University of the Chinese Academy of Sciences, Beijing, China
- Chinese Academy of Sciences Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- China National Center for Bioinformation, Beijing, China
| | - Qun Chu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Huifang Hu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Yusheng Cai
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Qiaoran Wang
- University of the Chinese Academy of Sciences, Beijing, China
- Chinese Academy of Sciences Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- China National Center for Bioinformation, Beijing, China
| | - Daoyuan Huang
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Zhejun Ji
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Jingyi Li
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | | | - Moshi Song
- University of the Chinese Academy of Sciences, Beijing, China.
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China.
| | - Weiqi Zhang
- University of the Chinese Academy of Sciences, Beijing, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.
- Chinese Academy of Sciences Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
- China National Center for Bioinformation, Beijing, China.
| | - Jing Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- University of Science and Technology of China, Hefei, China.
- University of the Chinese Academy of Sciences, Beijing, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China.
| | - Guang-Hui Liu
- University of the Chinese Academy of Sciences, Beijing, China.
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China.
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital, Capital Medical University, Beijing, China.
- Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital, Capital Medical University, Beijing, China.
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10
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Pappalardo XG, Barra V. Losing DNA methylation at repetitive elements and breaking bad. Epigenetics Chromatin 2021; 14:25. [PMID: 34082816 PMCID: PMC8173753 DOI: 10.1186/s13072-021-00400-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 05/21/2021] [Indexed: 02/08/2023] Open
Abstract
Background DNA methylation is an epigenetic chromatin mark that allows heterochromatin formation and gene silencing. It has a fundamental role in preserving genome stability (including chromosome stability) by controlling both gene expression and chromatin structure. Therefore, the onset of an incorrect pattern of DNA methylation is potentially dangerous for the cells. This is particularly important with respect to repetitive elements, which constitute the third of the human genome. Main body Repetitive sequences are involved in several cell processes, however, due to their intrinsic nature, they can be a source of genome instability. Thus, most repetitive elements are usually methylated to maintain a heterochromatic, repressed state. Notably, there is increasing evidence showing that repetitive elements (satellites, long interspersed nuclear elements (LINEs), Alus) are frequently hypomethylated in various of human pathologies, from cancer to psychiatric disorders. Repetitive sequences’ hypomethylation correlates with chromatin relaxation and unscheduled transcription. If these alterations are directly involved in human diseases aetiology and how, is still under investigation. Conclusions Hypomethylation of different families of repetitive sequences is recurrent in many different human diseases, suggesting that the methylation status of these elements can be involved in preservation of human health. This provides a promising point of view towards the research of therapeutic strategies focused on specifically tuning DNA methylation of DNA repeats.
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Affiliation(s)
- Xena Giada Pappalardo
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania, 95125, Catania, Italy.,National Council of Research, Institute for Biomedical Research and Innovation (IRIB), Unit of Catania, 95125, Catania, Italy
| | - Viviana Barra
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90128, Palermo, Italy.
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11
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Replication Stress, Genomic Instability, and Replication Timing: A Complex Relationship. Int J Mol Sci 2021; 22:ijms22094764. [PMID: 33946274 PMCID: PMC8125245 DOI: 10.3390/ijms22094764] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/26/2021] [Accepted: 04/28/2021] [Indexed: 12/29/2022] Open
Abstract
The replication-timing program constitutes a key element of the organization and coordination of numerous nuclear processes in eukaryotes. This program is established at a crucial moment in the cell cycle and occurs simultaneously with the organization of the genome, thus indicating the vital significance of this process. With recent technological achievements of high-throughput approaches, a very strong link has been confirmed between replication timing, transcriptional activity, the epigenetic and mutational landscape, and the 3D organization of the genome. There is also a clear relationship between replication stress, replication timing, and genomic instability, but the extent to which they are mutually linked to each other is unclear. Recent evidence has shown that replication timing is affected in cancer cells, although the cause and consequence of this effect remain unknown. However, in-depth studies remain to be performed to characterize the molecular mechanisms of replication-timing regulation and clearly identify different cis- and trans-acting factors. The results of these studies will potentially facilitate the discovery of new therapeutic pathways, particularly for personalized medicine, or new biomarkers. This review focuses on the complex relationship between replication timing, replication stress, and genomic instability.
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12
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Willaume S, Rass E, Fontanilla-Ramirez P, Moussa A, Wanschoor P, Bertrand P. A Link between Replicative Stress, Lamin Proteins, and Inflammation. Genes (Basel) 2021; 12:genes12040552. [PMID: 33918867 PMCID: PMC8070205 DOI: 10.3390/genes12040552] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/23/2021] [Accepted: 04/08/2021] [Indexed: 12/12/2022] Open
Abstract
Double-stranded breaks (DSB), the most toxic DNA lesions, are either a consequence of cellular metabolism, programmed as in during V(D)J recombination, or induced by anti-tumoral therapies or accidental genotoxic exposure. One origin of DSB sources is replicative stress, a major source of genome instability, especially when the integrity of the replication forks is not properly guaranteed. To complete stalled replication, restarting the fork requires complex molecular mechanisms, such as protection, remodeling, and processing. Recently, a link has been made between DNA damage accumulation and inflammation. Indeed, defects in DNA repair or in replication can lead to the release of DNA fragments in the cytosol. The recognition of this self-DNA by DNA sensors leads to the production of inflammatory factors. This beneficial response activating an innate immune response and destruction of cells bearing DNA damage may be considered as a novel part of DNA damage response. However, upon accumulation of DNA damage, a chronic inflammatory cellular microenvironment may lead to inflammatory pathologies, aging, and progression of tumor cells. Progress in understanding the molecular mechanisms of DNA damage repair, replication stress, and cytosolic DNA production would allow to propose new therapeutical strategies against cancer or inflammatory diseases associated with aging. In this review, we describe the mechanisms involved in DSB repair, the replicative stress management, and its consequences. We also focus on new emerging links between key components of the nuclear envelope, the lamins, and DNA repair, management of replicative stress, and inflammation.
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13
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Balzano E, Giunta S. Centromeres under Pressure: Evolutionary Innovation in Conflict with Conserved Function. Genes (Basel) 2020; 11:E912. [PMID: 32784998 PMCID: PMC7463522 DOI: 10.3390/genes11080912] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/04/2020] [Accepted: 08/04/2020] [Indexed: 12/22/2022] Open
Abstract
Centromeres are essential genetic elements that enable spindle microtubule attachment for chromosome segregation during mitosis and meiosis. While this function is preserved across species, centromeres display an array of dynamic features, including: (1) rapidly evolving DNA; (2) wide evolutionary diversity in size, shape and organization; (3) evidence of mutational processes to generate homogenized repetitive arrays that characterize centromeres in several species; (4) tolerance to changes in position, as in the case of neocentromeres; and (5) intrinsic fragility derived by sequence composition and secondary DNA structures. Centromere drive underlies rapid centromere DNA evolution due to the "selfish" pursuit to bias meiotic transmission and promote the propagation of stronger centromeres. Yet, the origins of other dynamic features of centromeres remain unclear. Here, we review our current understanding of centromere evolution and plasticity. We also detail the mutagenic processes proposed to shape the divergent genetic nature of centromeres. Changes to centromeres are not simply evolutionary relics, but ongoing shifts that on one side promote centromere flexibility, but on the other can undermine centromere integrity and function with potential pathological implications such as genome instability.
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Affiliation(s)
- Elisa Balzano
- Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, 00185 Roma, Italy;
| | - Simona Giunta
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
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14
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Zheng T, Zhou H, Li X, Peng D, Yang Y, Zeng Y, Liu H, Ren J, Zhao Y. RBMX is required for activation of ATR on repetitive DNAs to maintain genome stability. Cell Death Differ 2020; 27:3162-3176. [PMID: 32494026 DOI: 10.1038/s41418-020-0570-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 05/15/2020] [Accepted: 05/20/2020] [Indexed: 01/11/2023] Open
Abstract
ATR is a master regulator of cell response to replication stress. Adequate activation of ATR is essential for preventing genome aberrance induced by replication defect. However, the mechanism underlying ATR activation is not fully understood. Here, we identify that RBMX is an ssDNA binding protein that orchestrates a novel pathway to activate ATR. Using super-resolution STORM, we observe that RBMX and RPA bind to adjacent but nonoverlapping sites on ssDNA in response to replication stress. RBMX then binds to and facilitates positioning of TopBP1, which activates nearby ATR associated with RPA. In addition, ATR activation by ssDNA-RBMX-TopBP1 is independent of ssDNA-dsDNA junction and 9-1-1 complex. ChIP-seq analysis reveals that RBMX/RPA are highly enriched on repetitive DNAs, which are considered as fragile sites with high replication stress. RBMX depletion leads to defective localization of TopBP1 to replication stressed sites and inadequate activation of ATR. Furthermore, cells with deficient RBMX demonstrate replication defect, leading to formation of micronuclei and a high rate of sister-chromatin exchange, indicative of genome instability. Together, the results identify a new ssDNA-RBMX-TopBP1 pathway that is specifically required for activation of ATR on repetitive DNAs. Therefore, RBMX is a key factor to ensure genome stability during replication.
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Affiliation(s)
- Tian Zheng
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Haoxian Zhou
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Xiaocui Li
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Di Peng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510006, China
| | - Yiding Yang
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Yanru Zeng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510006, China
| | - Haiying Liu
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Jian Ren
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510006, China
| | - Yong Zhao
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China. .,State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510006, China.
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15
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Raposo CJ, McElroy KA, Fuchs SM. The Epithelial adhesin 1 tandem repeat region mediates protein display through multiple mechanisms. FEMS Yeast Res 2020; 20:foaa018. [PMID: 32301985 PMCID: PMC7199969 DOI: 10.1093/femsyr/foaa018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 04/15/2020] [Indexed: 01/18/2023] Open
Abstract
The pathogenic yeast Candida glabrata is reliant on a suite of cell surface adhesins that play a variety of roles necessary for transmission, establishment and proliferation during infection. One particular adhesin, Epithelial Adhesin 1 [Epa1p], is responsible for binding to host tissue, a process which is essential for fungal propagation. Epa1p structure consists of three domains: an N-terminal intercellular binding domain responsible for epithelial cell binding, a C-terminal GPI anchor for cell wall linkage and a serine/threonine-rich linker domain connecting these terminal domains. The linker domain contains a 40-amino acid tandem repeat region, which we have found to be variable in repeat copy number between isolates from clinical sources. We hypothesized that natural variation in Epa1p repeat copy may modulate protein function. To test this, we recombinantly expressed Epa1p with various repeat copy numbers in S. cerevisiae to determine how differences in repeat copy number affect Epa1p expression, surface display and binding to human epithelial cells. Our data suggest that repeat copy number variation has pleiotropic effects, influencing gene expression, protein surface display and shedding from the cell surface of the Epa1p adhesin. This study serves to demonstrate repeat copy number variation can modulate protein function through a number of mechanisms in order to contribute to pathogenicity of C. glabrata.
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Affiliation(s)
- Colin J Raposo
- Department of Biology , Tufts University, 200 Boston Ave Suite 4700, Medford, MA, USA 01255
| | - Kyle A McElroy
- Department of Biology , Tufts University, 200 Boston Ave Suite 4700, Medford, MA, USA 01255
- Allen Discovery Center, Tufts University, 200 Boston Ave Suite 4600, Medford, MA 02155
| | - Stephen M Fuchs
- Department of Biology , Tufts University, 200 Boston Ave Suite 4700, Medford, MA, USA 01255
- Allen Discovery Center, Tufts University, 200 Boston Ave Suite 4600, Medford, MA 02155
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16
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Wang ZL, Zhu YQ, Yan Q, Yan WY, Zheng HJ, Zeng ZJ. A Chromosome-Scale Assembly of the Asian Honeybee Apis cerana Genome. Front Genet 2020; 11:279. [PMID: 32292419 PMCID: PMC7119468 DOI: 10.3389/fgene.2020.00279] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 03/09/2020] [Indexed: 11/13/2022] Open
Abstract
Apis cerana is one of the main honeybee species in artificial farming, which is widely distributed in Asian countries. The genome of A. cerana has been sequenced by several different research groups using second generation sequencing technologies. However, it is still necessary to obtain more complete and accurate genome sequences. Here we present a chromosome-scale assembly of the A. cerana genome using single-molecule real-time (SMRT) Pacific Biosciences sequencing and high-throughput chromatin conformation capture (Hi-C) genome scaffolding. The updated assembly is 215.67 Mb in size with a contig N50 of 4.49 Mb, representing an 212-fold improvement over the previous Illumina-based version. Hi-C scaffolding resulted in 16 pseudochromosomes occupying 97.85% of the assembled genome sequences. A total of 10,741 protein-coding genes were predicted and 9,627 genes were annotated. Besides, 314 new genes were identified compared to the previous version. The improved high-quality A. cerana reference genome will provide precise sequence information for biological research of A. cerana.
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Affiliation(s)
- Zi-Long Wang
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, China
| | - Yong-Qiang Zhu
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Qing Yan
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Wei-Yu Yan
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, China
| | - Hua-Jun Zheng
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Zhi-Jiang Zeng
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, China
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17
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Del Mundo IMA, Cho EJ, Dalby KN, Vasquez KM. A 'light-up' intercalator displacement assay for detection of triplex DNA stabilizers. Chem Commun (Camb) 2020; 56:1996-1999. [PMID: 31960843 PMCID: PMC7323859 DOI: 10.1039/c9cc08817b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here, we developed a coralyne-based, 'light-up' intercalator displacement assay to identify molecular stabilizers of triplex DNA using a sequence from a chromosomal breakpoint hotspot in the human c-MYC oncogene. Its potential to identify triplex DNA ligands was demonstrated using BePI and doxorubicin. Identification of triplex-interacting ligands may allow the regulation of genetic instability in human genomes.
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Affiliation(s)
- Imee M A Del Mundo
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd., Austin, TX, USA.
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18
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Role of Rad51 and DNA repair in cancer: A molecular perspective. Pharmacol Ther 2020; 208:107492. [PMID: 32001312 DOI: 10.1016/j.pharmthera.2020.107492] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/13/2020] [Accepted: 01/22/2020] [Indexed: 12/24/2022]
Abstract
The maintenance of genome integrity is essential for any organism survival and for the inheritance of traits to offspring. To the purpose, cells have developed a complex DNA repair system to defend the genetic information against both endogenous and exogenous sources of damage. Accordingly, multiple repair pathways can be aroused from the diverse forms of DNA lesions, which can be effective per se or via crosstalk with others to complete the whole DNA repair process. Deficiencies in DNA healing resulting in faulty repair and/or prolonged DNA damage can lead to genes mutations, chromosome rearrangements, genomic instability, and finally carcinogenesis and/or cancer progression. Although it might seem paradoxical, at the same time such defects in DNA repair pathways may have therapeutic implications for potential clinical practice. Here we provide an overview of the main DNA repair pathways, with special focus on the role played by homologous repair and the RAD51 recombinase protein in the cellular DNA damage response. We next discuss the recombinase structure and function per se and in combination with all its principal mediators and regulators. Finally, we conclude with an analysis of the manifold roles that RAD51 plays in carcinogenesis, cancer progression and anticancer drug resistance, and conclude this work with a survey of the most promising therapeutic strategies aimed at targeting RAD51 in experimental oncology.
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19
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Schizosaccharomyces pombe Assays to Study Mitotic Recombination Outcomes. Genes (Basel) 2020; 11:genes11010079. [PMID: 31936815 PMCID: PMC7016768 DOI: 10.3390/genes11010079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/07/2020] [Accepted: 01/07/2020] [Indexed: 01/16/2023] Open
Abstract
The fission yeast—Schizosaccharomyces pombe—has emerged as a powerful tractable system for studying DNA damage repair. Over the last few decades, several powerful in vivo genetic assays have been developed to study outcomes of mitotic recombination, the major repair mechanism of DNA double strand breaks and stalled or collapsed DNA replication forks. These assays have significantly increased our understanding of the molecular mechanisms underlying the DNA damage response pathways. Here, we review the assays that have been developed in fission yeast to study mitotic recombination.
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20
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Hijazi H, Coelho FS, Gonzaga-Jauregui C, Bernardini L, Mar SS, Manning MA, Hanson-Kahn A, Naidu S, Srivastava S, Lee JA, Jones JR, Friez MJ, Alberico T, Torres B, Fang P, Cheung SW, Song X, Davis-Williams A, Jornlin C, Wight PA, Patyal P, Taube J, Poretti A, Inoue K, Zhang F, Pehlivan D, Carvalho CMB, Hobson GM, Lupski JR. Xq22 deletions and correlation with distinct neurological disease traits in females: Further evidence for a contiguous gene syndrome. Hum Mutat 2019; 41:150-168. [PMID: 31448840 DOI: 10.1002/humu.23902] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 08/14/2019] [Accepted: 08/22/2019] [Indexed: 01/24/2023]
Abstract
Xq22 deletions that encompass PLP1 (Xq22-PLP1-DEL) are notable for variable expressivity of neurological disease traits in females ranging from a mild late-onset form of spastic paraplegia type 2 (MIM# 312920), sometimes associated with skewed X-inactivation, to an early-onset neurological disease trait (EONDT) of severe developmental delay, intellectual disability, and behavioral abnormalities. Size and gene content of Xq22-PLP1-DEL vary and were proposed as potential molecular etiologies underlying variable expressivity in carrier females where two smallest regions of overlap (SROs) were suggested to influence disease. We ascertained a cohort of eight unrelated patients harboring Xq22-PLP1-DEL and performed high-density array comparative genomic hybridization and breakpoint-junction sequencing. Molecular characterization of Xq22-PLP1-DEL from 17 cases (eight herein and nine published) revealed an overrepresentation of breakpoints that reside within repeats (11/17, ~65%) and the clustering of ~47% of proximal breakpoints in a genomic instability hotspot with characteristic non-B DNA density. These findings implicate a potential role for genomic architecture in stimulating the formation of Xq22-PLP1-DEL. The correlation of Xq22-PLP1-DEL gene content with neurological disease trait in female cases enabled refinement of the associated SROs to a single genomic interval containing six genes. Our data support the hypothesis that genes contiguous to PLP1 contribute to EONDT.
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Affiliation(s)
- Hadia Hijazi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Fernanda S Coelho
- Programa de Pós-Graduação em Genética Departmento de Biologia Geral, UFMG, Belo Horizonte, Minas Gerais, Brazil.,Instituto René Rachou, FIOCRUZ, Belo Horizonte, Minas Gerais, Brazil
| | | | - Laura Bernardini
- Medical Genetics Division, IRCCS "Casa Sollievo della Sofferenza" Foundation, San Giovanni Rotondo (FG), Italy
| | - Soe S Mar
- Department of Neurology, Washington University School of Medicine, St. Louis, Missouri
| | - Melanie A Manning
- Division of Medical Genetics, Department of Pediatrics, Stanford University School of Medicine, Palo Alto, California.,Department of Pathology, Stanford University School of Medicine, Palo Alto, California
| | - Andrea Hanson-Kahn
- Division of Medical Genetics, Department of Pediatrics, Stanford University School of Medicine, Palo Alto, California.,Department of Genetics, Stanford University School of Medicine, Palo Alto, California
| | - SakkuBai Naidu
- Departments of Neurology and Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Neurogenetics, Kennedy Krieger Institute, Baltimore, Maryland
| | | | - Jennifer A Lee
- Molecular Diagnostic Laboratory, Greenwood Genetic Center, Greenwood, South Carolina
| | - Julie R Jones
- Molecular Diagnostic Laboratory, Greenwood Genetic Center, Greenwood, South Carolina
| | - Michael J Friez
- Molecular Diagnostic Laboratory, Greenwood Genetic Center, Greenwood, South Carolina
| | - Thomas Alberico
- Nemours Biomedical Research, Nemours/Alfred I. duPont Hospital for Children, Wilmington, Delaware
| | - Barbara Torres
- Medical Genetics Division, IRCCS "Casa Sollievo della Sofferenza" Foundation, San Giovanni Rotondo (FG), Italy
| | - Ping Fang
- Clinical Genomics, WuXi NextCODE, Cambridge, Massachusetts
| | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Xiaofei Song
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Angelique Davis-Williams
- Nemours Biomedical Research, Nemours/Alfred I. duPont Hospital for Children, Wilmington, Delaware
| | - Carly Jornlin
- Nemours Biomedical Research, Nemours/Alfred I. duPont Hospital for Children, Wilmington, Delaware
| | - Patricia A Wight
- Department of Physiology and Biophysics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Pankaj Patyal
- Department of Physiology and Biophysics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Jennifer Taube
- Nemours Biomedical Research, Nemours/Alfred I. duPont Hospital for Children, Wilmington, Delaware
| | - Andrea Poretti
- Departments of Neurology and Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ken Inoue
- Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Feng Zhang
- State Key Laboratory of Genetic Engineering at School of Life Sciences, Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Section of Neurology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Grace M Hobson
- Nemours Biomedical Research, Nemours/Alfred I. duPont Hospital for Children, Wilmington, Delaware
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas.,Texas Children's Hospital, Houston, Texas
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21
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Dunn MJ, Anderson MZ. To Repeat or Not to Repeat: Repetitive Sequences Regulate Genome Stability in Candida albicans. Genes (Basel) 2019; 10:genes10110866. [PMID: 31671659 PMCID: PMC6896093 DOI: 10.3390/genes10110866] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/15/2019] [Accepted: 10/23/2019] [Indexed: 12/18/2022] Open
Abstract
Genome instability often leads to cell death but can also give rise to innovative genotypic and phenotypic variation through mutation and structural rearrangements. Repetitive sequences and chromatin architecture in particular are critical modulators of recombination and mutability. In Candida albicans, four major classes of repeats exist in the genome: telomeres, subtelomeres, the major repeat sequence (MRS), and the ribosomal DNA (rDNA) locus. Characterization of these loci has revealed how their structure contributes to recombination and either promotes or restricts sequence evolution. The mechanisms of recombination that give rise to genome instability are known for some of these regions, whereas others are generally unexplored. More recent work has revealed additional repetitive elements, including expanded gene families and centromeric repeats that facilitate recombination and genetic innovation. Together, the repeats facilitate C. albicans evolution through construction of novel genotypes that underlie C. albicans adaptive potential and promote persistence across its human host.
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Affiliation(s)
- Matthew J. Dunn
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA;
| | - Matthew Z. Anderson
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA;
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA
- Correspondence: ; Tel.: +614-247-0058
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22
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Tiwari V, Wilson DM. DNA Damage and Associated DNA Repair Defects in Disease and Premature Aging. Am J Hum Genet 2019; 105:237-257. [PMID: 31374202 PMCID: PMC6693886 DOI: 10.1016/j.ajhg.2019.06.005] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 06/05/2019] [Indexed: 12/14/2022] Open
Abstract
Genetic information is constantly being attacked by intrinsic and extrinsic damaging agents, such as reactive oxygen species, atmospheric radiation, environmental chemicals, and chemotherapeutics. If DNA modifications persist, they can adversely affect the polymerization of DNA or RNA, leading to replication fork collapse or transcription arrest, or can serve as mutagenic templates during nucleic acid synthesis reactions. To combat the deleterious consequences of DNA damage, organisms have developed complex repair networks that remove chemical modifications or aberrant base arrangements and restore the genome to its original state. Not surprisingly, inherited or sporadic defects in DNA repair mechanisms can give rise to cellular outcomes that underlie disease and aging, such as transformation, apoptosis, and senescence. In the review here, we discuss several genetic disorders linked to DNA repair defects, attempting to draw correlations between the nature of the accumulating DNA damage and the pathological endpoints, namely cancer, neurological disease, and premature aging.
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Affiliation(s)
- Vinod Tiwari
- Laboratory of Molecular Gerontology, National Institute on Aging, Intramural Research Program, National Institutes of Health, 251 Bayview Boulevard, Suite 100, Baltimore, MD 21224, USA.
| | - David M Wilson
- Laboratory of Molecular Gerontology, National Institute on Aging, Intramural Research Program, National Institutes of Health, 251 Bayview Boulevard, Suite 100, Baltimore, MD 21224, USA.
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23
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24
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Guler GD, Rosenwaks Z, Gerhardt J. Human DNA Helicase B as a Candidate for Unwinding Secondary CGG Repeat Structures at the Fragile X Mental Retardation Gene. Front Mol Neurosci 2018; 11:138. [PMID: 29760651 PMCID: PMC5936766 DOI: 10.3389/fnmol.2018.00138] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 04/04/2018] [Indexed: 12/20/2022] Open
Abstract
The fragile X syndrome (FXS) is caused by a CGG repeat expansion at the fragile X mental retardation (FMR1) gene. FMR1 alleles with more than 200 CGG repeats bear chromosomal fragility when cells experience folate deficiency. CGG repeats were reported to be able to form secondary structures, such as hairpins, in vitro. When such secondary structures are formed, repeats can lead to replication fork stalling even in the absence of any additional perturbation. Indeed, it was recently shown that the replication forks stall at the endogenous FMR1 locus in unaffected and FXS cells, suggesting the formation of secondary repeat structures at the FMR1 gene in vivo. If not dealt with properly replication fork stalling can lead to polymerase slippage and repeat expansion as well as fragile site expression. Despite the presence of repeat structures at the FMR1 locus, chromosomal fragility is only expressed under replicative stress suggesting the existence of potential molecular mechanisms that help the replication fork progress through these repeat regions. DNA helicases are known to aid replication forks progress through repetitive DNA sequences. Yet, the identity of the DNA helicase(s) responsible for unwinding the CGG repeats at FMR1 locus is not known. We found that the human DNA helicase B (HDHB) may provide an answer for this question. We used chromatin-immunoprecipitation assay to study the FMR1 region and common fragile sites (CFS), and asked whether HDHB localizes at replication forks stalled at repetitive regions even in unperturbed cells. HDHB was strongly enriched in S-phase at the repetitive DNA at CFS and FMR1 gene but not in the flanking regions. Taken together, these results suggest that HDHB functions in preventing or repairing stalled replication forks that arise in repeat-rich regions even in unperturbed cells. Furthermore, we discuss the importance and potential role of HDHB and other helicases in the resolution of secondary CGG repeat structures.
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Affiliation(s)
- Gulfem D Guler
- Celgene Quanticel Research, San Francisco, CA, United States
| | - Zev Rosenwaks
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, Cornell University, New York, NY, United States
| | - Jeannine Gerhardt
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, Cornell University, New York, NY, United States.,Department of Obstetrics and Gynecology, Weill Cornell Medicine, Cornell University, New York, NY, United States
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