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Rojas P, Wang J, Guglielmi G, Sadurnì MM, Pavlou L, Leung GHD, Rajagopal V, Spill F, Saponaro M. Genome-wide identification of replication fork stalling/pausing sites and the interplay between RNA Pol II transcription and DNA replication progression. Genome Biol 2024; 25:126. [PMID: 38773641 PMCID: PMC11106976 DOI: 10.1186/s13059-024-03278-8] [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: 01/27/2023] [Accepted: 05/14/2024] [Indexed: 05/24/2024] Open
Abstract
BACKGROUND DNA replication progression can be affected by the presence of physical barriers like the RNA polymerases, leading to replication stress and DNA damage. Nonetheless, we do not know how transcription influences overall DNA replication progression. RESULTS To characterize sites where DNA replication forks stall and pause, we establish a genome-wide approach to identify them. This approach uses multiple timepoints during S-phase to identify replication fork/stalling hotspots as replication progresses through the genome. These sites are typically associated with increased DNA damage, overlapped with fragile sites and with breakpoints of rearrangements identified in cancers but do not overlap with replication origins. Overlaying these sites with a genome-wide analysis of RNA polymerase II transcription, we find that replication fork stalling/pausing sites inside genes are directly related to transcription progression and activity. Indeed, we find that slowing down transcription elongation slows down directly replication progression through genes. This indicates that transcription and replication can coexist over the same regions. Importantly, rearrangements found in cancers overlapping transcription-replication collision sites are detected in non-transformed cells and increase following treatment with ATM and ATR inhibitors. At the same time, we find instances where transcription activity favors replication progression because it reduces histone density. CONCLUSIONS Altogether, our findings highlight how transcription and replication overlap during S-phase, with both positive and negative consequences for replication fork progression and genome stability by the coexistence of these two processes.
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Affiliation(s)
- Patricia Rojas
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Jianming Wang
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Giovanni Guglielmi
- School of Mathematics, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Department of Biomedical Engineering, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Martina Mustè Sadurnì
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Lucas Pavlou
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Geoffrey Ho Duen Leung
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Vijay Rajagopal
- Department of Biomedical Engineering, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Fabian Spill
- School of Mathematics, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Marco Saponaro
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
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2
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Fenstermaker TK, Petruk S, Mazo A. An emerging paradigm in epigenetic marking: coordination of transcription and replication. Transcription 2024; 15:22-37. [PMID: 38378467 DOI: 10.1080/21541264.2024.2316965] [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] [Received: 12/22/2023] [Accepted: 02/06/2024] [Indexed: 02/22/2024] Open
Abstract
DNA replication and RNA transcription both utilize DNA as a template and therefore need to coordinate their activities. The predominant theory in the field is that in order for the replication fork to proceed, transcription machinery has to be evicted from DNA until replication is complete. If that does not occur, these machineries collide, and these collisions elicit various repair mechanisms which require displacement of one of the enzymes, often RNA polymerase, in order for replication to proceed. This model is also at the heart of the epigenetic bookmarking theory, which implies that displacement of RNA polymerase during replication requires gradual re-building of chromatin structure, which guides recruitment of transcriptional proteins and resumption of transcription. We discuss these theories but also bring to light newer data that suggest that these two processes may not be as detrimental to one another as previously thought. This includes findings suggesting that these processes can occur without fork collapse and that RNA polymerase may only be transiently displaced during DNA replication. We discuss potential mechanisms by which RNA polymerase may be retained at the replication fork and quickly rebind to DNA post-replication. These discoveries are important, not only as new evidence as to how these two processes are able to occur harmoniously but also because they have implications on how transcriptional programs are maintained through DNA replication. To this end, we also discuss the coordination of replication and transcription in light of revising the current epigenetic bookmarking theory of how the active gene status can be transmitted through S phase.
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Affiliation(s)
- Tyler K Fenstermaker
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Svetlana Petruk
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Alexander Mazo
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
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3
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Fenstermaker TK, Petruk S, Kovermann SK, Brock HW, Mazo A. RNA polymerase II associates with active genes during DNA replication. Nature 2023; 620:426-433. [PMID: 37468626 DOI: 10.1038/s41586-023-06341-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 06/19/2023] [Indexed: 07/21/2023]
Abstract
The transcriptional machinery is thought to dissociate from DNA during replication. Certain proteins, termed epigenetic marks, must be transferred from parent to daughter DNA strands in order to maintain the memory of transcriptional states1,2. These proteins are believed to re-initiate rebuilding of chromatin structure, which ultimately recruits RNA polymerase II (Pol II) to the newly replicated daughter strands. It is believed that Pol II is recruited back to active genes only after chromatin is rebuilt3,4. However, there is little experimental evidence addressing the central questions of when and how Pol II is recruited back to the daughter strands and resumes transcription. Here we show that immediately after passage of the replication fork, Pol II in complex with other general transcription proteins and immature RNA re-associates with active genes on both leading and lagging strands of nascent DNA, and rapidly resumes transcription. This suggests that the transcriptionally active Pol II complex is retained in close proximity to DNA, with a Pol II-PCNA interaction potentially underlying this retention. These findings indicate that the Pol II machinery may not require epigenetic marks to be recruited to the newly synthesized DNA during the transition from DNA replication to resumption of transcription.
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Affiliation(s)
- Tyler K Fenstermaker
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Svetlana Petruk
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Sina K Kovermann
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hugh W Brock
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alexander Mazo
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA.
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4
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Saponaro M. Transcription-Replication Coordination. Life (Basel) 2022; 12:108. [PMID: 35054503 PMCID: PMC8781949 DOI: 10.3390/life12010108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/06/2022] [Accepted: 01/10/2022] [Indexed: 12/02/2022] Open
Abstract
Transcription and replication are the two most essential processes that a cell does with its DNA: they allow cells to express the genomic content that is required for their functions and to create a perfect copy of this genomic information to pass on to the daughter cells. Nevertheless, these two processes are in a constant ambivalent relationship. When transcription and replication occupy the same regions, there is the possibility of conflicts between transcription and replication as transcription can impair DNA replication progression leading to increased DNA damage. Nevertheless, DNA replication origins are preferentially located in open chromatin next to actively transcribed regions, meaning that the possibility of conflicts is potentially an accepted incident for cells. Data in the literature point both towards the existence or not of coordination between these two processes to avoid the danger of collisions. Several reviews have been published on transcription-replication conflicts, but we focus here on the most recent findings that relate to how these two processes are coordinated in eukaryotes, considering advantages and disadvantages from coordination, how likely conflicts are at any given time, and which are their potential hotspots in the genome.
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Affiliation(s)
- Marco Saponaro
- Transcription Associated Genome Instability Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
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5
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Lalonde M, Trauner M, Werner M, Hamperl S. Consequences and Resolution of Transcription-Replication Conflicts. Life (Basel) 2021; 11:life11070637. [PMID: 34209204 PMCID: PMC8303131 DOI: 10.3390/life11070637] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 06/28/2021] [Accepted: 06/28/2021] [Indexed: 11/17/2022] Open
Abstract
Transcription–replication conflicts occur when the two critical cellular machineries responsible for gene expression and genome duplication collide with each other on the same genomic location. Although both prokaryotic and eukaryotic cells have evolved multiple mechanisms to coordinate these processes on individual chromosomes, it is now clear that conflicts can arise due to aberrant transcription regulation and premature proliferation, leading to DNA replication stress and genomic instability. As both are considered hallmarks of aging and human diseases such as cancer, understanding the cellular consequences of conflicts is of paramount importance. In this article, we summarize our current knowledge on where and when collisions occur and how these encounters affect the genome and chromatin landscape of cells. Finally, we conclude with the different cellular pathways and multiple mechanisms that cells have put in place at conflict sites to ensure the resolution of conflicts and accurate genome duplication.
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6
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Boldogkői Z, Balázs Z, Moldován N, Prazsák I, Tombácz D. Novel classes of replication-associated transcripts discovered in viruses. RNA Biol 2019; 16:166-175. [PMID: 30608222 PMCID: PMC6380287 DOI: 10.1080/15476286.2018.1564468] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The role of RNA molecules in the priming of DNA replication and in providing a template for telomerase extension has been known for decades. Since then, several transcripts have been discovered, which play diverse roles in governing replication, including regulation of RNA primer formation, the recruitment of replication origin (Ori) recognition complex, and the assembly of replication fork. Recent studies on viral transcriptomes have revealed novel classes of replication-associated (ra)RNAs, which are expressed from the genomic locations in close vicinity to the Ori. Many of them overlap the Ori, whereas others are terminated close to the replication origin. These novel transcripts can be both protein-coding and non-coding RNAs. The Ori-overlapping part of the mRNAs is generally either the 5ʹ-untranslated regions (UTRs), or the 3ʹ-UTRs of the longer isoforms. Several raRNAs have been identified in various viral families using primarily third-generation long-read sequencing. Hyper-editing of these transcripts has also been described.
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Affiliation(s)
- Zsolt Boldogkői
- a Department of Medical Biology, Faculty of Medicine , University of Szeged , Szeged , Hungary
| | - Zsolt Balázs
- a Department of Medical Biology, Faculty of Medicine , University of Szeged , Szeged , Hungary
| | - Norbert Moldován
- a Department of Medical Biology, Faculty of Medicine , University of Szeged , Szeged , Hungary
| | - István Prazsák
- a Department of Medical Biology, Faculty of Medicine , University of Szeged , Szeged , Hungary
| | - Dóra Tombácz
- a Department of Medical Biology, Faculty of Medicine , University of Szeged , Szeged , Hungary
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7
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Treen N, Heist T, Wang W, Levine M. Depletion of Maternal Cyclin B3 Contributes to Zygotic Genome Activation in the Ciona Embryo. Curr Biol 2018; 28:1150-1156.e4. [PMID: 29576477 PMCID: PMC5996753 DOI: 10.1016/j.cub.2018.02.046] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 12/18/2017] [Accepted: 02/16/2018] [Indexed: 10/17/2022]
Abstract
Most animal embryos display a delay in the activation of zygotic transcription during early embryogenesis [1]. This process is thought to help coordinate rapid increases in cell number during early development [2]. The timing of zygotic genome activation (ZGA) during the maternal-to-zygotic transition (MZT) remains uncertain despite extensive efforts. We explore ZGA in the simple protovertebrate, Ciona intestinalis. Single-cell RNA sequencing (RNA-seq) assays identified Cyclin B3 (Ccnb3) as a putative mediator of ZGA. Maternal Ccnb3 transcripts rapidly diminish in abundance during the onset of zygotic transcription at the 8-cell and 16-cell stages. Disruption of Ccnb3 activity results in precocious activation of zygotic transcription, while overexpression abolishes normal activation. These observations suggest that the depletion of maternal Cyclin B3 products is a critical component of the MZT and ZGA. We discuss evidence that this mechanism might play a conserved role in the MZT of other metazoans, including mice and humans.
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Affiliation(s)
- Nicholas Treen
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.
| | - Tyler Heist
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Wei Wang
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Michael Levine
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
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8
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Cucco F, Palumbo E, Camerini S, D’Alessio B, Quarantotti V, Casella ML, Rizzo IM, Cukrov D, Delia D, Russo A, Crescenzi M, Musio A. Separase prevents genomic instability by controlling replication fork speed. Nucleic Acids Res 2018; 46:267-278. [PMID: 29165708 PMCID: PMC5758895 DOI: 10.1093/nar/gkx1172] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 10/26/2017] [Accepted: 11/10/2017] [Indexed: 01/21/2023] Open
Abstract
Proper chromosome segregation is crucial for preserving genomic integrity, and errors in this process cause chromosome mis-segregation, which may contribute to cancer development. Sister chromatid separation is triggered by Separase, an evolutionary conserved protease that cleaves the cohesin complex, allowing the dissolution of sister chromatid cohesion. Here we provide evidence that Separase participates in genomic stability maintenance by controlling replication fork speed. We found that Separase interacted with the replication licensing factors MCM2-7, and genome-wide data showed that Separase co-localized with MCM complex and cohesin. Unexpectedly, the depletion of Separase increased the fork velocity about 1.5-fold and caused a strong acetylation of cohesin's SMC3 subunit and altered checkpoint response. Notably, Separase silencing triggered genomic instability in both HeLa and human primary fibroblast cells. Our results show a novel mechanism for fork progression mediated by Separase and thus the basis for genomic instability associated with tumorigenesis.
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Affiliation(s)
- Francesco Cucco
- Institute for Biomedical and Genetic Research, National Research Council, Pisa, Italy
| | - Elisa Palumbo
- Department of Biology, University of Padua, Padua, Italy
| | - Serena Camerini
- Department of Cell Biology and Neurosciences, National Institute of Health, Rome, Italy
| | - Barbara D’Alessio
- Institute for Biomedical and Genetic Research, National Research Council, Pisa, Italy
| | - Valentina Quarantotti
- Institute for Biomedical and Genetic Research, National Research Council, Pisa, Italy
| | - Maria Luisa Casella
- Department of Cell Biology and Neurosciences, National Institute of Health, Rome, Italy
| | - Ilaria Maria Rizzo
- Institute for Biomedical and Genetic Research, National Research Council, Pisa, Italy
| | - Dubravka Cukrov
- Institute for Biomedical and Genetic Research, National Research Council, Pisa, Italy
| | - Domenico Delia
- Fondazione IRCCS Istituto Nazionale Tumori, Department of Experimental Oncology, Milan, Italy
| | - Antonella Russo
- Department of Biology, University of Padua, Padua, Italy
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Marco Crescenzi
- Department of Cell Biology and Neurosciences, National Institute of Health, Rome, Italy
| | - Antonio Musio
- Institute for Biomedical and Genetic Research, National Research Council, Pisa, Italy
- Tumour Institute of Tuscany, Florence, Italy
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9
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Donlon TA, Morris BJ, Chen R, Masaki KH, Allsopp RC, Willcox DC, Elliott A, Willcox BJ. FOXO3 longevity interactome on chromosome 6. Aging Cell 2017; 16:1016-1025. [PMID: 28722347 PMCID: PMC5595686 DOI: 10.1111/acel.12625] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/07/2017] [Indexed: 01/07/2023] Open
Abstract
FOXO3 has been implicated in longevity in multiple populations. By DNA sequencing in long‐lived individuals, we identified all single nucleotide polymorphisms (SNPs) in FOXO3 and showed 41 were associated with longevity. Thirteen of these had predicted alterations in transcription factor binding sites. Those SNPs appeared to be in physical contact, via RNA polymerase II binding chromatin looping, with sites in the FOXO3 promoter, and likely function together as a cis‐regulatory unit. The SNPs exhibited a high degree of LD in the Asian population, in which they define a specific longevity haplotype that is relatively common. The haplotype was less frequent in whites and virtually nonexistent in Africans. We identified distant contact points between FOXO3 and 46 neighboring genes, through long‐range physical contacts via CCCTC‐binding factor zinc finger protein (CTCF) binding sites, over a 7.3 Mb distance on chromosome 6q21. When activated by cellular stress, we visualized movement of FOXO3 toward neighboring genes. FOXO3 resides at the center of this early‐replicating and highly conserved syntenic region of chromosome 6. Thus, in addition to its role as a transcription factor regulating gene expression genomewide, FOXO3 may function at the genomic level to help regulate neighboring genes by virtue of its central location in chromatin conformation via topologically associated domains. We believe that the FOXO3 ‘interactome’ on chromosome 6 is a chromatin domain that defines an aging hub. A more thorough understanding of the functions of these neighboring genes may help elucidate the mechanisms through which FOXO3 variants promote longevity and healthy aging.
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Affiliation(s)
- Timothy A. Donlon
- Department of Research; Genetics Laboratory; Honolulu Heart Program/Honolulu-Asia Aging Study (HAAS); Kuakini Medical Center; Honolulu Hawaii
- John A. Burns School of Medicine; University of Hawaii Manoa; Honolulu Hawaii
| | - Brian J. Morris
- Department of Research; Genetics Laboratory; Honolulu Heart Program/Honolulu-Asia Aging Study (HAAS); Kuakini Medical Center; Honolulu Hawaii
- Basic & Clinical Genomics Laboratory; School of Medical Sciences and Bosch Institute; University of Sydney; Sydney NSW Australia
- Department of Geriatric Medicine; John A. Burns School of Medicine; University of Hawaii; Honolulu Hawaii
| | - Randi Chen
- Department of Research; Genetics Laboratory; Honolulu Heart Program/Honolulu-Asia Aging Study (HAAS); Kuakini Medical Center; Honolulu Hawaii
| | - Kamal H. Masaki
- Department of Research; Genetics Laboratory; Honolulu Heart Program/Honolulu-Asia Aging Study (HAAS); Kuakini Medical Center; Honolulu Hawaii
- Department of Geriatric Medicine; John A. Burns School of Medicine; University of Hawaii; Honolulu Hawaii
| | - Richard C. Allsopp
- John A. Burns School of Medicine; University of Hawaii Manoa; Honolulu Hawaii
| | - D. Craig Willcox
- Department of Research; Genetics Laboratory; Honolulu Heart Program/Honolulu-Asia Aging Study (HAAS); Kuakini Medical Center; Honolulu Hawaii
- Department of Geriatric Medicine; John A. Burns School of Medicine; University of Hawaii; Honolulu Hawaii
- Department of Human Welfare; Okinawa International University; Okinawa Japan
| | - Ayako Elliott
- Department of Research; Genetics Laboratory; Honolulu Heart Program/Honolulu-Asia Aging Study (HAAS); Kuakini Medical Center; Honolulu Hawaii
| | - Bradley J. Willcox
- Department of Research; Genetics Laboratory; Honolulu Heart Program/Honolulu-Asia Aging Study (HAAS); Kuakini Medical Center; Honolulu Hawaii
- Department of Geriatric Medicine; John A. Burns School of Medicine; University of Hawaii; Honolulu Hawaii
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10
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Brackley CA, Johnson J, Kelly S, Cook PR, Marenduzzo D. Simulated binding of transcription factors to active and inactive regions folds human chromosomes into loops, rosettes and topological domains. Nucleic Acids Res 2016; 44:3503-12. [PMID: 27060145 PMCID: PMC4856988 DOI: 10.1093/nar/gkw135] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 02/22/2016] [Accepted: 02/24/2016] [Indexed: 01/12/2023] Open
Abstract
Biophysicists are modeling conformations of interphase chromosomes, often basing the strengths of interactions between segments distant on the genetic map on contact frequencies determined experimentally. Here, instead, we develop a fitting-free, minimal model: bivalent or multivalent red and green 'transcription factors' bind to cognate sites in strings of beads ('chromatin') to form molecular bridges stabilizing loops. In the absence of additional explicit forces, molecular dynamic simulations reveal that bound factors spontaneously cluster-red with red, green with green, but rarely red with green-to give structures reminiscent of transcription factories. Binding of just two transcription factors (or proteins) to active and inactive regions of human chromosomes yields rosettes, topological domains and contact maps much like those seen experimentally. This emergent 'bridging-induced attraction' proves to be a robust, simple and generic force able to organize interphase chromosomes at all scales.
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Affiliation(s)
- Chris A Brackley
- SUPA, School of Physics & Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK
| | - James Johnson
- SUPA, School of Physics & Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK
| | - Steven Kelly
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Peter R Cook
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Davide Marenduzzo
- SUPA, School of Physics & Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK
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11
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Papantonis A, Cook PR. Transcription factories: genome organization and gene regulation. Chem Rev 2013; 113:8683-705. [PMID: 23597155 DOI: 10.1021/cr300513p] [Citation(s) in RCA: 159] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Argyris Papantonis
- Sir William Dunn School of Pathology, University of Oxford , South Parks Road, Oxford OX1 3RE, United Kingdom
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12
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Dellino GI, Cittaro D, Piccioni R, Luzi L, Banfi S, Segalla S, Cesaroni M, Mendoza-Maldonado R, Giacca M, Pelicci PG. Genome-wide mapping of human DNA-replication origins: levels of transcription at ORC1 sites regulate origin selection and replication timing. Genome Res 2012. [PMID: 23187890 PMCID: PMC3530669 DOI: 10.1101/gr.142331.112] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We report the genome-wide mapping of ORC1 binding sites in mammals, by chromatin immunoprecipitation and parallel sequencing (ChIP-seq). ORC1 binding sites in HeLa cells were validated as active DNA replication origins (ORIs) using Repli-seq, a method that allows identification of ORI-containing regions by parallel sequencing of temporally ordered replicating DNA. ORC1 sites were universally associated with transcription start sites (TSSs) of coding or noncoding RNAs (ncRNAs). Transcription levels at the ORC1 sites directly correlated with replication timing, suggesting the existence of two classes of ORIs: those associated with moderate/high transcription levels (≥1 RNA copy/cell), firing in early S and mapping to the TSSs of coding RNAs; and those associated with low transcription levels (<1 RNA copy/cell), firing throughout the entire S and mapping to TSSs of ncRNAs. These findings are compatible with a scenario whereby TSS expression levels influence the efficiency of ORC1 recruitment at G1 and the probability of firing during S.
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Affiliation(s)
- Gaetano Ivan Dellino
- Department of Experimental Oncology, European Institute of Oncology, 20141 Milan, Italy.
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13
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Maya-Mendoza A, Olivares-Chauvet P, Shaw A, Jackson DA. S phase progression in human cells is dictated by the genetic continuity of DNA foci. PLoS Genet 2010; 6:e1000900. [PMID: 20386742 PMCID: PMC2851568 DOI: 10.1371/journal.pgen.1000900] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2009] [Accepted: 03/08/2010] [Indexed: 12/26/2022] Open
Abstract
DNA synthesis must be performed with extreme precision to maintain genomic integrity. In mammalian cells, different genomic regions are replicated at defined times, perhaps to preserve epigenetic information and cell differentiation status. However, the molecular principles that define this S phase program are unknown. By analyzing replication foci within discrete chromosome territories during interphase, we show that foci which are active during consecutive intervals of S phase are maintained as spatially adjacent neighbors throughout the cell cycle. Using extended DNA fibers, we demonstrate that this spatial continuity of replication foci correlates with the genetic continuity of adjacent replicon clusters along chromosomes. Finally, we used bioinformatic tools to compare the structure of DNA foci with DNA domains that are seen to replicate during discrete time intervals of S phase using genome-wide strategies. Data presented show that a major mechanism of S phase progression involves the sequential synthesis of regions of the genome because of their genetic continuity along the chromosomal fiber. Eukaryotic DNA synthesis is regulated with exquisite precision so that genomes are replicated exactly once before cell division occurs. In simple eukaryotes, chromosomal loci are preferentially replicated at specific times of S phase, in part because of their differential sensitivity to cell cycle regulators and in part as a result of random choice. Mammals, with ∼250-fold larger genomes, have more complex replication programs, within which different classes of chromatin replicate at defined times. While the basic regulatory mechanisms in higher eukaryotes are conserved, it is unclear how their much more complex timing program is maintained. We use replication precursor analogues, which can be visualized in living or fixed cells, to monitor the spatial relationship of DNA domains that are replicated at different times of S phase. Analyzing individual chromosome, we show that a major mechanism regulating transitions in the S phase timing program involves the sequential activation of replication domains based on their genetic continuity. Our analysis of the mechanism of S phase progression in single cells provides an alternative to genome-wide strategies, which define patterns of replication using cell populations. In combination, these complimentary strategies provide fundamental insight into the mechanisms of S phase timing in mammalian cells.
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Affiliation(s)
| | | | - Alex Shaw
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Dean A. Jackson
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
- * E-mail:
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14
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Vecchio L, Solimando L, Biggiogera M, Fakan S. Use of halogenated precursors for simultaneous DNA and RNA detection by means of immunoelectron and immunofluorescence microscopy. J Histochem Cytochem 2007; 56:45-55. [PMID: 17938284 DOI: 10.1369/jhc.7a7225.2007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
We have developed a novel approach for in situ labeling and detection of nucleic acids in cultured cells. It is based on in vivo incorporation of chlorouridine (ClU) or iododeoxyuridine (IdU) into Chinese hamster ovary cells with the aim of labeling RNA and DNA, respectively. The halogenated nucleotides are immunolabeled on ultrathin sections with anti-bromodeoxyuridine (BrdU) monoclonal antibodies that specifically react with either IdU or ClU. Furthermore, we combined ClU and IdU incubation to label simultaneously RNA and DNA in the same cell. Both were visualized by means of anti-BrdU antibodies exhibiting strong affinity for one of the two halogenated epitopes. Confocal imaging of interphase nuclei and electron microscopic analysis showed evidence of a partial colocalization of newly synthesized DNA and RNA inside the cell nucleus. RNase and DNase digestion of ultrathin sections after formaldehyde fixation and acrylic resin embedding confirmed the specificity of incorporation. Consequently, this method allows us to differentially label DNA and RNA on the same section. Using short pulses with the precursors, we could show that newly synthesized DNA and RNA both preferentially occur within the perichromatin region at the border of condensed chromatin domains.
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Affiliation(s)
- Lorella Vecchio
- Centre of Electron Microscopy, University of Lausanne, Rue du Bugnon 27, CH 1005 Lausanne, Switzerland
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15
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Rytkönen AK, Hillukkala T, Vaara M, Sokka M, Jokela M, Sormunen R, Nasheuer HP, Nethanel T, Kaufmann G, Pospiech H, Syväoja JE. DNA polymerase ε associates with the elongating form of RNA polymerase II and nascent transcripts. FEBS J 2006; 273:5535-49. [PMID: 17212775 DOI: 10.1111/j.1742-4658.2006.05544.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
DNA polymerase epsilon co-operates with polymerases alpha and delta in the replicative DNA synthesis of eukaryotic cells. We describe here a specific physical interaction between DNA polymerase epsilon and RNA polymerase II, evidenced by reciprocal immunoprecipitation experiments. The interacting RNA polymerase II was the hyperphosphorylated IIO form implicated in transcriptional elongation, as inferred from (a) its reduced electrophoretic mobility that was lost upon phosphatase treatment, (b) correlation of the interaction with phosphorylation of Ser5 of the C-terminal domain heptapeptide repeat, and (c) the ability of C-terminal domain kinase inhibitors to abolish it. Polymerase epsilon was also shown to UV crosslink specifically alpha-amanitin-sensitive transcripts, unlike DNA polymerase alpha that crosslinked only to RNA-primed nascent DNA. Immunofluorescence microscopy revealed partial colocalization of RNA polymerase IIO and DNA polymerase epsilon, and immunoelectron microscopy revealed RNA polymerase IIO and DNA polymerase epsilon in defined nuclear clusters at various cell cycle stages. The RNA polymerase IIO-DNA polymerase epsilon complex did not relocalize to specific sites of DNA damage after focal UV damage. Their interaction was also independent of active DNA synthesis or defined cell cycle stage.
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Affiliation(s)
- Anna K Rytkönen
- Biocenter Oulu and Department of Biochemistry, University of Oulu, Finland
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16
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Schwaiger M, Schübeler D. A question of timing: emerging links between transcription and replication. Curr Opin Genet Dev 2006; 16:177-83. [PMID: 16503127 DOI: 10.1016/j.gde.2006.02.007] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2005] [Accepted: 02/13/2006] [Indexed: 11/28/2022]
Abstract
The coordination of transcription and timing of DNA replication during the S phase of the cell cycle has recently been studied chromosome-wide in high resolution. This revealed that in the complex genome of higher eukaryotes actively transcribed genes are more likely to replicate early in S phase. Dynamic changes in chromatin structure and nuclear organization appear to provide the underlying mechanism to link transcription and replication. A possible evolutionary benefit for this connection might result from differential replication fidelity during S phase, and comparisons of the human and chimpanzee genomes are compatible with this hypothesis.
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Affiliation(s)
- Michaela Schwaiger
- Friedrich-Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
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17
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Pliss A, Koberna K, Vecerová J, Malínský J, Masata M, Fialová M, Raska I, Berezney R. Spatio-temporal dynamics at rDNA foci: Global switching between DNA replication and transcription. J Cell Biochem 2004; 94:554-65. [PMID: 15543556 DOI: 10.1002/jcb.20317] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
We have investigated the in situ organization of ribosomal gene (rDNA) transcription and replication in HeLa cells. Fluorescence in situ hybridization (FISH) revealed numerous rDNA foci in the nucleolus. Each rDNA focus corresponds to a higher order chromatin domain containing multiple ribosomal genes. Multi-channel labeling experiments indicated that, in the majority of cells, all the rDNA foci were active in transcription as demonstrated by co-localization with signals to transcription and fibrillarin, a protein involved in ribosomal RNA processing. In some cells, however, a small portion of the rDNA foci did not overlap with signals to transcription and fibrillarin. Labeling for DNA replication revealed that those rDNA foci inactive in transcription were restricted to the S-phase of the cell cycle and were replicated predominantly from mid to late S-phase. Electron microscopic analysis localized the nucleolar transcription, replication, and fibrillarin signals to the dense fibrillar components of the nucleolus and at the borders of the fibrillar centers. We propose that the rDNA foci are the functional units for coordinating replication and transcription of the rRNA genes in space and time. This involves a global switching mechanism, active from mid to late S-phase, for turning off transcription and turning on replication at individual rDNA foci. Once all the rRNA genes at individual foci are replicated, these higher order chromatin domains are reprogrammed for transcription.
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Affiliation(s)
- Artem Pliss
- Department of Cell Biology, Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, Albertov 4, CZ-12800 Prague 2, Czech Republic
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18
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Rudd S, Frisch M, Grote K, Meyers BC, Mayer K, Werner T. Genome-wide in silico mapping of scaffold/matrix attachment regions in Arabidopsis suggests correlation of intragenic scaffold/matrix attachment regions with gene expression. PLANT PHYSIOLOGY 2004; 135:715-22. [PMID: 15208419 PMCID: PMC514109 DOI: 10.1104/pp.103.037861] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2004] [Revised: 03/26/2004] [Accepted: 03/28/2004] [Indexed: 05/17/2023]
Abstract
We carried out a genome-wide prediction of scaffold/matrix attachment regions (S/MARs) in Arabidopsis. Results indicate no uneven distribution on the chromosomal level but a clear underrepresentation of S/MARs inside genes. In cases where S/MARs were predicted within genes, these intragenic S/MARs were preferentially located within the 5'-half, most prominently within introns 1 and 2. Using Arabidopsis whole-genome expression data generated by the massively parallel signature sequencing methodology, we found a negative correlation between S/MAR-containing genes and transcriptional abundance. Expressed sequence tag data correlated the same way with S/MAR-containing genes. Thus, intragenic S/MARs show a negative correlation with transcription level. For various genes it has been shown experimentally that S/MARs can function as transcriptional regulators and that they have an implication in stabilizing expression levels within transgenic plants. On the basis of a genome-wide in silico S/MAR analysis, we found a significant correlation between the presence of intragenic S/MARs and transcriptional down-regulation.
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Affiliation(s)
- Stephen Rudd
- Munich Information Center for Protein Sequences/Institute for Bioinformatics, GSF-National Research Center for Environment and Health, 85764 Neuherberg, Germany
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19
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Frouin I, Montecucco A, Spadari S, Maga G. DNA replication: a complex matter. EMBO Rep 2003; 4:666-70. [PMID: 12835753 PMCID: PMC1326325 DOI: 10.1038/sj.embor.embor886] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2003] [Accepted: 05/21/2003] [Indexed: 02/01/2023] Open
Abstract
In eukaryotic cells, the essential function of DNA replication is carried out by a network of enzymes and proteins, which work together to rapidly and accurately duplicate the genetic information of the cell. Many of the components of this DNA replication apparatus associate with other cellular factors as components of multiprotein complexes, which act cooperatively in networks to regulate cell cycle progression and checkpoint control, but are distinct from the pre-replication complexes that associate with the origins and regulate their firing. In this review, we summarize current knowledge about the composition and dynamics of these large multiprotein complexes in mammalian cells and their relationships to the replication factories.
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Affiliation(s)
- Isabelle Frouin
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, via Abbiategrasso 207, I-27100
Pavia, Italy
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zürich-Irchel, Winterthurerstrasse 190, CH-8050
Zürich, Switzerland
| | - Alessandra Montecucco
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, via Abbiategrasso 207, I-27100
Pavia, Italy
| | - Silvio Spadari
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, via Abbiategrasso 207, I-27100
Pavia, Italy
| | - Giovanni Maga
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, via Abbiategrasso 207, I-27100
Pavia, Italy
- Tel: +39 0382 546355; Fax: +39 0382 422286;
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20
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Affiliation(s)
- P O Jensen
- Finsen Laboratory, Finsen Center, Rigshospitalet, Copenhagen, Denmark
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21
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Antequera F, Bird A. CpG islands as genomic footprints of promoters that are associated with replication origins. Curr Biol 1999; 9:R661-7. [PMID: 10508580 DOI: 10.1016/s0960-9822(99)80418-7] [Citation(s) in RCA: 152] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The primary target for DNA methylation in mammalian genomes is cytosine in the dinucleotide CpG. High densities of CpG dinucleotides are found in CpG islands, but paradoxically CpG islands are normally in a non-methylated state. Here, we speculate why CpG islands are immune to methylation and why they are so rich in guanine and cytosine relative to the surrounding DNA. We propose that CpG islands are associated with promoters that are transcriptionally active at totipotent stages of development and can also act as origins of DNA replication. CpG islands may be 'footprints' caused by early DNA replication intermediates at dual function promoters of this kind.
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Affiliation(s)
- F Antequera
- Instituto de Microbiología Bioquímica, CSIC/Universidad de Salamanca, Edificio Departamental, Campus Miguel de Unamuno 37007, Salamanca, Spain.
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22
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Galande S, Kohwi-Shigematsu T. Poly(ADP-ribose) polymerase and Ku autoantigen form a complex and synergistically bind to matrix attachment sequences. J Biol Chem 1999; 274:20521-8. [PMID: 10400681 DOI: 10.1074/jbc.274.29.20521] [Citation(s) in RCA: 141] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Genomic sequences with a cluster of ATC sequence stretches where one strand consists exclusively of well mixed As, Ts, and Cs confer high base unpairing propensity under negative superhelical strain. Such base unpairing regions (BURs) are typically found in scaffold or matrix attachment regions (SARs/MARs) that are thought to contribute to the formation of the loop domain structure of chromatin. Several proteins, including cell type-specific proteins, have been identified that bind specifically to double-stranded BURs either in vitro or in vivo. By using BUR-affinity chromatography to isolate BUR-binding proteins from breast cancer SK-BR-3 cells, we almost exclusively obtained a complex of poly(ADP-ribose) polymerase (PARP) and DNA-dependent protein kinase (DNA-PK). Both PARP and DNA-PK are activated by DNA strand breaks and are implicated in DNA repair, recombination, DNA replication, and transcription. In contrast to the previous notion that PARP and Ku autoantigen, the DNA-binding subunit of DNA-PK, mainly bind to free ends of DNA, here we show that both proteins individually bind BURs with high affinity and specificity in an end-independent manner using closed circular BUR-containing DNA substrates. We further demonstrate that PARP and Ku autoantigen form a molecular complex in vivo and in vitro in the absence of DNA, and as a functional consequence, their affinity to the BURs are synergistically enhanced. ADP-ribosylation of the nuclear extract abrogated the BUR binding activity of this complex. These results provide a mechanistic link toward understanding the functional overlap of PARP and DNA-PK and suggest a novel role for these proteins in the regulation of chromatin structure and function.
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Affiliation(s)
- S Galande
- Life Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94720, USA
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23
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Sasaki T, Sawado T, Yamaguchi M, Shinomiya T. Specification of regions of DNA replication initiation during embryogenesis in the 65-kilobase DNApolalpha-dE2F locus of Drosophila melanogaster. Mol Cell Biol 1999; 19:547-55. [PMID: 9858578 PMCID: PMC83912 DOI: 10.1128/mcb.19.1.547] [Citation(s) in RCA: 114] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In the early stage of Drosophila embryogenesis, DNA replication initiates at unspecified sites in the chromosome. In contrast, DNA replication initiates in specified regions in cultured cells. We investigated when and where the initiation regions are specified during embryogenesis and compared them with those observed in cultured cells by two-dimensional gel methods. In the DNA polymerase alpha gene (DNApolalpha) locus, where an initiation region, oriDalpha, had been identified in cultured Kc cells, repression of origin activity in the coding region was detected after formation of cellular blastoderms, and the range of the initiation region had become confined by 5 h after fertilization. During this work we identified other initiation regions between oriDalpha and the Drosophila E2F gene (dE2F) downstream of DNApolalpha. At least four initiation regions showing replication bubbles were identified in the 65-kb DNApolalpha-dE2F locus in 5-h embryos, but only two were observed in Kc cells. These results suggest that the specification levels of origin usage in 5-h embryos are in the intermediate state compared to those in more differentiated cells. Further, we found a spatial correlation between the active promoter regions for dE2F and the active initiation zones of replication. In 5-h embryos, two known transcripts differing in their first exons were expressed, and two regions close to the respective promoter regions for both transcripts functioned as replication origins. In Kc cells, only one transcript was expressed and functional replication origins were observed only in the region including the promoter region for this transcript.
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Affiliation(s)
- T Sasaki
- Mitsubishi Kasei Institute of Life Sciences, Machida, Tokyo 194-8511, Japan
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24
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Wei X, Samarabandu J, Devdhar RS, Siegel AJ, Acharya R, Berezney R. Segregation of transcription and replication sites into higher order domains. Science 1998; 281:1502-6. [PMID: 9727975 DOI: 10.1126/science.281.5382.1502] [Citation(s) in RCA: 180] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Microscopy shows that individual sites of DNA replication and transcription of mammalian nuclei segregate into sets of roughly 22 and 16 higher order domains, respectively. Each domain set displayed a distinct network-like appearance, including regions of individual domains and interdigitation of domains between the two networks. These data support a dynamic mosaic model for the higher order arrangement of genomic function inside the cell nuclei.
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Affiliation(s)
- X Wei
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, NY 14260, USA
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25
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Abstract
Double-minute chromosomes (DMs) amplify oncogenes in human tumors. The organization of genomic DNA in four independently isolated DMs amplifying the DHFR (dihydrofolate reductase) gene has been compared by mapping locations of CpG islands. When cleaved with methylation-sensitive rare-cutting restriction endonucleases, three hypomethylated GC-rich DNA sequences were frequently found in specific regions in these DMs. One such zone was in the CpG island containing the divergently transcribed promoter separating the DHFR and the Rep-3 genes. The other two sites were approximately 500 kb upstream and 300 kb downstream of the DHFR gene. An approximately 800-kb amplified core genomic region containing the DHFR gene using DM-specific probes has been identified in this study. All the DMs consisted of the core amplified region combined with additional DNA fragments. These additional fragments are different for each DM. Therefore, while the DNAs in each of the DMs are different, they have common hypomethylated regions in similar locations. These results suggest a role for the location of hypomethylated GC-rich sites such as the CpG islands in genesis of DMs.
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Affiliation(s)
- R Rizwana
- Department of Radiation Oncology, State University of New York Health Science Center, Syracuse 13210, USA
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26
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Chen LF, Ito K, Murakami Y, Ito Y. The capacity of polyomavirus enhancer binding protein 2alphaB (AML1/Cbfa2) to stimulate polyomavirus DNA replication is related to its affinity for the nuclear matrix. Mol Cell Biol 1998; 18:4165-76. [PMID: 9632801 PMCID: PMC109001 DOI: 10.1128/mcb.18.7.4165] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The nuclear matrix is thought to play an important role in the DNA replication of eukaryotic cells, although direct evidence for such a role is still lacking. A nuclear matrix-associated transcription factor, polyomavirus (Py) enhancer binding protein 2alphaB1 (PEBP2alphaB1) (AML1/Cbfa2), was found to stimulate Py replication through its cognate binding site. The minimal replication activation domain (RAD) was identified between amino acid (aa) 302 and aa 371 by using a fusion protein containing the GAL4 DNA binding domain (GAL4-RAD). In addition, the region showed affinity for the nuclear matrix and, on the basis of competition studies, binding activity for one or more proteins involved in the initiation of Py DNA replication. A leukemogenic chimeric protein, AML1/ETO(MTG8), which does not contain this region of PEBP2alphaB1/AML1, was also localized in the nuclear matrix fraction and competed for nuclear matrix association with PEBP2alphaB1 and GAL4-RAD. Moreover, AML1/ETO inhibited Py DNA replication stimulated by PEBP2alphaB1 and GAL4-RAD. The inhibition was specific for replication mediated by PEBP2alphaB1 and GAL4-RAD, and proportional to the degree of loss of these activators from the nuclear matrix, suggesting a requirement for nuclear matrix targeting in the stimulation of Py DNA replication by RAD. These results are the first to suggest a molecular link between the initiation of DNA replication and the nuclear matrix compartment.
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Affiliation(s)
- L F Chen
- Department of Viral Oncology, Institute for Virus Research, Kyoto University, Shogoin, Sakyo-ku, Kyoto 606, Japan
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27
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Ali RB, Teo AK, Oh HK, Chuang LS, Ayi TC, Li BF. Implication of localization of human DNA repair enzyme O6-methylguanine-DNA methyltransferase at active transcription sites in transcription-repair coupling of the mutagenic O6-methylguanine lesion. Mol Cell Biol 1998; 18:1660-9. [PMID: 9488483 PMCID: PMC108881 DOI: 10.1128/mcb.18.3.1660] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
DNA lesions that halt RNA polymerase during transcription are preferentially repaired by the nucleotide excision repair pathway. This transcription-coupled repair is initiated by the arrested RNA polymerase at the DNA lesion. However, the mutagenic O6-methylguanine (6MG) lesion which is bypassed by RNA polymerase is also preferentially repaired at the transcriptionally active DNA. We report here a plausible explanation for this observation: the human 6MG repair enzyme O6-methylguanine-DNA methyltransferase (MGMT) is present as speckles concentrated at active transcription sites (as revealed by polyclonal antibodies specific for its N and C termini). Upon treatment of cells with low dosages of N-methylnitrosourea, which produces 6MG lesions in the DNA, these speckles rapidly disappear, accompanied by the formation of active-site methylated MGMT (the repair product of 6MG by MGMT). The ability of MGMT to target itself to active transcription sites, thus providing an effective means of repairing 6MG lesions, possibly at transcriptionally active DNA, indicates its crucial role in human cancer and chemotherapy by alkylating agents.
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Affiliation(s)
- R B Ali
- Chemical Carcinogenesis Laboratory, Institute of Molecular and Cell Biology, National University of Singapore, Republic of Singapore
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28
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Bouniol-Baly C, Nguyen E, Besombes D, Debey P. Dynamic organization of DNA replication in one-cell mouse embryos: relationship to transcriptional activation. Exp Cell Res 1997; 236:201-11. [PMID: 9344600 DOI: 10.1006/excr.1997.3708] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
We have analyzed the spatial and temporal relationship between transcription and replication sites during the first cell cycle in mouse embryos. Embryos were microinjected with both 5-bromouridine-5'-triphosphate and digoxygenin-11-deoxyuridine-5'-triphosphate to visualize transcription and replication sites respectively. We detected six different phases of replication during S phase and dated the onset of zygotic transcription at the end of the S phase. Using confocal microscopy, we showed that there is essentially no colocalization of replication and transcription sites at this stage of development. Moreover, studies on aphidicolin-treated embryos demonstrated that inhibition of DNA replication does not hinder transcriptional activation at the 1-cell stage.
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Affiliation(s)
- C Bouniol-Baly
- Laboratoire Associé Institut National de la Santé et de la Recherche Médicale (INSERM), Institut National de la Recherche Agronomique (INRA), Paris, France. bouniol@.ibpc.fr
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29
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Abstract
Pairing between homologous chromosomes is essential for successful meiosis; generally only paired homologs recombine and segregate correctly into haploid germ cells. Homologs also pair in some somatic cells (e.g. in diploid and polytene cells of Drosophila). How homologs find their partners is a mystery. First, I review some explanations of how they might do so; most involve base-pairing (i.e. DNA-DNA) interactions. Then I discuss the remarkable fact that chromosomes only pair when they are transcriptionally active. Finally, I present a general model for pairing based upon the DNA-protein interactions involved in transcription. Each chromosome in the haploid set has a unique array of transcription units strung along its length. Therefore, each chromatin fibre will be folded into a unique array of loops associated with clusters of polymerases and transcription factors; only homologs share similar arrays. As these loops and clusters, or transcription factories, move continually, they make and break contact with others. Correct pairing would be nucleated when a promoter in a loop tethered to one factory binds to a homologous polymerizing site in another factory, before transcription stabilizes the association. This increases the chances that adjacent promoters will bind to their homologs, so that chromosomes eventually become zipped together with their partners. Pairing is then the inevitable consequence of transcription of partially-condensed chromosomes.
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Affiliation(s)
- P R Cook
- CRC Nuclear Structure and Function Research Group, Sir William Dunn School of Pathology, University of Oxford, UK.
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30
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Abstract
Most models for transcription and replication involve polymerases that track along the template. We review here experiments that suggest an alternative in which polymerization occurs as the template slides past a polymerase fixed to a large structure in the eukaryotic nucleus--a "factory" attached to a nucleoskeleton. This means that higher-order structure dictates how and when DNA is replicated or transcribed.
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Affiliation(s)
- D A Jackson
- CRC Nuclear Structure and Function Research Group, Sir William Dunn School of Pathology, University of Oxford, United Kingdom
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31
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Fernandes DJ, Catapano CV. The nuclear matrix as a site of anticancer drug action. INTERNATIONAL REVIEW OF CYTOLOGY 1996; 162A:539-76. [PMID: 8575887 DOI: 10.1016/s0074-7696(08)61238-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Many nuclear functions, including the organization of the chromatin within the nucleus, depend upon the presence of a nuclear matrix. Nuclear matrix proteins are involved in the formation of chromatin loops, control of DNA supercoiling, and regulation and coordination of transcriptional and replicational activities within individual loops. Various structural and functional components of the nuclear matrix represent potential targets for anticancer agents. Alkylating agents and ionizing radiation interact preferentially with nuclear matrix proteins and matrix-associated DNA. Other chemotherapeutic agents, such as fludarabine phosphate and topoisomerase II-active drugs, interact specifically with matrix-associated enzymes, such as DNA primase and the DNA topoisomerase II alpha isozyme. The interactions of these agents at the level of the nuclear matrix may compromise multiple nuclear functions and be relevant to their antitumor activities.
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Affiliation(s)
- D J Fernandes
- Department of Experimental Oncology, Hollings Cancer Center, Medical University of South Carolina, Charleston 29425, USA
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32
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van Driel R, Wansink DG, van Steensel B, Grande MA, Schul W, de Jong L. Nuclear domains and the nuclear matrix. INTERNATIONAL REVIEW OF CYTOLOGY 1996; 162A:151-89. [PMID: 8575880 DOI: 10.1016/s0074-7696(08)61231-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
This overview describes the spatial distribution of several enzymatic machineries and functions in the interphase nucleus. Three general observations can be made. First, many components of the different nuclear machineries are distributed in the nucleus in a characteristic way for each component. They are often found concentrated in specific domains. Second, nuclear machineries for the synthesis and processing of RNA and DNA are associated with an insoluble nuclear structure, called nuclear matrix. Evidently, handling of DNA and RNA is done by immobilized enzyme systems. Finally, the nucleus seems to be divided in two major compartments. One is occupied by compact chromosomes, the other compartment is the space between the chromosomes. In the latter, transcription takes place at the surface of chromosomal domains and it houses the splicing machinery. The relevance of nuclear organization for efficient gene expression is discussed.
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Affiliation(s)
- R van Driel
- E. C. Slater Instituut, University of Amsterdam, The Netherlands
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33
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Junéra HR, Masson C, Géraud G, Hernandez-Verdun D. The three-dimensional organization of ribosomal genes and the architecture of the nucleoli vary with G1, S and G2 phases. J Cell Sci 1995; 108 ( Pt 11):3427-41. [PMID: 8586655 DOI: 10.1242/jcs.108.11.3427] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The three-dimensional (3-D) organization of the nucleolus, a defined nuclear territory containing tandem repeats of the ribosomal genes (rDNA), was investigated in PtK1 cells. Identification of the interphase stages was performed in single cells using DNA quantification by cytometry for the G1 and G2 phases while the S phase was identified by immunolabelling of the proliferating cell nuclear antigen (PCNA). The 3-D organization of the rDNA in the nucleolus was analyzed by fluorescence in situ hybridization using confocal microscopy. All the rDNA was located inside the nucleolar structures during all stages and the two rDNA loci were orthogonal. The rDNA was heterogeneously distributed in each nucleolus during G1, S and G2, with alternate sites of clustered genes (spots) and of genes in more extended configurations. The number of spots (4 to 6 in G1) increased during S phase (7 to 12) and their 3-D organization was progressively relaxed from G1 to G2. Double spots in G2 could reflect a similar gene organization of two chromatids. During mid-S phase, PCNA co-localized with some clustered genes (spots), indicating that rDNA replication occurs inside nucleoli and at different sites of the same locus simultaneously. The evaluation of the rDNA transcription units in 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB)-treated cells indicated a mean of 16 units per G1 nucleus and 25 units per G2 nucleus. For G1 and G2, the fine 3-D structure of nucleoli was reconstructed using ultrathin serial sections after specific contrast of DNA and RNA, digitization of the serial section images and computer-assisted 3-D architecture. Fibrillar centers (FCs) formed discrete structures (about 10 in G1 and 20 in G2) connected by a network of the dense fibrillar component. The 3-D arrangement of the FCs in G1 and G2 are similar to the rDNA spots. In conclusion, the architecture of the nucleoli during interphase reflects the distribution of the rDNA that is characterized by alternation of clustered and extended genes.
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Abstract
The basic structural elements of chromatin and chromosomes are reviewed. Then a model involving only three architectural motifs, nucleosomes, chromatin loops and transcription factories/chromomeres, is presented. Loops are tied through transcription factors and RNA polymerases to factories during interphase and to the remnants of those factories, chromomeres, during mitosis. On entry into mitosis, increased adhesiveness between nucleosomes and between factories drives a ‘sticky-end’ aggregation to the most compact and stable structure, a cylinder of nucleosomes around an axial chromomeric core.
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Affiliation(s)
- P R Cook
- CRC Nuclear Structure and Function Research Group, Sir William Dunn School of Pathology, University of Oxford, UK
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35
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Chadee DN, Taylor WR, Hurta RA, Allis CD, Wright JA, Davie JR. Increased phosphorylation of histone H1 in mouse fibroblasts transformed with oncogenes or constitutively active mitogen-activated protein kinase kinase. J Biol Chem 1995; 270:20098-105. [PMID: 7650028 DOI: 10.1074/jbc.270.34.20098] [Citation(s) in RCA: 91] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
We compared the nucleosomal organization, histone H1 subtypes, and histone H1 phosphorylated isoforms of ras-transformed and parental 10T1/2 mouse fibroblasts. In agreement with previous studies, we found that ras-transformed mouse fibroblasts have a less condensed chromatin structure than normal fibroblasts. ras-transformed and parental 10T1/2 cells had similar amounts of H1 subtypes, proteins that have a key role in the compaction of chromatin. However, labeling studies with 32P and Western blot experiments with an antiphosphorylated H1 antibody show that interphase ras-transformed cells have higher levels of phosphorylated H1 isoforms than parental cells. G1/S phase-arrested ras-transformed cells had higher amounts of phosphorylated H1 than G1/S phase-arrested parental cells. Mouse fibroblasts transformed with fes, mos, raf, myc, or constitutively active mitogen-activated protein (MAP) kinase kinase had increased levels of phosphorylated H1. These observations suggest that increased phosphorylation of H1 is one of the consequences of the persistent activation of the mitogen-activated protein kinase signal transduction pathway. Indirect immunofluorescent studies show that phosphorylated H1b is localized in centers of RNA splicing in the nucleus, suggesting that this modified H1 subtype is complexed to transcriptionally active chromatin.
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Affiliation(s)
- D N Chadee
- Manitoba Institute of Cell Biology, University of Manitoba, Winnipeg, Canada
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36
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Kristie TM, Pomerantz JL, Twomey TC, Parent SA, Sharp PA. The cellular C1 factor of the herpes simplex virus enhancer complex is a family of polypeptides. J Biol Chem 1995; 270:4387-94. [PMID: 7876203 DOI: 10.1074/jbc.270.9.4387] [Citation(s) in RCA: 96] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The alpha/immediate early genes of herpes simplex virus are regulated by the specific assembly of a multiprotein enhancer complex containing the Oct-1 POU domain protein, the viral alpha-transinduction factor alpha TIF, (VP16, ICP25), and the C1 cellular factor. The C1 factor from mammalian cells is a heterogeneous but related set of polypeptides that interact directly with the alpha-transinduction factor to form a heteromeric protein complex. The isolation of cDNAs encoding the polypeptides of the C1 factor suggests that these proteins are proteolytic products of a novel precursor. The sequence of the amino termini of these polypeptide products indicate that the proteins are generated by site-specific cleavages within a reiterated 20-amino acid sequence. Although the C1 factor appears to be ubiquitously expressed, it is localized to subnuclear structures in specific cell types.
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Affiliation(s)
- T M Kristie
- Laboratory of Viral Diseases, National Institutes of Health, Bethesda, Maryland 20892
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37
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Hendzel M, Sun J, Chen H, Rattner J, Davie J. Histone acetyltransferase is associated with the nuclear matrix. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)31729-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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38
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Hozák P, Jackson DA, Cook PR. Replication factories and nuclear bodies: the ultrastructural characterization of replication sites during the cell cycle. J Cell Sci 1994; 107 ( Pt 8):2191-202. [PMID: 7983177 DOI: 10.1242/jcs.107.8.2191] [Citation(s) in RCA: 109] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sites of replication in synchronized HeLa cells were visualized by light and electron microscopy; cells were permeabilized and incubated with biotin-16-dUTP, and incorporation sites were immunolabelled. Electron microscopy of thick resinless sections from which approximately 90% chromatin had been removed showed that most DNA synthesis occurs in specific dense structures (replication factories) attached to a diffuse nucleoskeleton. These factories appear at the end of G1-phase and quickly become active; as S-phase progresses, they increase in size and decrease in number like sites of incorporation seen by light microscopy. Electron microscopy of conventional thin sections proved that these factories are a subset of nuclear bodies; they changed in the same characteristic way and contained DNA polymerase alpha and proliferating cell nuclear antigen. As replication factories can be observed and labelled in non-permeabilized cells, they cannot be aggregation artifacts. Some replication occurs outside factories at discrete sites on the diffuse skeleton; it becomes significant by mid S-phase and later becomes concentrated beneath the lamina.
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Affiliation(s)
- P Hozák
- CRC Nuclear Structure and Function Research Group, Sir William Dunn School of Pathology, University of Oxford, UK
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Jackson DA, Hassan AB, Errington RJ, Cook PR. Sites in human nuclei where damage induced by ultraviolet light is repaired: localization relative to transcription sites and concentrations of proliferating cell nuclear antigen and the tumour suppressor protein, p53. J Cell Sci 1994; 107 ( Pt 7):1753-60. [PMID: 7983145 DOI: 10.1242/jcs.107.7.1753] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The repair of damage induced in DNA by ultraviolet light involves excision of the damaged sequence and synthesis of new DNA to repair the gap. Sites of such repair synthesis were visualized by incubating permeabilized HeLa or MRC-5 cells with the DNA precursor, biotin-dUTP, in a physiological buffer; then incorporated biotin was immunolabeled with fluorescent antibodies. Repair did not take place at sites that reflected the DNA distribution; rather, sites were focally concentrated in a complex pattern. This pattern changed with time; initially intense repair took place at transcriptionally active sites but when transcription became inhibited it continued at sites with little transcription. Repair synthesis in vitro also occurred in the absence of transcription. Repair sites generally contained a high concentration of proliferating cell nuclear antigen but not the tumour-suppressor protein, p53.
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Affiliation(s)
- D A Jackson
- CRC Nuclear Structure and Function Research Group, Sir William Dunn School of Pathology, University of Oxford, UK
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40
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Hassan AB, Cook PR. Does transcription by RNA polymerase play a direct role in the initiation of replication? J Cell Sci 1994; 107 ( Pt 6):1381-7. [PMID: 7525619 DOI: 10.1242/jcs.107.6.1381] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
RNA polymerases have been implicated in the initiation of replication in bacteria. The conflicting evidence for a role in initiation in eukaryotes is reviewed.
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Affiliation(s)
- A B Hassan
- CRC Nuclear Structure and Function Research Group, Sir William Dunn School of Pathology, University of Oxford, UK
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41
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Abstract
Current models for RNA synthesis involve an RNA polymerase that tracks along a static template. However, research on chromatin loops suggests that the template slides past a stationary polymerase; individual polymerases tie the chromatin fibre into loops and clusters of polymerases determine the basic structure of the interphase and metaphase chromosome. RNA polymerase is then both a player and a manager of the chromosome loop.
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Affiliation(s)
- P R Cook
- CRC Nuclear Structure and Function Research Group, Sir William Dunn School of Pathology, University of Oxford, UK
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