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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] [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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Reed TT, Kendal AH, Wozniak KJ, Simmons LA. DNA replication initiation timing is important for maintaining genome integrity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.18.599555. [PMID: 38948856 PMCID: PMC11212987 DOI: 10.1101/2024.06.18.599555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
DNA replication is regulated by factors that promote or inhibit initiation. In Bacillus subtilis, YabA is a negative regulator of DNA replication initiation while the newly identified kinase CcrZ is a positive regulator. The consequences of under-initiation or over-initiation of DNA replication to genome stability remain unclear. In this work, we measure origin to terminus ratios as a proxy for replication initiation activity. We show that ΔccrZ and several ccrZ alleles under-initiate DNA replication while ablation of yabA or overproduction of CcrZ leads to over-initiation. We find that cells under-initiating DNA replication have few incidents of replication fork stress as determined by low formation of RecA-GFP foci compared with wild type. In contrast, cells over-initiating DNA replication show levels of RecA-GFP foci formation analogous to cells directly challenged with DNA damaging agents. We show that cells under-initiating and over-initiating DNA replication were both sensitive to mitomycin C and that changes in replication initiation frequency cause increased sensitivity to genotoxic stress. With these results, we propose that cells under-initiating DNA replication are sensitive to DNA damage due to a shortage of DNA for repair through homologous recombination. For cells over-initiating DNA replication, we propose that an increase in the number of replication forks leads to replication fork stress which is further exacerbated by chromosomal DNA damage. Together, our study shows that DNA replication initiation frequency must be tightly controlled as changes in initiation influence replication fork fate and the capacity of cells to efficiently repair damage to their genetic material.
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Affiliation(s)
- Tristan T. Reed
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Abigail H. Kendal
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Katherine J Wozniak
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
- Present address: Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030
| | - Lyle A. Simmons
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
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3
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Struhl K. Non-canonical functions of enhancers: regulation of RNA polymerase III transcription, DNA replication, and V(D)J recombination. Trends Genet 2024; 40:471-479. [PMID: 38643034 PMCID: PMC11152991 DOI: 10.1016/j.tig.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 04/02/2024] [Indexed: 04/22/2024]
Abstract
Enhancers are the key regulators of other DNA-based processes by virtue of their unique ability to generate nucleosome-depleted regions in a highly regulated manner. Enhancers regulate cell-type-specific transcription of tRNA genes by RNA polymerase III (Pol III). They are also responsible for the binding of the origin replication complex (ORC) to DNA replication origins, thereby regulating origin utilization, replication timing, and replication-dependent chromosome breaks. Additionally, enhancers regulate V(D)J recombination by increasing access of the recombination-activating gene (RAG) recombinase to target sites and by generating non-coding enhancer RNAs and localized regions of trimethylated histone H3-K4 recognized by the RAG2 PHD domain. Thus, enhancers represent the first step in decoding the genome, and hence they regulate biological processes that, unlike RNA polymerase II (Pol II) transcription, do not have dedicated regulatory proteins.
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Affiliation(s)
- Kevin Struhl
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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4
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Rojas P, Wang J, Guglielmi G, Sadurnì MM, Pavlou L, Leung GHD, Rajagopal V, Spill F, Saponaro M. Genome-wide identification of replication fork stalling/pausing sites and the interplay between RNA Pol II transcription and DNA replication progression. Genome Biol 2024; 25:126. [PMID: 38773641 PMCID: PMC11106976 DOI: 10.1186/s13059-024-03278-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 05/14/2024] [Indexed: 05/24/2024] Open
Abstract
BACKGROUND DNA replication progression can be affected by the presence of physical barriers like the RNA polymerases, leading to replication stress and DNA damage. Nonetheless, we do not know how transcription influences overall DNA replication progression. RESULTS To characterize sites where DNA replication forks stall and pause, we establish a genome-wide approach to identify them. This approach uses multiple timepoints during S-phase to identify replication fork/stalling hotspots as replication progresses through the genome. These sites are typically associated with increased DNA damage, overlapped with fragile sites and with breakpoints of rearrangements identified in cancers but do not overlap with replication origins. Overlaying these sites with a genome-wide analysis of RNA polymerase II transcription, we find that replication fork stalling/pausing sites inside genes are directly related to transcription progression and activity. Indeed, we find that slowing down transcription elongation slows down directly replication progression through genes. This indicates that transcription and replication can coexist over the same regions. Importantly, rearrangements found in cancers overlapping transcription-replication collision sites are detected in non-transformed cells and increase following treatment with ATM and ATR inhibitors. At the same time, we find instances where transcription activity favors replication progression because it reduces histone density. CONCLUSIONS Altogether, our findings highlight how transcription and replication overlap during S-phase, with both positive and negative consequences for replication fork progression and genome stability by the coexistence of these two processes.
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Affiliation(s)
- Patricia Rojas
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Jianming Wang
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Giovanni Guglielmi
- School of Mathematics, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Department of Biomedical Engineering, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Martina Mustè Sadurnì
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Lucas Pavlou
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Geoffrey Ho Duen Leung
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Vijay Rajagopal
- Department of Biomedical Engineering, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Fabian Spill
- School of Mathematics, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Marco Saponaro
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
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Jin C, Einig E, Xu W, Kollampally RB, Schlosser A, Flentje M, Popov N. The dimeric deubiquitinase USP28 integrates 53BP1 and MYC functions to limit DNA damage. Nucleic Acids Res 2024; 52:3011-3030. [PMID: 38227944 PMCID: PMC11024517 DOI: 10.1093/nar/gkae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 12/21/2023] [Accepted: 01/04/2024] [Indexed: 01/18/2024] Open
Abstract
DNA replication is a major source of endogenous DNA damage in tumor cells and a key target of cellular response to genotoxic stress. DNA replication can be deregulated by oncoproteins, such as transcription factor MYC, aberrantly activated in many human cancers. MYC is stringently regulated by the ubiquitin system - for example, ubiquitination controls recruitment of the elongation factor PAF1c, instrumental in MYC activity. Curiously, a key MYC-targeting deubiquitinase USP28 also controls cellular response to DNA damage via the mediator protein 53BP1. USP28 forms stable dimers, but the biological role of USP28 dimerization is unknown. We show here that dimerization limits USP28 activity and restricts recruitment of PAF1c by MYC. Expression of monomeric USP28 stabilizes MYC and promotes PAF1c recruitment, leading to ectopic DNA synthesis and replication-associated DNA damage. USP28 dimerization is stimulated by 53BP1, which selectively binds USP28 dimers. Genotoxic stress diminishes 53BP1-USP28 interaction, promotes disassembly of USP28 dimers and stimulates PAF1c recruitment by MYC. This triggers firing of DNA replication origins during early response to genotoxins and exacerbates DNA damage. We propose that dimerization of USP28 prevents ectopic DNA replication at transcriptionally active chromatin to maintain genome stability.
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Affiliation(s)
- Chao Jin
- Department of Medical Oncology and Pulmonology, University Hospital Tübingen, Otfried-Müller-Str 14, 72076 Tübingen, Germany
- DFG Cluster of Excellence 2180 ‘Image-guided and Functionally Instructed Tumor Therapies’ (iFIT), University of Tübingen, Tübingen, Germany
| | - Elias Einig
- Department of Medical Oncology and Pulmonology, University Hospital Tübingen, Otfried-Müller-Str 14, 72076 Tübingen, Germany
- DFG Cluster of Excellence 2180 ‘Image-guided and Functionally Instructed Tumor Therapies’ (iFIT), University of Tübingen, Tübingen, Germany
| | - Wenshan Xu
- Department of Radiation Oncology, University Hospital Würzburg, Josef-Schneider-Str. 2, 97080 Würzburg, Germany
| | - Ravi Babu Kollampally
- Department of Medical Oncology and Pulmonology, University Hospital Tübingen, Otfried-Müller-Str 14, 72076 Tübingen, Germany
- DFG Cluster of Excellence 2180 ‘Image-guided and Functionally Instructed Tumor Therapies’ (iFIT), University of Tübingen, Tübingen, Germany
| | - Andreas Schlosser
- Rudolf Virchow Center, Center for Integrative and Translational Bioimaging, University of Würzburg, Josef-Schneider-Str 2, 97080 Würzburg, Germany
| | - Michael Flentje
- Department of Radiation Oncology, University Hospital Würzburg, Josef-Schneider-Str. 2, 97080 Würzburg, Germany
| | - Nikita Popov
- Department of Medical Oncology and Pulmonology, University Hospital Tübingen, Otfried-Müller-Str 14, 72076 Tübingen, Germany
- DFG Cluster of Excellence 2180 ‘Image-guided and Functionally Instructed Tumor Therapies’ (iFIT), University of Tübingen, Tübingen, Germany
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Vitarelli MDO, Franco TA, Pires DDS, Lima ARJ, Viala VL, Kraus AJ, de Azevedo IDLMJ, da Cunha JPC, Elias MC. Integrating high-throughput analysis to create an atlas of replication origins in Trypanosoma cruzi in the context of genome structure and variability. mBio 2024; 15:e0031924. [PMID: 38441981 PMCID: PMC11005370 DOI: 10.1128/mbio.00319-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 02/09/2024] [Indexed: 03/07/2024] Open
Abstract
Trypanosoma cruzi is the etiologic agent of the most prevalent human parasitic disease in Latin America, Chagas disease. Its genome is rich in multigenic families that code for virulent antigens and are present in the rapidly evolving genomic compartment named Disruptive. DNA replication is a meticulous biological process in which flaws can generate mutations and changes in chromosomal and gene copy numbers. Here, integrating high-throughput and single-molecule analyses, we were able to identify Predominant, Flexible, and Dormant Orc1Cdc6-dependent origins as well as Orc1Cdc6-independent origins. Orc1Cdc6-dependent origins were found in multigenic family loci, while independent origins were found in the Core compartment that contains conserved and hypothetical protein-coding genes, in addition to multigenic families. In addition, we found that Orc1Cdc6 density is related to the firing of origins and that Orc1Cdc6-binding sites within fired origins are depleted of a specific class of nucleosomes that we previously categorized as dynamic. Together, these data suggest that Orc1Cdc6-dependent origins may contribute to the rapid evolution of the Disruptive compartment and, therefore, to the success of T. cruzi infection and that the local epigenome landscape is also involved in this process.IMPORTANCETrypanosoma cruzi, responsible for Chagas disease, affects millions globally, particularly in Latin America. Lack of vaccine or treatment underscores the need for research. Parasite's genome, with virulent antigen-coding multigenic families, resides in the rapidly evolving Disruptive compartment. Study sheds light on the parasite's dynamic DNA replication, discussing the evolution of the Disruptive compartment. Therefore, the findings represent a significant stride in comprehending T. cruzi's biology and the molecular bases that contribute to the success of infection caused by this parasite.
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Affiliation(s)
- Marcela de Oliveira Vitarelli
- Cell Cycle Laboratory, Butantan Institute, Av. Vital Brazil, São Paulo, Brazil
- Center of Toxins, Immune Response and Cell Signaling (CeTICS), Butantan Institute, Av. Vital Brazil, São Paulo, Brazil
| | | | | | | | - Vincent Louis Viala
- Biochemistry Laboratory, Butantan Institute, Av. Vital Brazil, São Paulo, Brazil
| | - Amelie Johanna Kraus
- Division of Experimental Parasitology, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität in Munich, Planegg-Martinsried, Germany
- Biomedical Center, Division of Physiological Chemistry, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Planegg-Martinsried, Germany
| | | | - Julia Pinheiro Chagas da Cunha
- Cell Cycle Laboratory, Butantan Institute, Av. Vital Brazil, São Paulo, Brazil
- Center of Toxins, Immune Response and Cell Signaling (CeTICS), Butantan Institute, Av. Vital Brazil, São Paulo, Brazil
| | - Maria Carolina Elias
- Cell Cycle Laboratory, Butantan Institute, Av. Vital Brazil, São Paulo, Brazil
- Center of Toxins, Immune Response and Cell Signaling (CeTICS), Butantan Institute, Av. Vital Brazil, São Paulo, Brazil
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7
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Tian M, Wang Z, Su Z, Shibata E, Shibata Y, Dutta A, Zang C. Integrative analysis of DNA replication origins and ORC-/MCM-binding sites in human cells reveals a lack of overlap. eLife 2024; 12:RP89548. [PMID: 38567819 PMCID: PMC10990492 DOI: 10.7554/elife.89548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024] Open
Abstract
Based on experimentally determined average inter-origin distances of ~100 kb, DNA replication initiates from ~50,000 origins on human chromosomes in each cell cycle. The origins are believed to be specified by binding of factors like the origin recognition complex (ORC) or CTCF or other features like G-quadruplexes. We have performed an integrative analysis of 113 genome-wide human origin profiles (from five different techniques) and five ORC-binding profiles to critically evaluate whether the most reproducible origins are specified by these features. Out of ~7.5 million union origins identified by all datasets, only 0.27% (20,250 shared origins) were reproducibly obtained in at least 20 independent SNS-seq datasets and contained in initiation zones identified by each of three other techniques, suggesting extensive variability in origin usage and identification. Also, 21% of the shared origins overlap with transcriptional promoters, posing a conundrum. Although the shared origins overlap more than union origins with constitutive CTCF-binding sites, G-quadruplex sites, and activating histone marks, these overlaps are comparable or less than that of known transcription start sites, so that these features could be enriched in origins because of the overlap of origins with epigenetically open, promoter-like sequences. Only 6.4% of the 20,250 shared origins were within 1 kb from any of the ~13,000 reproducible ORC-binding sites in human cancer cells, and only 4.5% were within 1 kb of the ~11,000 union MCM2-7-binding sites in contrast to the nearly 100% overlap in the two comparisons in the yeast, Saccharomyces cerevisiae. Thus, in human cancer cell lines, replication origins appear to be specified by highly variable stochastic events dependent on the high epigenetic accessibility around promoters, without extensive overlap between the most reproducible origins and currently known ORC- or MCM-binding sites.
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Affiliation(s)
- Mengxue Tian
- Center for Public Health Genomics, University of Virginia School of MedicineCharlottesvilleUnited States
- Department of Biochemistry and Molecular Genetics, University of Virginia School of MedicineCharlottesvilleUnited States
| | - Zhenjia Wang
- Center for Public Health Genomics, University of Virginia School of MedicineCharlottesvilleUnited States
| | - Zhangli Su
- Department of Biochemistry and Molecular Genetics, University of Virginia School of MedicineCharlottesvilleUnited States
- Department of Genetics, University of Alabama at BirminghamBirminghamUnited States
| | - Etsuko Shibata
- Department of Biochemistry and Molecular Genetics, University of Virginia School of MedicineCharlottesvilleUnited States
- Department of Genetics, University of Alabama at BirminghamBirminghamUnited States
| | - Yoshiyuki Shibata
- Department of Biochemistry and Molecular Genetics, University of Virginia School of MedicineCharlottesvilleUnited States
- Department of Genetics, University of Alabama at BirminghamBirminghamUnited States
| | - Anindya Dutta
- Department of Biochemistry and Molecular Genetics, University of Virginia School of MedicineCharlottesvilleUnited States
- Department of Genetics, University of Alabama at BirminghamBirminghamUnited States
| | - Chongzhi Zang
- Center for Public Health Genomics, University of Virginia School of MedicineCharlottesvilleUnited States
- Department of Biochemistry and Molecular Genetics, University of Virginia School of MedicineCharlottesvilleUnited States
- Department of Public Health Sciences, University of VirginiaCharlottesvilleUnited States
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8
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Rivosecchi J, Jurikova K, Cusanelli E. Telomere-specific regulation of TERRA and its impact on telomere stability. Semin Cell Dev Biol 2024; 157:3-23. [PMID: 38088000 DOI: 10.1016/j.semcdb.2023.11.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 11/02/2023] [Indexed: 01/08/2024]
Abstract
TERRA is a class of telomeric repeat-containing RNAs that are expressed from telomeres in multiple organisms. TERRA transcripts play key roles in telomere maintenance and their physiological levels are essential to maintain the integrity of telomeric DNA. Indeed, deregulated TERRA expression or its altered localization can impact telomere stability by multiple mechanisms including fueling transcription-replication conflicts, promoting resection of chromosome ends, altering the telomeric chromatin, and supporting homologous recombination. Therefore, a fine-tuned control of TERRA is important to maintain the integrity of the genome. Several studies have reported that different cell lines express substantially different levels of TERRA. Most importantly, TERRA levels markedly vary among telomeres of a given cell type, indicating the existence of telomere-specific regulatory mechanisms which may help coordinate TERRA functions. TERRA molecules contain distinct subtelomeric sequences, depending on their telomere of origin, which may instruct specific post-transcriptional modifications or mediate distinct functions. In addition, all TERRA transcripts share a repetitive G-rich sequence at their 3' end which can form DNA:RNA hybrids and fold into G-quadruplex structures. Both structures are involved in TERRA functions and can critically affect telomere stability. In this review, we examine the mechanisms controlling TERRA levels and the impact of their telomere-specific regulation on telomere stability. We compare evidence obtained in different model organisms, discussing recent advances as well as controversies in the field. Furthermore, we discuss the importance of DNA:RNA hybrids and G-quadruplex structures in the context of TERRA biology and telomere maintenance.
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Affiliation(s)
- Julieta Rivosecchi
- Laboratory of Cell Biology and Molecular Genetics, Department CIBIO, University of Trento, via Sommarive 9, 38123 Trento, Italy
| | - Katarina Jurikova
- Laboratory of Cell Biology and Molecular Genetics, Department CIBIO, University of Trento, via Sommarive 9, 38123 Trento, Italy; Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina, 84215 Bratislava, Slovakia
| | - Emilio Cusanelli
- Laboratory of Cell Biology and Molecular Genetics, Department CIBIO, University of Trento, via Sommarive 9, 38123 Trento, Italy.
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9
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Jones RM, Reynolds-Winczura A, Gambus A. A Decade of Discovery-Eukaryotic Replisome Disassembly at Replication Termination. BIOLOGY 2024; 13:233. [PMID: 38666845 PMCID: PMC11048390 DOI: 10.3390/biology13040233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 03/23/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024]
Abstract
The eukaryotic replicative helicase (CMG complex) is assembled during DNA replication initiation in a highly regulated manner, which is described in depth by other manuscripts in this Issue. During DNA replication, the replicative helicase moves through the chromatin, unwinding DNA and facilitating nascent DNA synthesis by polymerases. Once the duplication of a replicon is complete, the CMG helicase and the remaining components of the replisome need to be removed from the chromatin. Research carried out over the last ten years has produced a breakthrough in our understanding, revealing that replication termination, and more specifically replisome disassembly, is indeed a highly regulated process. This review brings together our current understanding of these processes and highlights elements of the mechanism that are conserved or have undergone divergence throughout evolution. Finally, we discuss events beyond the classic termination of DNA replication in S-phase and go over the known mechanisms of replicative helicase removal from chromatin in these particular situations.
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Affiliation(s)
- Rebecca M. Jones
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, University of Birmingham, Birmingham B15 2TT, UK; (R.M.J.); (A.R.-W.)
- School of Biosciences, Aston University, Birmingham B4 7ET, UK
| | - Alicja Reynolds-Winczura
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, University of Birmingham, Birmingham B15 2TT, UK; (R.M.J.); (A.R.-W.)
| | - Agnieszka Gambus
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, University of Birmingham, Birmingham B15 2TT, UK; (R.M.J.); (A.R.-W.)
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10
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Muñoz S, Blanco-Romero E, González-Acosta D, Rodriguez-Acebes S, Megías D, Lopes M, Méndez J. RAD51 restricts DNA over-replication from re-activated origins. EMBO J 2024; 43:1043-1064. [PMID: 38360996 PMCID: PMC10942984 DOI: 10.1038/s44318-024-00038-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 01/11/2024] [Accepted: 01/12/2024] [Indexed: 02/17/2024] Open
Abstract
Eukaryotic cells rely on several mechanisms to ensure that the genome is duplicated precisely once in each cell division cycle, preventing DNA over-replication and genomic instability. Most of these mechanisms limit the activity of origin licensing proteins to prevent the reactivation of origins that have already been used. Here, we have investigated whether additional controls restrict the extension of re-replicated DNA in the event of origin re-activation. In a genetic screening in cells forced to re-activate origins, we found that re-replication is limited by RAD51 and enhanced by FBH1, a RAD51 antagonist. In the presence of chromatin-bound RAD51, forks stemming from re-fired origins are slowed down, leading to frequent events of fork reversal. Eventual re-initiation of DNA synthesis mediated by PRIMPOL creates ssDNA gaps that facilitate the partial elimination of re-duplicated DNA by MRE11 exonuclease. In the absence of RAD51, these controls are abrogated and re-replication forks progress much longer than in normal conditions. Our study uncovers a safeguard mechanism to protect genome stability in the event of origin reactivation.
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Affiliation(s)
- Sergio Muñoz
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Elena Blanco-Romero
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Daniel González-Acosta
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Sara Rodriguez-Acebes
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Diego Megías
- Confocal Microscopy Unit, Biotechnology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain
- Advanced Optical Microscopy Unit, Central Core Facilities, Instituto de Salud Carlos III, Madrid, Spain
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Juan Méndez
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain.
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11
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Yang Z, Mogre S, He R, Berdan EL, Ho Sui S, Hill S. The ORFIUS complex regulates ORC2 localization at replication origins. NAR Cancer 2024; 6:zcae003. [PMID: 38288445 PMCID: PMC10823580 DOI: 10.1093/narcan/zcae003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 12/18/2023] [Accepted: 01/09/2024] [Indexed: 01/31/2024] Open
Abstract
High-grade serous ovarian cancer (HGSC) is a lethal malignancy with elevated replication stress (RS) levels and defective RS and RS-associated DNA damage responses. Here we demonstrate that the bromodomain-containing protein BRD1 is a RS suppressing protein that forms a replication origin regulatory complex with the histone acetyltransferase HBO1, the BRCA1 tumor suppressor, and BARD1, ORigin FIring Under Stress (ORFIUS). BRD1 and HBO1 promote eventual origin firing by supporting localization of the origin licensing protein ORC2 at origins. In the absence of BRD1 and/or HBO1, both origin firing and nuclei with ORC2 foci are reduced. BRCA1 regulates BRD1, HBO1, and ORC2 localization at replication origins. In the absence of BRCA1, both origin firing and nuclei with BRD1, HBO1, and ORC2 foci are increased. In normal and non-HGSC ovarian cancer cells, the ORFIUS complex responds to ATR and CDC7 origin regulatory signaling and disengages from origins during RS. In BRCA1-mutant and sporadic HGSC cells, BRD1, HBO1, and ORC2 remain associated with replication origins, and unresponsive to RS, DNA damage, or origin regulatory kinase inhibition. ORFIUS complex dysregulation may promote HGSC cell survival by allowing for upregulated origin firing and cell cycle progression despite accumulating DNA damage, and may be a RS target.
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Affiliation(s)
- Zelei Yang
- Department of Medical Oncology and Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Saie Mogre
- Department of Medical Oncology and Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Ruiyang He
- Department of Medical Oncology and Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Emma L Berdan
- Harvard Chan Bioinformatics Core, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Shannan J Ho Sui
- Harvard Chan Bioinformatics Core, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Sarah J Hill
- Department of Medical Oncology and Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Harvard Medical School, Boston, MA 02115, USA
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12
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Castellano CM, Lacroix L, Mathis E, Prorok P, Hennion M, Lopez-Rubio JJ, Méchali M, Gomes A. The genetic landscape of origins of replication in P. falciparum. Nucleic Acids Res 2024; 52:660-676. [PMID: 38038269 PMCID: PMC10810204 DOI: 10.1093/nar/gkad1103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 10/18/2023] [Accepted: 11/01/2023] [Indexed: 12/02/2023] Open
Abstract
Various origin mapping approaches have enabled genome-wide identification of origins of replication (ORI) in model organisms, but only a few studies have focused on divergent organisms. By employing three complementary approaches we provide a high-resolution map of ORIs in Plasmodium falciparum, the deadliest human malaria parasite. We profiled the distribution of origin of recognition complex (ORC) binding sites by ChIP-seq of two PfORC subunits and mapped active ORIs using NFS and SNS-seq. We show that ORIs lack sequence specificity but are not randomly distributed, and group in clusters. Licensing is biased towards regions of higher GC content and associated with G-quadruplex forming sequences (G4FS). While strong transcription likely enhances firing, active origins are depleted from transcription start sites. Instead, most accumulate in transcriptionally active gene bodies. Single molecule analysis of nanopore reads containing multiple initiation events, which could have only come from individual nuclei, showed a relationship between the replication fork pace and the distance to the nearest origin. While some similarities were drawn with the canonic eukaryote model, the distribution of ORIs in P. falciparum is likely shaped by unique genomic features such as extreme AT-richness-a product of evolutionary pressure imposed by the parasitic lifestyle.
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Affiliation(s)
| | - Laurent Lacroix
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Paris, France
| | - Emilie Mathis
- LPHI, CNRS, Université de Montpellier, 34095 Montpellier, France
| | - Paulina Prorok
- Institute of Human Genetics, CNRS, 34396 Montpellier, France
| | - Magali Hennion
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, F-75013 Paris, France
| | | | - Marcel Méchali
- Institute of Human Genetics, CNRS, 34396 Montpellier, France
| | - Ana Rita Gomes
- LPHI, CNRS, Université de Montpellier, 34095 Montpellier, France
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13
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González-Acosta D, Lopes M. DNA replication and replication stress response in the context of nuclear architecture. Chromosoma 2024; 133:57-75. [PMID: 38055079 PMCID: PMC10904558 DOI: 10.1007/s00412-023-00813-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 10/23/2023] [Accepted: 10/24/2023] [Indexed: 12/07/2023]
Abstract
The DNA replication process needs to be coordinated with other DNA metabolism transactions and must eventually extend to the full genome, regardless of chromatin status, gene expression, secondary structures and DNA lesions. Completeness and accuracy of DNA replication are crucial to maintain genome integrity, limiting transformation in normal cells and offering targeting opportunities for proliferating cancer cells. DNA replication is thus tightly coordinated with chromatin dynamics and 3D genome architecture, and we are only beginning to understand the underlying molecular mechanisms. While much has recently been discovered on how DNA replication initiation is organised and modulated in different genomic regions and nuclear territories-the so-called "DNA replication program"-we know much less on how the elongation of ongoing replication forks and particularly the response to replication obstacles is affected by the local nuclear organisation. Also, it is still elusive how specific components of nuclear architecture participate in the replication stress response. Here, we review known mechanisms and factors orchestrating replication initiation, and replication fork progression upon stress, focusing on recent evidence linking genome organisation and nuclear architecture with the cellular responses to replication interference, and highlighting open questions and future challenges to explore this exciting new avenue of research.
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Affiliation(s)
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland.
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14
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Tye BK, Zhai Y. The Origin Recognition Complex: From Origin Selection to Replication Licensing in Yeast and Humans. BIOLOGY 2023; 13:13. [PMID: 38248444 PMCID: PMC10813338 DOI: 10.3390/biology13010013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/15/2023] [Accepted: 12/20/2023] [Indexed: 01/23/2024]
Abstract
Understanding human DNA replication through the study of yeast has been an extremely fruitful journey. The minichromosome maintenance (MCM) 2-7 genes that encode the catalytic core of the eukaryotic replisome were initially identified through forward yeast genetics. The origin recognition complexes (ORC) that load the MCM hexamers at replication origins were purified from yeast extracts. We have reached an age where high-resolution cryoEM structures of yeast and human replication complexes can be compared side-by-side. Their similarities and differences are converging as alternative strategies that may deviate in detail but are shared by both species.
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Affiliation(s)
- Bik-Kwoon Tye
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Yuanliang Zhai
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China;
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15
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Lebdy R, Canut M, Patouillard J, Cadoret JC, Letessier A, Ammar J, Basbous J, Urbach S, Miotto B, Constantinou A, Abou Merhi R, Ribeyre C. The nucleolar protein GNL3 prevents resection of stalled replication forks. EMBO Rep 2023; 24:e57585. [PMID: 37965896 DOI: 10.15252/embr.202357585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/16/2023] Open
Abstract
Faithful DNA replication requires specific proteins that protect replication forks and so prevent the formation of DNA lesions that may damage the genome. Identification of new proteins involved in this process is essential to understand how DNA lesions accumulate in cancer cells and how they tolerate them. Here, we show that human GNL3/nucleostemin, a GTP-binding protein localized mostly in the nucleolus and highly expressed in cancer cells, prevents nuclease-dependent resection of nascent DNA in response to replication stress. We demonstrate that inhibiting origin firing reduces resection. This suggests that the heightened replication origin activation observed upon GNL3 depletion largely drives the observed DNA resection probably due to the exhaustion of the available RPA pool. We show that GNL3 and DNA replication initiation factor ORC2 interact in the nucleolus and that the concentration of GNL3 in the nucleolus is required to limit DNA resection. We propose that the control of origin firing by GNL3 through the sequestration of ORC2 in the nucleolus is critical to prevent nascent DNA resection in response to replication stress.
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Affiliation(s)
- Rana Lebdy
- Institut de Génétique Humaine (UMR9002), CNRS, Université de Montpellier, Montpellier Cedex 5, France
- Faculty of Sciences, Genomics and Surveillance Biotherapy (GSBT) Laboratory, R. Hariri Campus, Lebanese University, Hadath, Lebanon
| | - Marine Canut
- Institut de Génétique Humaine (UMR9002), CNRS, Université de Montpellier, Montpellier Cedex 5, France
| | - Julie Patouillard
- Institut de Génétique Humaine (UMR9002), CNRS, Université de Montpellier, Montpellier Cedex 5, France
| | | | - Anne Letessier
- Université Paris Cité, Institut Cochin, INSERM, CNRS, Paris, France
| | - Josiane Ammar
- Institut de Génétique Humaine (UMR9002), CNRS, Université de Montpellier, Montpellier Cedex 5, France
| | - Jihane Basbous
- Institut de Génétique Humaine (UMR9002), CNRS, Université de Montpellier, Montpellier Cedex 5, France
| | - Serge Urbach
- Institut de Génomique Fonctionnelle, CNRS UMR 5203, Inserm U1191, Université de Montpellier, Montpellier Cedex 5, France
| | - Benoit Miotto
- Université Paris Cité, Institut Cochin, INSERM, CNRS, Paris, France
| | - Angelos Constantinou
- Institut de Génétique Humaine (UMR9002), CNRS, Université de Montpellier, Montpellier Cedex 5, France
| | - Raghida Abou Merhi
- Faculty of Sciences, Genomics and Surveillance Biotherapy (GSBT) Laboratory, R. Hariri Campus, Lebanese University, Hadath, Lebanon
| | - Cyril Ribeyre
- Institut de Génétique Humaine (UMR9002), CNRS, Université de Montpellier, Montpellier Cedex 5, France
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16
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Lee CSK, Weiβ M, Hamperl S. Where and when to start: Regulating DNA replication origin activity in eukaryotic genomes. Nucleus 2023; 14:2229642. [PMID: 37469113 PMCID: PMC10361152 DOI: 10.1080/19491034.2023.2229642] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 07/21/2023] Open
Abstract
In eukaryotic genomes, hundreds to thousands of potential start sites of DNA replication named origins are dispersed across each of the linear chromosomes. During S-phase, only a subset of origins is selected in a stochastic manner to assemble bidirectional replication forks and initiate DNA synthesis. Despite substantial progress in our understanding of this complex process, a comprehensive 'identity code' that defines origins based on specific nucleotide sequences, DNA structural features, the local chromatin environment, or 3D genome architecture is still missing. In this article, we review the genetic and epigenetic features of replication origins in yeast and metazoan chromosomes and highlight recent insights into how this flexibility in origin usage contributes to nuclear organization, cell growth, differentiation, and genome stability.
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Affiliation(s)
- Clare S K Lee
- Chromosome Dynamics and Genome Stability, Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
| | - Matthias Weiβ
- Chromosome Dynamics and Genome Stability, Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
| | - Stephan Hamperl
- Chromosome Dynamics and Genome Stability, Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
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17
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Capelson M. You are who your friends are-nuclear pore proteins as components of chromatin-binding complexes. FEBS Lett 2023; 597:2769-2781. [PMID: 37652464 PMCID: PMC11081553 DOI: 10.1002/1873-3468.14728] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/17/2023] [Accepted: 08/17/2023] [Indexed: 09/02/2023]
Abstract
Nuclear pore complexes are large multicomponent protein complexes that are embedded in the nuclear envelope, where they mediate nucleocytoplasmic transport. In addition to supporting transport, nuclear pore components, termed nucleoporins (Nups), can interact with chromatin and influence genome function. A subset of Nups can also localize to the nuclear interior and bind chromatin intranuclearly, providing an opportunity to investigate chromatin-associated functions of Nups outside of the transport context. This review focuses on the gene regulatory functions of such intranuclear Nups, with a particular emphasis on their identity as components of several chromatin regulatory complexes. Recent proteomic screens have identified Nups as interacting partners of active and repressive epigenetic machinery, architectural proteins, and DNA replication complexes, providing insight into molecular mechanisms via which Nups regulate gene expression programs. This review summarizes these interactions and discusses their potential functions in the broader framework of nuclear genome organization.
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Affiliation(s)
- Maya Capelson
- Cell and Molecular Biology Program, Department of Biology, San Diego State University, CA, USA
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18
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Bhowmick R, Hickson ID, Liu Y. Completing genome replication outside of S phase. Mol Cell 2023; 83:3596-3607. [PMID: 37716351 DOI: 10.1016/j.molcel.2023.08.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/03/2023] [Accepted: 08/17/2023] [Indexed: 09/18/2023]
Abstract
Mitotic DNA synthesis (MiDAS) is an unusual form of DNA replication that occurs during mitosis. Initially, MiDAS was characterized as a process associated with intrinsically unstable loci known as common fragile sites that occurs after cells experience DNA replication stress (RS). However, it is now believed to be a more widespread "salvage" mechanism that is called upon to complete the duplication of any under-replicated genomic region. Emerging data suggest that MiDAS is a DNA repair process potentially involving two or more pathways working in parallel or sequentially. In this review, we introduce the causes of RS, regions of the human genome known to be especially vulnerable to RS, and the strategies used to complete DNA replication outside of S phase. Additionally, because MiDAS is a prominent feature of aneuploid cancer cells, we will discuss how targeting MiDAS might potentially lead to improvements in cancer therapy.
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Affiliation(s)
- Rahul Bhowmick
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Panum Institute, Blegdamsvej 3B, 2200 Copenhagen N, Denmark; Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Ian D Hickson
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Panum Institute, Blegdamsvej 3B, 2200 Copenhagen N, Denmark.
| | - Ying Liu
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Panum Institute, Blegdamsvej 3B, 2200 Copenhagen N, Denmark.
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19
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Zhang W, Wang Y, Liu Y, Liu C, Wang Y, He L, Cheng X, Peng Y, Xia L, Wu X, Wu J, Zhang Y, Sun L, Chen P, Li G, Tu Q, Liang J, Shang Y. NFIB facilitates replication licensing by acting as a genome organizer. Nat Commun 2023; 14:5076. [PMID: 37604829 PMCID: PMC10442334 DOI: 10.1038/s41467-023-40846-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 08/12/2023] [Indexed: 08/23/2023] Open
Abstract
The chromatin-based rule governing the selection and activation of replication origins in metazoans remains to be investigated. Here we report that NFIB, a member of Nuclear Factor I (NFI) family that was initially purified in host cells to promote adenoviral DNA replication but has since mainly been investigated in transcription regulation, is physically associated with the pre-replication complex (pre-RC) in mammalian cells. Genomic analyses reveal that NFIB facilitates the assembly of the pre-RC by increasing chromatin accessibility. Nucleosome binding and single-molecule magnetic tweezers shows that NFIB binds to and opens up nucleosomes. Transmission electron microscopy indicates that NFIB promotes nucleosome eviction on parental chromatin. NFIB deficiency leads to alterations of chromosome contacts/compartments in both G1 and S phase and affects the firing of a subset of origins at early-replication domains. Significantly, cancer-associated NFIB overexpression provokes gene duplication and genomic alterations recapitulating the genetic aberrance in clinical breast cancer and empowering cancer cells to dynamically evolve growth advantage and drug resistance. Together, these results point a role for NFIB in facilitating replication licensing by acting as a genome organizer, shedding new lights on the biological function of NFIB and on the replication origin selection in eukaryotes.
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Affiliation(s)
- Wenting Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Yue Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Yongjie Liu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Cuifang Liu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yizhou Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Lin He
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Xiao Cheng
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Yani Peng
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Lu Xia
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Xiaodi Wu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
| | - Jiajing Wu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
| | - Yu Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Luyang Sun
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Ping Chen
- Department of Immunology, School of Basic Medical Sciences, Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, 100069, China
| | - Guohong Li
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qiang Tu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Jing Liang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
| | - Yongfeng Shang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, 311121, China.
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20
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Wu J, Liu Y, Zhangding Z, Liu X, Ai C, Gan T, Liang H, Guo Y, Chen M, Liu Y, Yin J, Zhang W, Hu J. Cohesin maintains replication timing to suppress DNA damage on cancer genes. Nat Genet 2023; 55:1347-1358. [PMID: 37500731 DOI: 10.1038/s41588-023-01458-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 06/26/2023] [Indexed: 07/29/2023]
Abstract
Cohesin loss-of-function mutations are frequently observed in tumors, but the mechanism underlying its role in tumorigenesis is unclear. Here, we found that depletion of RAD21, a core subunit of cohesin, leads to massive genome-wide DNA breaks and 147 translocation hotspot genes, co-mutated with cohesin in multiple cancers. Increased DNA damages are independent of RAD21-loss-induced transcription alteration and loop anchor disruption. However, damage-induced chromosomal translocations coincide with the asymmetrically distributed Okazaki fragments of DNA replication, suggesting that RAD21 depletion causes replication stresses evidenced by the slower replication speed and increased stalled forks. Mechanistically, approximately 30% of the human genome exhibits an earlier replication timing after RAD21 depletion, caused by the early initiation of >900 extra dormant origins. Correspondingly, most translocation hotspot genes lie in timing-altered regions. Therefore, we conclude that cohesin dysfunction causes replication stresses induced by excessive DNA replication initiation, resulting in gross DNA damages that may promote tumorigenesis.
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Affiliation(s)
- Jinchun Wu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing, China
| | - Yang Liu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing, China
| | - Zhengrong Zhangding
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing, China
| | - Xuhao Liu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing, China
| | - Chen Ai
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing, China
| | - Tingting Gan
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing, China
| | - Haoxin Liang
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing, China
| | - Yuefeng Guo
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing, China
| | - Mohan Chen
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing, China
| | - Yiyang Liu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing, China
| | - Jianhang Yin
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing, China
| | - Weiwei Zhang
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing, China
| | - Jiazhi Hu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Center for Life Sciences, Genome Editing Research Center, Peking University, Beijing, China.
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21
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Xu D, Huang Y, Luo L, Tang L, Lu M, Cao H, Wang F, Diao Y, Lyubchenko L, Kapranov P. Genome-Wide Profiling of Endogenous Single-Stranded DNA Using the SSiNGLe-P1 Method. Int J Mol Sci 2023; 24:12062. [PMID: 37569439 PMCID: PMC10418711 DOI: 10.3390/ijms241512062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/23/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
Endogenous single-stranded DNA (essDNA) can form in a mammalian genome as the result of a variety of molecular processes and can both play important roles inside the cell as well as have detrimental consequences to genome integrity, much of which remains to be fully understood. Here, we established the SSiNGLe-P1 approach based on limited digestion by P1 endonuclease for high-throughput genome-wide identification of essDNA regions. We applied this method to profile essDNA in both human mitochondrial and nuclear genomes. In the mitochondrial genome, the profiles of essDNA provide new evidence to support the strand-displacement model of mitochondrial DNA replication. In the nuclear genome, essDNA regions were found to be enriched in certain types of functional genomic elements, particularly, the origins of DNA replication, R-loops, and to a lesser degree, in promoters. Furthermore, interestingly, many of the essDNA regions identified by SSiNGLe-P1 have not been annotated and thus could represent yet unknown functional elements.
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Affiliation(s)
- Dongyang Xu
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen 361021, China; (D.X.)
| | - Yu Huang
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen 361021, China; (D.X.)
| | - Lingcong Luo
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen 361021, China; (D.X.)
| | - Lu Tang
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen 361021, China; (D.X.)
| | - Meng Lu
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen 361021, China; (D.X.)
| | - Huifen Cao
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen 361021, China; (D.X.)
| | - Fang Wang
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen 361021, China; (D.X.)
| | - Yong Diao
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen 361021, China; (D.X.)
| | - Liudmila Lyubchenko
- National Medical Research Center for Radiology, Ministry of Health of Russia, 125284 Moscow, Russia
| | - Philipp Kapranov
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen 361021, China; (D.X.)
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
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22
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Shih J, Sarmashghi S, Zhakula-Kostadinova N, Zhang S, Georgis Y, Hoyt SH, Cuoco MS, Gao GF, Spurr LF, Berger AC, Ha G, Rendo V, Shen H, Meyerson M, Cherniack AD, Taylor AM, Beroukhim R. Cancer aneuploidies are shaped primarily by effects on tumour fitness. Nature 2023; 619:793-800. [PMID: 37380777 PMCID: PMC10529820 DOI: 10.1038/s41586-023-06266-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 05/26/2023] [Indexed: 06/30/2023]
Abstract
Aneuploidies-whole-chromosome or whole-arm imbalances-are the most prevalent alteration in cancer genomes1,2. However, it is still debated whether their prevalence is due to selection or ease of generation as passenger events1,2. Here we developed a method, BISCUT, that identifies loci subject to fitness advantages or disadvantages by interrogating length distributions of telomere- or centromere-bounded copy-number events. These loci were significantly enriched for known cancer driver genes, including genes not detected through analysis of focal copy-number events, and were often lineage specific. BISCUT identified the helicase-encoding gene WRN as a haploinsufficient tumour-suppressor gene on chromosome 8p, which is supported by several lines of evidence. We also formally quantified the role of selection and mechanical biases in driving aneuploidy, finding that rates of arm-level copy-number alterations are most highly correlated with their effects on cellular fitness1,2. These results provide insight into the driving forces behind aneuploidy and its contribution to tumorigenesis.
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Affiliation(s)
- Juliann Shih
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Tufts University School of Medicine, Boston, MA, USA
- Department of Internal Medicine, Kirk Kerkorian School of Medicine at the University of Nevada, Las Vegas, NV, USA
| | - Shahab Sarmashghi
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Nadja Zhakula-Kostadinova
- Department of Pathology and Cell Biology, Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Genetics and Development, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Shu Zhang
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Yohanna Georgis
- Department of Pathology and Cell Biology, Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Stephanie H Hoyt
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michael S Cuoco
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Galen F Gao
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Liam F Spurr
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ashton C Berger
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Gavin Ha
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Veronica Rendo
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Hui Shen
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Matthew Meyerson
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Andrew D Cherniack
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alison M Taylor
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Pathology and Cell Biology, Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Rameen Beroukhim
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
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23
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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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24
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The human pre-replication complex is an open complex. Cell 2023; 186:98-111.e21. [PMID: 36608662 DOI: 10.1016/j.cell.2022.12.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 10/13/2022] [Accepted: 12/05/2022] [Indexed: 01/07/2023]
Abstract
In eukaryotes, DNA replication initiation requires assembly and activation of the minichromosome maintenance (MCM) 2-7 double hexamer (DH) to melt origin DNA strands. However, the mechanism for this initial melting is unknown. Here, we report a 2.59-Å cryo-electron microscopy structure of the human MCM-DH (hMCM-DH), also known as the pre-replication complex. In this structure, the hMCM-DH with a constricted central channel untwists and stretches the DNA strands such that almost a half turn of the bound duplex DNA is distorted with 1 base pair completely separated, generating an initial open structure (IOS) at the hexamer junction. Disturbing the IOS inhibits DH formation and replication initiation. Mapping of hMCM-DH footprints indicates that IOSs are distributed across the genome in large clusters aligning well with initiation zones designed for stochastic origin firing. This work unravels an intrinsic mechanism that couples DH formation with initial DNA melting to license replication initiation in human cells.
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25
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Colonnetta MM, Schedl P, Deshpande G. Germline/soma distinction in Drosophila embryos requires regulators of zygotic genome activation. eLife 2023; 12:78188. [PMID: 36598809 PMCID: PMC9812407 DOI: 10.7554/elife.78188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 12/23/2022] [Indexed: 01/05/2023] Open
Abstract
In Drosophila melanogaster embryos, somatic versus germline identity is the first cell fate decision. Zygotic genome activation (ZGA) orchestrates regionalized gene expression, imparting specific identity on somatic cells. ZGA begins with a minor wave that commences at nuclear cycle (NC)8 under the guidance of chromatin accessibility factors (Zelda, CLAMP, GAF), followed by the major wave during NC14. By contrast, primordial germ cell (PGC) specification requires maternally deposited and posteriorly anchored germline determinants. This is accomplished by a centrosome coordinated release and sequestration of germ plasm during the precocious cellularization of PGCs in NC10. Here, we report a novel requirement for Zelda and CLAMP during the establishment of the germline/soma distinction. When their activity is compromised, PGC determinants are not properly sequestered, and specification is disrupted. Conversely, the spreading of PGC determinants from the posterior pole adversely influences transcription in the neighboring somatic nuclei. These reciprocal aberrations can be correlated with defects in centrosome duplication/separation that are known to induce inappropriate transmission of the germ plasm. Interestingly, consistent with the ability of bone morphogenetic protein (BMP) signaling to influence specification of embryonic PGCs, reduction in the transcript levels of a BMP family ligand, decapentaplegic (dpp), is exacerbated at the posterior pole.
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Affiliation(s)
- Megan M Colonnetta
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
| | - Paul Schedl
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
| | - Girish Deshpande
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
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26
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Temporal regulation of head-on transcription at replication initiation sites. iScience 2022; 26:105791. [PMID: 36594032 PMCID: PMC9803852 DOI: 10.1016/j.isci.2022.105791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 09/14/2022] [Accepted: 12/08/2022] [Indexed: 12/13/2022] Open
Abstract
Head-on (HO) collisions between the DNA replication machinery and RNA polymerase over R-loop forming sequences (RLFS) are genotoxic, leading to replication fork blockage and DNA breaks. Current models suggest that HO collisions are avoided through replication initiation site (RIS) positioning upstream of active genes, ensuring co-orientation of replication fork movement and genic transcription. However, this model does not account for pervasive transcription, or intragenic RIS. Moreover, pervasive transcription initiation and CG-rich DNA is a feature of RIS, suggesting that HO transcription units (HO TUs) capable of forming R-loops might occur. Through mining phased GRO-seq data, and developing an informatics strategy to stringently identify RIS, we demonstrate that HO TUs containing RLFS occur at RIS in MCF-7 cells, and are downregulated at the G1/S phase boundary. Our analysis reveals a novel spatiotemporal relationship between transcription and replication, and supports the idea that HO collisions are avoided through transcriptional regulatory mechanisms.
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27
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Jodkowska K, Pancaldi V, Rigau M, Almeida R, Fernández-Justel J, Graña-Castro O, Rodríguez-Acebes S, Rubio-Camarillo M, Carrillo-de Santa Pau E, Pisano D, Al-Shahrour F, Valencia A, Gómez M, Méndez J. 3D chromatin connectivity underlies replication origin efficiency in mouse embryonic stem cells. Nucleic Acids Res 2022; 50:12149-12165. [PMID: 36453993 PMCID: PMC9757045 DOI: 10.1093/nar/gkac1111] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 10/31/2022] [Accepted: 11/25/2022] [Indexed: 12/03/2022] Open
Abstract
In mammalian cells, chromosomal replication starts at thousands of origins at which replisomes are assembled. Replicative stress triggers additional initiation events from 'dormant' origins whose genomic distribution and regulation are not well understood. In this study, we have analyzed origin activity in mouse embryonic stem cells in the absence or presence of mild replicative stress induced by aphidicolin, a DNA polymerase inhibitor, or by deregulation of origin licensing factor CDC6. In both cases, we observe that the majority of stress-responsive origins are also active in a small fraction of the cell population in a normal S phase, and stress increases their frequency of activation. In a search for the molecular determinants of origin efficiency, we compared the genetic and epigenetic features of origins displaying different levels of activation, and integrated their genomic positions in three-dimensional chromatin interaction networks derived from high-depth Hi-C and promoter-capture Hi-C data. We report that origin efficiency is directly proportional to the proximity to transcriptional start sites and to the number of contacts established between origin-containing chromatin fragments, supporting the organization of origins in higher-level DNA replication factories.
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Affiliation(s)
| | | | | | | | - José M Fernández-Justel
- Functional Organization of the Mammalian Genome Group, Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Madrid, Spain
| | - Osvaldo Graña-Castro
- Bioinformatics Unit, Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain,Institute of Applied Molecular Medicine (IMMA-Nemesio Díez), San Pablo-CEU University, Boadilla del Monte, Madrid, Spain
| | - Sara Rodríguez-Acebes
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Miriam Rubio-Camarillo
- Bioinformatics Unit, Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | | | - David Pisano
- Bioinformatics Unit, Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Fátima Al-Shahrour
- Bioinformatics Unit, Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Alfonso Valencia
- Computational Biology Life Sciences Group, Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - María Gómez
- Correspondence may also be addressed to María Gómez. Tel: +34 911964724; Fax: +34 911964420;
| | - Juan Méndez
- To whom correspondence should be addressed. Tel: +34 917328000; Fax: +34 917328033;
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28
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Mirceta M, Shum N, Schmidt MHM, Pearson CE. Fragile sites, chromosomal lesions, tandem repeats, and disease. Front Genet 2022; 13:985975. [PMID: 36468036 PMCID: PMC9714581 DOI: 10.3389/fgene.2022.985975] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 09/02/2022] [Indexed: 09/16/2023] Open
Abstract
Expanded tandem repeat DNAs are associated with various unusual chromosomal lesions, despiralizations, multi-branched inter-chromosomal associations, and fragile sites. Fragile sites cytogenetically manifest as localized gaps or discontinuities in chromosome structure and are an important genetic, biological, and health-related phenomena. Common fragile sites (∼230), present in most individuals, are induced by aphidicolin and can be associated with cancer; of the 27 molecularly-mapped common sites, none are associated with a particular DNA sequence motif. Rare fragile sites ( ≳ 40 known), ≤ 5% of the population (may be as few as a single individual), can be associated with neurodevelopmental disease. All 10 molecularly-mapped folate-sensitive fragile sites, the largest category of rare fragile sites, are caused by gene-specific CGG/CCG tandem repeat expansions that are aberrantly CpG methylated and include FRAXA, FRAXE, FRAXF, FRA2A, FRA7A, FRA10A, FRA11A, FRA11B, FRA12A, and FRA16A. The minisatellite-associated rare fragile sites, FRA10B, FRA16B, can be induced by AT-rich DNA-ligands or nucleotide analogs. Despiralized lesions and multi-branched inter-chromosomal associations at the heterochromatic satellite repeats of chromosomes 1, 9, 16 are inducible by de-methylating agents like 5-azadeoxycytidine and can spontaneously arise in patients with ICF syndrome (Immunodeficiency Centromeric instability and Facial anomalies) with mutations in genes regulating DNA methylation. ICF individuals have hypomethylated satellites I-III, alpha-satellites, and subtelomeric repeats. Ribosomal repeats and subtelomeric D4Z4 megasatellites/macrosatellites, are associated with chromosome location, fragility, and disease. Telomere repeats can also assume fragile sites. Dietary deficiencies of folate or vitamin B12, or drug insults are associated with megaloblastic and/or pernicious anemia, that display chromosomes with fragile sites. The recent discovery of many new tandem repeat expansion loci, with varied repeat motifs, where motif lengths can range from mono-nucleotides to megabase units, could be the molecular cause of new fragile sites, or other chromosomal lesions. This review focuses on repeat-associated fragility, covering their induction, cytogenetics, epigenetics, cell type specificity, genetic instability (repeat instability, micronuclei, deletions/rearrangements, and sister chromatid exchange), unusual heritability, disease association, and penetrance. Understanding tandem repeat-associated chromosomal fragile sites provides insight to chromosome structure, genome packaging, genetic instability, and disease.
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Affiliation(s)
- Mila Mirceta
- Program of Genetics and Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON, Canada
- Program of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Natalie Shum
- Program of Genetics and Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON, Canada
- Program of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Monika H. M. Schmidt
- Program of Genetics and Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON, Canada
- Program of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Christopher E. Pearson
- Program of Genetics and Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON, Canada
- Program of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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29
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Murat P, Perez C, Crisp A, van Eijk P, Reed SH, Guilbaud G, Sale JE. DNA replication initiation shapes the mutational landscape and expression of the human genome. SCIENCE ADVANCES 2022; 8:eadd3686. [PMID: 36351018 PMCID: PMC9645720 DOI: 10.1126/sciadv.add3686] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
The interplay between active biological processes and DNA repair is central to mutagenesis. Here, we show that the ubiquitous process of replication initiation is mutagenic, leaving a specific mutational footprint at thousands of early and efficient replication origins. The observed mutational pattern is consistent with two distinct mechanisms, reflecting the two-step process of origin activation, triggering the formation of DNA breaks at the center of origins and local error-prone DNA synthesis in their immediate vicinity. We demonstrate that these replication initiation-dependent mutational processes exert an influence on phenotypic diversity in humans that is disproportionate to the origins' genomic size: By increasing mutational loads at gene promoters and splice junctions, the presence of an origin significantly influences both gene expression and mRNA isoform usage. Last, we show that mutagenesis at origins not only drives the evolution of origin sequences but also contributes to sculpting regulatory domains of the human genome.
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Affiliation(s)
- Pierre Murat
- Division of Protein & Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Consuelo Perez
- Division of Protein & Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Alastair Crisp
- Division of Protein & Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Patrick van Eijk
- Broken String Biosciences Ltd., BioData Innovation Centre, Unit AB3-03, Level 3, Wellcome Genome Campus, Hinxton, Cambridge CB10 1DR, UK
- Division of Cancer & Genetics School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
| | - Simon H. Reed
- Broken String Biosciences Ltd., BioData Innovation Centre, Unit AB3-03, Level 3, Wellcome Genome Campus, Hinxton, Cambridge CB10 1DR, UK
- Division of Cancer & Genetics School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
| | - Guillaume Guilbaud
- Division of Protein & Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Julian E. Sale
- Division of Protein & Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
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30
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Richards L, Lord CL, Benton ML, Capra JA, Nordman JT. Nucleoporins facilitate ORC loading onto chromatin. Cell Rep 2022; 41:111590. [PMID: 36351393 PMCID: PMC10040217 DOI: 10.1016/j.celrep.2022.111590] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 08/10/2022] [Accepted: 10/11/2022] [Indexed: 11/11/2022] Open
Abstract
The origin recognition complex (ORC) binds throughout the genome to initiate DNA replication. In metazoans, it is still unclear how ORC is targeted to specific loci to facilitate helicase loading and replication initiation. Here, we perform immunoprecipitations coupled with mass spectrometry for ORC2 in Drosophila embryos. Surprisingly, we find that ORC2 associates with multiple subunits of the Nup107-160 subcomplex of the nuclear pore. Bioinformatic analysis reveals that, relative to all modENCODE factors, nucleoporins are among the most enriched factors at ORC2 binding sites. Critically, depletion of the nucleoporin Elys, a member of the Nup107-160 complex, decreases ORC2 loading onto chromatin. Depleting Elys also sensitizes cells to replication fork stalling, which could reflect a defect in establishing dormant replication origins. Our work reveals a connection between ORC, replication initiation, and nucleoporins, suggesting a function for nucleoporins in metazoan replication initiation.
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Affiliation(s)
- Logan Richards
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - Christopher L Lord
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | | | - John A Capra
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA; Bakar Computational Health Sciences Institute and Department of Epidemiology and Biostatistics, UCSF, San Francisco, CA 94143, USA
| | - Jared T Nordman
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA.
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31
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Dao FY, Lv H, Fullwood MJ, Lin H. Accurate Identification of DNA Replication Origin by Fusing Epigenomics and Chromatin Interaction Information. RESEARCH (WASHINGTON, D.C.) 2022; 2022:9780293. [PMID: 36405252 PMCID: PMC9667886 DOI: 10.34133/2022/9780293] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/30/2022] [Indexed: 07/29/2023]
Abstract
DNA replication initiation is a complex process involving various genetic and epigenomic signatures. The correct identification of replication origins (ORIs) could provide important clues for the study of a variety of diseases caused by replication. Here, we design a computational approach named iORI-Epi to recognize ORIs by incorporating epigenome-based features, sequence-based features, and 3D genome-based features. The iORI-Epi displays excellent robustness and generalization ability on both training datasets and independent datasets of K562 cell line. Further experiments confirm that iORI-Epi is highly scalable in other cell lines (MCF7 and HCT116). We also analyze and clarify the regulatory role of epigenomic marks, DNA motifs, and chromatin interaction in DNA replication initiation of eukaryotic genomes. Finally, we discuss gene enrichment pathways from the perspective of ORIs in different replication timing states and heuristically dissect the effect of promoters on replication initiation. Our computational methodology is worth extending to ORI identification in other eukaryotic species.
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Affiliation(s)
- Fu-Ying Dao
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
- School of Biological Sciences, Nanyang Technological University, Singapore 639798, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Dr, Singapore 117599, Singapore
| | - Hao Lv
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Melissa J. Fullwood
- School of Biological Sciences, Nanyang Technological University, Singapore 639798, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Dr, Singapore 117599, Singapore
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A∗STAR), Singapore 138673, Singapore
| | - Hao Lin
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
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32
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Ji F, Zhu X, Liao H, Ouyang L, Huang Y, Syeda MZ, Ying S. New Era of Mapping and Understanding Common Fragile Sites: An Updated Review on Origin of Chromosome Fragility. Front Genet 2022; 13:906957. [PMID: 35669181 PMCID: PMC9164283 DOI: 10.3389/fgene.2022.906957] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
Common fragile sites (CFSs) are specific genomic loci prone to forming gaps or breakages upon replication perturbation, which correlate well with chromosomal rearrangement and copy number variation. CFSs have been actively studied due to their important pathophysiological relevance in different diseases such as cancer and neurological disorders. The genetic locations and sequences of CFSs are crucial to understanding the origin of such unstable sites, which require reliable mapping and characterizing approaches. In this review, we will inspect the evolving techniques for CFSs mapping, especially genome-wide mapping and sequencing of CFSs based on current knowledge of CFSs. We will also revisit the well-established hypotheses on the origin of CFSs fragility, incorporating novel findings from the comprehensive analysis of finely mapped CFSs regarding their locations, sequences, and replication/transcription, etc. This review will present the most up-to-date picture of CFSs and, potentially, a new framework for future research of CFSs.
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Affiliation(s)
- Fang Ji
- International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu, China.,Department of Pharmacology and Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Key Laboratory of Respiratory Disease of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Xinli Zhu
- Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Key Laboratory of Respiratory Disease of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Hongwei Liao
- International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu, China.,Department of Pharmacology and Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Key Laboratory of Respiratory Disease of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Liujian Ouyang
- Department of Pharmacology and Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Key Laboratory of Respiratory Disease of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Yingfei Huang
- Department of Pharmacology and Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Key Laboratory of Respiratory Disease of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Madiha Zahra Syeda
- Department of Pharmacology and Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Key Laboratory of Respiratory Disease of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Songmin Ying
- International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu, China.,Department of Pharmacology and Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Key Laboratory of Respiratory Disease of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
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33
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Watzky M, Huard S, Juricek L, Dairou J, Chauvet C, Coumoul X, Letessier A, Miotto B. Hexokinase 2 is a transcriptional target and a positive modulator of AHR signalling. Nucleic Acids Res 2022; 50:5545-5564. [PMID: 35609998 PMCID: PMC9178003 DOI: 10.1093/nar/gkac360] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 04/20/2022] [Accepted: 05/16/2022] [Indexed: 12/14/2022] Open
Abstract
The aryl hydrocarbon receptor (AHR) regulates the expression of numerous genes in response to activation by agonists including xenobiotics. Although it is well appreciated that environmental signals and cell intrinsic features may modulate this transcriptional response, how it is mechanistically achieved remains poorly understood. We show that hexokinase 2 (HK2) a metabolic enzyme fuelling cancer cell growth, is a transcriptional target of AHR as well as a modulator of its activity. Expression of HK2 is positively regulated by AHR upon exposure to agonists both in human cells and in mice lung tissues. Conversely, over-expression of HK2 regulates the abundance of many proteins involved in the regulation of AHR signalling and these changes are linked with altered AHR expression levels and transcriptional activity. HK2 expression also shows a negative correlation with AHR promoter methylation in tumours, and these tumours with high HK2 expression and low AHR methylation are associated with a worse overall survival in patients. In sum, our study provides novel insights into how AHR signalling is regulated which may help our understanding of the context-specific effects of this pathway and may have implications in cancer.
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Affiliation(s)
- Manon Watzky
- Université Paris Cité, Institut Cochin, INSERM, U1016, CNRS, UMR8104, F-75014 Paris, France
| | - Solène Huard
- Université Paris Cité, Institut Cochin, INSERM, U1016, CNRS, UMR8104, F-75014 Paris, France
| | - Ludmila Juricek
- METATOX, T3S, Toxicologie Environnementale, Cibles thérapeutiques, Signalisation cellulaire et Biomarqueurs, INSERM UMR-S1124, F-75006 Paris, France
| | - Julien Dairou
- Université Paris Cité, UFR des Sciences Fondamentales et Biomédicales, Paris, France.,Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, CNRS, UMR 8601, Université Paris Cité, F-75006 Paris, France
| | - Caroline Chauvet
- METATOX, T3S, Toxicologie Environnementale, Cibles thérapeutiques, Signalisation cellulaire et Biomarqueurs, INSERM UMR-S1124, F-75006 Paris, France.,Université Paris Cité, UFR des Sciences Fondamentales et Biomédicales, Paris, France
| | - Xavier Coumoul
- METATOX, T3S, Toxicologie Environnementale, Cibles thérapeutiques, Signalisation cellulaire et Biomarqueurs, INSERM UMR-S1124, F-75006 Paris, France.,Université Paris Cité, UFR des Sciences Fondamentales et Biomédicales, Paris, France
| | - Anne Letessier
- Université Paris Cité, Institut Cochin, INSERM, U1016, CNRS, UMR8104, F-75014 Paris, France
| | - Benoit Miotto
- Université Paris Cité, Institut Cochin, INSERM, U1016, CNRS, UMR8104, F-75014 Paris, France
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LSD1 is required for euchromatic origin firing and replication timing. Signal Transduct Target Ther 2022; 7:102. [PMID: 35414135 PMCID: PMC9005705 DOI: 10.1038/s41392-022-00927-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 01/31/2022] [Accepted: 02/13/2022] [Indexed: 11/08/2022] Open
Abstract
The chromatin-based rule governing the selection and activation of replication origins remains to be elucidated. It is believed that DNA replication initiates from open chromatin domains; thus, replication origins reside in open and active chromatin. However, we report here that lysine-specific demethylase 1 (LSD1), which biochemically catalyzes H3K4me1/2 demethylation favoring chromatin condensation, interacts with the DNA replication machinery in human cells. We find that LSD1 level peaks in early S phase, when it is required for DNA replication by facilitating origin firing in euchromatic regions. Indeed, euchromatic zones enriched in H3K4me2 are the preferred sites for the pre-replicative complex (pre-RC) binding. Remarkably, LSD1 deficiency leads to a genome-wide switch of replication from early to late. We show that LSD1-engaged DNA replication is mechanistically linked to the loading of TopBP1-Interacting Checkpoint and Replication Regulator (TICRR) onto the pre-RC and subsequent recruitment of CDC45 during origin firing. Together, these results reveal an unexpected role for LSD1 in euchromatic origin firing and replication timing, highlighting the importance of epigenetic regulation in the activation of replication origins. As selective inhibitors of LSD1 are being exploited as potential cancer therapeutics, our study supports the importance of leveraging an appropriate level of LSD1 to curb the side effects of anti-LSD1 therapy.
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35
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Gatto A, Forest A, Quivy JP, Almouzni G. HIRA-dependent boundaries between H3 variants shape early replication in mammals. Mol Cell 2022; 82:1909-1923.e5. [PMID: 35381196 DOI: 10.1016/j.molcel.2022.03.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 12/16/2021] [Accepted: 03/09/2022] [Indexed: 10/18/2022]
Abstract
The lack of a consensus DNA sequence defining replication origins in mammals has led researchers to consider chromatin as a means to specify these regions. However, to date, there is no mechanistic understanding of how this could be achieved and maintained given that nucleosome disruption occurs with each fork passage and with transcription. Here, by genome-wide mapping of the de novo deposition of the histone variants H3.1 and H3.3 in human cells during S phase, we identified how their dual deposition mode ensures a stable marking with H3.3 flanked on both sides by H3.1. These H3.1/H3.3 boundaries correspond to the initiation zones of early origins. Loss of the H3.3 chaperone HIRA leads to the concomitant disruption of H3.1/H3.3 boundaries and initiation zones. We propose that the HIRA-dependent deposition of H3.3 preserves H3.1/H3.3 boundaries by protecting them from H3.1 invasion linked to fork progression, contributing to a chromatin-based definition of early replication zones.
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Affiliation(s)
- Alberto Gatto
- Institut Curie, PSL Research University, CNRS, Sorbonne Université, Nuclear Dynamics Unit, Equipe Labellisée Ligue contre le Cancer, 26 rue d'Ulm, 75005 Paris, France
| | - Audrey Forest
- Institut Curie, PSL Research University, CNRS, Sorbonne Université, Nuclear Dynamics Unit, Equipe Labellisée Ligue contre le Cancer, 26 rue d'Ulm, 75005 Paris, France
| | - Jean-Pierre Quivy
- Institut Curie, PSL Research University, CNRS, Sorbonne Université, Nuclear Dynamics Unit, Equipe Labellisée Ligue contre le Cancer, 26 rue d'Ulm, 75005 Paris, France.
| | - Geneviève Almouzni
- Institut Curie, PSL Research University, CNRS, Sorbonne Université, Nuclear Dynamics Unit, Equipe Labellisée Ligue contre le Cancer, 26 rue d'Ulm, 75005 Paris, France.
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36
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Thakur BL, Ray A, Redon CE, Aladjem MI. Preventing excess replication origin activation to ensure genome stability. Trends Genet 2022; 38:169-181. [PMID: 34625299 PMCID: PMC8752500 DOI: 10.1016/j.tig.2021.09.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/14/2021] [Accepted: 09/16/2021] [Indexed: 02/03/2023]
Abstract
Cells activate distinctive regulatory pathways that prevent excessive initiation of DNA replication to achieve timely and accurate genome duplication. Excess DNA synthesis is constrained by protein-DNA interactions that inhibit initiation at dormant origins. In parallel, specific modifications of pre-replication complexes prohibit post-replicative origin relicensing. Replication stress ensues when the controls that prevent excess replication are missing in cancer cells, which often harbor extrachromosomal DNA that can be further amplified by recombination-mediated processes to generate chromosomal translocations. The genomic instability that accompanies excess replication origin activation can provide a promising target for therapeutic intervention. Here we review molecular pathways that modulate replication origin dormancy, prevent excess origin activation, and detect, encapsulate, and eliminate persistent excess DNA.
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Affiliation(s)
- Bhushan L Thakur
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Anagh Ray
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Christophe E Redon
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Mirit I Aladjem
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
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37
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Balzano E, Di Tommaso E, Antoccia A, Pelliccia F, Giunta S. Characterization of Chromosomal Instability in Glioblastoma. Front Genet 2022; 12:810793. [PMID: 35154254 PMCID: PMC8831864 DOI: 10.3389/fgene.2021.810793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 12/23/2021] [Indexed: 11/13/2022] Open
Abstract
Glioblastoma multiforme (GBM) is a malignant tumor of the central nervous system (CNS). The poor prognosis of GBM due to resistance to therapy has been associated with high chromosomal instability (CIN). Replication stress is a major cause of CIN that manifests as chromosome rearrangements, fragility, and breaks, including those cytologically expressed within specific chromosome regions named common fragile sites (CFSs). In this work, we characterized the expression of human CFSs in the glioblastoma U-251 MG cell line upon treatment with the inhibitor of DNA polymerase alpha aphidicolin (APH). We observed 52 gaps/breaks located within previously characterized CFSs. We found 17 to be CFSs in GBM cells upon treatment with APH, showing a frequency equal to at least 1% of the total gaps/breaks. We report that two CFSs localized to regions FRA2E (2p13/p12) and FRA2F (2q22) were only found in U-251 MG cells, but not lymphocytes or fibroblasts, after APH treatment. Notably, these glioblastoma-specific CFSs had a relatively high expression compared to the other CFSs with breakage frequency between ∼7 and 9%. Presence of long genes, incomplete replication, and delayed DNA synthesis during mitosis (MiDAS) after APH treatment suggest that an impaired replication process may contribute to this loci-specific fragility in U-251 MG cells. Altogether, our work offers a characterization of common fragile site expression in glioblastoma U-251 MG cells that may be further exploited for cytogenetic and clinical studies to advance our understanding of this incurable cancer.
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Affiliation(s)
- Elisa Balzano
- Laboratory of Molecular Cytogenetics, Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Roma, Italy
- Laboratory of Genome Evolution, Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Roma, Italy
| | - Elena Di Tommaso
- Laboratory of Molecular Cytogenetics, Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Roma, Italy
- Laboratory of Genome Evolution, Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Roma, Italy
| | - Antonio Antoccia
- Laboratory of Genetics and Cytogenetics, Dipartimento di Scienze, Università Degli Studi Roma Tre, Roma, Italy
| | - Franca Pelliccia
- Laboratory of Molecular Cytogenetics, Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Roma, Italy
- *Correspondence: Franca Pelliccia, ; Simona Giunta,
| | - Simona Giunta
- Laboratory of Genome Evolution, Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Roma, Italy
- *Correspondence: Franca Pelliccia, ; Simona Giunta,
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38
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Mei L, Kedziora KM, Song EA, Purvis JE, Cook J. The consequences of differential origin licensing dynamics in distinct chromatin environments. Nucleic Acids Res 2022; 50:9601-9620. [PMID: 35079814 PMCID: PMC9508807 DOI: 10.1093/nar/gkac003] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/17/2021] [Accepted: 01/05/2022] [Indexed: 02/01/2023] Open
Abstract
Eukaryotic chromosomes contain regions of varying accessibility, yet DNA replication factors must access all regions. The first replication step is loading MCM complexes to license replication origins during the G1 cell cycle phase. It is not yet known how mammalian MCM complexes are adequately distributed to both accessible euchromatin regions and less accessible heterochromatin regions. To address this question, we combined time-lapse live-cell imaging with immunofluorescence imaging of single human cells to quantify the relative rates of MCM loading in euchromatin and heterochromatin throughout G1. We report here that MCM loading in euchromatin is faster than that in heterochromatin in early G1, but surprisingly, heterochromatin loading accelerates relative to euchromatin loading in middle and late G1. This differential acceleration allows both chromatin types to begin S phase with similar concentrations of loaded MCM. The different loading dynamics require ORCA-dependent differences in origin recognition complex distribution. A consequence of heterochromatin licensing dynamics is that cells experiencing a truncated G1 phase from premature cyclin E expression enter S phase with underlicensed heterochromatin, and DNA damage accumulates preferentially in heterochromatin in the subsequent S/G2 phase. Thus, G1 length is critical for sufficient MCM loading, particularly in heterochromatin, to ensure complete genome duplication and to maintain genome stability.
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Affiliation(s)
- Liu Mei
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Katarzyna M Kedziora
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Bioinformatics and Analytics Research Collaborative (BARC), University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Eun-Ah Song
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jeremy E Purvis
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jeanette Gowen Cook
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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39
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Super-resolution microscopy reveals stochastic initiation of replication in Drosophila polytene chromosomes. Chromosome Res 2022; 30:361-383. [PMID: 35226231 PMCID: PMC9771856 DOI: 10.1007/s10577-021-09679-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 01/25/2023]
Abstract
Studying the probability distribution of replication initiation along a chromosome is a huge challenge. Drosophila polytene chromosomes in combination with super-resolution microscopy provide a unique opportunity for analyzing the probabilistic nature of replication initiation at the ultrastructural level. Here, we developed a method for synchronizing S-phase induction among salivary gland cells. An analysis of the replication label distribution in the first minutes of S phase and in the following hours after the induction revealed the dynamics of replication initiation. Spatial super-resolution structured illumination microscopy allowed identifying multiple discrete replication signals and to investigate the behavior of replication signals in the first minutes of the S phase at the ultrastructural level. We identified replication initiation zones where initiation occurs stochastically. These zones differ significantly in the probability of replication initiation per time unit. There are zones in which initiation occurs on most strands of the polytene chromosome in a few minutes. In other zones, the initiation on all strands takes several hours. Compact bands are free of replication initiation events, and the replication runs from outer edges to the middle, where band shapes may alter.
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40
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Edgar RD, Perrone F, Foster AR, Payne F, Lewis S, Nayak KM, Kraiczy J, Cenier A, Torrente F, Salvestrini C, Heuschkel R, Hensel KO, Harris R, Jones DL, Zerbino DR, Zilbauer M. Culture-Associated DNA Methylation Changes Impact on Cellular Function of Human Intestinal Organoids. Cell Mol Gastroenterol Hepatol 2022; 14:1295-1310. [PMID: 36038072 PMCID: PMC9703134 DOI: 10.1016/j.jcmgh.2022.08.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 08/21/2022] [Accepted: 08/22/2022] [Indexed: 01/31/2023]
Abstract
BACKGROUND & AIMS Human intestinal epithelial organoids (IEOs) are a powerful tool to model major aspects of intestinal development, health, and diseases because patient-derived cultures retain many features found in vivo. A necessary aspect of the organoid model is the requirement to expand cultures in vitro through several rounds of passaging. This is of concern because the passaging of cells has been shown to affect cell morphology, ploidy, and function. METHODS Here, we analyzed 173 human IEO lines derived from the small and large bowel and examined the effect of culture duration on DNA methylation (DNAm). Furthermore, we tested the potential impact of DNAm changes on gene expression and cellular function. RESULTS Our analyses show a reproducible effect of culture duration on DNAm in a large discovery cohort as well as 2 publicly available validation cohorts generated in different laboratories. Although methylation changes were seen in only approximately 8% of tested cytosine-phosphate-guanine dinucleotides (CpGs) and global cellular function remained stable, a subset of methylation changes correlated with altered gene expression at baseline as well as in response to inflammatory cytokine exposure and withdrawal of Wnt agonists. Importantly, epigenetic changes were found to be enriched in genomic regions associated with colonic cancer and distant to the site of replication, indicating similarities to malignant transformation. CONCLUSIONS Our study shows distinct culture-associated epigenetic changes in mucosa-derived human IEOs, some of which appear to impact gene transcriptomic and cellular function. These findings highlight the need for future studies in this area and the importance of considering passage number as a potentially confounding factor.
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Affiliation(s)
- Rachel D Edgar
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Francesca Perrone
- Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - April R Foster
- Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom; Centre for Pathway Analysis, Milner Therapeutics Institute, University of Cambridge, Cambridge, United Kingdom
| | - Felicity Payne
- Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom; Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Sophia Lewis
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California; Eli and Edythe Broad Stem Cell Research Center, University of California Los Angeles, Los Angeles, California
| | - Komal M Nayak
- Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Judith Kraiczy
- Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Aurélie Cenier
- Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom; Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Franco Torrente
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Camilla Salvestrini
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Robert Heuschkel
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Kai O Hensel
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's Hospital, Cambridge, United Kingdom; Witten/Herdecke University, Department of Paediatrics, Helios Medical Centre Wuppertal, Children's Hospital, Wuppertal, Germany
| | - Rebecca Harris
- Centre for Pathway Analysis, Milner Therapeutics Institute, University of Cambridge, Cambridge, United Kingdom
| | - D Leanne Jones
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California; Eli and Edythe Broad Stem Cell Research Center, University of California Los Angeles, Los Angeles, California; Department of Anatomy and Medicine, Division of Geriatrics, University of California, San Francisco, San Francisco, California; Eli and Edythe Broad Center for Regeneration Medicine, University of California, San Francisco, San Francisco, California
| | - Daniel R Zerbino
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Matthias Zilbauer
- Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom; Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's Hospital, Cambridge, United Kingdom; Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom.
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41
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Hayashi-Takanaka Y, Hayashi Y, Hirano Y, Miyawaki-Kuwakado A, Ohkawa Y, Obuse C, Kimura H, Haraguchi T, Hiraoka Y. Chromatin loading of MCM hexamers is associated with di-/tri-methylation of histone H4K20 toward S phase entry. Nucleic Acids Res 2021; 49:12152-12166. [PMID: 34817054 PMCID: PMC8643670 DOI: 10.1093/nar/gkab1068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 09/29/2021] [Accepted: 10/20/2021] [Indexed: 12/30/2022] Open
Abstract
DNA replication is a key step in initiating cell proliferation. Loading hexameric complexes of minichromosome maintenance (MCM) helicase onto DNA replication origins during the G1 phase is essential for initiating DNA replication. Here, we examined MCM hexamer states during the cell cycle in human hTERT-RPE1 cells using multicolor immunofluorescence-based, single-cell plot analysis, and biochemical size fractionation. Experiments involving cell-cycle arrest at the G1 phase and release from the arrest revealed that a double MCM hexamer was formed via a single hexamer during G1 progression. A single MCM hexamer was recruited to chromatin in the early G1 phase. Another single hexamer was recruited to form a double hexamer in the late G1 phase. We further examined relationship between the MCM hexamer states and the methylation levels at lysine 20 of histone H4 (H4K20) and found that the double MCM hexamer state was correlated with di/trimethyl-H4K20 (H4K20me2/3). Inhibiting the conversion from monomethyl-H4K20 (H4K20me1) to H4K20me2/3 retained the cells in the single MCM hexamer state. Non-proliferative cells, including confluent cells or Cdk4/6 inhibitor-treated cells, also remained halted in the single MCM hexamer state. We propose that the single MCM hexamer state is a halting step in the determination of cell cycle progression.
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Affiliation(s)
- Yoko Hayashi-Takanaka
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita 565-0871, Japan
| | - Yuichiro Hayashi
- Institute of Biomedical Sciences, Kansai Medical University, 2-5-1 Shin-machi, Hirakata 573-1010, Japan
| | - Yasuhiro Hirano
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita 565-0871, Japan
| | - Atsuko Miyawaki-Kuwakado
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Chikashi Obuse
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka 560-0043, Japan
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8503, Japan
| | - Tokuko Haraguchi
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita 565-0871, Japan
| | - Yasushi Hiraoka
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita 565-0871, Japan
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42
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Higa M, Matsuda Y, Fujii J, Sugimoto N, Yoshida K, Fujita M. TRF2-mediated ORC recruitment underlies telomere stability upon DNA replication stress. Nucleic Acids Res 2021; 49:12234-12251. [PMID: 34761263 PMCID: PMC8643664 DOI: 10.1093/nar/gkab1004] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 10/07/2021] [Accepted: 10/12/2021] [Indexed: 12/12/2022] Open
Abstract
Telomeres are intrinsically difficult-to-replicate region of eukaryotic chromosomes. Telomeric repeat binding factor 2 (TRF2) binds to origin recognition complex (ORC) to facilitate the loading of ORC and the replicative helicase MCM complex onto DNA at telomeres. However, the biological significance of the TRF2–ORC interaction for telomere maintenance remains largely elusive. Here, we employed a TRF2 mutant with mutations in two acidic acid residues (E111A and E112A) that inhibited the TRF2–ORC interaction in human cells. The TRF2 mutant was impaired in ORC recruitment to telomeres and showed increased replication stress-associated telomeric DNA damage and telomere instability. Furthermore, overexpression of an ORC1 fragment (amino acids 244–511), which competitively inhibited the TRF2–ORC interaction, increased telomeric DNA damage under replication stress conditions. Taken together, these findings suggest that TRF2-mediated ORC recruitment contributes to the suppression of telomere instability.
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Affiliation(s)
- Mitsunori Higa
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yukihiro Matsuda
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Jumpei Fujii
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Nozomi Sugimoto
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Kazumasa Yoshida
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Masatoshi Fujita
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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43
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Hoffman RA, MacAlpine HK, MacAlpine DM. Disruption of origin chromatin structure by helicase activation in the absence of DNA replication. Genes Dev 2021; 35:1339-1355. [PMID: 34556529 PMCID: PMC8494203 DOI: 10.1101/gad.348517.121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 08/23/2021] [Indexed: 11/24/2022]
Abstract
Prior to initiation of DNA replication, the eukaryotic helicase, Mcm2-7, must be activated to unwind DNA at replication start sites in early S phase. To study helicase activation within origin chromatin, we constructed a conditional mutant of the polymerase α subunit Cdc17 (or Pol1) to prevent priming and block replication. Recovery of these cells at permissive conditions resulted in the generation of unreplicated gaps at origins, likely due to helicase activation prior to replication initiation. We used micrococcal nuclease (MNase)-based chromatin occupancy profiling under restrictive conditions to study chromatin dynamics associated with helicase activation. Helicase activation in the absence of DNA replication resulted in the disruption and disorganization of chromatin, which extends up to 1 kb from early, efficient replication origins. The CMG holohelicase complex also moves the same distance out from the origin, producing single-stranded DNA that activates the intra-S-phase checkpoint. Loss of the checkpoint did not regulate the progression and stalling of the CMG complex but rather resulted in the disruption of chromatin at both early and late origins. Finally, we found that the local sequence context regulates helicase progression in the absence of DNA replication, suggesting that the helicase is intrinsically less processive when uncoupled from replication.
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Affiliation(s)
- Rachel A Hoffman
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Heather K MacAlpine
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - David M MacAlpine
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
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44
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Foss EJ, Sripathy S, Gatbonton-Schwager T, Kwak H, Thiesen AH, Lao U, Bedalov A. Chromosomal Mcm2-7 distribution and the genome replication program in species from yeast to humans. PLoS Genet 2021; 17:e1009714. [PMID: 34473702 PMCID: PMC8443269 DOI: 10.1371/journal.pgen.1009714] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 09/15/2021] [Accepted: 07/13/2021] [Indexed: 01/24/2023] Open
Abstract
The spatio-temporal program of genome replication across eukaryotes is thought to be driven both by the uneven loading of pre-replication complexes (pre-RCs) across the genome at the onset of S-phase, and by differences in the timing of activation of these complexes during S phase. To determine the degree to which distribution of pre-RC loading alone could account for chromosomal replication patterns, we mapped the binding sites of the Mcm2-7 helicase complex (MCM) in budding yeast, fission yeast, mouse and humans. We observed similar individual MCM double-hexamer (DH) footprints across the species, but notable differences in their distribution: Footprints in budding yeast were more sharply focused compared to the other three organisms, consistent with the relative sequence specificity of replication origins in S. cerevisiae. Nonetheless, with some clear exceptions, most notably the inactive X-chromosome, much of the fluctuation in replication timing along the chromosomes in all four organisms reflected uneven chromosomal distribution of pre-replication complexes. Gene-rich regions of the genome tend to replicate earlier in S phase than do repetitive and other non-genic regions. This may be an evolutionary consequence of the fact that replication later in S phase is associated with higher frequencies of mutation and genome rearrangement. Replication timing along the chromosome is determined by 1) events prior to S-phase that specify the locations where DNA replication can be initiated, referred to as origin licensing; and 2) the timing of activation of these licensed origins during S-phase, referred to as origin firing. To determine the relative importance of these two mechanisms, here we identify both the binding sites and the abundance of a key component of the origin licensing machinery in budding yeast, fission yeast, mice, and humans, namely the replicative helicase complex. We discovered that, with a few notable exceptions, which include the inactive X chromosome in mammals, the program of replication timing can be largely explained simply on the basis of origin licensing. Our results support a model for replication timing that emphasizes stochastic firing of origins that have been licensed before S phase begins.
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Affiliation(s)
- Eric J. Foss
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Smitha Sripathy
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Tonibelle Gatbonton-Schwager
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Hyunchang Kwak
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Adam H. Thiesen
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Uyen Lao
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Antonio Bedalov
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Medicine, Department of Biochemistry, University of Washington, Seattle Washington, United States of America
- * E-mail:
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45
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Meiotic recombination mirrors patterns of germline replication in mice and humans. Cell 2021; 184:4251-4267.e20. [PMID: 34260899 DOI: 10.1016/j.cell.2021.06.025] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 04/02/2021] [Accepted: 06/21/2021] [Indexed: 12/29/2022]
Abstract
Genetic recombination generates novel trait combinations, and understanding how recombination is distributed across the genome is key to modern genetics. The PRDM9 protein defines recombination hotspots; however, megabase-scale recombination patterning is independent of PRDM9. The single round of DNA replication, which precedes recombination in meiosis, may establish these patterns; therefore, we devised an approach to study meiotic replication that includes robust and sensitive mapping of replication origins. We find that meiotic DNA replication is distinct; reduced origin firing slows replication in meiosis, and a distinctive replication pattern in human males underlies the subtelomeric increase in recombination. We detected a robust correlation between replication and both contemporary and historical recombination and found that replication origin density coupled with chromosome size determines the recombination potential of individual chromosomes. Our findings and methods have implications for understanding the mechanisms underlying DNA replication, genetic recombination, and the landscape of mammalian germline variation.
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Blin M, Lacroix L, Petryk N, Jaszczyszyn Y, Chen CL, Hyrien O, Le Tallec B. DNA molecular combing-based replication fork directionality profiling. Nucleic Acids Res 2021; 49:e69. [PMID: 33836085 PMCID: PMC8266662 DOI: 10.1093/nar/gkab219] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/15/2021] [Accepted: 03/19/2021] [Indexed: 01/05/2023] Open
Abstract
The replication strategy of metazoan genomes is still unclear, mainly because definitive maps of replication origins are missing. High-throughput methods are based on population average and thus may exclusively identify efficient initiation sites, whereas inefficient origins go undetected. Single-molecule analyses of specific loci can detect both common and rare initiation events along the targeted regions. However, these usually concentrate on positioning individual events, which only gives an overview of the replication dynamics. Here, we computed the replication fork directionality (RFD) profiles of two large genes in different transcriptional states in chicken DT40 cells, namely untranscribed and transcribed DMD and CCSER1 expressed at WT levels or overexpressed, by aggregating hundreds of oriented replication tracks detected on individual DNA fibres stretched by molecular combing. These profiles reconstituted RFD domains composed of zones of initiation flanking a zone of termination originally observed in mammalian genomes and were highly consistent with independent population-averaging profiles generated by Okazaki fragment sequencing. Importantly, we demonstrate that inefficient origins do not appear as detectable RFD shifts, explaining why dispersed initiation has remained invisible to population-based assays. Our method can both generate quantitative profiles and identify discrete events, thereby constituting a comprehensive approach to study metazoan genome replication.
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Affiliation(s)
- Marion Blin
- Département de Gastro-entérologie, pôle MAD, Assistance Publique des Hôpitaux de Marseille, Centre Hospitalier Universitaire de Marseille, Marseille, France
| | - Laurent Lacroix
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 46 rue d’Ulm, F-75005 Paris, France
| | - Nataliya Petryk
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 46 rue d’Ulm, F-75005 Paris, France
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), F-91198 Gif-sur-Yvette, France
| | - Yan Jaszczyszyn
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), F-91198 Gif-sur-Yvette, France
| | - Chun-Long Chen
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3244, F-75005 Paris, France
| | - Olivier Hyrien
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 46 rue d’Ulm, F-75005 Paris, France
| | - Benoît Le Tallec
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 46 rue d’Ulm, F-75005 Paris, France
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Ishihara S, Sasagawa Y, Kameda T, Yamashita H, Umeda M, Kotomura N, Abe M, Shimono Y, Nikaido I. Local states of chromatin compaction at transcription start sites control transcription levels. Nucleic Acids Res 2021; 49:8007-8023. [PMID: 34233004 PMCID: PMC8373074 DOI: 10.1093/nar/gkab587] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 06/12/2021] [Accepted: 06/30/2021] [Indexed: 11/16/2022] Open
Abstract
The ‘open’ and ‘compact’ regions of chromatin are considered to be regions of active and silent transcription, respectively. However, individual genes produce transcripts at different levels, suggesting that transcription output does not depend on the simple open-compact conversion of chromatin, but on structural variations in chromatin itself, which so far have remained elusive. In this study, weakly crosslinked chromatin was subjected to sedimentation velocity centrifugation, which fractionated the chromatin according to its degree of compaction. Open chromatin remained in upper fractions, while compact chromatin sedimented to lower fractions depending on the level of nucleosome assembly. Although nucleosomes were evenly detected in all fractions, histone H1 was more highly enriched in the lower fractions. H1 was found to self-associate and crosslinked to histone H3, suggesting that H1 bound to H3 interacts with another H1 in an adjacent nucleosome to form compact chromatin. Genome-wide analyses revealed that nearly the entire genome consists of compact chromatin without differences in compaction between repeat and non-repeat sequences; however, active transcription start sites (TSSs) were rarely found in compact chromatin. Considering the inverse correlation between chromatin compaction and RNA polymerase binding at TSSs, it appears that local states of chromatin compaction determine transcription levels.
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Affiliation(s)
- Satoru Ishihara
- Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Yohei Sasagawa
- Laboratory for Bioinformatics Research, RIKEN Center for Biosystems Dynamics Research, Wako, Saitama 351-0198, Japan.,Functional Genome Informatics, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Takeru Kameda
- Laboratory for Bioinformatics Research, RIKEN Center for Biosystems Dynamics Research, Wako, Saitama 351-0198, Japan.,Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Hayato Yamashita
- Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Mana Umeda
- Laboratory for Bioinformatics Research, RIKEN Center for Biosystems Dynamics Research, Wako, Saitama 351-0198, Japan
| | - Naoe Kotomura
- Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Masayuki Abe
- Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Yohei Shimono
- Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Itoshi Nikaido
- Laboratory for Bioinformatics Research, RIKEN Center for Biosystems Dynamics Research, Wako, Saitama 351-0198, Japan.,Functional Genome Informatics, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan.,Master's/Doctoral Program in Life Science Innovation (Bioinformatics), Degree Programs in Systems and Information Engineering, Graduate School of Science and Technology, University of Tsukuba, Wako, Saitama 351-0198, Japan
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48
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Técher H, Pasero P. The Replication Stress Response on a Narrow Path Between Genomic Instability and Inflammation. Front Cell Dev Biol 2021; 9:702584. [PMID: 34249949 PMCID: PMC8270677 DOI: 10.3389/fcell.2021.702584] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/03/2021] [Indexed: 02/06/2023] Open
Abstract
The genome of eukaryotic cells is particularly at risk during the S phase of the cell cycle, when megabases of chromosomal DNA are unwound to generate two identical copies of the genome. This daunting task is executed by thousands of micro-machines called replisomes, acting at fragile structures called replication forks. The correct execution of this replication program depends on the coordinated action of hundreds of different enzymes, from the licensing of replication origins to the termination of DNA replication. This review focuses on the mechanisms that ensure the completion of DNA replication under challenging conditions of endogenous or exogenous origin. It also covers new findings connecting the processing of stalled forks to the release of small DNA fragments into the cytoplasm, activating the cGAS-STING pathway. DNA damage and fork repair comes therefore at a price, which is the activation of an inflammatory response that has both positive and negative impacts on the fate of stressed cells. These new findings have broad implications for the etiology of interferonopathies and for cancer treatment.
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Affiliation(s)
- Hervé Técher
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue Contre le Cancer, Montpellier, France
| | - Philippe Pasero
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue Contre le Cancer, Montpellier, France
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49
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The structure of ORC-Cdc6 on an origin DNA reveals the mechanism of ORC activation by the replication initiator Cdc6. Nat Commun 2021; 12:3883. [PMID: 34162887 PMCID: PMC8222357 DOI: 10.1038/s41467-021-24199-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 06/07/2021] [Indexed: 01/31/2023] Open
Abstract
The Origin Recognition Complex (ORC) binds to sites in chromosomes to specify the location of origins of DNA replication. The S. cerevisiae ORC binds to specific DNA sequences throughout the cell cycle but becomes active only when it binds to the replication initiator Cdc6. It has been unclear at the molecular level how Cdc6 activates ORC, converting it to an active recruiter of the Mcm2-7 hexamer, the core of the replicative helicase. Here we report the cryo-EM structure at 3.3 Å resolution of the yeast ORC–Cdc6 bound to an 85-bp ARS1 origin DNA. The structure reveals that Cdc6 contributes to origin DNA recognition via its winged helix domain (WHD) and its initiator-specific motif. Cdc6 binding rearranges a short α-helix in the Orc1 AAA+ domain and the Orc2 WHD, leading to the activation of the Cdc6 ATPase and the formation of the three sites for the recruitment of Mcm2-7, none of which are present in ORC alone. The results illuminate the molecular mechanism of a critical biochemical step in the licensing of eukaryotic replication origins. Eukaryotic DNA replication is mediated by many proteins which are tightly regulated for an efficient firing of replication at each cell cycle. Here the authors report a cryo-EM structure of the yeast ORC–Cdc6 bound to an 85-bp ARS1 origin DNA revealing additional insights into how Cdc6 contributes to origin DNA recognition.
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50
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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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