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Cissé OH, Curran SJ, Folco HD, Liu Y, Bishop L, Wang H, Fischer ER, Davis AS, Combs C, Thapar S, Dekker JP, Grewal S, Cushion M, Ma L, Kovacs JA. Regional centromere configuration in the fungal pathogens of the Pneumocystis genus. mBio 2024; 15:e0318523. [PMID: 38380929 PMCID: PMC10936427 DOI: 10.1128/mbio.03185-23] [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: 11/29/2023] [Accepted: 01/31/2024] [Indexed: 02/22/2024] Open
Abstract
Centromeres are constricted chromosomal regions that are essential for cell division. In eukaryotes, centromeres display a remarkable architectural and genetic diversity. The basis of centromere-accelerated evolution remains elusive. Here, we focused on Pneumocystis species, a group of mammalian-specific fungal pathogens that form a sister taxon with that of the Schizosaccharomyces pombe, an important genetic model for centromere biology research. Methods allowing reliable continuous culture of Pneumocystis species do not currently exist, precluding genetic manipulation. CENP-A, a variant of histone H3, is the epigenetic marker that defines centromeres in most eukaryotes. Using heterologous complementation, we show that the Pneumocystis CENP-A ortholog is functionally equivalent to CENP-ACnp1 of S. pombe. Using organisms from a short-term in vitro culture or infected animal models and chromatin immunoprecipitation (ChIP)-Seq, we identified CENP-A bound regions in two Pneumocystis species that diverged ~35 million years ago. Each species has a unique short regional centromere (<10 kb) flanked by heterochromatin in 16-17 monocentric chromosomes. They span active genes and lack conserved DNA sequence motifs and repeats. These features suggest an epigenetic specification of centromere function. Analysis of centromeric DNA across multiple Pneumocystis species suggests a vertical transmission at least 100 million years ago. The common ancestry of Pneumocystis and S. pombe centromeres is untraceable at the DNA level, but the overall architectural similarity could be the result of functional constraint for successful chromosomal segregation.IMPORTANCEPneumocystis species offer a suitable genetic system to study centromere evolution in pathogens because of their phylogenetic proximity with the non-pathogenic yeast S. pombe, a popular model for cell biology. We used this system to explore how centromeres have evolved after the divergence of the two clades ~ 460 million years ago. To address this question, we established a protocol combining short-term culture and ChIP-Seq to characterize centromeres in multiple Pneumocystis species. We show that Pneumocystis have short epigenetic centromeres that function differently from those in S. pombe.
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Affiliation(s)
- Ousmane H. Cissé
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Shelly J. Curran
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - H. Diego Folco
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Yueqin Liu
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Lisa Bishop
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Honghui Wang
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Elizabeth R. Fischer
- Microscopy Unit, Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - A. Sally Davis
- Diagnostic Medicine/Pathobiology, Kansas State University College of Veterinary Medicine, Manhattan, Kansas, USA
| | - Christian Combs
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Sabrina Thapar
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - John P. Dekker
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, National Institute of Allergy, and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Shiv Grewal
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Melanie Cushion
- Department of Internal Medicine, College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
| | - Liang Ma
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Joseph A. Kovacs
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
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Nathanailidou P, Dhakshnamoorthy J, Xiao H, Zofall M, Holla S, O’Neill M, Andresson T, Wheeler D, Grewal SIS. Specialized replication of heterochromatin domains ensures self-templated chromatin assembly and epigenetic inheritance. Proc Natl Acad Sci U S A 2024; 121:e2315596121. [PMID: 38285941 PMCID: PMC10861883 DOI: 10.1073/pnas.2315596121] [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: 09/07/2023] [Accepted: 12/21/2023] [Indexed: 01/31/2024] Open
Abstract
Heterochromatin, defined by histone H3 lysine 9 methylation (H3K9me), spreads across large domains and can be epigenetically inherited in a self-propagating manner. Heterochromatin propagation depends upon a read-write mechanism, where the Clr4/Suv39h methyltransferase binds to preexisting trimethylated H3K9 (H3K9me3) and further deposits H3K9me. How the parental methylated histone template is preserved during DNA replication is not well understood. Here, we demonstrate using Schizosaccharomyces pombe that heterochromatic regions are specialized replication domains demarcated by their surrounding boundary elements. DNA replication throughout these domains is distinguished by an abundance of replisome components and is coordinated by Swi6/HP1. Although mutations in the replicative helicase subunit Mcm2 that affect histone binding impede the maintenance of a heterochromatin domain at an artificially targeted ectopic site, they have only a modest impact on heterochromatin propagation via the read-write mechanism at an endogenous site. Instead, our findings suggest a crucial role for the replication factor Mcl1 in retaining parental histones and promoting heterochromatin propagation via a mechanism involving the histone chaperone FACT. Engagement of FACT with heterochromatin requires boundary elements, which position the heterochromatic domain at the nuclear peripheral subdomain enriched for heterochromatin factors. Our findings highlight the importance of replisome components and boundary elements in creating a specialized environment for the retention of parental methylated histones, which facilitates epigenetic inheritance of heterochromatin.
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Affiliation(s)
- Patroula Nathanailidou
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD20892
| | - Jothy Dhakshnamoorthy
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD20892
| | - Hua Xiao
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD20892
| | - Martin Zofall
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD20892
| | - Sahana Holla
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD20892
| | - Maura O’Neill
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD21701
| | - Thorkell Andresson
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD21701
| | - David Wheeler
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD20892
| | - Shiv I. S. Grewal
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD20892
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Lee GE, Byun J, Lee CJ, Cho YY. Molecular Mechanisms for the Regulation of Nuclear Membrane Integrity. Int J Mol Sci 2023; 24:15497. [PMID: 37895175 PMCID: PMC10607757 DOI: 10.3390/ijms242015497] [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: 09/26/2023] [Revised: 10/19/2023] [Accepted: 10/22/2023] [Indexed: 10/29/2023] Open
Abstract
The nuclear membrane serves a critical role in protecting the contents of the nucleus and facilitating material and signal exchange between the nucleus and cytoplasm. While extensive research has been dedicated to topics such as nuclear membrane assembly and disassembly during cell division, as well as interactions between nuclear transmembrane proteins and both nucleoskeletal and cytoskeletal components, there has been comparatively less emphasis on exploring the regulation of nuclear morphology through nuclear membrane integrity. In particular, the role of type II integral proteins, which also function as transcription factors, within the nuclear membrane remains an area of research that is yet to be fully explored. The integrity of the nuclear membrane is pivotal not only during cell division but also in the regulation of gene expression and the communication between the nucleus and cytoplasm. Importantly, it plays a significant role in the development of various diseases. This review paper seeks to illuminate the biomolecules responsible for maintaining the integrity of the nuclear membrane. It will delve into the mechanisms that influence nuclear membrane integrity and provide insights into the role of type II membrane protein transcription factors in this context. Understanding these aspects is of utmost importance, as it can offer valuable insights into the intricate processes governing nuclear membrane integrity. Such insights have broad-reaching implications for cellular function and our understanding of disease pathogenesis.
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Affiliation(s)
- Ga-Eun Lee
- BK21-4th, and BRL, College of Pharmacy, The Catholic University of Korea, 43, Jibong-ro, Wonmi-gu, Bucheon-si 14662, Gyeonggi-do, Republic of Korea; (G.-E.L.); (J.B.)
| | - Jiin Byun
- BK21-4th, and BRL, College of Pharmacy, The Catholic University of Korea, 43, Jibong-ro, Wonmi-gu, Bucheon-si 14662, Gyeonggi-do, Republic of Korea; (G.-E.L.); (J.B.)
| | - Cheol-Jung Lee
- Research Center for Materials Analysis, Korea Basic Science Institute, 169-148, Gwahak-ro, Yuseong-gu, Daejeon 34133, Chungcheongnam-do, Republic of Korea
| | - Yong-Yeon Cho
- BK21-4th, and BRL, College of Pharmacy, The Catholic University of Korea, 43, Jibong-ro, Wonmi-gu, Bucheon-si 14662, Gyeonggi-do, Republic of Korea; (G.-E.L.); (J.B.)
- RCD Control and Material Research Institute, The Catholic University of Korea, 43, Jibong-ro, Wonmi-gu, Bucheon-si 14662, Gyeonggi-do, Republic of Korea
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Hori K, Yamazaki S, Ohtaka-Maruyama C, Ono T, Iguchi T, Masai H. Cdc7 kinase is required for postnatal brain development. Genes Cells 2023; 28:679-693. [PMID: 37584256 DOI: 10.1111/gtc.13059] [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: 04/10/2023] [Revised: 07/20/2023] [Accepted: 08/06/2023] [Indexed: 08/17/2023]
Abstract
The evolutionally conserved Cdc7 kinase plays crucial roles in initiation of DNA replication as well as in other chromosomal events. To examine the roles of Cdc7 in brain development, we have generated mice carrying Cdc7 knockout in neural stem cells by using Nestin-Cre. The Cdc7Fl/Fl NestinCre mice were born, but exhibited severe growth retardation and impaired postnatal brain development. These mice exhibited motor dysfunction within 9 days after birth and did not survive for more than 19 days. The cerebral cortical layer formation was impaired, although the cortical cell numbers were not altered in the mutant. In the cerebellum undergoing hypoplasia, granule cells (CGC) decreased in number in Cdc7Fl/F l NestinCre mice compared to the control at E15-18, suggesting that Cdc7 is required for DNA replication and cell proliferation of CGC at mid embryonic stage (before embryonic day 15). On the other hand, the Purkinje cell numbers were not altered but its layer formation was impaired in the mutant. These results indicate differential roles of Cdc7 in DNA replication/cell proliferation in brain. Furthermore, the defects of layer formation suggest a possibility that Cdc7 may play an additional role in cell migration during neural development.
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Affiliation(s)
- Karin Hori
- Genome Dynamics Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Satoshi Yamazaki
- Genome Dynamics Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Chiaki Ohtaka-Maruyama
- Developmental Neuroscience Project, Department of Brain and Neurosciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Tomio Ono
- Laboratory for Transgenic Technology, Center for Basic Technology Research, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Tomohiro Iguchi
- Genome Dynamics Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Hisao Masai
- Genome Dynamics Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
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Cissé OH, Curran S, Folco HD, Liu Y, Bishop L, Wang H, Fischer ER, Davis AS, Babb-Biernacki S, Doyle VP, Richards JK, Hassan SA, Dekker JP, Khil PP, Brenchley JM, Grewal S, Cushion M, Ma L, Kovacs JA. The Host Adapted Fungal Pathogens of Pneumocystis Genus Utilize Genic Regional Centromeres. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.12.540427. [PMID: 37425787 PMCID: PMC10327204 DOI: 10.1101/2023.05.12.540427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Centromeres are genomic regions that coordinate accurate chromosomal segregation during mitosis and meiosis. Yet, despite their essential function, centromeres evolve rapidly across eukaryotes. Centromeres are often the sites of chromosomal breaks which contribute to genome shuffling and promote speciation by inhibiting gene flow. How centromeres form in strongly host-adapted fungal pathogens has yet to be investigated. Here, we characterized the centromere structures in closely related species of mammalian-specific pathogens of the fungal phylum of Ascomycota. Methods allowing reliable continuous culture of Pneumocystis species do not currently exist, precluding genetic manipulation. CENP-A, a variant of histone H3, is the epigenetic marker that defines centromeres in most eukaryotes. Using heterologous complementation, we show that the Pneumocystis CENP-A ortholog is functionally equivalent to CENP-ACnp1 of Schizosaccharomyces pombe. Using organisms from a short-term in vitro culture or infected animal models and ChIP-seq, we identified centromeres in three Pneumocystis species that diverged ~100 million years ago. Each species has a unique short regional centromere (< 10kb) flanked by heterochromatin in 16-17 monocentric chromosomes. They span active genes and lack conserved DNA sequence motifs and repeats. CENP-C, a scaffold protein that links the inner centromere to the kinetochore appears dispensable in one species, suggesting a kinetochore rewiring. Despite the loss of DNA methyltransferases, 5-methylcytosine DNA methylation occurs in these species, though not related to centromere function. These features suggest an epigenetic specification of centromere function.
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Affiliation(s)
- Ousmane H Cissé
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Shelly Curran
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - H Diego Folco
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Yueqin Liu
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Lisa Bishop
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Honghui Wang
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Elizabeth R Fischer
- Microscopy Unit, Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - A Sally Davis
- Diagnostic Medicine/Pathobiology, Kansas State University College of Veterinary Medicine, Manhattan, USA
| | - Spenser Babb-Biernacki
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Vinson P Doyle
- Department of Plant Pathology and Crop Physiology, Lousiana State University AgCenter, Baton Rouge, Louisiana, USA
| | - Jonathan K Richards
- Department of Plant Pathology and Crop Physiology, Lousiana State University AgCenter, Baton Rouge, Louisiana, USA
| | - Sergio A Hassan
- Bioinformatics and Computational Biosciences Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - John P Dekker
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, National Institute of Allergy, and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Pavel P Khil
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, National Institute of Allergy, and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Jason M Brenchley
- Laboratory of Viral Diseases, National Institute of Allergy, and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Shiv Grewal
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Melanie Cushion
- Department of Internal Medicine, College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
| | - Liang Ma
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Joseph A Kovacs
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
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Arcangioli B, Gangloff S. The Fission Yeast Mating-Type Switching Motto: "One-for-Two" and "Two-for-One". Microbiol Mol Biol Rev 2023; 87:e0000821. [PMID: 36629411 PMCID: PMC10029342 DOI: 10.1128/mmbr.00008-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Schizosaccharomyces pombe is an ascomycete fungus that divides by medial fission; it is thus commonly referred to as fission yeast, as opposed to the distantly related budding yeast Saccharomyces cerevisiae. The reproductive lifestyle of S. pombe relies on an efficient genetic sex determination system generating a 1:1 sex ratio and using alternating haploid/diploid phases in response to environmental conditions. In this review, we address how one haploid cell manages to generate two sister cells with opposite mating types, a prerequisite to conjugation and meiosis. This mating-type switching process depends on two highly efficient consecutive asymmetric cell divisions that rely on DNA replication, repair, and recombination as well as the structure and components of heterochromatin. We pay special attention to the intimate interplay between the genetic and epigenetic partners involved in this process to underscore the importance of basic research and its profound implication for a better understanding of chromatin biology.
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Affiliation(s)
- Benoît Arcangioli
- Genome Dynamics Unit, Genomes and Genetics Department, Pasteur Institute, Paris, France
| | - Serge Gangloff
- Genome Dynamics Unit, Genomes and Genetics Department, Pasteur Institute, Paris, France
- UMR3525, Genetics of Genomes, CNRS-Pasteur Institute, Paris, France
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Rhind N. DNA replication timing: Biochemical mechanisms and biological significance. Bioessays 2022; 44:e2200097. [PMID: 36125226 PMCID: PMC9783711 DOI: 10.1002/bies.202200097] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/31/2022] [Accepted: 09/02/2022] [Indexed: 12/27/2022]
Abstract
The regulation of DNA replication is a fascinating biological problem both from a mechanistic angle-How is replication timing regulated?-and from an evolutionary one-Why is replication timing regulated? Recent work has provided significant insight into the first question. Detailed biochemical understanding of the mechanism and regulation of replication initiation has made possible robust hypotheses for how replication timing is regulated. Moreover, technical progress, including high-throughput, single-molecule mapping of replication initiation and single-cell assays of replication timing, has allowed for direct testing of these hypotheses in mammalian cells. This work has consolidated the conclusion that differential replication timing is a consequence of the varying probability of replication origin initiation. The second question is more difficult to directly address experimentally. Nonetheless, plausible hypotheses can be made and one-that replication timing contributes to the regulation of chromatin structure-has received new experimental support.
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Affiliation(s)
- Nicholas Rhind
- Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
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Sen S, Dodamani A, Nambiar M. Emerging mechanisms and roles of meiotic crossover repression at centromeres. Curr Top Dev Biol 2022; 151:155-190. [PMID: 36681469 DOI: 10.1016/bs.ctdb.2022.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Crossover events during recombination in meiosis are essential for generating genetic diversity as well as crucial to allow accurate chromosomal segregation between homologous chromosomes. Spatial control for the distribution of crossover events along the chromosomes is largely a tightly regulated process and involves many facets such as interference, repression as well as assurance, to make sure that not too many or too few crossovers are generated. Repression of crossover events at the centromeres is a highly conserved process across all species tested. Failure to inhibit such recombination events can result in chromosomal mis-segregation during meiosis resulting in aneuploid gametes that are responsible for infertility or developmental disorders such as Down's syndrome and other trisomies in humans. In the past few decades, studies to understand the molecular mechanisms behind this repression have shown the involvement of a multitude of factors ranging from the centromere-specific proteins such as the kinetochore to the flanking pericentric heterochromatin as well as DNA double-strand break repair pathways. In this chapter, we review the different mechanisms of pericentric repression mechanisms known till date as well as highlight the importance of understanding this regulation in the context of chromosomal segregation defects. We also discuss the clinical implications of dysregulation of this process, especially in human reproductive health and genetic diseases.
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Affiliation(s)
- Sucharita Sen
- Department of Biology, Indian Institute of Science Education and Research, Pune, India
| | - Ananya Dodamani
- Department of Biology, Indian Institute of Science Education and Research, Pune, India
| | - Mridula Nambiar
- Department of Biology, Indian Institute of Science Education and Research, Pune, India.
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Impact of Chromosomal Context on Origin Selection and the Replication Program. Genes (Basel) 2022; 13:genes13071244. [PMID: 35886027 PMCID: PMC9318681 DOI: 10.3390/genes13071244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/28/2022] [Accepted: 07/08/2022] [Indexed: 02/01/2023] Open
Abstract
Eukaryotic DNA replication is regulated by conserved mechanisms that bring about a spatial and temporal organization in which distinct genomic domains are copied at characteristic times during S phase. Although this replication program has been closely linked with genome architecture, we still do not understand key aspects of how chromosomal context modulates the activity of replication origins. To address this question, we have exploited models that combine engineered genomic rearrangements with the unique replication programs of post-quiescence and pre-meiotic S phases. Our results demonstrate that large-scale inversions surprisingly do not affect cell proliferation and meiotic progression, despite inducing a restructuring of replication domains on each rearranged chromosome. Remarkably, these alterations in the organization of DNA replication are entirely due to changes in the positions of existing origins along the chromosome, as their efficiencies remain virtually unaffected genome wide. However, we identified striking alterations in origin firing proximal to the fusion points of each inversion, suggesting that the immediate chromosomal neighborhood of an origin is a crucial determinant of its activity. Interestingly, the impact of genome reorganization on replication initiation is highly comparable in the post-quiescent and pre-meiotic S phases, despite the differences in DNA metabolism in these two physiological states. Our findings therefore shed new light on how origin selection and the replication program are governed by chromosomal architecture.
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f = m*a: A Framework for Investigating the Regulation of Replication Timing. Genes (Basel) 2022; 13:genes13020249. [PMID: 35205293 PMCID: PMC8872135 DOI: 10.3390/genes13020249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 01/21/2022] [Accepted: 01/24/2022] [Indexed: 12/04/2022] Open
Abstract
Stochastic models of replication timing posit that origin firing timing is regulated by origin firing probability, with early-firing origins having a high probability of firing and late-firing origins having a lower probability. However, they offer no insight into why one origin should have a higher firing probability than another. Here, a simple framework is suggested for how to approach the question by noting that the firing probability (f) must be the product of the stoichiometry of the MCM replicative helicase loaded at the origin (m) and the probability with which that MCM is activated (a). This framework emphasizes that mechanistic understanding of replication timing must focus on MCM loading and activation and can be simplified to the equation f = m*a.
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11
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Alavi S, Ghadiri H, Dabirmanesh B, Moriyama K, Khajeh K, Masai H. G-quadruplex binding protein Rif1, a key regulator of replication timing. J Biochem 2021; 169:1-14. [PMID: 33169133 DOI: 10.1093/jb/mvaa128] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/18/2020] [Indexed: 12/19/2022] Open
Abstract
DNA replication is spatially and temporally regulated during S phase to execute efficient and coordinated duplication of entire genome. Various epigenomic mechanisms operate to regulate the timing and locations of replication. Among them, Rif1 plays a major role to shape the 'replication domains' that dictate which segments of the genome are replicated when and where in the nuclei. Rif1 achieves this task by generating higher-order chromatin architecture near nuclear membrane and by recruiting a protein phosphatase. Rif1 is a G4 binding protein, and G4 binding activity of Rif1 is essential for replication timing regulation in fission yeast. In this article, we first summarize strategies by which cells regulate their replication timing and then describe how Rif1 and its interaction with G4 contribute to regulation of chromatin architecture and replication timing.
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Affiliation(s)
| | - Hamed Ghadiri
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Bahareh Dabirmanesh
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Kenji Moriyama
- Genome Dynamics Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, Japan
| | - Khosro Khajeh
- Department of Nanobiotechnology.,Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Hisao Masai
- Genome Dynamics Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, Japan
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12
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Dukaj L, Rhind N. The capacity of origins to load MCM establishes replication timing patterns. PLoS Genet 2021; 17:e1009467. [PMID: 33764973 PMCID: PMC8023499 DOI: 10.1371/journal.pgen.1009467] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 04/06/2021] [Accepted: 03/04/2021] [Indexed: 11/24/2022] Open
Abstract
Loading of the MCM replicative helicase at origins of replication is a highly regulated process that precedes DNA replication in all eukaryotes. The stoichiometry of MCM loaded at origins has been proposed to be a key determinant of when those origins initiate replication during S phase. Nevertheless, the genome-wide regulation of MCM loading stoichiometry and its direct effect on replication timing remain unclear. In order to investigate why some origins load more MCM than others, we perturbed MCM levels in budding yeast cells and, for the first time, directly measured MCM levels and replication timing in the same experiment. Reduction of MCM levels through degradation of Mcm4, one of the six obligate components of the MCM complex, slowed progression through S phase and increased sensitivity to replication stress. Reduction of MCM levels also led to differential loading at origins during G1, revealing origins that are sensitive to reductions in MCM and others that are not. Sensitive origins loaded less MCM under normal conditions and correlated with a weak ability to recruit the origin recognition complex (ORC). Moreover, reduction of MCM loading at specific origins of replication led to a delay in their replication during S phase. In contrast, overexpression of MCM had no effects on cell cycle progression, relative MCM levels at origins, or replication timing, suggesting that, under optimal growth conditions, cellular MCM levels are not limiting for MCM loading. Our results support a model in which the loading capacity of origins is the primary determinant of MCM stoichiometry in wild-type cells, but that stoichiometry is controlled by origins' ability to recruit ORC and compete for MCM when MCM becomes limiting.
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Affiliation(s)
- Livio Dukaj
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School Worcester, Massachusetts, United States of America
| | - Nicholas Rhind
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School Worcester, Massachusetts, United States of America
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13
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Yang J, Liu X, Huang Y, He L, Zhang W, Ren J, Wang Y, Wu J, Wu X, Shan L, Yang X, Sun L, Liang J, Zhang Y, Shang Y. TRPS1 drives heterochromatic origin refiring and cancer genome evolution. Cell Rep 2021; 34:108814. [PMID: 33691114 DOI: 10.1016/j.celrep.2021.108814] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 12/18/2020] [Accepted: 02/10/2021] [Indexed: 02/06/2023] Open
Abstract
Exploitation of naturally occurring genetic mutations could empower the discovery of novel aspects of established cancer genes. We report here that TRPS1, a gene linked to the tricho-rhino-phalangeal syndrome (TRPS) and recently identified as a potential breast cancer driver, promotes breast carcinogenesis through regulating replication. Epigenomic decomposition of TRPS1 landscape reveals nearly half of H3K9me3-marked heterochromatic origins are occupied by TRPS1, where it encourages the chromatin loading of APC/C, resulting in uncontrolled origin refiring. TRPS1 binds to the genome through its atypical H3K9me3 reading via GATA and IKAROS domains, while TRPS-related mutations affect its chromatin binding, replication boosting, and tumorigenicity. Concordantly, overexpression of wild-type but not TRPS-associated mutants of TRPS1 is sufficient to drive cancer genome amplifications, which experience an extrachromosomal route and dynamically evolve to confer therapeutic resistance. Together, these results uncover a critical function of TRPS1 in driving heterochromatin origin firing and breast cancer genome evolution.
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Affiliation(s)
- Jianguo Yang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Xiaoping Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Yunchao Huang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Lin He
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Wenting Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Jie Ren
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Yue Wang
- Department of Biochemistry and Molecular Biology, School of Medicine, Hangzhou Normal University, Hangzhou 311121, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Jiajing Wu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Xiaodi Wu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Lin Shan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Xiaohan Yang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Luyang Sun
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Jing Liang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Yu Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China.
| | - Yongfeng Shang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China; Department of Biochemistry and Molecular Biology, School of Medicine, Hangzhou Normal University, Hangzhou 311121, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China.
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14
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Yu H, Tsuchida M, Ando M, Hashizaki T, Shimada A, Takahata S, Murakami Y. Trimethylguanosine synthase 1 (Tgs1) is involved in Swi6/HP1-independent siRNA production and establishment of heterochromatin in fission yeast. Genes Cells 2021; 26:203-218. [PMID: 33527595 DOI: 10.1111/gtc.12833] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/22/2021] [Accepted: 01/25/2021] [Indexed: 11/27/2022]
Abstract
In fission yeast, siRNA generated by RNA interference (RNAi) factors plays critical roles in establishment and maintenance of heterochromatin. To achieve efficient siRNA synthesis, RNAi factors assemble on heterochromatin via association with Swi6, a homologue of heterochromatin protein 1 (HP1), and heterochromatic noncoding RNA (hncRNA) retained on chromatin. In addition, spliceosomes formed on hncRNA introns recruit RNAi factors to hncRNA and heterochromatin. Small nuclear RNAs, components of the spliceosome, have a trimethylguanosine (TMG) cap that is generated by Tgs1-dependent hypermethylation of the normal m7G cap; this cap is required for efficient splicing of some mRNAs in budding yeast and Drosophila. In this study, we found that loss of Tgs1 in fission yeast destabilizes centromeric heterochromatin. Tgs1 was required for Swi6-independent siRNA synthesis, as well as for the establishment of centromeric heterochromatin. Loss of Tgs1 affected the splicing efficiency of hncRNA introns in the absence of Swi6. Furthermore, some hncRNAs have a TMG cap, and we found that loss of Tgs1 diminished the chromatin binding of these hncRNAs. Together, these results suggest that the Tgs1-dependent TMG cap plays critical roles in establishment of heterochromatin by ensuring spliceosome-dependent recruitment of RNAi factors and regulating the binding between chromatin and hncRNA.
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Affiliation(s)
- Hiroki Yu
- Laboratory of Bioorganic Chemistry, Graduate school of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan.,Ambitious Leader's Program Fostering Future Leaders to Open New Frontiers in Materials Science (ALP), Hokkaido University, Sapporo, Hokkaido, Japan
| | - Mai Tsuchida
- Laboratory for Cell Regulation, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Motoyoshi Ando
- Laboratory of Bioorganic Chemistry, Graduate school of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan
| | - Tomoka Hashizaki
- Laboratory of Bioorganic Chemistry, Graduate school of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan
| | - Atsushi Shimada
- Laboratory for Cell Regulation, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Shinya Takahata
- Laboratory of Bioorganic Chemistry, Graduate school of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan.,Laboratory of Bioorganic Chemistry, Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Yota Murakami
- Laboratory of Bioorganic Chemistry, Graduate school of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan.,Laboratory of Bioorganic Chemistry, Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Japan
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15
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Ding Q, Koren A. Positive and Negative Regulation of DNA Replication Initiation. Trends Genet 2020; 36:868-879. [PMID: 32739030 PMCID: PMC7572746 DOI: 10.1016/j.tig.2020.06.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/28/2020] [Accepted: 06/30/2020] [Indexed: 12/25/2022]
Abstract
Genomic DNA is replicated every cell cycle by the programmed activation of replication origins at specific times and chromosomal locations. The factors that define the locations of replication origins and their typical activation times in eukaryotic cells are poorly understood. Previous studies highlighted the role of activating factors and epigenetic modifications in regulating replication initiation. Here, we review the role that repressive pathways - and their alleviation - play in establishing the genomic landscape of replication initiation. Several factors mediate this repression, in particular, factors associated with inactive chromatin. Repression can support organized, yet stochastic, replication initiation, and its absence could explain instances of rapid and random replication or re-replication.
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Affiliation(s)
- Qiliang Ding
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
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16
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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.
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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; , ,
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17
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Chromatin and Nuclear Architecture: Shaping DNA Replication in 3D. Trends Genet 2020; 36:967-980. [PMID: 32713597 DOI: 10.1016/j.tig.2020.07.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/26/2020] [Accepted: 07/02/2020] [Indexed: 12/13/2022]
Abstract
In eukaryotes, DNA replication progresses through a finely orchestrated temporal and spatial program. The 3D genome structure and nuclear architecture have recently emerged as fundamental determinants of the replication program. Factors with established roles in replication have been recognized as genome organization regulators. Exploiting paradigms from yeasts and mammals, we discuss how DNA replication is regulated in time and space through DNA-associated trans-acting factors, diffusible limiting replication initiation factors, higher-order chromatin folding, dynamic origin localization, and specific nuclear microenvironments. We present an integrated model for the regulation of DNA replication in 3D and highlight the importance of accurate spatio-temporal regulation of DNA replication in physiology and disease.
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18
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Takayama Y. Identification of Genes Encoding CENP-A and Heterochromatin Protein 1 of Lipomyces starkeyi and Functional Analysis Using Schizosaccharomyces pombe. Genes (Basel) 2020; 11:genes11070769. [PMID: 32650514 PMCID: PMC7397231 DOI: 10.3390/genes11070769] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/06/2020] [Accepted: 07/06/2020] [Indexed: 11/16/2022] Open
Abstract
Centromeres function as a platform for the assembly of multiple kinetochore proteins and are essential for chromosome segregation. An active centromere is characterized by the presence of a centromere-specific histone H3 variant, CENP-A. Faithful centromeric localization of CENP-A is supported by heterochromatin in almost all eukaryotes; however, heterochromatin proteins have been lost in most Saccharomycotina. Here, identification of CENP-A (CENP-AL.s.) and heterochromatin protein 1 (Lsw1) in a Saccharomycotina species, the oleaginous yeast Lipomyces starkeyi, is reported. To determine if these proteins are functional, the proteins in S. pombe, a species widely used to study centromeres, were ectopically expressed. CENP-AL.s. localizes to centromeres and can be replaced with S. pombe CENP-A, indicating that CENP-AL.s. is a functional centromere-specific protein. Lsw1 binds at heterochromatin regions, and chromatin binding is dependent on methylation of histone H3 at lysine 9. In other species, self-interaction of heterochromatin protein 1 is thought to cause folding of chromatin, triggering transcription repression and heterochromatin formation. Consistent with this, it was found that Lsw1 can self-interact. L. starkeyi chromatin contains the methylation of histone H3 at lysine 9. These results indicated that L. starkeyi has a primitive heterochromatin structure and is an attractive model for analysis of centromere heterochromatin evolution.
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Affiliation(s)
- Yuko Takayama
- Department of Biosciences, School of Science and Engineering, Teikyo University, 1-1 Toyosatodai, Utsunomiya, Tochigi 320–8551, Japan; ; Tel.: +81-28-627-7242
- Division of Integrated Science and Engineering, Graduate School of Science and Engineering, Teikyo University Graduate Schools, 1–1 Toyosatodai, Utsunomiya, Tochigi 320–8551, Japan
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19
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Abstract
The conserved serine-threonine kinase, Cdc7, plays a crucial role in initiation of DNA replication by facilitating the assembly of an initiation complex. Cdc7 is expressed at a high level and exhibits significant kinase activity not only during S-phase but also during G2/M-phases. A conserved mitotic kinase, Aurora B, is activated during M-phase by association with INCENP, forming the chromosome passenger complex with Borealin and Survivin. We show that Cdc7 phosphorylates and stimulates Aurora B kinase activity in vitro. We identified threonine-236 as a critical phosphorylation site on Aurora B that could be a target of Cdc7 or could be an autophosphorylation site stimulated by Cdc7-mediated phosphorylation elsewhere. We found that threonines at both 232 (that has been identified as an autophosphorylation site) and 236 are essential for the kinase activity of Aurora B. Cdc7 down regulation or inhibition reduced Aurora B activity in vivo and led to retarded M-phase progression. SAC imposed by paclitaxel was dramatically reversed by Cdc7 inhibition, similar to the effect of Aurora B inhibition under the similar situation. Our data show that Cdc7 contributes to M-phase progression and to spindle assembly checkpoint most likely through Aurora B activation.
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20
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Control of DNA replication timing in the 3D genome. Nat Rev Mol Cell Biol 2019; 20:721-737. [DOI: 10.1038/s41580-019-0162-y] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/18/2019] [Indexed: 12/27/2022]
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21
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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.
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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
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22
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Ren B, Tan HL, Nguyen TTT, Sayed AMM, Li Y, Mok YK, Yang H, Chen ES. Regulation of transcriptional silencing and chromodomain protein localization at centromeric heterochromatin by histone H3 tyrosine 41 phosphorylation in fission yeast. Nucleic Acids Res 2019; 46:189-202. [PMID: 29136238 PMCID: PMC5758876 DOI: 10.1093/nar/gkx1010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 10/13/2017] [Indexed: 12/29/2022] Open
Abstract
Heterochromatin silencing is critical for genomic integrity and cell survival. It is orchestrated by chromodomain (CD)-containing proteins that bind to methylated histone H3 lysine 9 (H3K9me), a hallmark of heterochromatin. Here, we show that phosphorylation of tyrosine 41 (H3Y41p)—a novel histone H3 modification—participates in the regulation of heterochromatin in fission yeast. We show that a loss-of-function mutant of H3Y41 can suppress heterochromatin de-silencing in the centromere and subtelomere repeat regions, suggesting a de-silencing role for H3Y41p on heterochromatin. Furthermore, we show both in vitro and in vivo that H3Y41p differentially regulates two CD-containing proteins without the change in the level of H3K9 methylation: it promotes the binding of Chp1 to histone H3 and the exclusion of Swi6. H3Y41p is preferentially enriched on centromeric heterochromatin during M- to early S phase, which coincides with the localization switch of Swi6/Chp1. The loss-of-function H3Y41 mutant could suppress the hypersensitivity of the RNAi mutants towards hydroxyurea (HU), which arrests replication in S phase. Overall, we describe H3Y41p as a novel histone modification that differentially regulates heterochromatin silencing in fission yeast via the binding of CD-containing proteins.
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Affiliation(s)
- Bingbing Ren
- Department of Biochemistry, National University of Singapore, Yong Loo Lin School of Medicine, Singapore
| | - Hwei Ling Tan
- Department of Biochemistry, National University of Singapore, Yong Loo Lin School of Medicine, Singapore
| | - Thi Thuy Trang Nguyen
- Department of Biochemistry, National University of Singapore, Yong Loo Lin School of Medicine, Singapore
| | | | - Ying Li
- Cancer Science Institute, National University of Singapore, Yong Loo Lin School of Medicine, Singapore
| | - Yu-Keung Mok
- Department of Biological Sciences, National University of Singapore
| | - Henry Yang
- Cancer Science Institute, National University of Singapore, Yong Loo Lin School of Medicine, Singapore.,National University Health System (NUHS), Singapore
| | - Ee Sin Chen
- Department of Biochemistry, National University of Singapore, Yong Loo Lin School of Medicine, Singapore.,National University Health System (NUHS), Singapore
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23
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Shen KF, Forsburg SL. Overlapping Roles in Chromosome Segregation for Heterochromatin Protein 1 (Swi6) and DDK in Schizosaccharomyces pombe. Genetics 2019; 212:417-430. [PMID: 31000521 PMCID: PMC6553818 DOI: 10.1534/genetics.119.302125] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 04/10/2019] [Indexed: 12/23/2022] Open
Abstract
Fission yeast Swi6 is a human HP1 homolog that plays important roles in multiple cellular processes. In addition to its role in maintaining heterochromatin silencing, Swi6 is required for cohesin enrichment at the pericentromere. Loss of Swi6 leads to abnormal mitosis, including defects in the establishment of bioriented sister kinetochores and microtubule attachment. Swi6 interacts with Dfp1, a regulatory subunit of DBF4-dependent kinase (DDK), and failure to recruit Dfp1 to the pericentromere results in late DNA replication. Using the dfp1-3A mutant allele, which specifically disrupts Swi6-Dfp1 association, we investigated how interaction between Swi6 and Dfp1 affects chromosome dynamics. We find that disrupting the interaction between Swi6 and Dfp1 delays mitotic progression in a spindle assembly checkpoint-dependent manner. Artificially tethering Dfp1 back to the pericentromere is sufficient to restore normal spindle length and rescue segregation defects in swi6-deleted cells. However, Swi6 is necessary for centromeric localization of Rad21-GFP independent of DDK. Our data indicate that DDK contributes to mitotic chromosome segregation in pathways that partly overlap with, but can be separated from both, Swi6 and the other HP1 homolog, Chp2.
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Affiliation(s)
- Kuo-Fang Shen
- Program in Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089-2910
| | - Susan L Forsburg
- Program in Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089-2910
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24
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Zhang H, Petrie MV, He Y, Peace JM, Chiolo IE, Aparicio OM. Dynamic relocalization of replication origins by Fkh1 requires execution of DDK function and Cdc45 loading at origins. eLife 2019; 8:45512. [PMID: 31084713 PMCID: PMC6533057 DOI: 10.7554/elife.45512] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 05/13/2019] [Indexed: 12/11/2022] Open
Abstract
Chromosomal DNA elements are organized into spatial domains within the eukaryotic nucleus. Sites undergoing DNA replication, high-level transcription, and repair of double-strand breaks coalesce into foci, although the significance and mechanisms giving rise to these dynamic structures are poorly understood. In S. cerevisiae, replication origins occupy characteristic subnuclear localizations that anticipate their initiation timing during S phase. Here, we link localization of replication origins in G1 phase with Fkh1 activity, which is required for their early replication timing. Using a Fkh1-dependent origin relocalization assay, we determine that execution of Dbf4-dependent kinase function, including Cdc45 loading, results in dynamic relocalization of a replication origin from the nuclear periphery to the interior in G1 phase. Origin mobility increases substantially with Fkh1-driven relocalization. These findings provide novel molecular insight into the mechanisms that govern dynamics and spatial organization of DNA replication origins and possibly other functional DNA elements.
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Affiliation(s)
- Haiyang Zhang
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, United States
| | - Meghan V Petrie
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, United States
| | - Yiwei He
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, United States
| | - Jared M Peace
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, United States
| | - Irene E Chiolo
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, United States
| | - Oscar M Aparicio
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, United States
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25
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Short-Homology-Mediated CRISPR/Cas9-Based Method for Genome Editing in Fission Yeast. G3-GENES GENOMES GENETICS 2019; 9:1153-1163. [PMID: 30755408 PMCID: PMC6469419 DOI: 10.1534/g3.118.200976] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The CRISPR/Cas9 system enables the editing of genomes of numerous organisms through the induction of the double-strand breaks (DSB) at specific chromosomal targets. We improved the CRISPR/Cas9 system to ease the direct introduction of a point mutation or a tagging sequence into the chromosome by combining it with the noncanonical homology-directed DNA repair (HDR) based genome editing in fission yeast. We constructed convenient cloning vectors, which possessed a guide RNA (gRNA) expression module, or the humanized Streptococcus pyogenes Cas9 gene that is expressed under the control of an inducible promoter to avoid the needless expression, or both a gRNA and Cas9 gene. Using this system, we attempted the short-homology-mediated genome editing and found that the HDR pathway provides high-frequency genome editing at target loci without the need of a long donor DNA. Using short oligonucleotides, we successfully introduced point mutations into two target genes at high frequency. We also precisely integrated the sequences for epitope and GFP tagging using donor DNA possessing short homology into the target loci, which enabled us to obtain cells expressing N-terminally tagged fusion proteins. This system could expedite genome editing in fission yeast, and could be applicable to other organisms.
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26
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Massey DJ, Kim D, Brooks KE, Smolka MB, Koren A. Next-Generation Sequencing Enables Spatiotemporal Resolution of Human Centromere Replication Timing. Genes (Basel) 2019; 10:genes10040269. [PMID: 30987063 PMCID: PMC6523654 DOI: 10.3390/genes10040269] [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: 02/14/2019] [Revised: 03/25/2019] [Accepted: 03/29/2019] [Indexed: 12/15/2022] Open
Abstract
Centromeres serve a critical function in preserving genome integrity across sequential cell divisions, by mediating symmetric chromosome segregation. The repetitive, heterochromatic nature of centromeres is thought to be inhibitory to DNA replication, but has also led to their underrepresentation in human reference genome assemblies. Consequently, centromeres have been excluded from genomic replication timing analyses, leaving their time of replication unresolved. However, the most recent human reference genome, hg38, included models of centromere sequences. To establish the experimental requirements for achieving replication timing profiles for centromeres, we sequenced G1- and S-phase cells from five human cell lines, and aligned the sequence reads to hg38. We were able to infer DNA replication timing profiles for the centromeres in each of the five cell lines, which showed that centromere replication occurs in mid-to-late S phase. Furthermore, we found that replication timing was more variable between cell lines in the centromere regions than expected, given the distribution of variation in replication timing genome-wide. These results suggest the potential of these, and future, sequence models to enable high-resolution studies of replication in centromeres and other heterochromatic regions.
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Affiliation(s)
- Dashiell J Massey
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
| | - Dongsung Kim
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA.
| | - Kayla E Brooks
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
| | - Marcus B Smolka
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA.
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
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27
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Hiratani I, Takahashi S. DNA Replication Timing Enters the Single-Cell Era. Genes (Basel) 2019; 10:genes10030221. [PMID: 30884743 PMCID: PMC6470765 DOI: 10.3390/genes10030221] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 03/12/2019] [Accepted: 03/12/2019] [Indexed: 12/20/2022] Open
Abstract
In mammalian cells, DNA replication timing is controlled at the level of megabase (Mb)-sized chromosomal domains and correlates well with transcription, chromatin structure, and three-dimensional (3D) genome organization. Because of these properties, DNA replication timing is an excellent entry point to explore genome regulation at various levels and a variety of studies have been carried out over the years. However, DNA replication timing studies traditionally required at least tens of thousands of cells, and it was unclear whether the replication domains detected by cell population analyses were preserved at the single-cell level. Recently, single-cell DNA replication profiling methods became available, which revealed that the Mb-sized replication domains detected by cell population analyses were actually well preserved in individual cells. In this article, we provide a brief overview of our current knowledge on DNA replication timing regulation in mammals based on cell population studies, outline the findings from single-cell DNA replication profiling, and discuss future directions and challenges.
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Affiliation(s)
- Ichiro Hiratani
- Laboratory for Developmental Epigenetics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Hyogo 650-0047, Japan.
| | - Saori Takahashi
- Laboratory for Developmental Epigenetics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Hyogo 650-0047, Japan.
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28
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Origin Firing Regulations to Control Genome Replication Timing. Genes (Basel) 2019; 10:genes10030199. [PMID: 30845782 PMCID: PMC6470937 DOI: 10.3390/genes10030199] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 02/25/2019] [Accepted: 02/28/2019] [Indexed: 12/19/2022] Open
Abstract
Complete genome duplication is essential for genetic homeostasis over successive cell generations. Higher eukaryotes possess a complex genome replication program that involves replicating the genome in units of individual chromatin domains with a reproducible order or timing. Two types of replication origin firing regulations ensure complete and well-timed domain-wise genome replication: (1) the timing of origin firing within a domain must be determined and (2) enough origins must fire with appropriate positioning in a short time window to avoid inter-origin gaps too large to be fully copied. Fundamental principles of eukaryotic origin firing are known. We here discuss advances in understanding the regulation of origin firing to control firing time. Work with yeasts suggests that eukaryotes utilise distinct molecular pathways to determine firing time of distinct sets of origins, depending on the specific requirements of the genomic regions to be replicated. Although the exact nature of the timing control processes varies between eukaryotes, conserved aspects exist: (1) the first step of origin firing, pre-initiation complex (pre-IC formation), is the regulated step, (2) many regulation pathways control the firing kinase Dbf4-dependent kinase, (3) Rif1 is a conserved mediator of late origin firing and (4) competition between origins for limiting firing factors contributes to firing timing. Characterization of the molecular timing control pathways will enable us to manipulate them to address the biological role of replication timing, for example, in cell differentiation and genome instability.
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29
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Abstract
Each genomic locus in a eukaryotic cell has a distinct average time of replication during S phase that depends on the spatial and temporal pattern of replication initiation events. Replication timing can affect genomic integrity because late replication is associated with an increased mutation rate. For most eukaryotes, the features of the genome that specify the location and timing of initiation events are unknown. To investigate these features for the fission yeast, Schizosaccharomyces pombe, we developed an integrative model to analyze large single-molecule and global genomic datasets. The model provides an accurate description of the complex dynamics of S. pombe DNA replication at high resolution. We present evidence that there are many more potential initiation sites in the S. pombe genome than previously identified and that the distribution of these sites is primarily determined by two factors: the sequence preferences of the origin recognition complex (ORC), and the interference of transcription with the assembly or stability of prereplication complexes (pre-RCs). We suggest that in addition to directly interfering with initiation, transcription has driven the evolution of the binding properties of ORC in S. pombe and other eukaryotic species to target pre-RC assembly to regions of the genome that are less likely to be transcribed.
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30
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Okita AK, Zafar F, Su J, Weerasekara D, Kajitani T, Takahashi TS, Kimura H, Murakami Y, Masukata H, Nakagawa T. Heterochromatin suppresses gross chromosomal rearrangements at centromeres by repressing Tfs1/TFIIS-dependent transcription. Commun Biol 2019; 2:17. [PMID: 30652128 PMCID: PMC6329695 DOI: 10.1038/s42003-018-0251-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 12/05/2018] [Indexed: 12/20/2022] Open
Abstract
Heterochromatin, characterized by histone H3 lysine 9 (H3K9) methylation, assembles on repetitive regions including centromeres. Although centromeric heterochromatin is important for correct segregation of chromosomes, its exact role in maintaining centromere integrity remains elusive. Here, we found in fission yeast that heterochromatin suppresses gross chromosomal rearrangements (GCRs) at centromeres. Mutations in Clr4/Suv39 methyltransferase increased the formation of isochromosomes, whose breakpoints were located in centromere repeats. H3K9A and H3K9R mutations also increased GCRs, suggesting that Clr4 suppresses centromeric GCRs via H3K9 methylation. HP1 homologs Swi6 and Chp2 and the RNAi component Chp1 were the chromodomain proteins essential for full suppression of GCRs. Remarkably, mutations in RNA polymerase II (RNAPII) or Tfs1/TFIIS, the transcription factor that facilitates restart of RNAPII after backtracking, specifically bypassed the requirement of Clr4 for suppressing GCRs. These results demonstrate that heterochromatin suppresses GCRs by repressing Tfs1-dependent transcription of centromere repeats.
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Affiliation(s)
- Akiko K. Okita
- 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
| | - Jie Su
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043 Japan
| | - Dayalini Weerasekara
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043 Japan
| | - Takuya Kajitani
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810 Japan
- Present Address: Department of Molecular Biology and Genetics, Cornell University, 526 Campus Road, Ithaca, NY 14853 USA
| | - Tatsuro S. Takahashi
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043 Japan
- Present Address: Department of Biology, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395 Japan
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, Kanagawa 226-8503 Japan
| | - Yota Murakami
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810 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
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31
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Ogawa S, Kido S, Handa T, Ogawa H, Asakawa H, Takahashi TS, Nakagawa T, Hiraoka Y, Masukata H. Shelterin promotes tethering of late replication origins to telomeres for replication-timing control. EMBO J 2018; 37:embj.201898997. [PMID: 29997179 DOI: 10.15252/embj.201898997] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 05/19/2018] [Accepted: 06/19/2018] [Indexed: 12/12/2022] Open
Abstract
DNA replication initiates at many discrete loci on eukaryotic chromosomes, and individual replication origins are regulated under a spatiotemporal program. However, the underlying mechanisms of this regulation remain largely unknown. In the fission yeast Schizosaccharomyces pombe, the telomere-binding protein Taz1, ortholog of human TRF1/TRF2, regulates a subset of late replication origins by binding to the telomere-like sequence near the origins. Here, we showed using a lacO/LacI-GFP system that Taz1-dependent late origins were predominantly localized at the nuclear periphery throughout interphase, and were localized adjacent to the telomeres in the G1/S phase. The peripheral localization that depended on the nuclear membrane protein Bqt4 was not necessary for telomeric association and replication-timing control of the replication origins. Interestingly, the shelterin components Rap1 and Poz1 were required for replication-timing control and telomeric association of Taz1-dependent late origins, and this requirement was bypassed by a minishelterin Tpz1-Taz1 fusion protein. Our results suggest that Taz1 suppresses replication initiation through shelterin-mediated telomeric association of the origins at the onset of S phase.
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Affiliation(s)
- Shiho Ogawa
- Graduate School of Science, Osaka University, Toyonaka Osaka, Japan
| | - Sayuri Kido
- Graduate School of Science, Osaka University, Toyonaka Osaka, Japan
| | - Tetsuya Handa
- Graduate School of Science, Osaka University, Toyonaka Osaka, Japan
| | - Hidesato Ogawa
- Graduate School of Frontier Biosciences, Osaka University, Suita Osaka, Japan
| | - Haruhiko Asakawa
- Graduate School of Frontier Biosciences, Osaka University, Suita Osaka, Japan
| | | | - Takuro Nakagawa
- Graduate School of Science, Osaka University, Toyonaka Osaka, Japan
| | - Yasushi Hiraoka
- Graduate School of Frontier Biosciences, Osaka University, Suita Osaka, Japan
| | - Hisao Masukata
- Graduate School of Science, Osaka University, Toyonaka Osaka, Japan .,Graduate School of Frontier Biosciences, Osaka University, Suita Osaka, Japan
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32
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Ebrahimi H, Masuda H, Jain D, Cooper JP. Distinct 'safe zones' at the nuclear envelope ensure robust replication of heterochromatic chromosome regions. eLife 2018; 7:32911. [PMID: 29722648 PMCID: PMC5933923 DOI: 10.7554/elife.32911] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 03/30/2018] [Indexed: 12/24/2022] Open
Abstract
Chromosome replication and transcription occur within a complex nuclear milieu whose functional subdomains are beginning to be mapped out. Here we delineate distinct domains of the fission yeast nuclear envelope (NE), focusing on regions enriched for the inner NE protein, Bqt4, or the lamin interacting domain protein, Lem2. Bqt4 is relatively mobile around the NE and acts in two capacities. First, Bqt4 tethers chromosome termini and the mat locus to the NE specifically while these regions are replicating. This positioning is required for accurate heterochromatin replication. Second, Bqt4 mobilizes a subset of Lem2 molecules around the NE to promote pericentric heterochromatin maintenance. Opposing Bqt4-dependent Lem2 mobility are factors that stabilize Lem2 beneath the centrosome, where Lem2 plays a crucial role in kinetochore maintenance. Our data prompt a model in which Bqt4-rich nuclear subdomains are 'safe zones' in which collisions between transcription and replication are averted and heterochromatin is reassembled faithfully.
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Affiliation(s)
- Hani Ebrahimi
- Telomere Biology Section, Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, United States
| | - Hirohisa Masuda
- Telomere Biology Section, Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, United States
| | - Devanshi Jain
- Telomere Biology Section, Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, United States
| | - Julia Promisel Cooper
- Telomere Biology Section, Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, United States
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33
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Lin FM, Kumar S, Ren J, Karami S, Bahnassy S, Li Y, Zheng X, Wang J, Bawa-Khalfe T. SUMOylation of HP1α supports association with ncRNA to define responsiveness of breast cancer cells to chemotherapy. Oncotarget 2017; 7:30336-49. [PMID: 27107417 PMCID: PMC5058684 DOI: 10.18632/oncotarget.8733] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 04/03/2016] [Indexed: 01/19/2023] Open
Abstract
Epigenetic reprogramming allows cancer cells to bypass normal checkpoints and potentiate aberrant proliferation. Several chromatin regulators are subject to reversible SUMO-modification but little is known about how SUMOylation of chromatin-remodelers modulates the cancer epigenome. Recently, we demonstrated that SUMO-protease SENP7L is upregulated in aggressive BCa and maintains hypoSUMOylated heterochromatin protein 1-α (HP1α). Canonical models define HP1α as a "reader" of repressive H3K9m3 marks that supports constitutive heterochromatin. It is unclear how SUMOylation affects HP1α function in BCa cells. This report shows HP1α SUMO-dynamics are closely regulated in a complex with SENP7L and SUMO-E3 Polycomb-2 (PC2/CBX4). This complex accumulates at H3K9m3 sites, hypoSUMOylates HP1α and PC2, and reduces PC2's SUMO-E3 activity. HyperSUMO conditions cause complex dissociation, SUMOylation of PC2 and HP1α, and recruitment of SUMOylated HP1α to multiple DNA-repair genes including Rad51C. SUMOylated HP1α's enrichment at euchromatin requires chromatin-bound non-coding RNA (ncRNA), reduces Rad51C protein, and increases DNA-breaks in BCa cells. Hence, HP1α SUMOylation and consistently low SENP7L increase efficacy of DNA-damaging chemotherapeutic agents. BCa patients on chemotherapy that express low SENP7L exhibit greater survival rates than patients with high SENP7L. Collectively, these studies suggest that SUMOylated HP1α is a critical epigenetic-regulator of DNA-repair in BCa that could define chemotherapy responsiveness.
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Affiliation(s)
- Feng-Ming Lin
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Santosh Kumar
- Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Jing Ren
- Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Samaneh Karami
- Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Shaymaa Bahnassy
- Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Yue Li
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Xiaofeng Zheng
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jing Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tasneem Bawa-Khalfe
- Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
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34
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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.
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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.
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35
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Aladjem MI, Redon CE. Order from clutter: selective interactions at mammalian replication origins. Nat Rev Genet 2017; 18:101-116. [PMID: 27867195 PMCID: PMC6596300 DOI: 10.1038/nrg.2016.141] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Mammalian chromosome duplication progresses in a precise order and is subject to constraints that are often relaxed in developmental disorders and malignancies. Molecular information about the regulation of DNA replication at the chromatin level is lacking because protein complexes that initiate replication seem to bind chromatin indiscriminately. High-throughput sequencing and mathematical modelling have yielded detailed genome-wide replication initiation maps. Combining these maps and models with functional genetic analyses suggests that distinct DNA-protein interactions at subgroups of replication initiation sites (replication origins) modulate the ubiquitous replication machinery and supports an emerging model that delineates how indiscriminate DNA-binding patterns translate into a consistent, organized replication programme.
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Affiliation(s)
- Mirit I Aladjem
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, 37 Convent Drive, Bethesda, Maryland 20892, USA
| | - Christophe E Redon
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, 37 Convent Drive, Bethesda, Maryland 20892, USA
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36
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Toteva T, Mason B, Kanoh Y, Brøgger P, Green D, Verhein-Hansen J, Masai H, Thon G. Establishment of expression-state boundaries by Rif1 and Taz1 in fission yeast. Proc Natl Acad Sci U S A 2017; 114:1093-1098. [PMID: 28096402 PMCID: PMC5293076 DOI: 10.1073/pnas.1614837114] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The Shelterin component Rif1 has emerged as a global regulator of the replication-timing program in all eukaryotes examined to date, possibly by modulating the 3D-organization of the genome. In fission yeast a second Shelterin component, Taz1, might share similar functions. Here, we identified unexpected properties for Rif1 and Taz1 by conducting high-throughput genetic screens designed to identify cis- and trans-acting factors capable of creating heterochromatin-euchromatin boundaries in fission yeast. The preponderance of cis-acting elements identified in the screens originated from genomic loci bound by Taz1 and associated with origins of replication whose firing is repressed by Taz1 and Rif1. Boundary formation and gene silencing by these elements required Taz1 and Rif1 and coincided with altered replication timing in the region. Thus, small chromosomal elements sensitive to Taz1 and Rif1 (STAR) could simultaneously regulate gene expression and DNA replication over a large domain, at the edge of which they established a heterochromatin-euchromatin boundary. Taz1, Rif1, and Rif1-associated protein phosphatases Sds21 and Dis2 were each sufficient to establish a boundary when tethered to DNA. Moreover, efficient boundary formation required the amino-terminal domain of the Mcm4 replicative helicase onto which the antagonistic activities of the replication-promoting Dbf4-dependent kinase and Rif1-recruited phosphatases are believed to converge to control replication origin firing. Altogether these observations provide an insight into a coordinated control of DNA replication and organization of the genome into expression domains.
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Affiliation(s)
- Tea Toteva
- Department of Biology, BioCenter, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Bethany Mason
- Department of Biology, BioCenter, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Yutaka Kanoh
- Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamkitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Peter Brøgger
- Department of Biology, BioCenter, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Daniel Green
- Department of Biology, BioCenter, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Janne Verhein-Hansen
- Department of Biology, BioCenter, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Hisao Masai
- Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamkitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Geneviève Thon
- Department of Biology, BioCenter, University of Copenhagen, 2200 Copenhagen N, Denmark;
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37
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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.
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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.
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38
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Kelly T. Historical Perspective of Eukaryotic DNA Replication. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1042:1-41. [PMID: 29357051 DOI: 10.1007/978-981-10-6955-0_1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The replication of the genome of a eukaryotic cell is a complex process requiring the ordered assembly of multiprotein replisomes at many chromosomal sites. The process is strictly controlled during the cell cycle to ensure the complete and faithful transmission of genetic information to progeny cells. Our current understanding of the mechanisms of eukaryotic DNA replication has evolved over a period of more than 30 years through the efforts of many investigators. The aim of this perspective is to provide a brief history of the major advances during this period.
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Affiliation(s)
- Thomas Kelly
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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39
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Lin SJ, Tapia-Alveal C, Jabado OJ, Germain D, O'Connell MJ. An acetyltransferase-independent function of Eso1 regulates centromere cohesion. Mol Biol Cell 2016; 27:4002-4010. [PMID: 27798241 PMCID: PMC5156541 DOI: 10.1091/mbc.e16-08-0596] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 10/11/2016] [Accepted: 10/12/2016] [Indexed: 12/21/2022] Open
Abstract
Eukaryotes contain three essential Structural Maintenance of Chromosomes (SMC) complexes: cohesin, condensin, and Smc5/6. Cohesin forms a ring-shaped structure that embraces sister chromatids to promote their cohesion. The cohesiveness of cohesin is promoted by acetylation of N-terminal lysines of the Smc3 subunit by the acetyltransferases Eco1 in Saccharomyces cerevisiae and the homologue, Eso1, in Schizosaccharomyces pombe. In both yeasts, these acetyltransferases are essential for cell viability. However, whereas nonacetylatable Smc3 mutants are lethal in S. cerevisiae, they are not in S. pombe We show that the lethality of a temperature-sensitive allele of eso1 (eso1-H17) is due to activation of the spindle assembly checkpoint (SAC) and is associated with premature centromere separation. The lack of cohesion at the centromeres does not correlate with Psm3 acetylation or cohesin levels at the centromeres, but is associated ith significantly reduced recruitment of the cohesin regulator Pds5. The SAC activation in this context is dependent on Smc5/6 function, which is required to remove cohesin from chromosome arms but not centromeres. The mitotic defects caused by Smc5/6 and Eso1 dysfunction are cosuppressed in double mutants. This identifies a novel function (or functions) for Eso1 and Smc5/6 at centromeres and extends the functional relationships between these SMC complexes.
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Affiliation(s)
- Su-Jiun Lin
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Claudia Tapia-Alveal
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Omar J Jabado
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Doris Germain
- Department of Hematology and Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Matthew J O'Connell
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
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40
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Feng W, Michaels SD. Accessing the Inaccessible: The Organization, Transcription, Replication, and Repair of Heterochromatin in Plants. Annu Rev Genet 2016; 49:439-59. [PMID: 26631514 DOI: 10.1146/annurev-genet-112414-055048] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Eukaryotic genomes often contain large quantities of potentially deleterious sequences, such as transposons. One strategy for mitigating this risk is to package such sequences into so-called constitutive heterochromatin, where the dense chromatin environment is thought to inhibit transcription by excluding transcription factors and RNA polymerase. This type of model makes it tempting to think of heterochromatin as an inert region that is isolated from the rest of the nucleus. Recent work on heterochromatin, however, reveals that it is a dynamic environment. Despite its dense packaging, heterochromatin must remain accessible for a host of processes, including DNA replication and repair, and, paradoxically, transcription. In plants, transcripts produced by specialized RNA polymerases are used to target regions of the genome for silencing via DNA methylation. Thus, the maintenance of heterochromatin requires a careful balancing act of access and exclusion, which is achieved through the action of a host of interrelated pathways.
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Affiliation(s)
- Wei Feng
- Carnegie Institution for Science, Department of Plant Biology, Stanford, California 94305;
| | - Scott D Michaels
- Department of Biology, Indiana University, Bloomington, Indiana 47405;
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41
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Son M, Lee Y, Kim KH. The Transcription Cofactor Swi6 of the Fusarium graminearum Is Involved in Fusarium Graminearum Virus 1 Infection-Induced Phenotypic Alterations. THE PLANT PATHOLOGY JOURNAL 2016; 32:281-289. [PMID: 27493603 PMCID: PMC4968638 DOI: 10.5423/ppj.oa.12.2015.0267] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 02/24/2016] [Accepted: 02/24/2016] [Indexed: 06/06/2023]
Abstract
The transcription cofactor Swi6 plays important roles in regulating vegetative growth and meiosis in Saccharomyces cerevisiae. Functions of Swi6 ortholog were also characterized in Fusarium graminearum which is one of the devastating plant pathogenic fungi. Here, we report possible role of FgSwi6 in the interaction between F. graminearum and Fusarium graminearum virus 1 (FgV1) strain DK21. FgV1 perturbs biological characteristics of host fungi such as vegetative growth, sporulation, pigmentation, and reduction of the virulence (hypovirulence) of its fungal host. To characterize function(s) of FgSWI6 gene during FgV1 infection, targeted deletion, over-expression, and complementation mutants were generated and further infected successfully with FgV1. Deletion of FgSwi6 led to severe reduction of vegetative growth even aerial mycelia while over-expression did not affect any remarkable alteration of phenotype in virus-free isolates. Virus-infected (VI) FgSWI6 deletion isolate exhibited completely delayed vegetative growth. However, VI FgSWI6 over-expression mutant grew faster than any other VI isolates. To verify whether these different growth patterns in VI isolates, viral RNA quantification was carried out using qRT-PCR. Surprisingly, viral RNA accumulations in VI isolates were similar regardless of introduced mutations. These results provide evidence that FgSWI6 might play important role(s) in FgV1 induced phenotype alteration such as delayed vegetative growth.
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Affiliation(s)
- Moonil Son
- Department of Agricultural Biotechnology and Center for Fungal Pathogenesis, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826,
Korea
- Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826,
Korea
| | - Yoonseung Lee
- Department of Applied Biology and Chemistry, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826,
Korea
| | - Kook-Hyung Kim
- Department of Agricultural Biotechnology and Center for Fungal Pathogenesis, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826,
Korea
- Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826,
Korea
- Department of Applied Biology and Chemistry, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826,
Korea
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42
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Tripathi VP, Dubey DD. A replication-time-controlling sequence element in Schizosaccharomyces pombe. Chromosoma 2016; 126:465-471. [DOI: 10.1007/s00412-016-0606-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 06/09/2016] [Accepted: 06/14/2016] [Indexed: 12/31/2022]
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43
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The Histone Variant H3.3 Is Enriched at Drosophila Amplicon Origins but Does Not Mark Them for Activation. G3-GENES GENOMES GENETICS 2016; 6:1661-71. [PMID: 27172191 PMCID: PMC4889662 DOI: 10.1534/g3.116.028068] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Eukaryotic DNA replication begins from multiple origins. The origin recognition complex (ORC) binds origin DNA and scaffolds assembly of a prereplicative complex (pre-RC), which is subsequently activated to initiate DNA replication. In multicellular eukaryotes, origins do not share a strict DNA consensus sequence, and their activity changes in concert with chromatin status during development, but mechanisms are ill-defined. Previous genome-wide analyses in Drosophila and other organisms have revealed a correlation between ORC binding sites and the histone variant H3.3. This correlation suggests that H3.3 may designate origin sites, but this idea has remained untested. To address this question, we examined the enrichment and function of H3.3 at the origins responsible for developmental gene amplification in the somatic follicle cells of the Drosophila ovary. We found that H3.3 is abundant at these amplicon origins. H3.3 levels remained high when replication initiation was blocked, indicating that H3.3 is abundant at the origins before activation of the pre-RC. H3.3 was also enriched at the origins during early oogenesis, raising the possibility that H3.3 bookmarks sites for later amplification. However, flies null mutant for both of the H3.3 genes in Drosophila did not have overt defects in developmental gene amplification or genomic replication, suggesting that H3.3 is not essential for the assembly or activation of the pre-RC at origins. Instead, our results imply that the correlation between H3.3 and ORC sites reflects other chromatin attributes that are important for origin function.
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44
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Xu YJ. Inner nuclear membrane protein Lem2 facilitates Rad3-mediated checkpoint signaling under replication stress induced by nucleotide depletion in fission yeast. Cell Signal 2016; 28:235-45. [PMID: 26746798 PMCID: PMC4753118 DOI: 10.1016/j.cellsig.2015.12.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Revised: 12/02/2015] [Accepted: 12/17/2015] [Indexed: 01/19/2023]
Abstract
DNA replication checkpoint is a highly conserved cellular signaling pathway critical for maintaining genome integrity in eukaryotes. It is activated when DNA replication is perturbed. In Schizosaccharomyces pombe, perturbed replication forks activate the sensor kinase Rad3 (ATR/Mec1), which works cooperatively with mediator Mrc1 and the 9-1-1 checkpoint clamp to phosphorylate the effector kinase Cds1 (CHK2/Rad53). Phosphorylation of Cds1 promotes autoactivation of the kinase. Activated Cds1 diffuses away from the forks and stimulates most of the checkpoint responses under replication stress. Although this signaling pathway has been well understood in fission yeast, how the signaling is initiated and thus regulated remains incompletely understood. Previous studies have shown that deletion of lem2(+) sensitizes cells to the inhibitor of ribonucleotide reductase, hydroxyurea. However, the underlying mechanism is still not well understood. This study shows that in the presence of hydroxyurea, Lem2 facilitates Rad3-mediated checkpoint signaling for Cds1 activation. Without Lem2, all known Rad3-dependent phosphorylations critical for replication checkpoint signaling are seriously compromised, which likely causes the aberrant mitosis and drug sensitivity observed in this mutant. Interestingly, the mutant is not very sensitive to DNA damage and the DNA damage checkpoint remains largely intact, suggesting that the main function of Lem2 is to facilitate checkpoint signaling in response to replication stress. Since Lem2 is an inner nuclear membrane protein, these results also suggest that the replication checkpoint may be spatially regulated inside the nucleus, a previously unknown mechanism.
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Affiliation(s)
- Yong-Jie Xu
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, 3640 Colonel Glenn Hwy., Dayton OH 45435, USA.
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45
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Quantitative BrdU immunoprecipitation method demonstrates that Fkh1 and Fkh2 are rate-limiting activators of replication origins that reprogram replication timing in G1 phase. Genome Res 2016; 26:365-75. [PMID: 26728715 PMCID: PMC4772018 DOI: 10.1101/gr.196857.115] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 12/17/2015] [Indexed: 01/31/2023]
Abstract
The Saccharomyces cerevisiaeForkhead Box (FOX) proteins, Fkh1 and Fkh2, regulate diverse cellular processes including transcription, long-range DNA interactions during homologous recombination, and replication origin timing and long-range origin clustering. We hypothesized that, as stimulators of early origin activation, Fkh1 and Fkh2 abundance limits the rate of origin activation genome-wide. Existing methods, however, are not well-suited to quantitative, genome-wide measurements of origin firing between strains and conditions. To overcome this limitation, we developed qBrdU-seq, a quantitative method for BrdU incorporation analysis of replication dynamics, and applied it to show that overexpression of Fkh1 and Fkh2 advances the initiation timing of many origins throughout the genome resulting in a higher total level of origin initiations in early S phase. The higher initiation rate is accompanied by slower replication fork progression, thereby maintaining a normal length of S phase without causing detectable Rad53 checkpoint kinase activation. The advancement of origin firing time, including that of origins in heterochromatic domains, was established in late G1 phase, indicating that origin timing can be reset subsequently to origin licensing. These results provide novel insights into the mechanisms of origin timing regulation by identifying Fkh1 and Fkh2 as rate-limiting factors for origin firing that determine the ability of replication origins to accrue limiting factors and have the potential to reprogram replication timing late in G1 phase.
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46
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Hutchins JRA, Aze A, Coulombe P, Méchali M. Characteristics of Metazoan DNA Replication Origins. DNA REPLICATION, RECOMBINATION, AND REPAIR 2016. [PMCID: PMC7120227 DOI: 10.1007/978-4-431-55873-6_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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47
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Abstract
DNA replication begins with the assembly of pre-replication complexes (pre-RCs) at thousands of DNA replication origins during the G1 phase of the cell cycle. At the G1-S-phase transition, pre-RCs are converted into pre-initiation complexes, in which the replicative helicase is activated, leading to DNA unwinding and initiation of DNA synthesis. However, only a subset of origins are activated during any S phase. Recent insights into the mechanisms underlying this choice reveal how flexibility in origin usage and temporal activation are linked to chromosome structure and organization, cell growth and differentiation, and replication stress.
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48
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Liu J, Zimmer K, Rusch DB, Paranjape N, Podicheti R, Tang H, Calvi BR. DNA sequence templates adjacent nucleosome and ORC sites at gene amplification origins in Drosophila. Nucleic Acids Res 2015; 43:8746-61. [PMID: 26227968 PMCID: PMC4605296 DOI: 10.1093/nar/gkv766] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 07/16/2015] [Indexed: 12/12/2022] Open
Abstract
Eukaryotic origins of DNA replication are bound by the origin recognition complex (ORC), which scaffolds assembly of a pre-replicative complex (pre-RC) that is then activated to initiate replication. Both pre-RC assembly and activation are strongly influenced by developmental changes to the epigenome, but molecular mechanisms remain incompletely defined. We have been examining the activation of origins responsible for developmental gene amplification in Drosophila. At a specific time in oogenesis, somatic follicle cells transition from genomic replication to a locus-specific replication from six amplicon origins. Previous evidence indicated that these amplicon origins are activated by nucleosome acetylation, but how this affects origin chromatin is unknown. Here, we examine nucleosome position in follicle cells using micrococcal nuclease digestion with Ilumina sequencing. The results indicate that ORC binding sites and other essential origin sequences are nucleosome-depleted regions (NDRs). Nucleosome position at the amplicons was highly similar among developmental stages during which ORC is or is not bound, indicating that being an NDR is not sufficient to specify ORC binding. Importantly, the data suggest that nucleosomes and ORC have opposite preferences for DNA sequence and structure. We propose that nucleosome hyperacetylation promotes pre-RC assembly onto adjacent DNA sequences that are disfavored by nucleosomes but favored by ORC.
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Affiliation(s)
- Jun Liu
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Kurt Zimmer
- School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA
| | - Douglas B Rusch
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA
| | - Neha Paranjape
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Ram Podicheti
- School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA
| | - Haixu Tang
- School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA
| | - Brian R Calvi
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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49
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Musiałek MW, Rybaczek D. Behavior of replication origins in Eukaryota - spatio-temporal dynamics of licensing and firing. Cell Cycle 2015; 14:2251-64. [PMID: 26030591 DOI: 10.1080/15384101.2015.1056421] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Although every organism shares some common features of replication, this process varies greatly among eukaryotic species. Current data show that mathematical models of the organization of origins based on possibility theory may be applied (and remain accurate) in every model organism i.e. from yeast to humans. The major differences lie within the dynamics of origin firing and the regulation mechanisms that have evolved to meet new challenges throughout the evolution of the organism. This article elaborates on the relations between chromatin structure, organization of origins, their firing times and the impact that these features can have on genome stability, showing both differences and parallels inside the eukaryotic domain.
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Key Words
- APC, anaphase promoting complex
- ARS, autonomously replicating sequences
- ATR, ataxia telangiectasia mutated and Rad3-related kinase
- C-Frag, chromosome fragmentation
- CDK, cyclin-dependent kinase
- CDT, C-terminus domain
- CEN, centromere
- CFSs, chromosome fragile sites
- CIN, chromosome instability
- CMG, Cdc45-MCM-GINS complex
- Cdc45, cell division control protein 45
- Cdc6, cell division control protein 6
- Cdt1, chromatin licensing and DNA replication factor 1
- Chk1, checkpoint kinase 1
- Clb2, G2/mitotic-specific cyclin Clb2
- DCR, Ddb1-Cu14a-Roc1 complex
- DDK, Dbf-4-dependent kinase
- DSBs, double strand breaks
- Dbf4, protein Dbf4 homolog A
- Dfp1, Hsk1-Dfp1 kinase complex regulatory subunit Dfp1
- Dpb11, DNA replication regulator Dpb11
- E2F, E2F transcription factor
- EL, early to late origins transition
- ETG1, E2F target gene 1/replisome factor
- Fkh, fork head domain protein
- GCN5, histone acetyltransferase GCN5
- GINS, go-ichi-ni-san
- LE, late to early origins transition
- MCM2–7, minichromosome maintenance helicase complex
- NDT, N-terminus domain
- ORC, origin recognition complex
- ORCA, origin recognition complex subunit A
- PCC, premature chromosome condensation
- PCNA, proliferating cell nuclear antigen
- RO, replication origin
- RPD3, histone deacetylase 3
- RTC, replication timing control
- Rif1, replication timing regulatory factor 1
- SCF, Skp1-Cullin-F-Box ligase
- SIR, sulfite reductase
- Sld2, replication regulator Sld2
- Sld3, replication regulator Sld3
- Swi6, chromatin-associated protein swi6
- Taz1, telomere length regulator taz1
- YKU70, yeast Ku protein.
- dormant origins
- mathematical models of replication
- ori, origin
- origin competence
- origin efficiency
- origin firing
- origin licensing
- p53, tumor suppressor protein p53
- replication timing
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Affiliation(s)
- Marcelina W Musiałek
- a Department of Cytophysiology ; Institute of Experimental Biology; Faculty of Biology and Environmental Protection; University of Łódź ; Łódź , Poland
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50
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Brancucci NMB, Bertschi NL, Zhu L, Niederwieser I, Chin WH, Wampfler R, Freymond C, Rottmann M, Felger I, Bozdech Z, Voss TS. Heterochromatin protein 1 secures survival and transmission of malaria parasites. Cell Host Microbe 2015; 16:165-176. [PMID: 25121746 DOI: 10.1016/j.chom.2014.07.004] [Citation(s) in RCA: 186] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Revised: 04/28/2014] [Accepted: 06/06/2014] [Indexed: 12/14/2022]
Abstract
Clonally variant expression of surface antigens allows the malaria parasite Plasmodium falciparum to evade immune recognition during blood stage infection and secure malaria transmission. We demonstrate that heterochromatin protein 1 (HP1), an evolutionary conserved regulator of heritable gene silencing, controls expression of numerous P. falciparum virulence genes as well as differentiation into the sexual forms that transmit to mosquitoes. Conditional depletion of P. falciparum HP1 (PfHP1) prevents mitotic proliferation of blood stage parasites and disrupts mutually exclusive expression and antigenic variation of the major virulence factor PfEMP1. Additionally, PfHP1-dependent regulation of PfAP2-G, a transcription factor required for gametocyte conversion, controls the switch from asexual proliferation to sexual differentiation, providing insight into the epigenetic mechanisms underlying gametocyte commitment. These findings show that PfHP1 is centrally involved in clonally variant gene expression and sexual differentiation in P. falciparum and have major implications for developing antidisease and transmission-blocking interventions against malaria.
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Affiliation(s)
- Nicolas M B Brancucci
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Socinstrasse 57, Basel 4051, Switzerland; University of Basel, Petersplatz 1, Basel 4003, Switzerland
| | - Nicole L Bertschi
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Socinstrasse 57, Basel 4051, Switzerland; University of Basel, Petersplatz 1, Basel 4003, Switzerland
| | - Lei Zhu
- School of Biological Sciences, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Igor Niederwieser
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Socinstrasse 57, Basel 4051, Switzerland; University of Basel, Petersplatz 1, Basel 4003, Switzerland
| | - Wai Hoe Chin
- School of Biological Sciences, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Rahel Wampfler
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Socinstrasse 57, Basel 4051, Switzerland; University of Basel, Petersplatz 1, Basel 4003, Switzerland
| | - Céline Freymond
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Socinstrasse 57, Basel 4051, Switzerland; University of Basel, Petersplatz 1, Basel 4003, Switzerland
| | - Matthias Rottmann
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Socinstrasse 57, Basel 4051, Switzerland; University of Basel, Petersplatz 1, Basel 4003, Switzerland
| | - Ingrid Felger
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Socinstrasse 57, Basel 4051, Switzerland; University of Basel, Petersplatz 1, Basel 4003, Switzerland
| | - Zbynek Bozdech
- School of Biological Sciences, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Till S Voss
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Socinstrasse 57, Basel 4051, Switzerland; University of Basel, Petersplatz 1, Basel 4003, Switzerland.
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