1
|
Cook D, Kozmin SG, Yeh E, Petes TD, Bloom K. Dicentric chromosomes are resolved through breakage and repair at their centromeres. Chromosoma 2024; 133:117-134. [PMID: 38165460 PMCID: PMC11180013 DOI: 10.1007/s00412-023-00814-6] [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: 11/11/2023] [Accepted: 12/21/2023] [Indexed: 01/03/2024]
Abstract
Chromosomes with two centromeres provide a unique opportunity to study chromosome breakage and DNA repair using completely endogenous cellular machinery. Using a conditional transcriptional promoter to control the second centromere, we are able to activate the dicentric chromosome and follow the appearance of DNA repair products. We find that the rate of appearance of DNA repair products resulting from homology-based mechanisms exceeds the expected rate based on their limited centromere homology (340 bp) and distance from one another (up to 46.3 kb). In order to identify whether DNA breaks originate in the centromere, we introduced 12 single-nucleotide polymorphisms (SNPs) into one of the centromeres. Analysis of the distribution of SNPs in the recombinant centromeres reveals that recombination was initiated with about equal frequency within the conserved centromere DNA elements CDEII and CDEIII of the two centromeres. The conversion tracts range from about 50 bp to the full length of the homology between the two centromeres (340 bp). Breakage and repair events within and between the centromeres can account for the efficiency and distribution of DNA repair products. We propose that in addition to providing a site for kinetochore assembly, the centromere may be a point of stress relief in the face of genomic perturbations.
Collapse
Affiliation(s)
- Diana Cook
- Department of Biology, University of North Carolina Chapel Hill, Chapel Hill, NC, 27599-3280, USA
| | - Stanislav G Kozmin
- Department of Molecular Genetics & Microbiology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Elaine Yeh
- Department of Biology, University of North Carolina Chapel Hill, Chapel Hill, NC, 27599-3280, USA
| | - Thomas D Petes
- Department of Molecular Genetics & Microbiology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Kerry Bloom
- Department of Biology, University of North Carolina Chapel Hill, Chapel Hill, NC, 27599-3280, USA.
| |
Collapse
|
2
|
Showman S, Talbert PB, Xu Y, Adeyemi RO, Henikoff S. Expansion of human centromeric arrays in cells undergoing break-induced replication. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.11.566714. [PMID: 38014305 PMCID: PMC10680626 DOI: 10.1101/2023.11.11.566714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Human centromeres are located within α-satellite arrays and evolve rapidly, which can lead to individual variation in array lengths. Proposed mechanisms for such alterations in lengths are unequal cross-over between sister chromatids, gene conversion, and break-induced replication. However, the underlying molecular mechanisms responsible for the massive, complex, and homogeneous organization of centromeric arrays have not been experimentally validated. Here, we use droplet digital PCR assays to demonstrate that centromeric arrays can expand and contract within ~20 somatic cell divisions of a cell line. We find that the frequency of array variation among single-cell-derived subclones ranges from a minimum of ~7% to a maximum of ~100%. Further clonal evolution revealed that centromere expansion is favored over contraction. We find that the homologous recombination protein RAD52 and the helicase PIF1 are required for extensive array change, suggesting that centromere sequence evolution can occur via break-induced replication.
Collapse
Affiliation(s)
- Soyeon Showman
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Paul B. Talbert
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Yiling Xu
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Richard O. Adeyemi
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| |
Collapse
|
3
|
Ivessa AS, Singh S. The increase in cell death rates in caloric restricted cells of the yeast helicase mutant rrm3 is Sir complex dependent. Sci Rep 2023; 13:17832. [PMID: 37857740 PMCID: PMC10587150 DOI: 10.1038/s41598-023-45125-z] [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: 11/29/2022] [Accepted: 10/16/2023] [Indexed: 10/21/2023] Open
Abstract
Calorie restriction (CR), which is a reduction in calorie intake without malnutrition, usually extends lifespan and improves tissue integrity. This report focuses on the relationship between nuclear genomic instability and dietary-restriction and its effect on cell survival. We demonstrate that the cell survival rates of the genomic instability yeast mutant rrm3 change under metabolic restricted conditions. Rrm3 is a DNA helicase, chromosomal replication slows (and potentially stalls) in its absence with increased rates at over 1400 natural pause sites including sites within ribosomal DNA and tRNA genes. Whereas rrm3 mutant cells have lower cell death rates compared to wild type (WT) in growth medium containing normal glucose levels (i.e., 2%), under CR growth conditions cell death rates increase in the rrm3 mutant to levels, which are higher than WT. The silent-information-regulatory (Sir) protein complex and mitochondrial oxidative stress are required for the increase in cell death rates in the rrm3 mutant when cells are transferred from growth medium containing 2% glucose to CR-medium. The Rad53 checkpoint protein is highly phosphorylated in the rrm3 mutant in response to genomic instability in growth medium containing 2% glucose. Under CR, Rad53 phosphorylation is largely reduced in the rrm3 mutant in a Sir-complex dependent manner. Since CR is an adjuvant treatment during chemotherapy, which may target genomic instability in cancer cells, our studies may gain further insight into how these therapy strategies can be improved.
Collapse
Affiliation(s)
- Andreas S Ivessa
- Department of Cell Biology and Molecular Medicine, Rutgers New Jersey Medical School, Rutgers Biomedical and Health Sciences, 185 South Orange Avenue, Newark, NJ, 07101-1709, USA.
| | - Sukhwinder Singh
- Pathology and Laboratory Medicine/Flow Cytometry and Immunology Core Laboratory, Rutgers New Jersey Medical School, Rutgers Biomedical and Health Sciences, 185 South Orange Avenue, Newark, NJ, 07101-1709, USA
| |
Collapse
|
4
|
Abstract
Centromeres, the chromosomal loci where spindle fibers attach during cell division to segregate chromosomes, are typically found within satellite arrays in plants and animals. Satellite arrays have been difficult to analyze because they comprise megabases of tandem head-to-tail highly repeated DNA sequences. Much evidence suggests that centromeres are epigenetically defined by the location of nucleosomes containing the centromere-specific histone H3 variant cenH3, independently of the DNA sequences where they are located; however, the reason that cenH3 nucleosomes are generally found on rapidly evolving satellite arrays has remained unclear. Recently, long-read sequencing technology has clarified the structures of satellite arrays and sparked rethinking of how they evolve, and new experiments and analyses have helped bring both understanding and further speculation about the role these highly repeated sequences play in centromere identification.
Collapse
Affiliation(s)
- Paul B Talbert
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Steven Henikoff
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| |
Collapse
|
5
|
Narayanan A, Vadnala RN, Ganguly P, Selvakumar P, Rudramurthy SM, Prasad R, Chakrabarti A, Siddharthan R, Sanyal K. Functional and Comparative Analysis of Centromeres Reveals Clade-Specific Genome Rearrangements in Candida auris and a Chromosome Number Change in Related Species. mBio 2021; 12:e00905-21. [PMID: 33975937 PMCID: PMC8262905 DOI: 10.1128/mbio.00905-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 04/01/2021] [Indexed: 12/22/2022] Open
Abstract
The thermotolerant multidrug-resistant ascomycete Candida auris rapidly emerged since 2009 causing systemic infections worldwide and simultaneously evolved in different geographical zones. The molecular events that orchestrated this sudden emergence of the killer fungus remain mostly elusive. Here, we identify centromeres in C. auris and related species, using a combined approach of chromatin immunoprecipitation and comparative genomic analyses. We find that C. auris and multiple other species in the Clavispora/Candida clade shared a conserved small regional GC-poor centromere landscape lacking pericentromeres or repeats. Further, a centromere inactivation event led to karyotypic alterations in this species complex. Interspecies genome analysis identified several structural chromosomal changes around centromeres. In addition, centromeres are found to be rapidly evolving loci among the different geographical clades of the same species of C. auris Finally, we reveal an evolutionary trajectory of the unique karyotype associated with clade 2 that consists of the drug-susceptible isolates of C. aurisIMPORTANCECandida auris, the killer fungus, emerged as different geographical clades, exhibiting multidrug resistance and high karyotype plasticity. Chromosomal rearrangements are known to play key roles in the emergence of new species, virulence, and drug resistance in pathogenic fungi. Centromeres, the genomic loci where microtubules attach to separate the sister chromatids during cell division, are known to be hot spots of breaks and downstream rearrangements. We identified the centromeres in C. auris and related species to study their involvement in the evolution and karyotype diversity reported in C. auris We report conserved centromere features in 10 related species and trace the events that occurred at the centromeres during evolution. We reveal a centromere inactivation-mediated chromosome number change in these closely related species. We also observe that one of the geographical clades, the East Asian clade, evolved along a unique trajectory, compared to the other clades and related species.
Collapse
Affiliation(s)
- Aswathy Narayanan
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Rakesh Netha Vadnala
- Computational Biology, The Institute of Mathematical Sciences/HBNI, Chennai, India
| | - Promit Ganguly
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Pavitra Selvakumar
- Computational Biology, The Institute of Mathematical Sciences/HBNI, Chennai, India
| | - Shivaprakash M Rudramurthy
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Rajendra Prasad
- Amity Institute of Biotechnology, Amity University Haryana, Haryana, India
| | - Arunaloke Chakrabarti
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Rahul Siddharthan
- Computational Biology, The Institute of Mathematical Sciences/HBNI, Chennai, India
| | - Kaustuv Sanyal
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
- Osaka University, Suita, Japan
| |
Collapse
|
6
|
Cook D, Long S, Stanton J, Cusick P, Lawrimore C, Yeh E, Grant S, Bloom K. Behavior of dicentric chromosomes in budding yeast. PLoS Genet 2021; 17:e1009442. [PMID: 33735169 PMCID: PMC8009378 DOI: 10.1371/journal.pgen.1009442] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 03/30/2021] [Accepted: 02/24/2021] [Indexed: 12/15/2022] Open
Abstract
DNA double-strand breaks arise in vivo when a dicentric chromosome (two centromeres on one chromosome) goes through mitosis with the two centromeres attached to opposite spindle pole bodies. Repair of the DSBs generates phenotypic diversity due to the range of monocentric derivative chromosomes that arise. To explore whether DSBs may be differentially repaired as a function of their spatial position in the chromosome, we have examined the structure of monocentric derivative chromosomes from cells containing a suite of dicentric chromosomes in which the distance between the two centromeres ranges from 6.5 kb to 57.7 kb. Two major classes of repair products, homology-based (homologous recombination (HR) and single-strand annealing (SSA)) and end-joining (non-homologous (NHEJ) and micro-homology mediated (MMEJ)) were identified. The distribution of repair products varies as a function of distance between the two centromeres. Genetic dependencies on double strand break repair (Rad52), DNA ligase (Lif1), and S phase checkpoint (Mrc1) are indicative of distinct repair pathway choices for DNA breaks in the pericentromeric chromatin versus the arms. A challenge in chromosome biology is to integrate the linear code with spatial organization and chromosome dynamics within the nucleus. The major sub-division of function in the nucleus is the nucleolus, the site of ribosomal RNA synthesis. We report that the pericentromere DNA surrounding the centromere is another region of confined biochemistry. We have found that chromosome breaks between two centromeres that both lie within the pericentromeric region of the chromosomes are repaired via pathways that do not rely on sequence homology (MMEJ or NHEJ). Chromosome breaks in dicentric chromosomes whose centromeres are separated by > 20 kb are repaired via pathways that rely mainly on sequence homology (HR, SSA). The repair of breaks in the pericentromere versus breaks in the arms are differentially dependent on Rad52, Lif1, and Mrc1, further indicative of spatial control over DNA repair pathways.
Collapse
Affiliation(s)
- Diana Cook
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Sarah Long
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - John Stanton
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Patrick Cusick
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Colleen Lawrimore
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Elaine Yeh
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Sarah Grant
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Kerry Bloom
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail:
| |
Collapse
|
7
|
Kara N, Krueger F, Rugg-Gunn P, Houseley J. Genome-wide analysis of DNA replication and DNA double-strand breaks using TrAEL-seq. PLoS Biol 2021; 19:e3000886. [PMID: 33760805 PMCID: PMC8021198 DOI: 10.1371/journal.pbio.3000886] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 04/05/2021] [Accepted: 02/17/2021] [Indexed: 02/07/2023] Open
Abstract
Faithful replication of the entire genome requires replication forks to copy large contiguous tracts of DNA, and sites of persistent replication fork stalling present a major threat to genome stability. Understanding the distribution of sites at which replication forks stall, and the ensuing fork processing events, requires genome-wide methods that profile replication fork position and the formation of recombinogenic DNA ends. Here, we describe Transferase-Activated End Ligation sequencing (TrAEL-seq), a method that captures single-stranded DNA 3' ends genome-wide and with base pair resolution. TrAEL-seq labels both DNA breaks and replication forks, providing genome-wide maps of replication fork progression and fork stalling sites in yeast and mammalian cells. Replication maps are similar to those obtained by Okazaki fragment sequencing; however, TrAEL-seq is performed on asynchronous populations of wild-type cells without incorporation of labels, cell sorting, or biochemical purification of replication intermediates, rendering TrAEL-seq far simpler and more widely applicable than existing replication fork direction profiling methods. The specificity of TrAEL-seq for DNA 3' ends also allows accurate detection of double-strand break sites after the initiation of DNA end resection, which we demonstrate by genome-wide mapping of meiotic double-strand break hotspots in a dmc1Δ mutant that is competent for end resection but not strand invasion. Overall, TrAEL-seq provides a flexible and robust methodology with high sensitivity and resolution for studying DNA replication and repair, which will be of significant use in determining mechanisms of genome instability.
Collapse
Affiliation(s)
- Neesha Kara
- Epigenetics Programme, Babraham Institute, Cambridge, United Kingdom
| | - Felix Krueger
- Babraham Bioinformatics, Babraham Institute, Cambridge, United Kingdom
| | - Peter Rugg-Gunn
- Epigenetics Programme, Babraham Institute, Cambridge, United Kingdom
| | - Jonathan Houseley
- Epigenetics Programme, Babraham Institute, Cambridge, United Kingdom
| |
Collapse
|
8
|
Pérez-Arnaiz P, Dattani A, Smith V, Allers T. Haloferax volcanii-a model archaeon for studying DNA replication and repair. Open Biol 2020; 10:200293. [PMID: 33259746 PMCID: PMC7776575 DOI: 10.1098/rsob.200293] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 11/09/2020] [Indexed: 12/16/2022] Open
Abstract
The tree of life shows the relationship between all organisms based on their common ancestry. Until 1977, it comprised two major branches: prokaryotes and eukaryotes. Work by Carl Woese and other microbiologists led to the recategorization of prokaryotes and the proposal of three primary domains: Eukarya, Bacteria and Archaea. Microbiological, genetic and biochemical techniques were then needed to study the third domain of life. Haloferax volcanii, a halophilic species belonging to the phylum Euryarchaeota, has provided many useful tools to study Archaea, including easy culturing methods, genetic manipulation and phenotypic screening. This review will focus on DNA replication and DNA repair pathways in H. volcanii, how this work has advanced our knowledge of archaeal cellular biology, and how it may deepen our understanding of bacterial and eukaryotic processes.
Collapse
Affiliation(s)
| | | | | | - Thorsten Allers
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, UK
| |
Collapse
|
9
|
Guin K, Sreekumar L, Sanyal K. Implications of the Evolutionary Trajectory of Centromeres in the Fungal Kingdom. Annu Rev Microbiol 2020; 74:835-853. [PMID: 32706633 DOI: 10.1146/annurev-micro-011720-122512] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Chromosome segregation during the cell cycle is an evolutionarily conserved, fundamental biological process. Dynamic interaction between spindle microtubules and the kinetochore complex that assembles on centromere DNA is required for faithful chromosome segregation. The first artificial minichromosome was constructed by cloning the centromere DNA of the budding yeast Saccharomyces cerevisiae. Since then, centromeres have been identified in >60 fungal species. The DNA sequence and organization of the sequence elements are highly diverse across these fungal centromeres. In this article, we provide a comprehensive view of the evolution of fungal centromeres. Studies of this process facilitated the identification of factors influencing centromere specification, maintenance, and propagation through many generations. Additionally, we discuss the unique features and plasticity of centromeric chromatin and the involvement of centromeres in karyotype evolution. Finally, we discuss the implications of recurrent loss of RNA interference (RNAi) and/or heterochromatin components on the trajectory of the evolution of fungal centromeres and propose the centromere structure of the last common ancestor of three major fungal phyla-Ascomycota, Basidiomycota, and Mucoromycota.
Collapse
Affiliation(s)
- Krishnendu Guin
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, Karnataka 560064, India; , ,
| | - Lakshmi Sreekumar
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, Karnataka 560064, India; , ,
| | - Kaustuv Sanyal
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, Karnataka 560064, India; , ,
| |
Collapse
|
10
|
Ahmed Ezzat H, Price C. Characterisation of unessential genes required for survival under conditions of DNA stress. J Genet Eng Biotechnol 2020; 18:14. [PMID: 32372157 PMCID: PMC7201005 DOI: 10.1186/s43141-020-00025-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 03/11/2020] [Indexed: 11/10/2022]
Abstract
BACKGROUND Genomic instability is a hallmark of cancer. Cancer progression depends on the development and amplification of mutations that alter the cellular response to threats to the genome. This can lead to DNA replication stress and the potential loss of genetic integrity of the newly formed cells. This study utilised fission yeast to map the interactions occurring in some of the most crucial pathways in both DNA replication and checkpoint monitoring involving Rad4, the Schizosaccharomyces pombe (S. pombe) TopBP1 homologue. We have modelled conditions of replication stress in the genetically tractable fission yeast, S. pombe using the hypomorphic rad4-116 allele. Synthetic genetic analysis was used to identify processes required for cell survival under conditions of DNA replication stress. With the aim of mapping the genetic interactions of rad4 and its mutant allele, rad4-116, several genes that could have an interaction with rad4 during replication stress have emerged as attractive. RESULTS Interactions with genes involved in chromatin remodelling, such as hip1, and replication fork stalling resolution, such as mrc1, swi1 and swi3 were explored and confirmed. The interactions of Rad4 with each of the genes provided separate and distinct tumour formation pathways, as evident in the synthetically lethal interactions. Even within the same complex, rad4-116 double mutants behaved differently proving that Rad4 interacts at different levels and functions with the same proteins. CONCLUSION Results from this study provide a novel view of the rad4 interactions, the association of Rad4 with the replisome. The study also provides the groundwork on a theoretical and practical level for the exploration and separation of interactions of TopBP1 with the histone chaperone family and the replisome.
Collapse
Affiliation(s)
- Hassan Ahmed Ezzat
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, UK.
| | - Clive Price
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, UK
| |
Collapse
|
11
|
Talbert PB, Henikoff S. What makes a centromere? Exp Cell Res 2020; 389:111895. [PMID: 32035948 DOI: 10.1016/j.yexcr.2020.111895] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 01/18/2020] [Accepted: 02/05/2020] [Indexed: 12/26/2022]
Abstract
Centromeres are the eukaryotic chromosomal sites at which the kinetochore forms and attaches to spindle microtubules to orchestrate chromosomal segregation in mitosis and meiosis. Although centromeres are essential for cell division, their sequences are not conserved and evolve rapidly. Centromeres vary dramatically in size and organization. Here we categorize their diversity and explore the evolutionary forces shaping them. Nearly all centromeres favor AT-rich DNA that is gene-free and transcribed at a very low level. Repair of frequent centromere-proximal breaks probably contributes to their rapid sequence evolution. Point centromeres are only ~125 bp and are specified by common protein-binding motifs, whereas short regional centromeres are 1-5 kb, typically have unique sequences, and may have pericentromeric repeats adapted to facilitate centromere clustering. Transposon-rich centromeres are often ~100-300 kb and are favored by RNAi machinery that silences transposons, by suppression of meiotic crossovers at centromeres, and by the ability of some transposons to target centromeres. Megabase-length satellite centromeres arise in plants and animals with asymmetric female meiosis that creates centromere competition, and favors satellite monomers one or two nucleosomes in length that position and stabilize centromeric nucleosomes. Holocentromeres encompass the length of a chromosome and may differ dramatically between mitosis and meiosis. We propose a model in which low level transcription of centromeres facilitates the formation of non-B DNA that specifies centromeres and promotes loading of centromeric nucleosomes.
Collapse
Affiliation(s)
- Paul B Talbert
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
| | - Steven Henikoff
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA.
| |
Collapse
|
12
|
Sankaranarayanan SR, Ianiri G, Coelho MA, Reza MH, Thimmappa BC, Ganguly P, Vadnala RN, Sun S, Siddharthan R, Tellgren-Roth C, Dawson TL, Heitman J, Sanyal K. Loss of centromere function drives karyotype evolution in closely related Malassezia species. eLife 2020; 9:e53944. [PMID: 31958060 PMCID: PMC7025860 DOI: 10.7554/elife.53944] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 01/20/2020] [Indexed: 12/14/2022] Open
Abstract
Genomic rearrangements associated with speciation often result in variation in chromosome number among closely related species. Malassezia species show variable karyotypes ranging between six and nine chromosomes. Here, we experimentally identified all eight centromeres in M. sympodialis as 3-5-kb long kinetochore-bound regions that span an AT-rich core and are depleted of the canonical histone H3. Centromeres of similar sequence features were identified as CENP-A-rich regions in Malassezia furfur, which has seven chromosomes, and histone H3 depleted regions in Malassezia slooffiae and Malassezia globosa with nine chromosomes each. Analysis of synteny conservation across centromeres with newly generated chromosome-level genome assemblies suggests two distinct mechanisms of chromosome number reduction from an inferred nine-chromosome ancestral state: (a) chromosome breakage followed by loss of centromere DNA and (b) centromere inactivation accompanied by changes in DNA sequence following chromosome-chromosome fusion. We propose that AT-rich centromeres drive karyotype diversity in the Malassezia species complex through breakage and inactivation.
Collapse
Affiliation(s)
- Sundar Ram Sankaranarayanan
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific ResearchBengaluruIndia
| | - Giuseppe Ianiri
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
| | - Marco A Coelho
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
| | - Md Hashim Reza
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific ResearchBengaluruIndia
| | - Bhagya C Thimmappa
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific ResearchBengaluruIndia
| | - Promit Ganguly
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific ResearchBengaluruIndia
| | | | - Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
| | | | - Christian Tellgren-Roth
- National Genomics Infrastructure, Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala UniversityUppsalaSweden
| | - Thomas L Dawson
- Skin Research Institute Singapore, Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- Department of Drug Discovery, Medical University of South Carolina, School of PharmacyCharlestonUnited States
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
| | - Kaustuv Sanyal
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific ResearchBengaluruIndia
| |
Collapse
|
13
|
Lawrimore CJ, Bloom K. Common Features of the Pericentromere and Nucleolus. Genes (Basel) 2019; 10:E1029. [PMID: 31835574 PMCID: PMC6947172 DOI: 10.3390/genes10121029] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 12/05/2019] [Accepted: 12/07/2019] [Indexed: 12/20/2022] Open
Abstract
Both the pericentromere and the nucleolus have unique characteristics that distinguish them amongst the rest of genome. Looping of pericentromeric DNA, due to structural maintenance of chromosome (SMC) proteins condensin and cohesin, drives its ability to maintain tension during metaphase. Similar loops are formed via condensin and cohesin in nucleolar ribosomal DNA (rDNA). Condensin and cohesin are also concentrated in transfer RNA (tRNA) genes, genes which may be located within the pericentromere as well as tethered to the nucleolus. Replication fork stalling, as well as downstream consequences such as genomic recombination, are characteristic of both the pericentromere and rDNA. Furthermore, emerging evidence suggests that the pericentromere may function as a liquid-liquid phase separated domain, similar to the nucleolus. We therefore propose that the pericentromere and nucleolus, in part due to their enrichment of SMC proteins and others, contain similar domains that drive important cellular activities such as segregation, stability, and repair.
Collapse
Affiliation(s)
| | - Kerry Bloom
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA;
| |
Collapse
|
14
|
Chen CF, Pohl TJ, Chan A, Slocum JS, Zakian VA. Saccharomyces cerevisiae Centromere RNA Is Negatively Regulated by Cbf1 and Its Unscheduled Synthesis Impacts CenH3 Binding. Genetics 2019; 213:465-479. [PMID: 31391265 PMCID: PMC6781895 DOI: 10.1534/genetics.119.302528] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 07/19/2019] [Indexed: 12/12/2022] Open
Abstract
Two common features of centromeres are their transcription into noncoding centromere RNAs (cen-RNAs) and their assembly into nucleosomes that contain a centromere-specific histone H3 (cenH3). Here, we show that Saccharomyces cerevisiae cen-RNA was present in low amounts in wild-type (WT) cells, and that its appearance was tightly cell cycle-regulated, appearing and disappearing in a narrow window in S phase after centromere replication. In cells lacking Cbf1, a centromere-binding protein, cen-RNA was 5-12 times more abundant throughout the cell cycle. In WT cells, cen-RNA appearance occurred at the same time as loss of Cbf1's centromere binding, arguing that the physical presence of Cbf1 inhibits cen-RNA production. Binding of the Pif1 DNA helicase, which happens in mid-late S phase, occurred at about the same time as Cbf1 loss from the centromere, suggesting that Pif1 may facilitate this loss by its known ability to displace proteins from DNA. Cen-RNAs were more abundant in rnh1Δ cells but only in mid-late S phase. However, fork pausing at centromeres was not elevated in rnh1Δ cells but rather was due to centromere-binding proteins, including Cbf1 Strains with increased cen-RNA lost centromere plasmids at elevated rates. In cbf1Δ cells, where both the levels and the cell cycle-regulated appearance of cen-RNA were disrupted, the timing and levels of cenH3 centromere binding were perturbed. Thus, cen-RNAs are highly regulated, and disruption of this regulation correlates with changes in centromere structure and function.
Collapse
Affiliation(s)
- Chi-Fu Chen
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, New Jersey 08544
| | - Thomas J Pohl
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, New Jersey 08544
| | - Angela Chan
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, New Jersey 08544
| | - Joshua S Slocum
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, New Jersey 08544
| | - Virginia A Zakian
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, New Jersey 08544
| |
Collapse
|
15
|
Lawrimore J, Bloom K. The regulation of chromosome segregation via centromere loops. Crit Rev Biochem Mol Biol 2019; 54:352-370. [PMID: 31573359 PMCID: PMC6856439 DOI: 10.1080/10409238.2019.1670130] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/02/2019] [Accepted: 09/17/2019] [Indexed: 12/14/2022]
Abstract
Biophysical studies of the yeast centromere have shown that the organization of the centromeric chromatin plays a crucial role in maintaining proper tension between sister kinetochores during mitosis. While centromeric chromatin has traditionally been considered a simple spring, recent work reveals the centromere as a multifaceted, tunable shock absorber. Centromeres can differ from other regions of the genome in their heterochromatin state, supercoiling state, and enrichment of structural maintenance of chromosomes (SMC) protein complexes. Each of these differences can be utilized to alter the effective stiffness of centromeric chromatin. In budding yeast, the SMC protein complexes condensin and cohesin stiffen chromatin by forming and cross-linking chromatin loops, respectively, into a fibrous structure resembling a bottlebrush. The high density of the loops compacts chromatin while spatially isolating the tension from spindle pulling forces to a subset of the chromatin. Paradoxically, the molecular crowding of chromatin via cohesin and condensin also causes an outward/poleward force. The structure allows the centromere to act as a shock absorber that buffers the variable forces generated by dynamic spindle microtubules. Based on the distribution of SMCs from bacteria to human and the conserved distance between sister kinetochores in a wide variety of organisms (0.4 to 1 micron), we propose that the bottlebrush mechanism is the foundational principle for centromere function in eukaryotes.
Collapse
Affiliation(s)
- Josh Lawrimore
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kerry Bloom
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| |
Collapse
|
16
|
Pohl TJ, Zakian VA. Pif1 family DNA helicases: A helpmate to RNase H? DNA Repair (Amst) 2019; 84:102633. [PMID: 31231063 DOI: 10.1016/j.dnarep.2019.06.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/14/2019] [Accepted: 06/14/2019] [Indexed: 01/21/2023]
Abstract
An R-loop is a structure that forms when an RNA transcript stays bound to the DNA strand that encodes it and leaves the complementary strand exposed as a loop of single stranded DNA. R-loops accumulate when the processing of RNA transcripts is impaired. The failure to remove these RNA-DNA hybrids can lead to replication fork stalling and genome instability. Resolution of R-loops is thought to be mediated mainly by RNase H enzymes through the removal and degradation of the RNA in the hybrid. However, DNA helicases can also dismantle R-loops by displacing the bound RNA. In particular, the Pif1 family DNA helicases have been shown to regulate R-loop formation at specific genomic loci, such as tRNA genes and centromeres. Here we review the roles of Pif1 family helicases in vivo and in vitro and discuss evidence that Pif1 family helicases act on RNA-DNA hybrids and highlight their potential roles in complementing RNase H for R-loop resolution.
Collapse
Affiliation(s)
- Thomas J Pohl
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, United States
| | - Virginia A Zakian
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, United States.
| |
Collapse
|
17
|
Black EM, Giunta S. Repetitive Fragile Sites: Centromere Satellite DNA As a Source of Genome Instability in Human Diseases. Genes (Basel) 2018; 9:E615. [PMID: 30544645 PMCID: PMC6315641 DOI: 10.3390/genes9120615] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 12/03/2018] [Accepted: 12/03/2018] [Indexed: 12/31/2022] Open
Abstract
Maintenance of an intact genome is essential for cellular and organismal homeostasis. The centromere is a specialized chromosomal locus required for faithful genome inheritance at each round of cell division. Human centromeres are composed of large tandem arrays of repetitive alpha-satellite DNA, which are often sites of aberrant rearrangements that may lead to chromosome fusions and genetic abnormalities. While the centromere has an essential role in chromosome segregation during mitosis, the long and repetitive nature of the highly identical repeats has greatly hindered in-depth genetic studies, and complete annotation of all human centromeres is still lacking. Here, we review our current understanding of human centromere genetics and epigenetics as well as recent investigations into the role of centromere DNA in disease, with a special focus on cancer, aging, and human immunodeficiency⁻centromeric instability⁻facial anomalies (ICF) syndrome. We also highlight the causes and consequences of genomic instability at these large repetitive arrays and describe the possible sources of centromere fragility. The novel connection between alpha-satellite DNA instability and human pathological conditions emphasizes the importance of obtaining a truly complete human genome assembly and accelerating our understanding of centromere repeats' role in physiology and beyond.
Collapse
Affiliation(s)
- Elizabeth M Black
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
| | - Simona Giunta
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
| |
Collapse
|
18
|
Dna2 nuclease deficiency results in large and complex DNA insertions at chromosomal breaks. Nature 2018; 564:287-290. [PMID: 30518856 PMCID: PMC6346745 DOI: 10.1038/s41586-018-0769-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 10/23/2018] [Indexed: 11/22/2022]
Abstract
Insertions of mobile elements1-4, mitochondrial
DNA5 and fragments of
nuclear chromosomes6 at DNA
double strand breaks (DSBs) threaten genome integrity and are common in
cancer7-9. Insertions of chromosome fragments at
V(D)J loci can stimulate antibody diversification10. The origin of insertions of chromosomal
fragments and the mechanisms that prevent such insertions remain unknown. Here
we found the first mutant, lacking evolutionarily conserved Dna2 nuclease, that
shows frequent insertions of ~0.1-1.5 kb long sequences into DSBs with
many events carrying multiple DNA fragments joined together. Sequencing of
~500 DNA inserts revealed that they originate from Ty retrotransposons
(~8%), rDNA (~15%) and from throughout the genome with preference
for fragile regions such as origins of replication, R-loops, centromeres,
telomeres or replication fork barriers. Inserted fragments are not lost from
their original loci and therefore represent duplications. These duplications
depend on nonhomologous end-joining (NHEJ) and Pol4. We propose a model in which
alternative processing of DNA structures arising in Dna2-deficient cells can
result in the release of DNA fragments and their capture at DSBs.Similar DNA
insertions at DSBs are expected in any cells with linear extrachromosomal DNA
fragments.
Collapse
|
19
|
Two Pif1 Family DNA Helicases Cooperate in Centromere Replication and Segregation in Saccharomyces cerevisiae. Genetics 2018; 211:105-119. [PMID: 30442759 PMCID: PMC6325707 DOI: 10.1534/genetics.118.301710] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 11/06/2018] [Indexed: 02/07/2023] Open
Abstract
Pif1 family helicases are found in virtually all eukaryotes. Saccharomyces cerevisiae (Sc) encodes two Pif1 family helicases, ScPif1 and Rrm3 ScPif1 is multifunctional, required not only for maintenance of mitochondrial DNA but also for multiple distinct nuclear functions. Rrm3 moves with the replication fork and promotes movement of the fork through ∼1400 hard-to-replicate sites, including centromeres. Here we show that ScPif1, like Rrm3, bound robustly to yeast centromeres but only if the centromere was active. While Rrm3 binding to centromeres occurred in early to mid S phase, about the same time as centromere replication, ScPif1 binding occurred later in the cell cycle when replication of most centromeres is complete. However, the timing of Rrm3 and ScPif1 centromere binding was altered by the absence of the other helicase, such that Rrm3 centromere binding occurred later in pif1-m2 cells and ScPif1 centromere binding occurred earlier in rrm3Δ cells. As shown previously, the modest pausing of replication forks at centromeres seen in wild-type cells was increased in the absence of Rrm3 While a lack of ScPif1 did not result in increased fork pausing at centromeres, pausing was even higher in rrm3Δ pif1Δ cells than in rrm3Δ cells. Likewise, centromere function as monitored by the loss rate of a centromere plasmid was increased in rrm3Δ but not pif1Δ cells, and was even higher in rrm3Δ pif1Δ cells than in rrm3Δ cells. Thus, ScPif1 promotes centromere replication and segregation, but only in the absence of Rrm3 These data also hint at a potential post-S phase function for ScPif1 at centromeres. These studies add to the growing list of ScPif1 functions that promote chromosome stability.
Collapse
|
20
|
Barra V, Fachinetti D. The dark side of centromeres: types, causes and consequences of structural abnormalities implicating centromeric DNA. Nat Commun 2018; 9:4340. [PMID: 30337534 PMCID: PMC6194107 DOI: 10.1038/s41467-018-06545-y] [Citation(s) in RCA: 164] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 09/06/2018] [Indexed: 12/18/2022] Open
Abstract
Centromeres are the chromosomal domains required to ensure faithful transmission of the genome during cell division. They have a central role in preventing aneuploidy, by orchestrating the assembly of several components required for chromosome separation. However, centromeres also adopt a complex structure that makes them susceptible to being sites of chromosome rearrangements. Therefore, preservation of centromere integrity is a difficult, but important task for the cell. In this review, we discuss how centromeres could potentially be a source of genome instability and how centromere aberrations and rearrangements are linked with human diseases such as cancer.
Collapse
Affiliation(s)
- V Barra
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, F-75005, Paris, France
| | - D Fachinetti
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, F-75005, Paris, France.
| |
Collapse
|
21
|
Abstract
The spatiotemporal organization of chromatin plays central roles in cellular function. The ribosomal DNA (rDNA) chromatin undergoes dynamic structural changes during mitosis and stress. Here, we developed a CRISPR-based imaging system and tracked the condensation dynamics of rDNA chromatin in live yeast cells under glucose starvation. We found that acute glucose starvation triggers rapid condensation of rDNA. Time-lapse microscopy revealed two stages for rDNA condensation: a “primary stage,” when relaxed rDNA chromatin forms higher order loops or rings, and a “secondary stage,” when the rDNA rings further condense into compact clusters. Twisting of rDNA rings accompanies the secondary stage. The condensin complex, but not the cohesin complex, is required for efficient rDNA condensation in response to glucose starvation. Furthermore, we found that the DNA helicase Sgs1 is essential for the survival of cells expressing rDNA-bound dCas9, suggesting a role for helicases in facilitating DNA replication at dCas9-binding sites. A CRISPR-based imaging system allows tracking of rDNA condensation in single cells Glucose starvation triggers rDNA condensation in two prominent stages Condensin contributes to efficient rDNA condensation caused by glucose starvation Sgs1 helicase is required for normal rDNA replication at dCas9-binding sites
Collapse
Affiliation(s)
- Yuan Xue
- Department of Molecular Cellular and Developmental Biology, Yale University, 850 West Campus Drive, West Haven, CT 06516, USA
- Systems Biology Institute, Yale University, 850 West Campus Drive, West Haven, CT 06516, USA
| | - Murat Acar
- Department of Molecular Cellular and Developmental Biology, Yale University, 850 West Campus Drive, West Haven, CT 06516, USA
- Systems Biology Institute, Yale University, 850 West Campus Drive, West Haven, CT 06516, USA
- Department of Physics, Yale University, 217 Prospect Street, New Haven, CT 06511, USA
- Corresponding author
| |
Collapse
|
22
|
Zafar F, Okita AK, Onaka AT, Su J, Katahira Y, Nakayama JI, Takahashi TS, Masukata H, Nakagawa T. Regulation of mitotic recombination between DNA repeats in centromeres. Nucleic Acids Res 2017; 45:11222-11235. [PMID: 28977643 PMCID: PMC5737691 DOI: 10.1093/nar/gkx763] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 08/17/2017] [Indexed: 12/18/2022] Open
Abstract
Centromeres that are essential for faithful segregation of chromosomes consist of unique DNA repeats in many eukaryotes. Although recombination is under-represented around centromeres during meiosis, little is known about recombination between centromere repeats in mitotic cells. Here, we compared spontaneous recombination that occurs between ade6B/ade6X inverted repeats integrated at centromere 1 (cen1) or at a non-centromeric ura4 locus in fission yeast. Remarkably, distinct mechanisms of homologous recombination (HR) were observed in centromere and non-centromere regions. Rad51-dependent HR that requires Rad51, Rad54 and Rad52 was predominant in the centromere, whereas Rad51-independent HR that requires Rad52 also occurred in the arm region. Crossovers between inverted repeats (i.e. inversions) were under-represented in the centromere as compared to the arm region. While heterochromatin was dispensable, Mhf1/CENP–S, Mhf2/CENP–X histone-fold proteins and Fml1/FANCM helicase were required to suppress crossovers. Furthermore, Mhf1 and Fml1 were found to prevent gross chromosomal rearrangements mediated by centromere repeats. These data uncovered the regulation of mitotic recombination between DNA repeats in centromeres and its physiological role in maintaining genome integrity.
Collapse
Affiliation(s)
- Faria Zafar
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Akiko K Okita
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Atsushi T Onaka
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Jie Su
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Yasuhiro Katahira
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Jun-Ichi Nakayama
- Division of Chromatin Regulation, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 44-8585, Japan
| | - Tatsuro S Takahashi
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Hisao Masukata
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Takuro Nakagawa
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| |
Collapse
|
23
|
Cabral M, Cheng X, Singh S, Ivessa AS. Absence of Non-histone Protein Complexes at Natural Chromosomal Pause Sites Results in Reduced Replication Pausing in Aging Yeast Cells. Cell Rep 2017; 17:1747-1754. [PMID: 27829146 DOI: 10.1016/j.celrep.2016.10.050] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 09/08/2016] [Accepted: 10/14/2016] [Indexed: 11/26/2022] Open
Abstract
There is substantial evidence that genomic instability increases during aging. Replication pausing (and stalling) at difficult-to-replicate chromosomal sites may induce genomic instability. Interestingly, in aging yeast cells, we observed reduced replication pausing at various natural replication pause sites (RPSs) in ribosomal DNA (rDNA) and non-rDNA locations (e.g., silent replication origins and tRNA genes). The reduced pausing occurs independent of the DNA helicase Rrm3p, which facilitates replication past these non-histone protein-complex-bound RPSs, and is independent of the deacetylase Sir2p. Conditions of caloric restriction (CR), which extend life span, also cause reduced replication pausing at the 5S rDNA and at tRNA genes. In aged and CR cells, the RPSs are less occupied by their specific non-histone protein complexes (e.g., the preinitiation complex TFIIIC), likely because members of these complexes have primarily cytosolic localization. These conditions may lead to reduced replication pausing and may lower replication stress at these sites during aging.
Collapse
Affiliation(s)
- Marleny Cabral
- Department of Cell Biology and Molecular Medicine, Rutgers New Jersey Medical School, Rutgers Biomedical and Health Sciences, 185 South Orange Avenue, Newark, NJ 07101-1709, USA
| | - Xin Cheng
- Department of Cell Biology and Molecular Medicine, Rutgers New Jersey Medical School, Rutgers Biomedical and Health Sciences, 185 South Orange Avenue, Newark, NJ 07101-1709, USA
| | - Sukhwinder Singh
- Pathology and Laboratory Medicine/Flow Cytometry and Immunology Core Laboratory, Rutgers New Jersey Medical School, Rutgers Biomedical and Health Sciences, 185 South Orange Avenue, Newark, NJ 07101-1709, USA
| | - Andreas S Ivessa
- Department of Cell Biology and Molecular Medicine, Rutgers New Jersey Medical School, Rutgers Biomedical and Health Sciences, 185 South Orange Avenue, Newark, NJ 07101-1709, USA.
| |
Collapse
|
24
|
Muñoz-Galván S, García-Rubio M, Ortega P, Ruiz JF, Jimeno S, Pardo B, Gómez-González B, Aguilera A. A new role for Rrm3 in repair of replication-born DNA breakage by sister chromatid recombination. PLoS Genet 2017; 13:e1006781. [PMID: 28475600 PMCID: PMC5438189 DOI: 10.1371/journal.pgen.1006781] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 05/19/2017] [Accepted: 04/26/2017] [Indexed: 11/19/2022] Open
Abstract
Replication forks stall at different DNA obstacles such as those originated by transcription. Fork stalling can lead to DNA double-strand breaks (DSBs) that will be preferentially repaired by homologous recombination when the sister chromatid is available. The Rrm3 helicase is a replisome component that promotes replication upon fork stalling, accumulates at highly transcribed regions and prevents not only transcription-induced replication fork stalling but also transcription-associated hyper-recombination. This led us to explore the possible role of Rrm3 in the repair of DSBs when originating at the passage of the replication fork. Using a mini-HO system that induces mainly single-stranded DNA breaks, we show that rrm3Δ cells are defective in DSB repair. The defect is clearly seen in sister chromatid recombination, the major repair pathway of replication-born DSBs. Our results indicate that Rrm3 recruitment to replication-born DSBs is crucial for viability, uncovering a new role for Rrm3 in the repair of broken replication forks. DNA replication needs to be precise to ensure cell survival and to avoid genetic instability. Different DNA obstacles, such as those originated by transcription, frequently hamper replication fork progression leading to fork stalling or even fork breakage. This requires the homologous recombination machinery to repair the damage. Here, we uncovered a role for yeast Rrm3, a replisome component known to promote replication upon fork stalling, in the repair of replication-born double strand breaks. In particular, rrm3Δ cells show a defect in the recombination with the sister chromatid, the preferred template for the maintenance of genome integrity. Our results support the possibility that the known accumulation of Rrm3 at sites of active transcription reflects an active role of Rrm3 in the repair of broken forks.
Collapse
Affiliation(s)
- Sandra Muñoz-Galván
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville, Spain
| | - María García-Rubio
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville, Spain
| | - Pedro Ortega
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville, Spain
| | - Jose F. Ruiz
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville, Spain
| | - Sonia Jimeno
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville, Spain
| | - Benjamin Pardo
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville, Spain
| | - Belén Gómez-González
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville, Spain
- * E-mail: (AA); (BGG)
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville, Spain
- * E-mail: (AA); (BGG)
| |
Collapse
|
25
|
Gadaleta MC, Noguchi E. Regulation of DNA Replication through Natural Impediments in the Eukaryotic Genome. Genes (Basel) 2017; 8:genes8030098. [PMID: 28272375 PMCID: PMC5368702 DOI: 10.3390/genes8030098] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 03/03/2017] [Indexed: 02/07/2023] Open
Abstract
All living organisms need to duplicate their genetic information while protecting it from unwanted mutations, which can lead to genetic disorders and cancer development. Inaccuracies during DNA replication are the major cause of genomic instability, as replication forks are prone to stalling and collapse, resulting in DNA damage. The presence of exogenous DNA damaging agents as well as endogenous difficult-to-replicate DNA regions containing DNA–protein complexes, repetitive DNA, secondary DNA structures, or transcribing RNA polymerases, increases the risk of genomic instability and thus threatens cell survival. Therefore, understanding the cellular mechanisms required to preserve the genetic information during S phase is of paramount importance. In this review, we will discuss our current understanding of how cells cope with these natural impediments in order to prevent DNA damage and genomic instability during DNA replication.
Collapse
Affiliation(s)
- Mariana C Gadaleta
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA.
| | - Eishi Noguchi
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA.
| |
Collapse
|
26
|
Forsburg SL, Shen KF. Centromere Stability: The Replication Connection. Genes (Basel) 2017; 8:genes8010037. [PMID: 28106789 PMCID: PMC5295031 DOI: 10.3390/genes8010037] [Citation(s) in RCA: 7] [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: 12/19/2016] [Revised: 01/10/2017] [Accepted: 01/12/2017] [Indexed: 11/16/2022] Open
Abstract
The fission yeast centromere, which is similar to metazoan centromeres, contains highly repetitive pericentromere sequences that are assembled into heterochromatin. This is required for the recruitment of cohesin and proper chromosome segregation. Surprisingly, the pericentromere replicates early in the S phase. Loss of heterochromatin causes this domain to become very sensitive to replication fork defects, leading to gross chromosome rearrangements. This review examines the interplay between components of DNA replication, heterochromatin assembly, and cohesin dynamics that ensures maintenance of genome stability and proper chromosome segregation.
Collapse
Affiliation(s)
- Susan L Forsburg
- Program in Molecular & Computational Biology, University of Southern California, Los Angeles, CA 90089-2910, USA.
| | - Kuo-Fang Shen
- Program in Molecular & Computational Biology, University of Southern California, Los Angeles, CA 90089-2910, USA.
| |
Collapse
|
27
|
Abstract
DNA topological transitions occur when replication forks encounter other DNA transactions such as transcription. Failure in resolving such conflicts leads to generation of aberrant replication and transcription intermediates that might have adverse effects on genome stability. Cells have evolved numerous surveillance mechanisms to avoid, tolerate, and resolve such replication-transcription conflicts. Defects or non-coordination in such cellular mechanisms might have catastrophic effect on cell viability. In this chapter, we review consequences of replication encounters with transcription and its associated events, topological challenges, and how these inevitable conflicts alter the genome structure and functions.
Collapse
|
28
|
Romeo F, Falbo L, Costanzo V. Replication, checkpoint suppression and structure of centromeric DNA. Nucleus 2016; 7:540-546. [PMID: 27893298 DOI: 10.1080/19491034.2016.1255836] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Human centromeres contain large amounts of repetitive DNA sequences known as α satellite DNA, which can be difficult to replicate and whose functional role is unclear. Recently, we have characterized protein composition, structural organization and checkpoint response to stalled replication forks of centromeric chromatin reconstituted in Xenopus laevis egg extract. We showed that centromeric DNA has high affinity for SMC2-4 subunits of condensins and for CENP-A, it is enriched for DNA repair factors and suppresses the ATR checkpoint to ensure its efficient replication. We also showed that centromeric chromatin forms condensins enriched and topologically constrained DNA loops, which likely contribute to the overall structure of the centromere. These findings have important implications on how chromosomes are organized and genome stability is maintained in mammalian cells.
Collapse
Affiliation(s)
- Francesco Romeo
- a DNA metabolism laboratory, IFOM, The FIRC institute for Molecular Oncology , Milan , Italy
| | - Lucia Falbo
- a DNA metabolism laboratory, IFOM, The FIRC institute for Molecular Oncology , Milan , Italy
| | - Vincenzo Costanzo
- a DNA metabolism laboratory, IFOM, The FIRC institute for Molecular Oncology , Milan , Italy
| |
Collapse
|
29
|
Onaka AT, Toyofuku N, Inoue T, Okita AK, Sagawa M, Su J, Shitanda T, Matsuyama R, Zafar F, Takahashi TS, Masukata H, Nakagawa T. Rad51 and Rad54 promote noncrossover recombination between centromere repeats on the same chromatid to prevent isochromosome formation. Nucleic Acids Res 2016; 44:10744-10757. [PMID: 27697832 PMCID: PMC5159554 DOI: 10.1093/nar/gkw874] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 09/06/2016] [Accepted: 09/21/2016] [Indexed: 12/14/2022] Open
Abstract
Centromeres consist of DNA repeats in many eukaryotes. Non-allelic homologous recombination (HR) between them can result in gross chromosomal rearrangements (GCRs). In fission yeast, Rad51 suppresses isochromosome formation that occurs between inverted repeats in the centromere. However, how the HR enzyme prevents homology-mediated GCRs remains unclear. Here, we provide evidence that Rad51 with the aid of the Swi/Snf-type motor protein Rad54 promotes non-crossover recombination between centromere repeats to prevent isochromosome formation. Mutations in Rad51 and Rad54 epistatically increased the rates of isochromosome formation and chromosome loss. In sharp contrast, these mutations decreased gene conversion between inverted repeats in the centromere. Remarkably, analysis of recombinant DNAs revealed that rad51 and rad54 increase the proportion of crossovers. In the absence of Rad51, deletion of the structure-specific endonuclease Mus81 decreased both crossovers and isochromosomes, while the cdc27/pol32-D1 mutation, which impairs break-induced replication, did not. We propose that Rad51 and Rad54 promote non-crossover recombination between centromere repeats on the same chromatid, thereby suppressing crossover between non-allelic repeats on sister chromatids that leads to chromosomal rearrangements. Furthermore, we found that Rad51 and Rad54 are required for gene silencing in centromeres, suggesting that HR also plays a role in the structure and function of centromeres.
Collapse
Affiliation(s)
- Atsushi T Onaka
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Naoko Toyofuku
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Takahiro Inoue
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Akiko K Okita
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Minami Sagawa
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Jie Su
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Takeshi Shitanda
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Rei Matsuyama
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Faria Zafar
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Tatsuro S Takahashi
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Hisao Masukata
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Takuro Nakagawa
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| |
Collapse
|
30
|
Muñoz S, Méndez J. DNA replication stress: from molecular mechanisms to human disease. Chromosoma 2016; 126:1-15. [PMID: 26797216 DOI: 10.1007/s00412-016-0573-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Revised: 01/04/2016] [Accepted: 01/05/2016] [Indexed: 12/29/2022]
Abstract
The genome of proliferating cells must be precisely duplicated in each cell division cycle. Chromosomal replication entails risks such as the possibility of introducing breaks and/or mutations in the genome. Hence, DNA replication requires the coordinated action of multiple proteins and regulatory factors, whose deregulation causes severe developmental diseases and predisposes to cancer. In recent years, the concept of "replicative stress" (RS) has attracted much attention as it impinges directly on genomic stability and offers a promising new avenue to design anticancer therapies. In this review, we summarize recent progress in three areas: (1) endogenous and exogenous factors that contribute to RS, (2) molecular mechanisms that mediate the cellular responses to RS, and (3) the large list of diseases that are directly or indirectly linked to RS.
Collapse
Affiliation(s)
- Sergio Muñoz
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, E-28029, Madrid, Spain
| | - Juan Méndez
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, E-28029, Madrid, Spain.
| |
Collapse
|
31
|
Scott KC, Bloom KS. Lessons learned from counting molecules: how to lure CENP-A into the kinetochore. Open Biol 2015; 4:rsob.140191. [PMID: 25500356 PMCID: PMC4281711 DOI: 10.1098/rsob.140191] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Affiliation(s)
- Kristin C Scott
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| | - Kerry S Bloom
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| |
Collapse
|
32
|
Replication stress in Mammalian cells and its consequences for mitosis. Genes (Basel) 2015; 6:267-98. [PMID: 26010955 PMCID: PMC4488665 DOI: 10.3390/genes6020267] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 05/15/2015] [Accepted: 05/18/2015] [Indexed: 12/23/2022] Open
Abstract
The faithful transmission of genetic information to daughter cells is central to maintaining genomic stability and relies on the accurate and complete duplication of genetic material during each cell cycle. However, the genome is routinely exposed to endogenous and exogenous stresses that can impede the progression of replication. Such replication stress can be an early cause of cancer or initiate senescence. Replication stress, which primarily occurs during S phase, results in consequences during mitosis, jeopardizing chromosome segregation and, in turn, genomic stability. The traces of replication stress can be detected in the daughter cells during G1 phase. Alterations in mitosis occur in two types: 1) local alterations that correspond to breaks, rearrangements, intertwined DNA molecules or non-separated sister chromatids that are confined to the region of the replication dysfunction; 2) genome-wide chromosome segregation resulting from centrosome amplification (although centrosomes do not contain DNA), which amplifies the local replication stress to the entire genome. Here, we discuss the endogenous causes of replication perturbations, the mechanisms of replication fork restart and the consequences for mitosis, chromosome segregation and genomic stability.
Collapse
|
33
|
Kochenova OV, Daee DL, Mertz TM, Shcherbakova PV. DNA polymerase ζ-dependent lesion bypass in Saccharomyces cerevisiae is accompanied by error-prone copying of long stretches of adjacent DNA. PLoS Genet 2015; 11:e1005110. [PMID: 25826305 PMCID: PMC4380420 DOI: 10.1371/journal.pgen.1005110] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 02/27/2015] [Indexed: 11/24/2022] Open
Abstract
Translesion synthesis (TLS) helps cells to accomplish chromosomal replication in the presence of unrepaired DNA lesions. In eukaryotes, the bypass of most lesions involves a nucleotide insertion opposite the lesion by either a replicative or a specialized DNA polymerase, followed by extension of the resulting distorted primer terminus by DNA polymerase ζ (Polζ). The subsequent events leading to disengagement of the error-prone Polζ from the primer terminus and its replacement with an accurate replicative DNA polymerase remain largely unknown. As a first step toward understanding these events, we aimed to determine the length of DNA stretches synthesized in an error-prone manner during the Polζ-dependent lesion bypass. We developed new in vivo assays to identify the products of mutagenic TLS through a plasmid-borne tetrahydrofuran lesion and a UV-induced chromosomal lesion. We then surveyed the region downstream of the lesion site (in respect to the direction of TLS) for the presence of mutations indicative of an error-prone polymerase activity. The bypass of both lesions was associated with an approximately 300,000-fold increase in the mutation rate in the adjacent DNA segment, in comparison to the mutation rate during normal replication. The hypermutated tract extended 200 bp from the lesion in the plasmid-based assay and as far as 1 kb from the lesion in the chromosome-based assay. The mutation rate in this region was similar to the rate of errors produced by purified Polζ during copying of undamaged DNA in vitro. Further, no mutations downstream of the lesion were observed in rare TLS products recovered from Polζ-deficient cells. This led us to conclude that error-prone Polζ synthesis continues for several hundred nucleotides after the lesion bypass is completed. These results provide insight into the late steps of TLS and show that error-prone TLS tracts span a substantially larger region than previously appreciated. Genomic instability is associated with multiple genetic diseases. Endogenous and exogenous DNA-damaging factors constitute a major source of genomic instability. Mutations occur when DNA lesions are bypassed by specialized translesion synthesis (TLS) DNA polymerases that are less accurate than the normal replicative polymerases. The discovery of the remarkable infidelity of the TLS enzymes at the turn of the century immediately suggested that their contribution to replication must be tightly restricted to sites of DNA damage to avoid excessive mutagenesis. The actual extent of error-prone synthesis that accompanies TLS in vivo has never been estimated. We describe a novel genetic approach to measure the length of DNA synthesized by TLS polymerases upon their recruitment to sites of DNA damage. We show that stretches of error-prone synthesis associated with the bypass of a single damaged nucleotide span at least 200 and sometimes up to 1,000 nucleotide-long segments, resulting in more than a 300,000-fold increase in mutagenesis in the surrounding region. We speculate that processive synthesis of long DNA stretches by error-prone polymerases could contribute to clustered mutagenesis, a phenomenon that allows for rapid genome changes without significant loss of fitness and plays an important role in tumorigenesis, the immune response and adaptation.
Collapse
Affiliation(s)
- Olga V. Kochenova
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Danielle L. Daee
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Tony M. Mertz
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Polina V. Shcherbakova
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- * E-mail:
| |
Collapse
|
34
|
Accessory Replicative Helicases and the Replication of Protein-Bound DNA. J Mol Biol 2014; 426:3917-3928. [DOI: 10.1016/j.jmb.2014.10.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 09/29/2014] [Accepted: 10/06/2014] [Indexed: 12/29/2022]
|
35
|
Genome-wide mapping of yeast histone chaperone anti-silencing function 1 reveals its role in condensin binding with chromatin. PLoS One 2014; 9:e108652. [PMID: 25264624 PMCID: PMC4181348 DOI: 10.1371/journal.pone.0108652] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 09/01/2014] [Indexed: 12/23/2022] Open
Abstract
Genome-wide participation and importance of the histone chaperone Asf1 (Anti-Silencing Function 1) in diverse DNA transactions like replication, repair, heterochromatic silencing and transcription are well documented. Yet its genome-wide targets have not been reported. Using ChIP-seq method, we found that yeast Asf1 associates with 590 unique targets including centromeres, telomeres and condensin-binding sites. It is found selectively on highly transcribed regions, which include replication fork pause sites. Asf1 preferentially associates with the genes transcribed by RNA polymerase (pol) III where its presence affects RNA production and replication-independent histone exchange. On pol II-transcribed genes, a negative correlation is found between Asf1 and nucleosome occupancy. It is not enriched on most of the reported sites of histone exchange or on the genes, which are misregulated in the asf1Δ cells. Interestingly, chromosome-wide distributions of Asf1 and one of the condensin subunits, Brn1 show a nearly identical pattern. Moreover, Brn1 shows reduced occupancy at various condensin-binding sites in asf1Δ cells. These results along with high association of Asf1 with heterochromatic centromeres and telomeres ascribe novel roles to Asf1 in condensin loading and chromatin dynamics.
Collapse
|
36
|
Topoisomerase 2 is dispensable for the replication and segregation of small yeast artificial chromosomes (YACs). PLoS One 2014; 9:e104995. [PMID: 25115861 PMCID: PMC4130621 DOI: 10.1371/journal.pone.0104995] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 07/15/2014] [Indexed: 11/19/2022] Open
Abstract
DNA topoisomerases are thought to play a critical role in transcription, replication and recombination as well as in the condensation and segregation of sister duplexes during cell division. Here, we used high-resolution two-dimensional agarose gel electrophoresis to study the replication intermediates and final products of small circular and linear minichromosomes of Saccharomyces cerevisiae in the presence and absence of DNA topoisomerase 2. The results obtained confirmed that whereas for circular minichromosomes, catenated sister duplexes accumulated in the absence of topoisomerase 2, linear YACs were able to replicate and segregate regardless of this topoisomerase. The patterns of replication intermediates for circular and linear YACs displayed significant differences suggesting that DNA supercoiling might play a key role in the modulation of replication fork progression. Altogether, this data supports the notion that for linear chromosomes the torsional tension generated by transcription and replication dissipates freely throughout the telomeres.
Collapse
|
37
|
Singh J. Role of DNA replication in establishment and propagation of epigenetic states of chromatin. Semin Cell Dev Biol 2014; 30:131-43. [PMID: 24794003 DOI: 10.1016/j.semcdb.2014.04.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 04/03/2014] [Indexed: 10/25/2022]
Abstract
DNA replication is the fundamental process of duplication of the genetic information that is vital for survival of all living cells. The basic mechanistic steps of replication initiation, elongation and termination are conserved among bacteria, lower eukaryotes, like yeast and metazoans. However, the details of the mechanisms are different. Furthermore, there is a close coordination between chromatin assembly pathways and various components of replication machinery whereby DNA replication is coupled to "chromatin replication" during cell cycle. Thereby, various epigenetic modifications associated with different states of gene expression in differentiated cells and the related chromatin structures are faithfully propagated during the cell division through tight coupling with the DNA replication machinery. Several examples are found in lower eukaryotes like budding yeast and fission yeast with close parallels in metazoans.
Collapse
Affiliation(s)
- Jagmohan Singh
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, India.
| |
Collapse
|
38
|
Mitra S, Gómez-Raja J, Larriba G, Dubey DD, Sanyal K. Rad51-Rad52 mediated maintenance of centromeric chromatin in Candida albicans. PLoS Genet 2014; 10:e1004344. [PMID: 24762765 PMCID: PMC3998917 DOI: 10.1371/journal.pgen.1004344] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 03/19/2014] [Indexed: 11/29/2022] Open
Abstract
Specification of the centromere location in most eukaryotes is not solely dependent on the DNA sequence. However, the non-genetic determinants of centromere identity are not clearly defined. While multiple mechanisms, individually or in concert, may specify centromeres epigenetically, most studies in this area are focused on a universal factor, a centromere-specific histone H3 variant CENP-A, often considered as the epigenetic determinant of centromere identity. In spite of variable timing of its loading at centromeres across species, a replication coupled early S phase deposition of CENP-A is found in most yeast centromeres. Centromeres are the earliest replicating chromosomal regions in a pathogenic budding yeast Candida albicans. Using a 2-dimensional agarose gel electrophoresis assay, we identify replication origins (ORI7-LI and ORI7-RI) proximal to an early replicating centromere (CEN7) in C. albicans. We show that the replication forks stall at CEN7 in a kinetochore dependent manner and fork stalling is reduced in the absence of the homologous recombination (HR) proteins Rad51 and Rad52. Deletion of ORI7-RI causes a significant reduction in the stalled fork signal and an increased loss rate of the altered chromosome 7. The HR proteins, Rad51 and Rad52, have been shown to play a role in fork restart. Confocal microscopy shows declustered kinetochores in rad51 and rad52 mutants, which are evidence of kinetochore disintegrity. CENP-ACaCse4 levels at centromeres, as determined by chromatin immunoprecipitation (ChIP) experiments, are reduced in absence of Rad51/Rad52 resulting in disruption of the kinetochore structure. Moreover, western blot analysis reveals that delocalized CENP-A molecules in HR mutants degrade in a similar fashion as in other kinetochore mutants described before. Finally, co-immunoprecipitation assays indicate that Rad51 and Rad52 physically interact with CENP-ACaCse4in vivo. Thus, the HR proteins Rad51 and Rad52 epigenetically maintain centromere functioning by regulating CENP-ACaCse4 levels at the programmed stall sites of early replicating centromeres. The epigenetic mark of centromeres, CENP-A, is deposited in S phase in most yeasts by a mechanism that is not completely understood. Here, we identify two CEN7 flanking replication origins, ORI7-L1 and ORI7-RI, proximal to an early replicating centromere (CEN7) in a budding yeast Candida albicans. Replication forks starting from these origins stall randomly at CEN7 by the kinetochore that serves as a barrier to fork progression. We observe that centromeric fork stalling is reduced in absence of the HR proteins, Rad51 and Rad52, known to play a role in restarting stalled forks. Further, we demonstrate that Rad51 and Rad52 physically interact with CENP-ACaCse4in vivo. CENP-ACaCse4 levels are reduced in absence of Rad51 or Rad52, which results in disruption of the kinetochore structure. Here we propose a novel DNA replication-coupled mechanism mediated by HR proteins which epigenetically maintains centromere identity by regulating CENP-A deposition. A direct role of DNA repair proteins in centromere function offers insights into the mechanisms of centromere mis-regulation that leads to widespread aneuploidy in cancer cells.
Collapse
Affiliation(s)
- Sreyoshi Mitra
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, India
| | - Jonathan Gómez-Raja
- Departamento Ciencias Biomédicas Área de Microbiología, Universidad de Extremadura, Badajoz, Spain
| | - Germán Larriba
- Departamento Ciencias Biomédicas Área de Microbiología, Universidad de Extremadura, Badajoz, Spain
| | | | - Kaustuv Sanyal
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, India
- * E-mail:
| |
Collapse
|
39
|
Mankouri HW, Huttner D, Hickson ID. How unfinished business from S-phase affects mitosis and beyond. EMBO J 2013; 32:2661-71. [PMID: 24065128 PMCID: PMC3801442 DOI: 10.1038/emboj.2013.211] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 09/05/2013] [Indexed: 12/17/2022] Open
Abstract
The eukaryotic cell cycle is conventionally viewed as comprising several discrete steps, each of which must be completed before the next one is initiated. However, emerging evidence suggests that incompletely replicated, or unresolved, chromosomes from S-phase can persist into mitosis, where they present a potential threat to the faithful segregation of sister chromatids. In this review, we provide an overview of the different classes of loci where this 'unfinished S-phase business' can lead to a variety of cytogenetically distinct DNA structures throughout the various steps of mitosis. Furthermore, we discuss the potential ways in which cells might not only tolerate this inevitable aspect of chromosome biology, but also exploit it to assist in the maintenance of genome stability.
Collapse
Affiliation(s)
- Hocine W Mankouri
- Department of Cellular and Molecular Medicine, Nordea Center for Healthy Aging, Copenhagen N, Denmark
| | - Diana Huttner
- Department of Cellular and Molecular Medicine, Nordea Center for Healthy Aging, Copenhagen N, Denmark
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen N, Denmark
| | - Ian D Hickson
- Department of Cellular and Molecular Medicine, Nordea Center for Healthy Aging, Copenhagen N, Denmark
| |
Collapse
|
40
|
Jõers P, Lewis SC, Fukuoh A, Parhiala M, Ellilä S, Holt IJ, Jacobs HT. Mitochondrial transcription terminator family members mTTF and mTerf5 have opposing roles in coordination of mtDNA synthesis. PLoS Genet 2013; 9:e1003800. [PMID: 24068965 PMCID: PMC3778013 DOI: 10.1371/journal.pgen.1003800] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Accepted: 07/30/2013] [Indexed: 12/19/2022] Open
Abstract
All genomes require a system for avoidance or handling of collisions between the machineries of DNA replication and transcription. We have investigated the roles in this process of the mTERF (mitochondrial transcription termination factor) family members mTTF and mTerf5 in Drosophila melanogaster. The two mTTF binding sites in Drosophila mtDNA, which also bind mTerf5, were found to coincide with major sites of replication pausing. RNAi-mediated knockdown of either factor resulted in mtDNA depletion and developmental arrest. mTTF knockdown decreased site-specific replication pausing, but led to an increase in replication stalling and fork regression in broad zones around each mTTF binding site. Lagging-strand DNA synthesis was impaired, with extended RNA/DNA hybrid segments seen in replication intermediates. This was accompanied by the accumulation of recombination intermediates and nicked/broken mtDNA species. Conversely, mTerf5 knockdown led to enhanced replication pausing at mTTF binding sites, a decrease in fragile replication intermediates containing single-stranded segments, and the disappearance of species containing segments of RNA/DNA hybrid. These findings indicate an essential and previously undescribed role for proteins of the mTERF family in the integration of transcription and DNA replication, preventing unregulated collisions and facilitating productive interactions between the two machineries that are inferred to be essential for completion of lagging-strand DNA synthesis.
Collapse
Affiliation(s)
- Priit Jõers
- Institute of Biomedical Technology and Tampere University Hospital, Tampere, Finland
- Estonian Biocentre, Tartu, Estonia
| | - Samantha C. Lewis
- Institute of Biomedical Technology and Tampere University Hospital, Tampere, Finland
- Department of Biology, University of California, Riverside, California, United States of America
| | - Atsushi Fukuoh
- Institute of Biomedical Technology and Tampere University Hospital, Tampere, Finland
- Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
- Department of Medical Laboratory Science, Junshin Gakuen University, Fukuoka, Japan
| | - Mikael Parhiala
- Institute of Biomedical Technology and Tampere University Hospital, Tampere, Finland
| | - Simo Ellilä
- Institute of Biomedical Technology and Tampere University Hospital, Tampere, Finland
| | - Ian J. Holt
- MRC National Institute of Medical Research, London, United Kingdom
| | - Howard T. Jacobs
- Institute of Biomedical Technology and Tampere University Hospital, Tampere, Finland
- Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland
- * E-mail:
| |
Collapse
|
41
|
Jõers P, Jacobs HT. Analysis of replication intermediates indicates that Drosophila melanogaster mitochondrial DNA replicates by a strand-coupled theta mechanism. PLoS One 2013; 8:e53249. [PMID: 23308172 PMCID: PMC3537619 DOI: 10.1371/journal.pone.0053249] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Accepted: 11/28/2012] [Indexed: 11/18/2022] Open
Abstract
Mitochondrial DNA synthesis is necessary for the normal function of the organelle and for the eukaryotic organism as a whole. Here we demonstrate, using two-dimensional agarose gel electrophoresis to analyse replication intermediates, that unidirectional, strand-coupled DNA synthesis is the prevalent mode of mtDNA replication in Drosophila melanogaster. Commencing within the single, extended non-coding region (NCR), replication proceeds around the circular genome, manifesting an irregular rate of elongation, and pausing frequently in specific regions. Evidence for a limited contribution of strand-asynchronous DNA synthesis was found in a subset of mtDNA molecules, but confined to the ribosomal RNA gene region, just downstream of the NCR. Our findings imply that strand-coupled replication is widespread amongst metazoans, and should inform future research on mtDNA metabolism in D. melanogaster.
Collapse
Affiliation(s)
- Priit Jõers
- Institute of Biomedical Technology and Tampere University Hospital, University of Tampere, Tampere, Finland
| | - Howard T. Jacobs
- Institute of Biomedical Technology and Tampere University Hospital, University of Tampere, Tampere, Finland
- * E-mail:
| |
Collapse
|
42
|
Yong-Gonzales V, Hang LE, Castellucci F, Branzei D, Zhao X. The Smc5-Smc6 complex regulates recombination at centromeric regions and affects kinetochore protein sumoylation during normal growth. PLoS One 2012; 7:e51540. [PMID: 23284708 PMCID: PMC3527468 DOI: 10.1371/journal.pone.0051540] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 11/08/2012] [Indexed: 11/22/2022] Open
Abstract
The Smc5-Smc6 complex in Saccharomyces cerevisiae is both essential for growth and important for coping with genotoxic stress. While it facilitates damage tolerance throughout the genome under genotoxin treatment, its function during unperturbed growth is mainly documented for repetitive DNA sequence maintenance. Here we provide physical and genetic evidence showing that the Smc5–Smc6 complex regulates recombination at non-repetitive loci such as centromeres in the absence of DNA damaging agents. Mutating Smc6 results in the accumulation of recombination intermediates at centromeres and other unique sequences as assayed by 2D gel analysis. In addition, smc6 mutant cells exhibit increased levels of Rad52 foci that co-localize with centromere markers. A rad52 mutation that decreases centromeric, but not overall, levels of Rad52 foci in smc6 mutants suppresses the nocodazole sensitivity of these cells, suggesting that the Smc6-mediated regulation of recombination at centromeric regions impacts centromere-related functions. In addition to influencing recombination, the SUMO ligase subunit of the Smc5–Smc6 complex promotes the sumoylation of two kinetochore proteins and affects mitotic spindles. These results suggest that the Smc5–Smc6 complex regulates both recombination and kinetochore sumoylation to facilitate chromosomal maintenance during growth.
Collapse
Affiliation(s)
- Vladimir Yong-Gonzales
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Lisa E. Hang
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
- Programs in Biochemistry, Cell and Molecular Biology, Weill Cornell Graduate School of Medical Sciences, New York, New York, United States of America
| | | | - Dana Branzei
- IFOM, FIRC Institute of Molecular Oncology, Milan, Italy
| | - Xiaolan Zhao
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
- * E-mail:
| |
Collapse
|
43
|
Abstract
The conserved PIF helicase family appears to function in replication to ensure termination and passage through regions that slow or arrest replication fork movement. Findings in fission yeast extend evidence from budding yeast, and argue for universal mechanisms that ensure replication integrity.
Collapse
Affiliation(s)
- Kenji Shimada
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
| | | |
Collapse
|
44
|
Topoisomerase I poisoning results in PARP-mediated replication fork reversal. Nat Struct Mol Biol 2012; 19:417-23. [DOI: 10.1038/nsmb.2258] [Citation(s) in RCA: 351] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Accepted: 02/07/2012] [Indexed: 12/30/2022]
|
45
|
Paeschke K, Capra JA, Zakian VA. DNA replication through G-quadruplex motifs is promoted by the Saccharomyces cerevisiae Pif1 DNA helicase. Cell 2011; 145:678-91. [PMID: 21620135 DOI: 10.1016/j.cell.2011.04.015] [Citation(s) in RCA: 442] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Revised: 02/10/2011] [Accepted: 03/23/2011] [Indexed: 11/28/2022]
Abstract
G-quadruplex (G4) DNA structures are extremely stable four-stranded secondary structures held together by noncanonical G-G base pairs. Genome-wide chromatin immunoprecipitation was used to determine the in vivo binding sites of the multifunctional Saccharomyces cerevisiae Pif1 DNA helicase, a potent unwinder of G4 structures in vitro. G4 motifs were a significant subset of the high-confidence Pif1-binding sites. Replication slowed in the vicinity of these motifs, and they were prone to breakage in Pif1-deficient cells, whereas non-G4 Pif1-binding sites did not show this behavior. Introducing many copies of G4 motifs caused slow growth in replication-stressed Pif1-deficient cells, which was relieved by spontaneous mutations that eliminated their ability to form G4 structures, bind Pif1, slow DNA replication, and stimulate DNA breakage. These data suggest that G4 structures form in vivo and that they are resolved by Pif1 to prevent replication fork stalling and DNA breakage.
Collapse
Affiliation(s)
- Katrin Paeschke
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | | | | |
Collapse
|
46
|
Fachinetti D, Bermejo R, Cocito A, Minardi S, Katou Y, Kanoh Y, Shirahige K, Azvolinsky A, Zakian VA, Foiani M. Replication termination at eukaryotic chromosomes is mediated by Top2 and occurs at genomic loci containing pausing elements. Mol Cell 2010; 39:595-605. [PMID: 20797631 DOI: 10.1016/j.molcel.2010.07.024] [Citation(s) in RCA: 119] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Revised: 05/05/2010] [Accepted: 06/08/2010] [Indexed: 01/19/2023]
Abstract
Chromosome replication initiates at multiple replicons and terminates when forks converge. In E. coli, the Tus-TER complex mediates polar fork converging at the terminator region, and aberrant termination events challenge chromosome integrity and segregation. Since in eukaryotes, termination is less characterized, we used budding yeast to identify the factors assisting fork fusion at replicating chromosomes. Using genomic and mechanistic studies, we have identified and characterized 71 chromosomal termination regions (TERs). TERs contain fork pausing elements that influence fork progression and merging. The Rrm3 DNA helicase assists fork progression across TERs, counteracting the accumulation of X-shaped structures. The Top2 DNA topoisomerase associates at TERs in S phase, and G2/M facilitates fork fusion and prevents DNA breaks and genome rearrangements at TERs. We propose that in eukaryotes, replication fork barriers, Rrm3, and Top2 coordinate replication fork progression and fusion at TERs, thus counteracting abnormal genomic transitions.
Collapse
Affiliation(s)
- Daniele Fachinetti
- Fondazione IFOM, Istituto FIRC di Oncologia Molecolare (IFOM-IEO Campus), Via Adamello 16, 20139 Milan, Italy
| | | | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Rozenzhak S, Mejía-Ramírez E, Williams JS, Schaffer L, Hammond JA, Head SR, Russell P. Rad3 decorates critical chromosomal domains with gammaH2A to protect genome integrity during S-Phase in fission yeast. PLoS Genet 2010; 6:e1001032. [PMID: 20661445 PMCID: PMC2908685 DOI: 10.1371/journal.pgen.1001032] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2010] [Accepted: 06/17/2010] [Indexed: 01/24/2023] Open
Abstract
Schizosaccharomyces pombe Rad3 checkpoint kinase and its human ortholog ATR are essential for maintaining genome integrity in cells treated with genotoxins that damage DNA or arrest replication forks. Rad3 and ATR also function during unperturbed growth, although the events triggering their activation and their critical functions are largely unknown. Here, we use ChIP-on-chip analysis to map genomic loci decorated by phosphorylated histone H2A (gammaH2A), a Rad3 substrate that establishes a chromatin-based recruitment platform for Crb2 and Brc1 DNA repair/checkpoint proteins. Unexpectedly, gammaH2A marks a diverse array of genomic features during S-phase, including natural replication fork barriers and a fork breakage site, retrotransposons, heterochromatin in the centromeres and telomeres, and ribosomal RNA (rDNA) repeats. gammaH2A formation at the centromeres and telomeres is associated with heterochromatin establishment by Clr4 histone methyltransferase. We show that gammaH2A domains recruit Brc1, a factor involved in repair of damaged replication forks. Brc1 C-terminal BRCT domain binding to gammaH2A is crucial in the absence of Rqh1(Sgs1), a RecQ DNA helicase required for rDNA maintenance whose human homologs are mutated in patients with Werner, Bloom, and Rothmund-Thomson syndromes that are characterized by cancer-predisposition or accelerated aging. We conclude that Rad3 phosphorylates histone H2A to mobilize Brc1 to critical genomic domains during S-phase, and this pathway functions in parallel with Rqh1 DNA helicase in maintaining genome integrity.
Collapse
Affiliation(s)
- Sophie Rozenzhak
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Eva Mejía-Ramírez
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Jessica S. Williams
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
| | - Lana Schaffer
- DNA Array Core Facility, The Scripps Research Institute, La Jolla, California, United States of America
| | - Jennifer A. Hammond
- DNA Array Core Facility, The Scripps Research Institute, La Jolla, California, United States of America
| | - Steven R. Head
- DNA Array Core Facility, The Scripps Research Institute, La Jolla, California, United States of America
| | - Paul Russell
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California, United States of America
| |
Collapse
|
48
|
Szilard RK, Jacques PE, Laramée L, Cheng B, Galicia S, Bataille AR, Yeung M, Mendez M, Bergeron M, Robert F, Durocher D. Systematic identification of fragile sites via genome-wide location analysis of gamma-H2AX. Nat Struct Mol Biol 2010; 17:299-305. [PMID: 20139982 DOI: 10.1038/nsmb.1754] [Citation(s) in RCA: 154] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Accepted: 11/30/2009] [Indexed: 12/11/2022]
Abstract
Phosphorylation of histone H2AX is an early response to DNA damage in eukaryotes. In Saccharomyces cerevisiae, DNA damage or replication-fork stalling results in phosphorylation of histone H2A yielding gamma-H2A (yeast gamma-H2AX) in a Mec1 (ATR)- and Tel1 (ATM)-dependent manner. Here, we describe the genome-wide location analysis of gamma-H2A as a strategy to identify loci prone to engaging the Mec1 and Tel1 pathways. Notably, gamma-H2A enrichment overlaps with loci prone to replication-fork stalling and is caused by the action of Mec1 and Tel1, indicating that these loci are prone to breakage. Moreover, about half the sites enriched for gamma-H2A map to repressed protein-coding genes, and histone deacetylases are necessary for formation of gamma-H2A at these loci. Finally, our work indicates that high-resolution mapping of gamma-H2AX is a fruitful route to map fragile sites in eukaryotic genomes.
Collapse
Affiliation(s)
- Rachel K Szilard
- [1] Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada. [2] These authors contributed equally to this work
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Morohashi H, Maculins T, Labib K. The amino-terminal TPR domain of Dia2 tethers SCF(Dia2) to the replisome progression complex. Curr Biol 2009; 19:1943-9. [PMID: 19913425 DOI: 10.1016/j.cub.2009.09.062] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2009] [Revised: 09/23/2009] [Accepted: 09/25/2009] [Indexed: 10/20/2022]
Abstract
Eukaryotic cells contain multiple versions of the E3 ubiquitin ligase known as the SCF (Skp1/cullin/F box), each of which is distinguished by a different F box protein that uses a domain at the carboxyl terminus to recognize substrates [1, 2]. The F box protein Dia2 is an important determinant of genome stability in budding yeast [3-5], but its mode of action is poorly understood. Here we show that SCF(Dia2) associates with the replisome progression complex (RPC) that assembles around the MCM2-7 helicase at DNA replication forks [6]. This interaction requires the RPC components Mrc1 and Ctf4, both of which associate with a tetratricopeptide repeat (TPR) domain located at the amino terminus of Dia2. Our data indicate that the TPR domain of Dia2 tethers SCF(Dia2) to the RPC, probably increasing the local concentration of the ligase at DNA replication forks. This regulation becomes important in cells that accumulate stalled DNA replication forks at protein-DNA barriers, perhaps aiding the interaction of SCF(Dia2) with key substrates. Our findings suggest that the amino-terminal domains of other F box proteins might also play an analogous regulatory role, controlling the localization of the cognate SCF complexes.
Collapse
Affiliation(s)
- Hiroko Morohashi
- Cancer Research UK Paterson Institute for Cancer Research, University of Manchester, UK
| | | | | |
Collapse
|
50
|
Gari K, Constantinou A. The role of the Fanconi anemia network in the response to DNA replication stress. Crit Rev Biochem Mol Biol 2009; 44:292-325. [PMID: 19728769 DOI: 10.1080/10409230903154150] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Fanconi anemia is a genetically heterogeneous disorder associated with chromosome instability and a highly elevated risk for developing cancer. The mutated genes encode proteins involved in the cellular response to DNA replication stress. Fanconi anemia proteins are extensively connected with DNA caretaker proteins, and appear to function as a hub for the coordination of DNA repair with DNA replication and cell cycle progression. At a molecular level, however, the raison d'être of Fanconi anemia proteins still remains largely elusive. The thirteen Fanconi anemia proteins identified to date have not been embraced into a single and defined biological process. To help put the Fanconi anemia puzzle into perspective, we begin this review with a summary of the strategies employed by prokaryotes and eukaryotes to tolerate obstacles to the progression of replication forks. We then summarize what we know about Fanconi anemia with an emphasis on biochemical aspects, and discuss how the Fanconi anemia network, a late acquisition in evolution, may function to permit the faithful and complete duplication of our very large vertebrate chromosomes.
Collapse
Affiliation(s)
- Kerstin Gari
- DNA Damage Response Laboratory, Cancer Research UK, London Research Institute, Clare Hall Laboratories, South Mimms, UK
| | | |
Collapse
|