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Zhu X, Kanemaki MT. Replication initiation sites and zones in the mammalian genome: Where are they located and how are they defined? DNA Repair (Amst) 2024; 141:103713. [PMID: 38959715 DOI: 10.1016/j.dnarep.2024.103713] [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: 04/19/2024] [Revised: 06/14/2024] [Accepted: 06/15/2024] [Indexed: 07/05/2024]
Abstract
Eukaryotic DNA replication is a tightly controlled process that occurs in two main steps, i.e., licensing and firing, which take place in the G1 and S phases of the cell cycle, respectively. In Saccharomyces cerevisiae, the budding yeast, replication origins contain consensus sequences that are recognized and bound by the licensing factor Orc1-6, which then recruits the replicative Mcm2-7 helicase. By contrast, mammalian initiation sites lack such consensus sequences, and the mammalian ORC does not exhibit sequence specificity. Studies performed over the past decades have identified replication initiation sites in the mammalian genome using sequencing-based assays, raising the question of whether replication initiation occurs at confined sites or in broad zones across the genome. Although recent reports have shown that the licensed MCMs in mammalian cells are broadly distributed, suggesting that ORC-dependent licensing may not determine the initiation sites/zones, they are predominantly located upstream of actively transcribed genes. This review compares the mechanism of replication initiation in yeast and mammalian cells, summarizes the sequencing-based technologies used for the identification of initiation sites/zones, and proposes a possible mechanism of initiation-site/zone selection in mammalian cells. Future directions and challenges in this field are also discussed.
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Affiliation(s)
- Xiaoxuan Zhu
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Yata 1111, Shizuoka, Mishima 411-8540, Japan.
| | - Masato T Kanemaki
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Yata 1111, Shizuoka, Mishima 411-8540, Japan; Graduate Institute for Advanced Studies, SOKENDAI, Yata 1111, Shizuoka, Mishima 411-8540, Japan; Department of Biological Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan.
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2
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Jaksik R, Wheeler DA, Kimmel M. Detection and characterization of constitutive replication origins defined by DNA polymerase epsilon. BMC Biol 2023; 21:41. [PMID: 36829160 PMCID: PMC9960419 DOI: 10.1186/s12915-023-01527-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 01/24/2023] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND Despite the process of DNA replication being mechanistically highly conserved, the location of origins of replication (ORI) may vary from one tissue to the next, or between rounds of replication in eukaryotes, suggesting flexibility in the choice of locations to initiate replication. Lists of human ORI therefore vary widely in number and location, and there are currently no methods available to compare them. Here, we propose a method of detection of ORI based on somatic mutation patterns generated by the mutator phenotype of damaged DNA polymerase epsilon (POLE). RESULTS We report the genome-wide localization of constitutive ORI in POLE-mutated human tumors using whole genome sequencing data. Mutations accumulated after many rounds of replication of unsynchronized dividing cell populations in tumors allow to identify constitutive origins, which we show are shared with high fidelity between individuals and tumor types. Using a Smith-Waterman-like dynamic programming approach, we compared replication origin positions obtained from multiple different methods. The comparison allowed us to define a consensus set of replication origins, identified consistently by multiple ORI detection methods. Many DNA features co-localized with the consensus set of ORI, including chromatin loop anchors, G-quadruplexes, S/MARs, and CpGs. Among all features, the H2A.Z histone exhibited the most significant association. CONCLUSIONS Our results show that mutation-based detection of replication origins is a viable approach to determining their location and associated sequence features.
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Affiliation(s)
- Roman Jaksik
- Department of Systems Biology and Engineering and Biotechnology Centre, Silesian University of Technology, Gliwice, Poland.
| | - David A. Wheeler
- grid.39382.330000 0001 2160 926XHuman Genome Sequencing Centre, Baylor College of Medicine, Houston, TX USA ,grid.240871.80000 0001 0224 711XPresent Address: Clinical Genomics Group, Department of Computational Biology, St Jude Children’s Research Hospital, Memphis, TN 38103 USA
| | - Marek Kimmel
- grid.6979.10000 0001 2335 3149Department of Systems Biology and Engineering and Biotechnology Centre, Silesian University of Technology, Gliwice, Poland ,grid.21940.3e0000 0004 1936 8278Department of Statistics, Rice University, Houston, TX USA ,grid.21940.3e0000 0004 1936 8278Department of Bioengineering, Rice University, Houston, TX USA
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3
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Wang W, Klein KN, Proesmans K, Yang H, Marchal C, Zhu X, Borrman T, Hastie A, Weng Z, Bechhoefer J, Chen CL, Gilbert DM, Rhind N. Genome-wide mapping of human DNA replication by optical replication mapping supports a stochastic model of eukaryotic replication. Mol Cell 2021; 81:2975-2988.e6. [PMID: 34157308 DOI: 10.1016/j.molcel.2021.05.024] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 03/08/2021] [Accepted: 05/20/2021] [Indexed: 12/27/2022]
Abstract
The heterogeneous nature of eukaryotic replication kinetics and the low efficiency of individual initiation sites make mapping the location and timing of replication initiation in human cells difficult. To address this challenge, we have developed optical replication mapping (ORM), a high-throughput single-molecule approach, and used it to map early-initiation events in human cells. The single-molecule nature of our data and a total of >2,500-fold coverage of the human genome on 27 million fibers averaging ∼300 kb in length allow us to identify initiation sites and their firing probability with high confidence. We find that the distribution of human replication initiation is consistent with inefficient, stochastic activation of heterogeneously distributed potential initiation complexes enriched in accessible chromatin. These observations are consistent with stochastic models of initiation-timing regulation and suggest that stochastic regulation of replication kinetics is a fundamental feature of eukaryotic replication, conserved from yeast to humans.
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Affiliation(s)
- Weitao Wang
- Institut Curie, PSL Research University, CNRS UMR 3244, Paris 75005, France
| | - Kyle N Klein
- Florida State University, Department of Biological Science, Tallahassee, FL 32306, USA
| | - Karel Proesmans
- Simon Fraser University, Department of Physics, Burnaby, BC V5A 1S6, Canada
| | - Hongbo Yang
- Northwestern University, Feinberg School of Medicine, Department of Biochemistry and Molecular Genetics, Chicago, IL 60208, USA
| | - Claire Marchal
- Florida State University, Department of Biological Science, Tallahassee, FL 32306, USA
| | - Xiaopeng Zhu
- Carnegie Mellon University, Computational Biology Department, Pittsburgh, PA 15213, USA
| | - Tyler Borrman
- University of Massachusetts Medical School, Program in Bioinformatics and Integrated Biology, Worcester, MA 01605, USA
| | | | - Zhiping Weng
- University of Massachusetts Medical School, Program in Bioinformatics and Integrated Biology, Worcester, MA 01605, USA
| | - John Bechhoefer
- Simon Fraser University, Department of Physics, Burnaby, BC V5A 1S6, Canada.
| | - Chun-Long Chen
- Institut Curie, PSL Research University, CNRS UMR 3244, Paris 75005, France; Sorbonne University, Paris 75005, France.
| | - David M Gilbert
- Florida State University, Department of Biological Science, Tallahassee, FL 32306, USA.
| | - Nicholas Rhind
- University of Massachusetts Medical School, Department of Biochemistry and Molecular Pharmacology, Worcester, MA 01605, USA.
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4
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Kumagai A, Dunphy WG. Binding of the Treslin-MTBP Complex to Specific Regions of the Human Genome Promotes the Initiation of DNA Replication. Cell Rep 2021; 32:108178. [PMID: 32966791 PMCID: PMC7523632 DOI: 10.1016/j.celrep.2020.108178] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 06/12/2020] [Accepted: 08/31/2020] [Indexed: 12/16/2022] Open
Abstract
The processes that control where higher eukaryotic cells initiate DNA replication throughout the genome are not understood clearly. In metazoans, the Treslin-MTBP complex mediates critical final steps in formation of the activated replicative helicase prior to initiation of replication. Here, we map the genome-wide distribution of the MTBP subunit of this complex in human cells. Our results indicate that MTBP binds to at least 30,000 sites in the genome. A majority of these sites reside in regions of open chromatin that contain transcriptional-regulatory elements (e.g., promoters, enhancers, and super-enhancers), which are known to be preferred areas for initiation of replication. Furthermore, many binding sites encompass two genomic features: a nucleosome-free DNA sequence (e.g., G-quadruplex DNA or AP-1 motif) and a nucleosome bearing histone marks characteristic of open chromatin, such as H3K4me2. Taken together, these findings indicate that Treslin-MTBP associates coordinately with multiple genomic signals to promote initiation of replication. Kumagai and Dunphy show that Treslin-MTBP, activator of the replicative helicase, binds to at least 30,000 sites in the human genome. Many sites contain a nucleosome with active chromatin marks and nucleosome-free DNA (G-quadruplex or AP-1 site). Thus, Treslin-MTBP associates with multiple genomic elements to promote initiation of DNA replication.
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Affiliation(s)
- Akiko Kumagai
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - William G Dunphy
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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5
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Silva Cascales H, Burdova K, Middleton A, Kuzin V, Müllers E, Stoy H, Baranello L, Macurek L, Lindqvist A. Cyclin A2 localises in the cytoplasm at the S/G2 transition to activate PLK1. Life Sci Alliance 2021; 4:e202000980. [PMID: 33402344 PMCID: PMC7812317 DOI: 10.26508/lsa.202000980] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 12/22/2020] [Accepted: 12/23/2020] [Indexed: 01/23/2023] Open
Abstract
Cyclin A2 is a key regulator of the cell cycle, implicated both in DNA replication and mitotic entry. Cyclin A2 participates in feedback loops that activate mitotic kinases in G2 phase, but why active Cyclin A2-CDK2 during the S phase does not trigger mitotic kinase activation remains unclear. Here, we describe a change in localisation of Cyclin A2 from being only nuclear to both nuclear and cytoplasmic at the S/G2 border. We find that Cyclin A2-CDK2 can activate the mitotic kinase PLK1 through phosphorylation of Bora, and that only cytoplasmic Cyclin A2 interacts with Bora and PLK1. Expression of predominately cytoplasmic Cyclin A2 or phospho-mimicking PLK1 T210D can partially rescue a G2 arrest caused by Cyclin A2 depletion. Cytoplasmic presence of Cyclin A2 is restricted by p21, in particular after DNA damage. Cyclin A2 chromatin association during DNA replication and additional mechanisms contribute to Cyclin A2 localisation change in the G2 phase. We find no evidence that such mechanisms involve G2 feedback loops and suggest that cytoplasmic appearance of Cyclin A2 at the S/G2 transition functions as a trigger for mitotic kinase activation.
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Affiliation(s)
| | - Kamila Burdova
- Laboratory of Cancer Cell Biology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Anna Middleton
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Vladislav Kuzin
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Erik Müllers
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Henriette Stoy
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Laura Baranello
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Libor Macurek
- Laboratory of Cancer Cell Biology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Arne Lindqvist
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
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6
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Shin G, Jeong D, Kim H, Im JS, Lee JK. RecQL4 tethering on the pre-replicative complex induces unscheduled origin activation and replication stress in human cells. J Biol Chem 2019; 294:16255-16265. [PMID: 31519754 DOI: 10.1074/jbc.ra119.009996] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 09/09/2019] [Indexed: 12/15/2022] Open
Abstract
Sequential activation of DNA replication origins is precisely programmed and critical to maintaining genome stability. RecQL4, a member of the conserved RecQ family of helicases, plays an essential role in the initiation of DNA replication in mammalian cells. Here, we showed that RecQL4 protein tethered on the pre-replicative complex (pre-RC) induces early activation of late replicating origins during S phase. Tethering of RecQL4 or its N terminus on pre-RCs via fusion with Orc4 protein resulted in the recruitment of essential initiation factors, such as Mcm10, And-1, Cdc45, and GINS, increasing nascent DNA synthesis in late replicating origins during early S phase. In this origin activation process, tethered RecQL4 was able to recruit Cdc45 even in the absence of cyclin-dependent kinase (CDK) activity, whereas CDK phosphorylation of RecQL4 N terminus was required for interaction with and origin recruitment of And-1 and GINS. In addition, forced activation of replication origins by RecQL4 tethering resulted in increased replication stress and the accumulation of ssDNAs, which can be recovered by transcription inhibition. Collectively, these results suggest that recruitment of RecQL4 to replication origins is an important step for temporal activation of replication origins during S phase. Further, perturbation of replication timing control by unscheduled origin activation significantly induces replication stress, which is mostly caused by transcription-replication conflicts.
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Affiliation(s)
- Gwangsu Shin
- Interdisciplinary Graduate Program in Genetic Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Dongsoo Jeong
- Interdisciplinary Graduate Program in Genetic Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyunsup Kim
- Interdisciplinary Graduate Program in Genetic Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jun-Sub Im
- Department of Biology Education, Seoul National University, Seoul, 08826, Republic of Korea
| | - Joon-Kyu Lee
- Interdisciplinary Graduate Program in Genetic Engineering, Seoul National University, Seoul, 08826, Republic of Korea .,Department of Biology Education, Seoul National University, Seoul, 08826, Republic of Korea
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7
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Cheung MH, Amin A, Wu R, Qin Y, Zou L, Yu Z, Liang C. Human NOC3 is essential for DNA replication licensing in human cells. Cell Cycle 2019; 18:605-620. [PMID: 30741601 DOI: 10.1080/15384101.2019.1578522] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Noc3p (Nucleolar Complex-associated protein) is an essential protein in budding yeast DNA replication licensing. Noc3p mediates the loading of Cdc6p and MCM proteins onto replication origins during the M-to-G1 transition by interacting with ORC (Origin Recognition Complex) and MCM (Minichromosome Maintenance) proteins. FAD24 (Factor for Adipocyte Differentiation, clone number 24), the human homolog of Noc3p (hNOC3), was previously reported to play roles in the regulation of DNA replication and proliferation in human cells. However, the role of hNOC3 in replication licensing was unclear. Here we report that hNOC3 physically interacts with multiple human pre-replicative complex (pre-RC) proteins and associates with known replication origins throughout the cell cycle. Moreover, knockdown of hNOC3 in HeLa cells abrogates the chromatin association of other pre-RC proteins including hCDC6 and hMCM, leading to DNA replication defects and eventual apoptosis in an abortive S-phase. In comparison, specific inhibition of the ribosome biogenesis pathway by preventing pre-rRNA synthesis, does not lead to any cell cycle or DNA replication defect or apoptosis in the same timeframe as the hNOC3 knockdown experiments. Our findings strongly suggest that hNOC3 plays an essential role in pre-RC formation and the initiation of DNA replication independent of its potential role in ribosome biogenesis in human cells.
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Affiliation(s)
- Man-Hei Cheung
- a Division of Life Science, Center for Cancer Research and State Key Lab for Molecular Neuroscience , Hong Kong University of Science and Technology , Hong Kong , China.,b Guangzhou HKUST Fok Ying Tung Research Institute , Guangzhou , China.,c Shenzhen-PKU-HKUST Medical Center , Biomedical Research Institute , Shenzhen , China
| | - Aftab Amin
- a Division of Life Science, Center for Cancer Research and State Key Lab for Molecular Neuroscience , Hong Kong University of Science and Technology , Hong Kong , China.,b Guangzhou HKUST Fok Ying Tung Research Institute , Guangzhou , China.,d School of Chinese Medicine , Hong Kong Baptist University , Hong Kong , China
| | - Rentian Wu
- a Division of Life Science, Center for Cancer Research and State Key Lab for Molecular Neuroscience , Hong Kong University of Science and Technology , Hong Kong , China
| | - Yan Qin
- a Division of Life Science, Center for Cancer Research and State Key Lab for Molecular Neuroscience , Hong Kong University of Science and Technology , Hong Kong , China
| | - Lan Zou
- a Division of Life Science, Center for Cancer Research and State Key Lab for Molecular Neuroscience , Hong Kong University of Science and Technology , Hong Kong , China.,e Intelgen Limited , Hong Kong-Guangzhou-Foshan , China
| | - Zhiling Yu
- d School of Chinese Medicine , Hong Kong Baptist University , Hong Kong , China
| | - Chun Liang
- a Division of Life Science, Center for Cancer Research and State Key Lab for Molecular Neuroscience , Hong Kong University of Science and Technology , Hong Kong , China.,b Guangzhou HKUST Fok Ying Tung Research Institute , Guangzhou , China.,c Shenzhen-PKU-HKUST Medical Center , Biomedical Research Institute , Shenzhen , China.,e Intelgen Limited , Hong Kong-Guangzhou-Foshan , China
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8
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Kaposi's Sarcoma-Associated Herpesvirus Deregulates Host Cellular Replication during Lytic Reactivation by Disrupting the MCM Complex through ORF59. J Virol 2018; 92:JVI.00739-18. [PMID: 30158293 DOI: 10.1128/jvi.00739-18] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 08/23/2018] [Indexed: 12/13/2022] Open
Abstract
Minichromosome maintenance proteins (MCMs) play an important role in DNA replication by binding to the origins as helicase and recruiting polymerases for DNA synthesis. During the S phase, MCM complex is loaded to limit DNA replication once per cell cycle. We identified MCMs as ORF59 binding partners in our protein pulldown assays, which led us to hypothesize that this interaction influences DNA replication. ORF59's interactions with MCMs were confirmed in both endogenous and overexpression systems, which showed its association with MCM3, MCM4, MCM5, and MCM6. Interestingly, MCM6 interacted with both the N- and C-terminal domains of ORF59, and its depletion in BCBL-1 and BC3 cells led to an increase in viral genome copies, viral late gene transcripts, and virion production compared to the control cells following reactivation. MCMs perform their function by loading onto the replication competent DNA, and one means of regulating chromatin loading/unloading, in addition to enzymatic activity of the MCM complex, is by posttranslational modifications, including phosphorylation of these factors. Interestingly, a hypophosphorylated form of MCM3, which is associated with reduced loading onto the chromatin, was detected during lytic reactivation and correlated with its inability to associate with histones in reactivated cells. Additionally, chromatin immunoprecipitation showed lower levels of MCM3 and MCM4 association at cellular origins of replication and decreased levels of cellular DNA synthesis in cells undergoing reactivation. Taken together, these findings suggest a mechanism in which KSHV ORF59 disrupts the assembly and functions of MCM complex to stall cellular DNA replication and promote viral replication.IMPORTANCE KSHV is the causative agent of various lethal malignancies affecting immunocompromised individuals. Both lytic and latent phases of the viral life cycle contribute to the progression of these cancers. A better understanding of how viral proteins disrupt functions of a normal healthy cell to cause oncogenesis is warranted. One crucial lytic protein produced early during lytic reactivation is the multifunctional ORF59. In this report, we elucidated an important role of ORF59 in manipulating the cellular environment conducive for viral DNA replication by deregulating the normal functions of the host MCM proteins. ORF59 binds to specific MCMs and sequesters them away from replication origins in order to sabotage cellular DNA replication. Blocking cellular DNA replication ensures that cellular resources are utilized for transcription and replication of viral DNA.
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9
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Balasubramaniam M, Reis RJS, Ayyadevara S, Wang X, Ganne A, Khaidakov M. Involvement of tRNAs in replication of human mitochondrial DNA and modifying effects of telomerase. Mech Ageing Dev 2017; 166:55-63. [PMID: 28765009 DOI: 10.1016/j.mad.2017.07.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 07/14/2017] [Accepted: 07/17/2017] [Indexed: 01/07/2023]
Abstract
Overexpression of telomerase has been shown to significantly increase the lifespan of mice. When mechanistically attributed to repair of critically short telomeres, the lifespan extending action of telomerase cannot be reconciled with the observation that telomerase-null mice do not exhibit shortening of lifespan for at least two generations. We hypothesized that telomerase may interfere with replication of mitochondrial DNA (mtDNA) in a way that reduces formation of deletions - the primary cause of age-dependent cell attrition in non-renewable cells such as myocytes and neurons. Here we show that several tRNA genes may function as alternative origins of replication (ORIs). We also show that telomerase interacts with canonical light strand ORI (ORIL) and tRNAs and modifies their activities. Our results suggest that replication of mitochondrial DNA (mtDNA) proceeds through a variety of mechanisms resulting in a mixture of classic strand-displacement mode, and coupled replication of heavy and light strands. Our results also suggest that effects of telomerase may arise from binding ORIL and thus limiting contribution of the deletion-prone strand displacement mode to mtDNA synthesis. These findings imply that it may be possible to uncouple detrimental and beneficial effects of telomerase, and thereby to improve telomerase-based strategies to extend lifespan.
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Affiliation(s)
- Meenakshisundaram Balasubramaniam
- Reynolds Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR 72205, United States; Central Arkansas Veterans Healthcare System, Little Rock, AR 72205, United States
| | - Robert J Shmookler Reis
- Reynolds Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR 72205, United States; Central Arkansas Veterans Healthcare System, Little Rock, AR 72205, United States
| | - Srinivas Ayyadevara
- Reynolds Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR 72205, United States; Central Arkansas Veterans Healthcare System, Little Rock, AR 72205, United States
| | - Xianwei Wang
- Xinxiang Medical University, Xinxiang, Henan, People's Republic of China
| | - Akshatha Ganne
- Reynolds Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR 72205, United States; University of Arkansas at Little Rock-University of Arkansas for Medical Sciences Bioinformatics Program, United States
| | - Magomed Khaidakov
- Central Arkansas Veterans Healthcare System, Little Rock, AR 72205, United States; Xinxiang Medical University, Xinxiang, Henan, People's Republic of China; Department of Medicine, Division of Gastroenterology and Hepatology, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, United States.
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10
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Langley AR, Gräf S, Smith JC, Krude T. Genome-wide identification and characterisation of human DNA replication origins by initiation site sequencing (ini-seq). Nucleic Acids Res 2016; 44:10230-10247. [PMID: 27587586 PMCID: PMC5137433 DOI: 10.1093/nar/gkw760] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 08/18/2016] [Accepted: 08/20/2016] [Indexed: 12/25/2022] Open
Abstract
Next-generation sequencing has enabled the genome-wide identification of human DNA replication origins. However, different approaches to mapping replication origins, namely (i) sequencing isolated small nascent DNA strands (SNS-seq); (ii) sequencing replication bubbles (bubble-seq) and (iii) sequencing Okazaki fragments (OK-seq), show only limited concordance. To address this controversy, we describe here an independent high-resolution origin mapping technique that we call initiation site sequencing (ini-seq). In this approach, newly replicated DNA is directly labelled with digoxigenin-dUTP near the sites of its initiation in a cell-free system. The labelled DNA is then immunoprecipitated and genomic locations are determined by DNA sequencing. Using this technique we identify >25,000 discrete origin sites at sub-kilobase resolution on the human genome, with high concordance between biological replicates. Most activated origins identified by ini-seq are found at transcriptional start sites and contain G-quadruplex (G4) motifs. They tend to cluster in early-replicating domains, providing a correlation between early replication timing and local density of activated origins. Origins identified by ini-seq show highest concordance with sites identified by SNS-seq, followed by OK-seq and bubble-seq. Furthermore, germline origins identified by positive nucleotide distribution skew jumps overlap with origins identified by ini-seq and OK-seq more frequently and more specifically than do sites identified by either SNS-seq or bubble-seq.
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Affiliation(s)
- Alexander R Langley
- Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, London NW7 1AA, UK
| | - Stefan Gräf
- Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK
- Department of Haematology, University of Cambridge, Cambridge CB2 0PT, UK
| | - James C Smith
- Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, London NW7 1AA, UK
| | - Torsten Krude
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
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11
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Stevanoni M, Palumbo E, Russo A. The Replication of Frataxin Gene Is Assured by Activation of Dormant Origins in the Presence of a GAA-Repeat Expansion. PLoS Genet 2016; 12:e1006201. [PMID: 27447727 PMCID: PMC4957762 DOI: 10.1371/journal.pgen.1006201] [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: 06/26/2015] [Accepted: 06/27/2016] [Indexed: 12/17/2022] Open
Abstract
It is well known that DNA replication affects the stability of several trinucleotide repeats, but whether replication profiles of human loci carrying an expanded repeat differ from those of normal alleles is poorly understood in the endogenous context. We investigated this issue using cell lines from Friedreich's ataxia patients, homozygous for a GAA-repeat expansion in intron 1 of the Frataxin gene. By interphase, FISH we found that in comparison to the normal Frataxin sequence the replication of expanded alleles is slowed or delayed. According to molecular combing, origins never fired within the normal Frataxin allele. In contrast, in mutant alleles dormant origins are recruited within the gene, causing a switch of the prevalent fork direction through the expanded repeat. Furthermore, a global modification of the replication profile, involving origin choice and a differential distribution of unidirectional forks, was observed in the surrounding 850 kb region. These data provide a wide-view of the interplay of events occurring during replication of genes carrying an expanded repeat.
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Affiliation(s)
| | - Elisa Palumbo
- Department of Biology, University of Padova, Padova, Italy
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12
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Huang Y, Amin A, Qin Y, Wang Z, Jiang H, Liang L, Shi L, Liang C. A Role of hIPI3 in DNA Replication Licensing in Human Cells. PLoS One 2016; 11:e0151803. [PMID: 27057756 PMCID: PMC4825987 DOI: 10.1371/journal.pone.0151803] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 03/06/2016] [Indexed: 01/08/2023] Open
Abstract
The yeast Ipi3p is required for DNA replication and cell viability in Sacharomyces cerevisiae. It is an essential component of the Rix1 complex (Rix1p/Ipi2p-Ipi1p-Ipi3p) that is required for the processing of 35S pre-rRNA in pre-60S ribosomal particles and for the initiation of DNA replication. The human IPI3 homolog is WDR18 (WD repeat domain 18), which shares significant homology with yIpi3p. Here we report that knockdown of hIPI3 resulted in substantial defects in the chromatin association of the MCM complex, DNA replication, cell cycle progression and cell proliferation. Importantly, hIPI3 silencing did not result in a reduction of the protein level of hCDC6, hMCM7, or the ectopically expressed GFP protein, indicating that protein synthesis was not defective in the same time frame of the DNA replication and cell cycle defects. Furthermore, the mRNA and protein levels of hIPI3 fluctuate in the cell cycle, with the highest levels from M phase to early G1 phase, similar to other pre-replicative (pre-RC) proteins. Moreover, hIPI3 interacts with other replication-initiation proteins, co-localizes with hMCM7 in the nucleus, and is important for the nuclear localization of hMCM7. We also found that hIPI3 preferentially binds to the origins of DNA replication including those at the c-Myc, Lamin-B2 and β-Globin loci. These results indicate that hIPI3 is involved in human DNA replication licensing independent of its role in ribosome biogenesis.
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Affiliation(s)
- Yining Huang
- Biomedical Research Institute, Shenzhen-PKU-HKUST Medical Center, Shenzhen, China
- Division of Life Science, Center for Cancer Research and State Key Lab for Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
- HKUST Fok Ying Tung Research Institute, Guangzhou, China
| | - Aftab Amin
- Division of Life Science, Center for Cancer Research and State Key Lab for Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Yan Qin
- Division of Life Science, Center for Cancer Research and State Key Lab for Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Ziyi Wang
- Biomedical Research Institute, Shenzhen-PKU-HKUST Medical Center, Shenzhen, China
- Division of Life Science, Center for Cancer Research and State Key Lab for Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
- HKUST Fok Ying Tung Research Institute, Guangzhou, China
| | - Huadong Jiang
- Division of Life Science, Center for Cancer Research and State Key Lab for Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Lu Liang
- Division of Life Science, Center for Cancer Research and State Key Lab for Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Linjing Shi
- Division of Life Science, Center for Cancer Research and State Key Lab for Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Chun Liang
- Biomedical Research Institute, Shenzhen-PKU-HKUST Medical Center, Shenzhen, China
- Division of Life Science, Center for Cancer Research and State Key Lab for Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
- HKUST Fok Ying Tung Research Institute, Guangzhou, China
- Intelgen Ltd., Hong Kong-Guangzhou-Foshan, China
- * E-mail:
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13
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Isolation of restriction fragments containing origins of replication from complex genomes. Methods Mol Biol 2016; 1300:279-92. [PMID: 25916718 DOI: 10.1007/978-1-4939-2596-4_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The identification and isolation of origins of replication from mammalian genomes has been a demanding task owing to the great complexity of these genomes. However, two methods have been refined in recent years each of which allows significant enrichment of recently activated origins of replication from asynchronous cell cultures. In one of these, nascent strands are melted from the long template DNA, and the small, origin-centered strands are isolated on sucrose gradients. The second method involves the selective entrapment of bubble-containing fragments in gelling agarose and their subsequent recovery and isolation by molecular cloning. Libraries prepared by this method from Chinese hamster and human cells have been shown to be extremely pure, and provide a renewable resource of origins that can be used as probes on microarrays or sequenced by high-throughput techniques to localize them within the genomic source. The bubble-trapping method is described here for asynchronous mammalian cells that grow with reasonable doubling times and from which nuclear matrices can be reliably prepared. The method for nuclear matrix preparation and enrichment of replication intermediates is described in an accompanying chapter entitled "Purification of restriction fragments containing replication intermediates from mammalian cells for 2-D gel analysis" (Chapter 16 ).
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14
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Cayrou C, Ballester B, Peiffer I, Fenouil R, Coulombe P, Andrau JC, van Helden J, Méchali M. The chromatin environment shapes DNA replication origin organization and defines origin classes. Genome Res 2015; 25:1873-85. [PMID: 26560631 PMCID: PMC4665008 DOI: 10.1101/gr.192799.115] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Accepted: 10/14/2015] [Indexed: 12/22/2022]
Abstract
To unveil the still-elusive nature of metazoan replication origins, we identified them genome-wide and at unprecedented high-resolution in mouse ES cells. This allowed initiation sites (IS) and initiation zones (IZ) to be differentiated. We then characterized their genetic signatures and organization and integrated these data with 43 chromatin marks and factors. Our results reveal that replication origins can be grouped into three main classes with distinct organization, chromatin environment, and sequence motifs. Class 1 contains relatively isolated, low-efficiency origins that are poor in epigenetic marks and are enriched in an asymmetric AC repeat at the initiation site. Late origins are mainly found in this class. Class 2 origins are particularly rich in enhancer elements. Class 3 origins are the most efficient and are associated with open chromatin and polycomb protein-enriched regions. The presence of Origin G-rich Repeated elements (OGRE) potentially forming G-quadruplexes (G4) was confirmed at most origins. These coincide with nucleosome-depleted regions located upstream of the initiation sites, which are associated with a labile nucleosome containing H3K64ac. These data demonstrate that specific chromatin landscapes and combinations of specific signatures regulate origin localization. They explain the frequently observed links between DNA replication and transcription. They also emphasize the plasticity of metazoan replication origins and suggest that in multicellular eukaryotes, the combination of distinct genetic features and chromatin configurations act in synergy to define and adapt the origin profile.
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Affiliation(s)
| | - Benoit Ballester
- INSERM, U1090 TAGC, Marseille F-13288, France; Aix Marseille University, U1090 TAGC, Marseille F-13288, France
| | | | - Romain Fenouil
- Centre d'Immunologie de Marseille-Luminy (CIML), 13009 Marseille, France
| | | | | | - Jacques van Helden
- INSERM, U1090 TAGC, Marseille F-13288, France; Aix Marseille University, U1090 TAGC, Marseille F-13288, France
| | - Marcel Méchali
- Institute of Human Genetics, CNRS, 34396 Montpellier, France
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15
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Urban JM, Foulk MS, Casella C, Gerbi SA. The hunt for origins of DNA replication in multicellular eukaryotes. F1000PRIME REPORTS 2015; 7:30. [PMID: 25926981 PMCID: PMC4371235 DOI: 10.12703/p7-30] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Origins of DNA replication (ORIs) occur at defined regions in the genome. Although DNA sequence defines the position of ORIs in budding yeast, the factors for ORI specification remain elusive in metazoa. Several methods have been used recently to map ORIs in metazoan genomes with the hope that features for ORI specification might emerge. These methods are reviewed here with analysis of their advantages and shortcomings. The various factors that may influence ORI selection for initiation of DNA replication are discussed.
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Affiliation(s)
- John M. Urban
- Division of Biology and Medicine, Department of Molecular Biology, Cell Biology and Biochemistry, Brown UniversitySidney Frank Hall, 185 Meeting Street, Providence, RI 02912USA
| | - Michael S. Foulk
- Division of Biology and Medicine, Department of Molecular Biology, Cell Biology and Biochemistry, Brown UniversitySidney Frank Hall, 185 Meeting Street, Providence, RI 02912USA
- Department of Biology, Mercyhurst University501 East 38th Street, Erie, PA 16546USA
| | - Cinzia Casella
- Division of Biology and Medicine, Department of Molecular Biology, Cell Biology and Biochemistry, Brown UniversitySidney Frank Hall, 185 Meeting Street, Providence, RI 02912USA
- Institute for Molecular Medicine, University of Southern DenmarkJB Winsloews Vej 25, 5000 Odense CDenmark
| | - Susan A. Gerbi
- Division of Biology and Medicine, Department of Molecular Biology, Cell Biology and Biochemistry, Brown UniversitySidney Frank Hall, 185 Meeting Street, Providence, RI 02912USA
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16
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Hyrien O. Peaks cloaked in the mist: the landscape of mammalian replication origins. J Cell Biol 2015; 208:147-60. [PMID: 25601401 PMCID: PMC4298691 DOI: 10.1083/jcb.201407004] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 12/16/2014] [Indexed: 12/23/2022] Open
Abstract
Replication of mammalian genomes starts at sites termed replication origins, which historically have been difficult to locate as a result of large genome sizes, limited power of genetic identification schemes, and rareness and fragility of initiation intermediates. However, origins are now mapped by the thousands using microarrays and sequencing techniques. Independent studies show modest concordance, suggesting that mammalian origins can form at any DNA sequence but are suppressed by read-through transcription or that they can overlap the 5' end or even the entire gene. These results require a critical reevaluation of whether origins form at specific DNA elements and/or epigenetic signals or require no such determinants.
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Affiliation(s)
- Olivier Hyrien
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique UMR8197 and Institut National de la Santé et de la Recherche Médicale U1024, 75005 Paris, France
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17
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Puzzi L, Marchetti L, Peverali FA, Biamonti G, Giacca M. DNA-protein interaction dynamics at the Lamin B2 replication origin. Cell Cycle 2015; 14:64-73. [PMID: 25483070 PMCID: PMC4352957 DOI: 10.4161/15384101.2014.973337] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 09/30/2014] [Indexed: 12/24/2022] Open
Abstract
To date, a complete understanding of the molecular events leading to DNA replication origin activation in mammalian cells still remains elusive. In this work, we report the results of a high resolution chromatin immunoprecipitation study to detect proteins interacting with the human Lamin B2 replication origin. In addition to the pre-RC component ORC4 and to the transcription factors USF and HOXC13, we found that 2 components of the AP-1 transcription factor, c-Fos and c-Jun, are also associated with the origin DNA during the late G1 phase of the cell cycle and that these factors interact with ORC4. Both DNA replication and AP-1 factor binding to the origin region were perturbed by cell treatment with merbarone, a topoisomerase II inhibitor, suggesting that DNA topology is essential for determining origin function.
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Affiliation(s)
- Luca Puzzi
- Molecular Biology Laboratory; Scuola Normale Superiore; Pisa, Italy
- Molecular Medicine Laboratory; International Centre for Genetic Engineering and Biotechnology (ICGEB); Trieste, Italy
| | - Laura Marchetti
- NEST; Scuola Normale Superiore and Istituto Nanoscienze-CNR; Pisa, Italy
| | - Fiorenzo A Peverali
- Istituto di Genetica Molecolare (IGM); Consiglio Nazionale delle Ricerche (CNR); Pavia, Italy
| | - Giuseppe Biamonti
- Istituto di Genetica Molecolare (IGM); Consiglio Nazionale delle Ricerche (CNR); Pavia, Italy
| | - Mauro Giacca
- Molecular Medicine Laboratory; International Centre for Genetic Engineering and Biotechnology (ICGEB); Trieste, Italy
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18
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Shinbrot E, Henninger EE, Weinhold N, Covington KR, Göksenin AY, Schultz N, Chao H, Doddapaneni H, Muzny DM, Gibbs RA, Sander C, Pursell ZF, Wheeler DA. Exonuclease mutations in DNA polymerase epsilon reveal replication strand specific mutation patterns and human origins of replication. Genome Res 2014; 24:1740-50. [PMID: 25228659 PMCID: PMC4216916 DOI: 10.1101/gr.174789.114] [Citation(s) in RCA: 203] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Tumors with somatic mutations in the proofreading exonuclease domain of DNA polymerase epsilon (POLE-exo*) exhibit a novel mutator phenotype, with markedly elevated TCT→TAT and TCG→TTG mutations and overall mutation frequencies often exceeding 100 mutations/Mb. Here, we identify POLE-exo* tumors in numerous cancers and classify them into two groups, A and B, according to their mutational properties. Group A mutants are found only in POLE, whereas Group B mutants are found in POLE and POLD1 and appear to be nonfunctional. In Group A, cell-free polymerase assays confirm that mutations in the exonuclease domain result in high mutation frequencies with a preference for C→A mutation. We describe the patterns of amino acid substitutions caused by POLE-exo* and compare them to other tumor types. The nucleotide preference of POLE-exo* leads to increased frequencies of recurrent nonsense mutations in key tumor suppressors such as TP53, ATM, and PIK3R1. We further demonstrate that strand-specific mutation patterns arise from some of these POLE-exo* mutants during genome duplication. This is the first direct proof of leading strand-specific replication by human POLE, which has only been demonstrated in yeast so far. Taken together, the extremely high mutation frequency and strand specificity of mutations provide a unique identifier of eukaryotic origins of replication.
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Affiliation(s)
- Eve Shinbrot
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Erin E Henninger
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana 70112, USA
| | - Nils Weinhold
- Department of Computational Biology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Kyle R Covington
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - A Yasemin Göksenin
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana 70112, USA
| | - Nikolaus Schultz
- Department of Computational Biology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Hsu Chao
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | | | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Chris Sander
- Department of Computational Biology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Zachary F Pursell
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana 70112, USA
| | - David A Wheeler
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA;
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19
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Mukhopadhyay R, Lajugie J, Fourel N, Selzer A, Schizas M, Bartholdy B, Mar J, Lin CM, Martin MM, Ryan M, Aladjem MI, Bouhassira EE. Allele-specific genome-wide profiling in human primary erythroblasts reveal replication program organization. PLoS Genet 2014; 10:e1004319. [PMID: 24787348 PMCID: PMC4006724 DOI: 10.1371/journal.pgen.1004319] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 03/10/2014] [Indexed: 11/19/2022] Open
Abstract
We have developed a new approach to characterize allele-specific timing of DNA replication genome-wide in human primary basophilic erythroblasts. We show that the two chromosome homologs replicate at the same time in about 88% of the genome and that large structural variants are preferentially associated with asynchronous replication. We identified about 600 megabase-sized asynchronously replicated domains in two tested individuals. The longest asynchronously replicated domains are enriched in imprinted genes suggesting that structural variants and parental imprinting are two causes of replication asynchrony in the human genome. Biased chromosome X inactivation in one of the two individuals tested was another source of detectable replication asynchrony. Analysis of high-resolution TimEX profiles revealed small variations termed timing ripples, which were undetected in previous, lower resolution analyses. Timing ripples reflect highly reproducible, variations of the timing of replication in the 100 kb-range that exist within the well-characterized megabase-sized replication timing domains. These ripples correspond to clusters of origins of replication that we detected using novel nascent strands DNA profiling methods. Analysis of the distribution of replication origins revealed dramatic differences in initiation of replication frequencies during S phase and a strong association, in both synchronous and asynchronous regions, between origins of replication and three genomic features: G-quadruplexes, CpG Islands and transcription start sites. The frequency of initiation in asynchronous regions was similar in the two homologs. Asynchronous regions were richer in origins of replication than synchronous regions. DNA replication in mammalian cells proceeds according to a distinct order. Genes that are expressed tend to replicate before genes that are not expressed. We report here that we have developed a method to measure the timing of replication of the maternal and paternal chromosomes separately. We found that the paternal and maternal chromosomes replicate at exactly the same time in the large majority of the genome and that the 12% of the genome that replicated asynchronously was enriched in imprinted genes and in structural variants. Previous experiments have shown that chromosomes could be divided into replication timing domains that are a few hundred thousand to a few megabases in size. We show here that these domains can be divided into sub-domains defined by ripples in the timing profile. These ripples corresponded to clusters of origins of replication. Finally, we show that the frequency of initiation in asynchronous regions was similar in the two homologs.
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Affiliation(s)
- Rituparna Mukhopadhyay
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Julien Lajugie
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Nicolas Fourel
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Ari Selzer
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Michael Schizas
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Boris Bartholdy
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Jessica Mar
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Chii Mei Lin
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Melvenia M. Martin
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Michael Ryan
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Mirit I. Aladjem
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Eric E. Bouhassira
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America
- * E-mail:
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20
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Li B, Su T, Ferrari R, Li JY, Kurdistani SK. A unique epigenetic signature is associated with active DNA replication loci in human embryonic stem cells. Epigenetics 2013; 9:257-67. [PMID: 24172870 DOI: 10.4161/epi.26870] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The cellular epigenetic landscape changes as pluripotent stem cells differentiate to somatic cells or when differentiated cells transform to a cancerous state. These epigenetic changes are commonly correlated with differences in gene expression. Whether active DNA replication is also associated with distinct chromatin environments in these developmentally and phenotypically diverse cell types has not been known. Here, we used BrdU-seq to map active DNA replication loci in human embryonic stem cells (hESCs), normal primary fibroblasts and a cancer cell line, and correlated these maps to the epigenome. In all cell lines, the majority of BrdU peaks were enriched in euchromatin and at DNA repetitive elements, especially at microsatellite repeats, and coincided with previously determined replication origins. The most prominent BrdU peaks were shared between all cells but a sizable fraction of the peaks were specific to each cell type and associated with cell type-specific genes. Surprisingly, the BrdU peaks that were common to all cell lines were associated with H3K18ac, H3K56ac, and H4K20me1 histone marks only in hESCs but not in normal fibroblasts or cancer cells. Depletion of the histone acetyltransferases for H3K18 and H3K56 dramatically decreased the number and intensity of BrdU peaks in hESCs. Our data reveal a unique epigenetic signature that distinguishes active replication loci in hESCs from normal somatic or malignant cells.
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Affiliation(s)
- Bing Li
- Department of Biological Chemistry; University of California; Los Angeles, CA USA
| | - Trent Su
- Department of Biological Chemistry; University of California; Los Angeles, CA USA; Division of Oral Biology and Medicine; School of Dentistry; University of California; Los Angeles, CA USA
| | - Roberto Ferrari
- Department of Biological Chemistry; University of California; Los Angeles, CA USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research; David Geffen School of Medicine; University of California; Los Angeles, CA USA
| | - Jing-Yu Li
- Department of Biological Chemistry; University of California; Los Angeles, CA USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research; David Geffen School of Medicine; University of California; Los Angeles, CA USA
| | - Siavash K Kurdistani
- Department of Biological Chemistry; University of California; Los Angeles, CA USA; Molecular Biology Institute; University of California; Los Angeles, CA USA; Department of Pathology and Laboratory Medicine; University of California; Los Angeles, CA USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research; David Geffen School of Medicine; University of California; Los Angeles, CA USA
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21
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Specification of DNA replication origins and genomic base composition in fission yeasts. J Mol Biol 2013; 425:4706-13. [PMID: 24095860 DOI: 10.1016/j.jmb.2013.09.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 09/17/2013] [Accepted: 09/19/2013] [Indexed: 11/21/2022]
Abstract
In the "Replicon Theory", Jacob, Brenner and Cuzin proposed the existence of replicators and initiators as the two major actors in DNA replication. Over the years, many protein components of initiators have been shown to be conserved in different organisms during evolution. By contrast, replicator DNA sequences (often referred to as replication origins) have diverged beyond possible comparison between eukaryotic genomes. Replication origins in the fission yeast Schizosaccharomyces pombe are made up of A+T-rich sequences that do not share any consensus elements. The information encoded in these replicators is interpreted by the Orc4 subunit of the ORC (origin recognition complex), which is unique among eukaryotes in that it contains a large domain harboring nine AT-hook subdomains that target ORC to a great variety of A+T-rich sequences along the chromosomes. Recently, the genomes of other Schizosaccharomyces species have been sequenced and the regions encompassing their replication origins have been identified. DNA sequence analysis and comparison of the organization of their Orc4 proteins have revealed species-specific differences that contribute to our understanding of how the specification of replication origins has evolved during the phylogenetic divergence of fission yeasts.
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22
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Lombraña R, Almeida R, Revuelta I, Madeira S, Herranz G, Saiz N, Bastolla U, Gómez M. High-resolution analysis of DNA synthesis start sites and nucleosome architecture at efficient mammalian replication origins. EMBO J 2013; 32:2631-44. [PMID: 23995398 DOI: 10.1038/emboj.2013.195] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 08/07/2013] [Indexed: 11/09/2022] Open
Abstract
DNA replication origins are poorly characterized genomic regions that are essential to recruit and position the initiation complex to start DNA synthesis. Despite the lack of specific replicator sequences, initiation of replication does not occur at random sites in the mammalian genome. This has lead to the view that DNA accessibility could be a major determinant of mammalian origins. Here, we performed a high-resolution analysis of nucleosome architecture and initiation sites along several origins of different genomic location and firing efficiencies. We found that mammalian origins are highly variable in nucleosome conformation and initiation patterns. Strikingly, initiation sites at efficient CpG island-associated origins always occur at positions of high-nucleosome occupancy. Origin recognition complex (ORC) binding sites, however, occur at adjacent but distinct positions marked by labile nucleosomes. We also found that initiation profiles mirror nucleosome architecture, both at endogenous origins and at a transgene in a heterologous system. Our studies provide a unique insight into the relationship between chromatin structure and initiation sites in the mammalian genome that has direct implications for how the replication programme can be accommodated to diverse epigenetic scenarios.
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Affiliation(s)
- Rodrigo Lombraña
- 1Functional Organization of the Genome Group, Centro de Biología Molecular 'Severo Ochoa', Consejo Superior de Investigaciones Científicas/Universidad Autónoma de Madrid (CSIC/UAM), Madrid, Spain
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23
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Yanga W, Lib X. Next-generation sequencing of Okazaki fragments extracted from Saccharomyces cerevisiae. FEBS Lett 2013; 587:2441-7. [PMID: 23792162 DOI: 10.1016/j.febslet.2013.06.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 06/11/2013] [Indexed: 11/19/2022]
Abstract
Genome-wide Okazaki fragment distribution can differentiate the discontinuous from the semi-discontinuous DNA replication model. Here, we investigated the genome-wide Okazaki fragment distribution in Saccharomyces cerevisiae S288C. We improved the method based upon lambda exonuclease digestion to purify Okazaki fragments from S288C yeast cells, followed by Illumina sequencing. The distribution of Okazaki fragments around confirmed replication origins, including two highly efficient replication origins, supported the discontinuous DNA replication model. In S. cerevisiae mitochondria, Okazaki fragments were overrepresented in the transcribed regions, indicating the interplay between transcription and DNA replication.
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Affiliation(s)
- Wenchao Yanga
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China.
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24
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Abdelbaqi K, Di Paola D, Rampakakis E, Zannis-Hadjopoulos M. Ku protein levels, localization and association to replication origins in different stages of breast tumor progression. J Cancer 2013; 4:358-70. [PMID: 23781282 PMCID: PMC3677623 DOI: 10.7150/jca.6289] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 05/23/2013] [Indexed: 11/05/2022] Open
Abstract
Human origins of DNA replication are specific sequences within the genome whereby DNA replication is initiated. A select group of proteins, known as the pre-replication (pre-RC) complex, in whose formation the Ku protein (Ku70/Ku86) was shown to play a role, bind to replication origins to initiate DNA replication. In this study, we have examined the involvement of Ku in breast tumorigenesis and tumor progression and found that the Ku protein expression levels in human breast metastatic (MCF10AC1a) cells were higher in the chromatin fraction compared to hyperplastic (MCF10AT) and normal (MCF10A) human breast cells, but remained constant in both the nuclear and cytoplasmic fractions. In contrast, in human intestinal cells, the Ku expression level was relatively constant for all cell fractions. Nascent DNA abundance and chromatin association of Ku70/86 revealed that the c-myc origin activity in MCF10AC1a is 2.5 to 5-fold higher than in MCF10AT and MCF10A, respectively, and Ku was bound to the c-myc origin more abundantly in MCF10AC1a, by approximately 1.5 to 4.2-fold higher than in MCF10AT and MCF10A, respectively. In contrast, similar nascent DNA abundance and chromatin association was found for all cell lines for the lamin B2 origin, associated with the constitutively active housekeeping lamin B2 gene. Electrophoretic mobility shift assays (EMSAs) performed on the nuclear extracts (NEs) of the three cell types revealed the presence of protein-DNA replication complexes on both the c-myc and lamin B2 origins, but an increase in binding activity was observed from normal, to transformed, to cancer cells for the c-myc origin, whereas no such difference was seen for the lamin B2 origin. Overall, the results suggest that increased Ku chromatin association, beyond wild type levels, alters cellular processes, which have been implicated in tumorigenesis.
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Affiliation(s)
- Khalil Abdelbaqi
- 1. Goodman Cancer Research Center, McGill University, Montreal, Quebec, Canada H3G 1Y6; ; 2. Department of Biochemistry, McGill University, Montreal, Quebec, Canada H3G 1Y6
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Evertts AG, Coller HA. Back to the origin: reconsidering replication, transcription, epigenetics, and cell cycle control. Genes Cancer 2013; 3:678-96. [PMID: 23634256 DOI: 10.1177/1947601912474891] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
In bacteria, replication is a carefully orchestrated event that unfolds the same way for each bacterium and each cell division. The process of DNA replication in bacteria optimizes cell growth and coordinates high levels of simultaneous replication and transcription. In metazoans, the organization of replication is more enigmatic. The lack of a specific sequence that defines origins of replication has, until recently, severely limited our ability to define the organizing principles of DNA replication. This question is of particular importance as emerging data suggest that replication stress is an important contributor to inherited genetic damage and the genomic instability in tumors. We consider here the replication program in several different organisms including recent genome-wide analyses of replication origins in humans. We review recent studies on the role of cytosine methylation in replication origins, the role of transcriptional looping and gene gating in DNA replication, and the role of chromatin's 3-dimensional structure in DNA replication. We use these new findings to consider several questions surrounding DNA replication in metazoans: How are origins selected? What is the relationship between replication and transcription? How do checkpoints inhibit origin firing? Why are there early and late firing origins? We then discuss whether oncogenes promote cancer through a role in DNA replication and whether errors in DNA replication are important contributors to the genomic alterations and gene fusion events observed in cancer. We conclude with some important areas for future experimentation.
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Affiliation(s)
- Hoyun Lee
- Tumour Biology Group, Northeast Cancer Centre, Sudbury, Ontario Canada.
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Cayrou C, Coulombe P, Puy A, Rialle S, Kaplan N, Segal E, Méchali M. New insights into replication origin characteristics in metazoans. Cell Cycle 2012; 11:658-67. [PMID: 22373526 DOI: 10.4161/cc.11.4.19097] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We recently reported the identification and characterization of DNA replication origins (Oris) in metazoan cell lines. Here, we describe additional bioinformatic analyses showing that the previously identified GC-rich sequence elements form origin G-rich repeated elements (OGREs) that are present in 67% to 90% of the DNA replication origins from Drosophila to human cells, respectively. Our analyses also show that initiation of DNA synthesis takes place precisely at 160 bp (Drosophila) and 280 bp (mouse) from the OGRE. We also found that in most CpG islands, an OGRE is positioned in opposite orientation on each of the two DNA strands and detected two sites of initiation of DNA synthesis upstream or downstream of each OGRE. Conversely, Oris not associated with CpG islands have a single initiation site. OGRE density along chromosomes correlated with previously published replication timing data. Ori sequences centered on the OGRE are also predicted to have high intrinsic nucleosome occupancy. Finally, OGREs predict G-quadruplex structures at Oris that might be structural elements controlling the choice or activation of replication origins.
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28
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Vaara M, Itkonen H, Hillukkala T, Liu Z, Nasheuer HP, Schaarschmidt D, Pospiech H, Syväoja JE. Segregation of replicative DNA polymerases during S phase: DNA polymerase ε, but not DNA polymerases α/δ, are associated with lamins throughout S phase in human cells. J Biol Chem 2012; 287:33327-38. [PMID: 22887995 DOI: 10.1074/jbc.m112.357996] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
DNA polymerases (Pol) α, δ, and ε replicate the bulk of chromosomal DNA in eukaryotic cells, Pol ε being the main leading strand and Pol δ the lagging strand DNA polymerase. By applying chromatin immunoprecipitation (ChIP) and quantitative PCR we found that at G(1)/S arrest, all three DNA polymerases were enriched with DNA containing the early firing lamin B2 origin of replication and, 2 h after release from the block, with DNA containing the origin at the upstream promoter region of the MCM4 gene. Pol α, δ, and ε were released from these origins upon firing. All three DNA polymerases, Mcm3 and Cdc45, but not Orc2, still formed complexes in late S phase. Reciprocal ChIP of the three DNA polymerases revealed that at G(1)/S arrest and early in S phase, Pol α, δ, and ε were associated with the same nucleoprotein complexes, whereas in late S phase Pol ε and Pol α/δ were largely associated with distinct complexes. At G(1)/S arrest, the replicative DNA polymerases were associated with lamins, but in late S phase only Pol ε, not Pol α/δ, remained associated with lamins. Consistently, Pol ε, but not Pol δ, was found in nuclear matrix fraction throughout the cell cycle. Therefore, Pol ε and Pol α/δ seem to pursue their functions at least in part independently in late S phase, either by physical uncoupling of lagging strand maturation from the fork progression, or by recruitment of Pol δ, but not Pol ε, to post-replicative processes such as translesion synthesis or post-replicative repair.
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Affiliation(s)
- Markku Vaara
- Department of Biology, University of Eastern Finland, Joensuu, Finland
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29
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Valenzuela MS, Hu L, Lueders J, Walker R, Meltzer PS. Broader utilization of origins of DNA replication in cancer cell lines along a 78 kb region of human chromosome 2q34. J Cell Biochem 2012; 113:132-40. [PMID: 21898540 DOI: 10.1002/jcb.23336] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Human DNA replication depends on the activation of thousands of origins distributed within the genome. The actual distribution of origins is not known, nor whether this distribution is unique to a cell type, or if it changes with the proliferative state of the cell. In this study, we have employed a real-time PCR-based nascent strand DNA abundance assay, to determine the location of origins along a 78 kb region on Chr2q34. Preliminary studies using nascent DNA strands isolated from either HeLa and normal skin fibroblast cells showed that in both cell lines peaks of high origin activity mapped in similar locations. However, the overall origin profile in HeLa cells corresponded to broad origin activation zones, whereas in fibroblasts a more punctuated profile of origin activation was observed. To investigate the relevance of this differential origin profile, we compared the origin distribution profiles in breast cancer cell lines MDA-MB-231, BT-474, and MCF-7, to their normal counterpart MCF-10A. In addition, the CRL7250 cell line was also used as a normal control. Our results validated our earlier observation and showed that the origin profile in normal cell lines exhibited a punctuated pattern, in contrast to broader zone profiles observed in the cancer cell lines. A quantitative analysis of origin peaks revealed that the number of activated origins in cancer cells is statistically larger than that obtained in normal cells, suggesting that the flexibility of origin usage is significantly increased in cancer cells compared to their normal counterparts.
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Affiliation(s)
- Manuel S Valenzuela
- Department of Biochemistry and Cancer Biology, School of Medicine, Meharry Medical College, Nashville, TN 37208, USA.
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30
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Cayrou C, Grégoire D, Coulombe P, Danis E, Méchali M. Genome-scale identification of active DNA replication origins. Methods 2012; 57:158-64. [DOI: 10.1016/j.ymeth.2012.06.015] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Revised: 06/21/2012] [Accepted: 06/25/2012] [Indexed: 12/15/2022] Open
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Valenzuela MS. Initiation of DNA Replication in the Human Genome. HEREDITARY GENETICS : CURRENT RESEARCH 2012; Suppl 1:4903. [PMID: 24511453 PMCID: PMC3915928 DOI: 10.4172/2161-1041.s1-003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Replication of the human genome relies on the presence of thousands of origins distributed along each of the chromosomes. The activation of these origins occurs in a highly regulated manner to ensure that chromosomes are faithfully duplicated only once during each cell cycle. Failure in this regulation can lead to abnormal cell proliferation, or/and genomic instability, the hallmarks of cancer cells. The mechanisms determining how, when, and where origins are activated remains still a mystery. However recent technological advances have facilitated the study of DNA replication in a genome-wide scale, and have provided a wealth of information on several features of this process. Here we present an overview of the current progress on our understanding of the initiation step of DNA replication in human cells, and its relationship to abnormal cell proliferation.
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Affiliation(s)
- Manuel S. Valenzuela
- Department of Biochemistry and Cancer Biology, School of Medicine, Meharry Medical College, 1005 D.B. Todd Jr. Boulevard, Nashville, TN 37208, USA
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Abstract
The origin recognition complex (ORC) was first discovered in the baker's yeast in 1992. Identification of ORC opened up a path for subsequent molecular level investigations on how eukaryotic cells initiate and control genome duplication each cell cycle. Twenty years after the first biochemical isolation, ORC is now taking on a three-dimensional shape, although a very blurry shape at the moment, thanks to the recent electron microscopy and image reconstruction efforts. In this chapter, we outline the current biochemical knowledge about ORC from several eukaryotic systems, with emphasis on the most recent structural and biochemical studies. Despite many species-specific properties, an emerging consensus is that ORC is an ATP-dependent machine that recruits other key proteins to form pre-replicative complexes (pre-RCs) at many origins of DNA replication, enabling the subsequent initiation of DNA replication in S phase.
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Affiliation(s)
- Huilin Li
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA, And, Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA, , Tel: 631-344-2931, Fax: 631-344-3407
| | - Bruce Stillman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA, , Tel: 516-367-8383
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Sugimoto N, Yugawa T, Iizuka M, Kiyono T, Fujita M. Chromatin remodeler sucrose nonfermenting 2 homolog (SNF2H) is recruited onto DNA replication origins through interaction with Cdc10 protein-dependent transcript 1 (Cdt1) and promotes pre-replication complex formation. J Biol Chem 2011; 286:39200-10. [PMID: 21937426 DOI: 10.1074/jbc.m111.256123] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
From late mitosis to the G(1) phase of the cell cycle, ORC, CDC6, and Cdt1 form the machinery necessary to load MCM2-7 complexes onto DNA. Here, we show that SNF2H, a member of the ATP-dependent chromatin-remodeling complex, is recruited onto DNA replication origins in human cells in a Cdt1-dependent manner and positively regulates MCM loading. SNF2H physically interacted with Cdt1. ChIP assays indicated that SNF2H associates with replication origins specifically during the G(1) phase. Binding of SNF2H at origins was decreased by Cdt1 silencing and, conversely, enhanced by Cdt1 overexpression. Furthermore, SNF2H silencing prevented MCM loading at origins and moderately inhibited S phase progression. Although neither SNF2H overexpression nor SNF2H silencing appeared to impact rereplication induced by Cdt1 overexpression, Cdt1-induced checkpoint activation was inhibited by SNF2H silencing. Collectively, these data suggest that SNF2H may promote MCM loading at DNA replication origins via interaction with Cdt1 in human cells. Because efficient loading of excess MCM complexes is thought to be required for cells to tolerate replication stress, Cdt1- and SNF2H-mediated promotion of MCM loading may be biologically relevant for the regulation of DNA replication.
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Affiliation(s)
- Nozomi Sugimoto
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashiku, Fukuoka 812-8582, Japan
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Rajewska M, Wegrzyn K, Konieczny I. AT-rich region and repeated sequences - the essential elements of replication origins of bacterial replicons. FEMS Microbiol Rev 2011; 36:408-34. [PMID: 22092310 DOI: 10.1111/j.1574-6976.2011.00300.x] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Accepted: 07/07/2011] [Indexed: 11/27/2022] Open
Abstract
Repeated sequences are commonly present in the sites for DNA replication initiation in bacterial, archaeal, and eukaryotic replicons. Those motifs are usually the binding places for replication initiation proteins or replication regulatory factors. In prokaryotic replication origins, the most abundant repeated sequences are DnaA boxes which are the binding sites for chromosomal replication initiation protein DnaA, iterons which bind plasmid or phage DNA replication initiators, defined motifs for site-specific DNA methylation, and 13-nucleotide-long motifs of a not too well-characterized function, which are present within a specific region of replication origin containing higher than average content of adenine and thymine residues. In this review, we specify methods allowing identification of a replication origin, basing on the localization of an AT-rich region and the arrangement of the origin's structural elements. We describe the regularity of the position and structure of the AT-rich regions in bacterial chromosomes and plasmids. The importance of 13-nucleotide-long repeats present at the AT-rich region, as well as other motifs overlapping them, was pointed out to be essential for DNA replication initiation including origin opening, helicase loading and replication complex assembly. We also summarize the role of AT-rich region repeated sequences for DNA replication regulation.
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Affiliation(s)
- Magdalena Rajewska
- Department of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology, University of Gdansk, Gdansk, Poland
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35
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Ding Q, MacAlpine DM. Defining the replication program through the chromatin landscape. Crit Rev Biochem Mol Biol 2011; 46:165-79. [PMID: 21417598 DOI: 10.3109/10409238.2011.560139] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
DNA replication is an essential cell cycle event required for the accurate and timely duplication of the chromosomes. It is essential that the genome is replicated accurately and completely within the confines of S-phase. Failure to completely copy the genome has the potential to result in catastrophic genomic instability. Replication initiates in a coordinated manner from multiple locations, termed origins of replication, distributed across each of the chromosomes. The selection of these origins of replication is a dynamic process responding to both developmental and tissue-specific signals. In this review, we explore the role of the local chromatin environment in regulating the DNA replication program at the level of origin selection and activation. Finally, there is increasing molecular evidence that the DNA replication program itself affects the chromatin landscape, suggesting that DNA replication is critical for both genetic and epigenetic inheritance.
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Affiliation(s)
- Queying Ding
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA
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36
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Cayrou C, Coulombe P, Vigneron A, Stanojcic S, Ganier O, Peiffer I, Rivals E, Puy A, Laurent-Chabalier S, Desprat R, Méchali M. Genome-scale analysis of metazoan replication origins reveals their organization in specific but flexible sites defined by conserved features. Genome Res 2011; 21:1438-49. [PMID: 21750104 DOI: 10.1101/gr.121830.111] [Citation(s) in RCA: 248] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In metazoans, thousands of DNA replication origins (Oris) are activated at each cell cycle. Their genomic organization and their genetic nature remain elusive. Here, we characterized Oris by nascent strand (NS) purification and a genome-wide analysis in Drosophila and mouse cells. We show that in both species most CpG islands (CGI) contain Oris, although methylation is nearly absent in Drosophila, indicating that this epigenetic mark is not crucial for defining the activated origin. Initiation of DNA synthesis starts at the borders of CGI, resulting in a striking bimodal distribution of NS, suggestive of a dual initiation event. Oris contain a unique nucleotide skew around NS peaks, characterized by G/T and C/A overrepresentation at the 5' and 3' of Ori sites, respectively. Repeated GC-rich elements were detected, which are good predictors of Oris, suggesting that common sequence features are part of metazoan Oris. In the heterochromatic chromosome 4 of Drosophila, Oris correlated with HP1 binding sites. At the chromosome level, regions rich in Oris are early replicating, whereas Ori-poor regions are late replicating. The genome-wide analysis was coupled with a DNA combing analysis to unravel the organization of Oris. The results indicate that Oris are in a large excess, but their activation does not occur at random. They are organized in groups of site-specific but flexible origins that define replicons, where a single origin is activated in each replicon. This organization provides both site specificity and Ori firing flexibility in each replicon, allowing possible adaptation to environmental cues and cell fates.
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37
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Valenzuela MS, Chen Y, Davis S, Yang F, Walker RL, Bilke S, Lueders J, Martin MM, Aladjem MI, Massion PP, Meltzer PS. Preferential localization of human origins of DNA replication at the 5'-ends of expressed genes and at evolutionarily conserved DNA sequences. PLoS One 2011; 6:e17308. [PMID: 21602917 PMCID: PMC3094316 DOI: 10.1371/journal.pone.0017308] [Citation(s) in RCA: 38] [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: 10/07/2010] [Accepted: 01/27/2011] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Replication of mammalian genomes requires the activation of thousands of origins which are both spatially and temporally regulated by as yet unknown mechanisms. At the most fundamental level, our knowledge about the distribution pattern of origins in each of the chromosomes, among different cell types, and whether the physiological state of the cells alters this distribution is at present very limited. METHODOLOGY/PRINCIPAL FINDINGS We have used standard λ-exonuclease resistant nascent DNA preparations in the size range of 0.7-1.5 kb obtained from the breast cancer cell line MCF-7 hybridized to a custom tiling array containing 50-60 nt probes evenly distributed among genic and non-genic regions covering about 1% of the human genome. A similar DNA preparation was used for high-throughput DNA sequencing. Array experiments were also performed with DNA obtained from BT-474 and H520 cell lines. By determining the sites showing nascent DNA enrichment, we have localized several thousand origins of DNA replication. Our major findings are: (a) both array and DNA sequencing assay methods produced essentially the same origin distribution profile; (b) origin distribution is largely conserved (>70%) in all cell lines tested; (c) origins are enriched at the 5'ends of expressed genes and at evolutionarily conserved intergenic sequences; and (d) ChIP on chip experiments in MCF-7 showed an enrichment of H3K4Me3 and RNA Polymerase II chromatin binding sites at origins of DNA replication. CONCLUSIONS/SIGNIFICANCE Our results suggest that the program for origin activation is largely conserved among different cell types. Also, our work supports recent studies connecting transcription initiation with replication, and in addition suggests that evolutionarily conserved intergenic sequences have the potential to participate in origin selection. Overall, our observations suggest that replication origin selection is a stochastic process significantly dependent upon local accessibility to replication factors.
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Affiliation(s)
- Manuel S. Valenzuela
- Genetics Branch, Center for Cancer Research,
National Cancer Institute, National Institutes of Health, Bethesda, Maryland,
United States of America
- Department of Biochemistry and Cancer Biology,
Meharry Medical College, Nashville, Tennessee, United States of
America
- * E-mail: (MSV); (PSM)
| | - Yidong Chen
- Genetics Branch, Center for Cancer Research,
National Cancer Institute, National Institutes of Health, Bethesda, Maryland,
United States of America
| | - Sean Davis
- Genetics Branch, Center for Cancer Research,
National Cancer Institute, National Institutes of Health, Bethesda, Maryland,
United States of America
| | - Fan Yang
- Genetics Branch, Center for Cancer Research,
National Cancer Institute, National Institutes of Health, Bethesda, Maryland,
United States of America
| | - Robert L. Walker
- Genetics Branch, Center for Cancer Research,
National Cancer Institute, National Institutes of Health, Bethesda, Maryland,
United States of America
| | - Sven Bilke
- Genetics Branch, Center for Cancer Research,
National Cancer Institute, National Institutes of Health, Bethesda, Maryland,
United States of America
| | - John Lueders
- Genetics Branch, Center for Cancer Research,
National Cancer Institute, National Institutes of Health, Bethesda, Maryland,
United States of America
| | - Melvenia M. Martin
- Laboratory of Molecular Pharmacology, Center
for Cancer Research, National Cancer Institute, National Institutes of Health,
Bethesda, Maryland, United States of America
| | - Mirit I. Aladjem
- Laboratory of Molecular Pharmacology, Center
for Cancer Research, National Cancer Institute, National Institutes of Health,
Bethesda, Maryland, United States of America
| | - Pierre P. Massion
- Division of Allergy, Pulmonary and Critical
Care Medicine, Vanderbilt Ingram Cancer Center, Vanderbilt University,
Nashville, Tennessee, United States of America
| | - Paul S. Meltzer
- Genetics Branch, Center for Cancer Research,
National Cancer Institute, National Institutes of Health, Bethesda, Maryland,
United States of America
- * E-mail: (MSV); (PSM)
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Mesner LD, Valsakumar V, Karnani N, Dutta A, Hamlin JL, Bekiranov S. Bubble-chip analysis of human origin distributions demonstrates on a genomic scale significant clustering into zones and significant association with transcription. Genome Res 2010; 21:377-89. [PMID: 21173031 DOI: 10.1101/gr.111328.110] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
We have used a novel bubble-trapping procedure to construct nearly pure and comprehensive human origin libraries from early S- and log-phase HeLa cells, and from log-phase GM06990, a karyotypically normal lymphoblastoid cell line. When hybridized to ENCODE tiling arrays, these libraries illuminated 15.3%, 16.4%, and 21.8% of the genome in the ENCODE regions, respectively. Approximately half of the origin fragments cluster into zones, and their signals are generally higher than those of isolated fragments. Interestingly, initiation events are distributed about equally between genic and intergenic template sequences. While only 13.2% and 14.0% of genes within the ENCODE regions are actually transcribed in HeLa and GM06990 cells, 54.5% and 25.6% of zonal origin fragments overlap transcribed genes, most with activating chromatin marks in their promoters. Our data suggest that cell synchronization activates a significant number of inchoate origins. In addition, HeLa and GM06990 cells activate remarkably different origin populations. Finally, there is only moderate concordance between the log-phase HeLa bubble map and published maps of small nascent strands for this cell line.
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Affiliation(s)
- Larry D Mesner
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA
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Lubelsky Y, Sasaki T, Kuipers MA, Lucas I, Le Beau MM, Carignon S, Debatisse M, Prinz JA, Dennis JH, Gilbert DM. Pre-replication complex proteins assemble at regions of low nucleosome occupancy within the Chinese hamster dihydrofolate reductase initiation zone. Nucleic Acids Res 2010; 39:3141-55. [PMID: 21148149 PMCID: PMC3082903 DOI: 10.1093/nar/gkq1276] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Genome-scale mapping of pre-replication complex proteins has not been reported in mammalian cells. Poor enrichment of these proteins at specific sites may be due to dispersed binding, poor epitope availability or cell cycle stage-specific binding. Here, we have mapped sites of biotin-tagged ORC and MCM protein binding in G1-synchronized populations of Chinese hamster cells harboring amplified copies of the dihydrofolate reductase (DHFR) locus, using avidin-affinity purification of biotinylated chromatin followed by high-density microarray analysis across the DHFR locus. We have identified several sites of significant enrichment for both complexes distributed throughout the previously identified initiation zone. Analysis of the frequency of initiations across stretched DNA fibers from the DHFR locus confirmed a broad zone of de-localized initiation activity surrounding the sites of ORC and MCM enrichment. Mapping positions of mononucleosomal DNA empirically and computing nucleosome-positioning information in silico revealed that ORC and MCM map to regions of low measured and predicted nucleosome occupancy. Our results demonstrate that specific sites of ORC and MCM enrichment can be detected within a mammalian intitiation zone, and suggest that initiation zones may be regions of generally low nucleosome occupancy where flexible nucleosome positioning permits flexible pre-RC assembly sites.
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Affiliation(s)
- Yoav Lubelsky
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
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40
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Mendoza-Maldonado R, Paolinelli R, Galbiati L, Giadrossi S, Giacca M. Interaction of the retinoblastoma protein with Orc1 and its recruitment to human origins of DNA replication. PLoS One 2010; 5:e13720. [PMID: 21085491 PMCID: PMC2976706 DOI: 10.1371/journal.pone.0013720] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2010] [Accepted: 10/05/2010] [Indexed: 02/02/2023] Open
Abstract
Background The retinoblastoma protein (Rb) is a crucial regulator of cell cycle progression by binding with E2F transcription factor and repressing the expression of a variety of genes required for the G1-S phase transition. Methodology/Principal Findings Here we show that Rb and E2F1 directly participate in the control of initiation of DNA replication in human HeLa, U2OS and T98G cells by specifically binding to origins of DNA replication in a cell cycle regulated manner. We show that, both in vitro and inside the cells, the largest subunit of the origin recognition complex (Orc1) specifically binds hypo-phosphorylated Rb and that this interaction is competitive with the binding of Rb to E2F1. The displacement of Rb-bound Orc1 by E2F1 at origins of DNA replication marks the progression of the G1 phase of the cell cycle toward the G1-S border. Conclusions/Significance The participation of Rb and E2F1 in the formation of the multiprotein complex that binds origins of DNA replication in mammalian cells appears to represent an effective mechanism to couple the expression of genes required for cell cycle progression to the activation of DNA replication.
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Affiliation(s)
- Ramiro Mendoza-Maldonado
- Molecular Medicine Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | | | - Laura Galbiati
- Molecular Medicine Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Sara Giadrossi
- Molecular Medicine Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Mauro Giacca
- Molecular Medicine Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
- Department of Biomedicine, University of Trieste, Faculty of Medicine, Trieste, Italy
- * E-mail:
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Cleary JD, Tomé S, López Castel A, Panigrahi GB, Foiry L, Hagerman KA, Sroka H, Chitayat D, Gourdon G, Pearson CE. Tissue- and age-specific DNA replication patterns at the CTG/CAG-expanded human myotonic dystrophy type 1 locus. Nat Struct Mol Biol 2010; 17:1079-87. [DOI: 10.1038/nsmb.1876] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2010] [Accepted: 06/24/2010] [Indexed: 01/30/2023]
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Genome-wide mapping of nuclear mitochondrial DNA sequences links DNA replication origins to chromosomal double-strand break formation in Schizosaccharomyces pombe. Genome Res 2010; 20:1250-61. [PMID: 20688779 DOI: 10.1101/gr.104513.109] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Chromosomal double-strand breaks (DSBs) threaten genome integrity and repair of these lesions is often mutagenic. How and where DSBs are formed is a major question conveniently addressed in simple model organisms like yeast. NUMTs, nuclear DNA sequences of mitochondrial origin, are present in most eukaryotic genomes and probably result from the capture of mitochondrial DNA (mtDNA) fragments into chromosomal breaks. NUMT formation is ongoing and was reported to cause de novo human genetic diseases. Study of NUMTs is likely to contribute to the understanding of naturally occurring chromosomal breaks. We show that Schizosaccharomyces pombe NUMTs are exclusively located in noncoding regions with no preference for gene promoters and, when located into promoters, do not affect gene transcription level. Strikingly, most noncoding regions comprising NUMTs are also associated with a DNA replication origin (ORI). Chromatin immunoprecipitation experiments revealed that chromosomal NUMTs are probably not acting as ORI on their own but that mtDNA insertions occurred directly next to ORIs, suggesting that these loci may be prone to DSB formation. Accordingly, induction of excessive DNA replication origin firing, a phenomenon often associated with human tumor formation, resulted in frequent nucleotide deletion events within ORI3001 subtelomeric chromosomal locus, illustrating a novel aspect of DNA replication-driven genomic instability. How mtDNA is fragmented is another important issue that we addressed by sequencing experimentally induced NUMTs. This highlighted regions of S. pombe mtDNA prone to breaking. Together with an analysis of human NUMTs, we propose that these fragile sites in mtDNA may correspond to replication pause sites.
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Palumbo E, Matricardi L, Tosoni E, Bensimon A, Russo A. Replication dynamics at common fragile site FRA6E. Chromosoma 2010; 119:575-87. [PMID: 20585795 DOI: 10.1007/s00412-010-0279-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Revised: 05/21/2010] [Accepted: 05/25/2010] [Indexed: 11/30/2022]
Abstract
The replication dynamics at common fragile site FRA6E has been evaluated by molecular combing and interphase fluorescent in situ hybridisation (FISH) in primary human lymphocytes cultured under normal or aphidicolin-induced stress conditions. FRA6E is one of the most frequently expressed common fragile sites of the human genome. It harbours several genes, PARK2 being regarded as the most relevant one. According to the results obtained from interphase FISH analysis, FRA6E can be considered a mid-late-replicating sequence characterised by heterogeneous replication timing. Molecular combing did not reveal specific replication parameters at the fragile site: fork rates were highly comparable to those detected at an early replicating locus (LMNB2) used as control and in very good agreement with the whole-genome data obtained in parallel. The same indication applied to the density of initiation zones, the inter-origin distances from adjacent ongoing forks, the frequencies of unidirectional forks, fork arrest events and asynchronous forks. Interestingly, PARK2 appeared embedded in an early/late replication transition zone, corresponding to intron 8 (162 kb) and to the fragility core of FRA6E. In cells exposed to aphidicolin, few forks progressing at a rather slow rate were observed, the majority of them being unidirectional, but again a specific response of the fragile site was not observed. In summary, at FRA6E the replication process is not impaired per se, but chromosome breakages occur preferentially at an early/late replication transition zone. Aphidicolin might increase the occurrence of breakage events at FRA6E by prolonging the time interval separating the replication of early and late replication domains. These results may be of general significance to address the problem of fragile site instability.
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Affiliation(s)
- Elisa Palumbo
- Department of Biology, University of Padova, Via U. Bassi 58/b, 35131, Padova, Italy
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Abstract
Studies in our laboratory over the last three decades have shown that the Chinese hamster dihydrofolate reductase (DHFR) origin of replication corresponds to a broad zone of inefficient initiation sites distributed throughout the spacer between the convergently transcribed DHFR and 2BE2121 genes. It is clear from mutational analysis that none of these sites is genetically required for controlling origin activity. However, the integrity of the promoter of the DHFR gene is needed to activate the downstream origin, while the 3' processing signals prevent invasion and inactivation of the downstream origin by transcription forks. Several other origins in metazoans have been shown to correspond to zones of inefficient sites, while a different subset appears to be similar to the fixed replicators that characterize origins in S. cerevisiae and lower organisms. These observations have led us to suggest a model in which the mammalian genome is dotted with a hierarchy of degenerate, redundant, and inefficient replicators at intervals of a kilobase or less, some of which may have evolved to be highly circumscribed and efficient. The activities of initiation sites are proposed to be largely regulated by local transcription and chromatin architecture. Recently, we and others have devised strategies for identifying active origins on a genome-wide scale in order to define their distributions between fixed and dispersive origin types and to detect relationships among origins, genes, and epigenetic markers. The global pictures emerging are suggestive but far from complete and appear to be plagued by some of the same uncertainties that have led to conflicting views of individual origins in the past (particularly DHFR). In this paper, we will trace the history of origin discovery in mammalian genomes, primarily using the well-studied DHFR origin as a model, because it has been analyzed by nearly every available origin mapping technique in several different laboratories, while many origins have been identified by only one. We will address the strengths and shortcomings of the various methods utilized to identify and characterize origins in complex genomes and will point out how we and others were sometimes led astray by false assumptions and biases, as well as insufficient information. The goal is to help guide future experiments that will provide a truly comprehensive and accurate portrait of origins and their regulation. After all, in the words of George Santayana, "Those who do not learn from history are doomed to repeat it."
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Schepers A, Papior P. Why are we where we are? Understanding replication origins and initiation sites in eukaryotes using ChIP-approaches. Chromosome Res 2010; 18:63-77. [PMID: 19904620 DOI: 10.1007/s10577-009-9087-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
DNA replication initiates from origins of replication following a strict sequential activation programme and a conserved temporal order of activation. The number of replication initiation sites varies between species, according to the complexity of the genomes, with an average spacing of 100,000 bp. In contrast to yeast genomes, the location and definition of origins in mammalian genomes has been elusive. Historically, mammalian replication initiation sites have been mapped in situ by systematically searching specific genomic loci for sites that preferentially initiated DNA replication, potential origins by start-site mapping and autonomously replicating sequence experiments, and potential ORC and pre-replicative complex (pre-RC) sites by chromatin immunoprecipitation (ChIP) using antibodies for pre-RC proteins. In the past decade, ChIP has become an important method for analyzing protein/DNA interactions. Classically, ChIP is combined with Southern blotting or PCR. Recently, whole genome-ChIP methods have been very successful in unicellular eukaryotes to understand molecular mechanisms coordinating replication initiation and its flexibility in response to environmental changes. However, in mammalian systems, ChIP with pre-RC antibodies has often been challenging and genome-wide studies are scarce. In this review, we will appraise the progress that has been made in understanding replication origin organization using immunoprecipitation of the ORC and Mcm2-7 complexes. A special focus will be on the advantages and disadvantages of genome-wide ChIP-technologies and their potential impact on understanding metazoan replicators.
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Affiliation(s)
- Aloys Schepers
- Department of Gene Vectors, Helmholtz Zentrum München-German Research Center for Environmental Health, Marchioninistrasse 25, 81377, München, Germany.
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Falaschi A, Abdurashidova G, Biamonti G. DNA replication, development and cancer: a homeotic connection? Crit Rev Biochem Mol Biol 2010; 45:14-22. [PMID: 19919294 DOI: 10.3109/10409230903365608] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The homeotic proteins are transcription factors, highly conserved in metazoan organisms, exerting a pivotal role in development and differentiation. They individually display a loose specificity for the DNA sequence they can bind, but operate mainly in multi-molecular associations that assure their target and function specificity. Homeotic proteins are known to play a role in the positive or negative regulation of cell proliferation. Furthermore, many homeotic proteins are actually proto-oncogenes, since different translocations involving their genes cause tumors, particularly in the hematopoietic system. A one-hybrid screen to detect proteins with affinity for the lamin B2 replication origin identified three homeotic proteins, namely HoxA13, HoxC10 and HoxC13. Recent data demonstrate that the HoxC13 oncoprotein specifically associates with replication foci and binds in vitro and in vivo to several human DNA replication origins. Moreover, Hox proteins interact with geminin, a regulator of cell cycle progression, and control the interaction of this protein with the DNA replication licensing factor Ctd1. Thus, the homeotic proteins, by participating directly in the function of DNA replication origins, may provide a direct link between the accurate regulation of DNA replication required by the morphogenetic program and the deregulation of this process typical of cancer.
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Thangavel S, Mendoza-Maldonado R, Tissino E, Sidorova JM, Yin J, Wang W, Monnat RJ, Falaschi A, Vindigni A. Human RECQ1 and RECQ4 helicases play distinct roles in DNA replication initiation. Mol Cell Biol 2010; 30:1382-96. [PMID: 20065033 PMCID: PMC2832491 DOI: 10.1128/mcb.01290-09] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2009] [Revised: 10/26/2009] [Accepted: 12/29/2009] [Indexed: 11/20/2022] Open
Abstract
Cellular and biochemical studies support a role for all five human RecQ helicases in DNA replication; however, their specific functions during this process are unclear. Here we investigate the in vivo association of the five human RecQ helicases with three well-characterized human replication origins. We show that only RECQ1 (also called RECQL or RECQL1) and RECQ4 (also called RECQL4) associate with replication origins in a cell cycle-regulated fashion in unperturbed cells. RECQ4 is recruited to origins at late G(1), after ORC and MCM complex assembly, while RECQ1 and additional RECQ4 are loaded at origins at the onset of S phase, when licensed origins begin firing. Both proteins are lost from origins after DNA replication initiation, indicating either disassembly or tracking with the newly formed replisome. Nascent-origin DNA synthesis and the frequency of origin firing are reduced after RECQ1 depletion and, to a greater extent, after RECQ4 depletion. Depletion of RECQ1, though not that of RECQ4, also suppresses replication fork rates in otherwise unperturbed cells. These results indicate that RECQ1 and RECQ4 are integral components of the human replication complex and play distinct roles in DNA replication initiation and replication fork progression in vivo.
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Affiliation(s)
- Saravanabhavan Thangavel
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy, Laboratorio di Biologia Molecolare, Scuola Normale Superiore, Via Moruzzi 1, Pisa I-56124, Italy, Departments of Pathology, Genome Sciences, University of Washington, Seattle, Washington 98195-7705, Laboratory of Genetics, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, Baltimore, Maryland 21224, Istituto di Fisiologia Clinica, CNR, Via Moruzzi 1, I-56124 Pisa, Italy
| | - Ramiro Mendoza-Maldonado
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy, Laboratorio di Biologia Molecolare, Scuola Normale Superiore, Via Moruzzi 1, Pisa I-56124, Italy, Departments of Pathology, Genome Sciences, University of Washington, Seattle, Washington 98195-7705, Laboratory of Genetics, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, Baltimore, Maryland 21224, Istituto di Fisiologia Clinica, CNR, Via Moruzzi 1, I-56124 Pisa, Italy
| | - Erika Tissino
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy, Laboratorio di Biologia Molecolare, Scuola Normale Superiore, Via Moruzzi 1, Pisa I-56124, Italy, Departments of Pathology, Genome Sciences, University of Washington, Seattle, Washington 98195-7705, Laboratory of Genetics, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, Baltimore, Maryland 21224, Istituto di Fisiologia Clinica, CNR, Via Moruzzi 1, I-56124 Pisa, Italy
| | - Julia M. Sidorova
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy, Laboratorio di Biologia Molecolare, Scuola Normale Superiore, Via Moruzzi 1, Pisa I-56124, Italy, Departments of Pathology, Genome Sciences, University of Washington, Seattle, Washington 98195-7705, Laboratory of Genetics, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, Baltimore, Maryland 21224, Istituto di Fisiologia Clinica, CNR, Via Moruzzi 1, I-56124 Pisa, Italy
| | - Jinhu Yin
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy, Laboratorio di Biologia Molecolare, Scuola Normale Superiore, Via Moruzzi 1, Pisa I-56124, Italy, Departments of Pathology, Genome Sciences, University of Washington, Seattle, Washington 98195-7705, Laboratory of Genetics, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, Baltimore, Maryland 21224, Istituto di Fisiologia Clinica, CNR, Via Moruzzi 1, I-56124 Pisa, Italy
| | - Weidong Wang
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy, Laboratorio di Biologia Molecolare, Scuola Normale Superiore, Via Moruzzi 1, Pisa I-56124, Italy, Departments of Pathology, Genome Sciences, University of Washington, Seattle, Washington 98195-7705, Laboratory of Genetics, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, Baltimore, Maryland 21224, Istituto di Fisiologia Clinica, CNR, Via Moruzzi 1, I-56124 Pisa, Italy
| | - Raymond J. Monnat
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy, Laboratorio di Biologia Molecolare, Scuola Normale Superiore, Via Moruzzi 1, Pisa I-56124, Italy, Departments of Pathology, Genome Sciences, University of Washington, Seattle, Washington 98195-7705, Laboratory of Genetics, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, Baltimore, Maryland 21224, Istituto di Fisiologia Clinica, CNR, Via Moruzzi 1, I-56124 Pisa, Italy
| | - Arturo Falaschi
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy, Laboratorio di Biologia Molecolare, Scuola Normale Superiore, Via Moruzzi 1, Pisa I-56124, Italy, Departments of Pathology, Genome Sciences, University of Washington, Seattle, Washington 98195-7705, Laboratory of Genetics, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, Baltimore, Maryland 21224, Istituto di Fisiologia Clinica, CNR, Via Moruzzi 1, I-56124 Pisa, Italy
| | - Alessandro Vindigni
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy, Laboratorio di Biologia Molecolare, Scuola Normale Superiore, Via Moruzzi 1, Pisa I-56124, Italy, Departments of Pathology, Genome Sciences, University of Washington, Seattle, Washington 98195-7705, Laboratory of Genetics, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, Baltimore, Maryland 21224, Istituto di Fisiologia Clinica, CNR, Via Moruzzi 1, I-56124 Pisa, Italy
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Cotobal C, Segurado M, Antequera F. Structural diversity and dynamics of genomic replication origins in Schizosaccharomyces pombe. EMBO J 2010; 29:934-42. [PMID: 20094030 DOI: 10.1038/emboj.2009.411] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Accepted: 12/21/2009] [Indexed: 11/09/2022] Open
Abstract
DNA replication origins (ORI) in Schizosaccharomyces pombe colocalize with adenine and thymine (A+T)-rich regions, and earlier analyses have established a size from 0.5 to over 3 kb for a DNA fragment to drive replication in plasmid assays. We have asked what are the requirements for ORI function in the chromosomal context. By designing artificial ORIs, we have found that A+T-rich fragments as short as 100 bp without homology to S. pombe DNA are able to initiate replication in the genome. On the other hand, functional dissection of endogenous ORIs has revealed that some of them span a few kilobases and include several modules that may be as short as 25-30 contiguous A+Ts capable of initiating replication from ectopic chromosome positions. The search for elements with these characteristics across the genome has uncovered an earlier unnoticed class of low-efficiency ORIs that fire late during S phase. These results indicate that ORI specification and dynamics varies widely in S. pombe, ranging from very short elements to large regions reminiscent of replication initiation zones in mammals.
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Affiliation(s)
- Cristina Cotobal
- Instituto de Microbiología Bioquímica, CSIC/Universidad de Salamanca, Edificio Departamental, Salamanca, Spain
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Guan Z, Hughes CM, Kosiyatrakul S, Norio P, Sen R, Fiering S, Allis CD, Bouhassira EE, Schildkraut CL. Decreased replication origin activity in temporal transition regions. ACTA ACUST UNITED AC 2010; 187:623-35. [PMID: 19951913 PMCID: PMC2806585 DOI: 10.1083/jcb.200905144] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Experimental attempts to activate replication origins within the temporal transition region in the IgH locus in mouse embryonic stem cells were not successful, and thus, why and how they become activated in B cells remains unclear. In the mammalian genome, early- and late-replicating domains are often separated by temporal transition regions (TTRs) with novel properties and unknown functions. We identified a TTR in the mouse immunoglobulin heavy chain (Igh) locus, which contains replication origins that are silent in embryonic stem cells but activated during B cell development. To investigate which factors contribute to origin activation during B cell development, we systematically modified the genetic and epigenetic status of the endogenous Igh TTR and used a single-molecule approach to analyze DNA replication. Introduction of a transcription unit into the Igh TTR, activation of gene transcription, and enhancement of local histone modifications characteristic of active chromatin did not lead to origin activation. Moreover, very few replication initiation events were observed when two ectopic replication origin sequences were inserted into the TTR. These findings indicate that the Igh TTR represents a repressive compartment that inhibits replication initiation, thus maintaining the boundaries between early and late replication domains.
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Affiliation(s)
- Zeqiang Guan
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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50
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Das-Bradoo S, Bielinsky AK. Replication initiation point mapping: approach and implications. Methods Mol Biol 2009; 521:105-20. [PMID: 19563103 DOI: 10.1007/978-1-60327-815-7_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Duplication of eukaryotic chromosomes begins from multiple sites called origins of replication, with DNA synthesis proceeding bidirectionally away from the origin. There is little detailed information available pertaining to whether replication initiates at specific sites or anywhere within a given origin. The development of replication initiation point (RIP) mapping has made it possible to map start sites for DNA synthesis at the nucleotide level. The key step in RIP mapping is the purification of nascent DNA, which is initiated by small RNA primers. For the removal of broken DNA fragments, we utilize lambda-exonuclease, which digests DNA, but leaves nascent strands intact as long as they have the RNA primer still attached. RIP mapping is a sensitive technique and has been successfully applied to single copy loci in both budding and fission yeast, archaebacteria, and human cells. Studies in yeast have shown that the binding site for the initiator, the origin recognition complex (ORC), lies immediately adjacent to the replication start point, which suggests that ORC directs the initiation machinery to a distinct site. Here, we present a detailed step-by-step protocol for RIP mapping of replication origins in budding yeast.
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Affiliation(s)
- Sapna Das-Bradoo
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
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