1
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Zhu X, Kanemaki MT. Replication initiation sites and zones in the mammalian genome: Where are they located and how are they defined? DNA Repair (Amst) 2024; 141:103713. [PMID: 38959715 DOI: 10.1016/j.dnarep.2024.103713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 06/14/2024] [Accepted: 06/15/2024] [Indexed: 07/05/2024]
Abstract
Eukaryotic DNA replication is a tightly controlled process that occurs in two main steps, i.e., licensing and firing, which take place in the G1 and S phases of the cell cycle, respectively. In Saccharomyces cerevisiae, the budding yeast, replication origins contain consensus sequences that are recognized and bound by the licensing factor Orc1-6, which then recruits the replicative Mcm2-7 helicase. By contrast, mammalian initiation sites lack such consensus sequences, and the mammalian ORC does not exhibit sequence specificity. Studies performed over the past decades have identified replication initiation sites in the mammalian genome using sequencing-based assays, raising the question of whether replication initiation occurs at confined sites or in broad zones across the genome. Although recent reports have shown that the licensed MCMs in mammalian cells are broadly distributed, suggesting that ORC-dependent licensing may not determine the initiation sites/zones, they are predominantly located upstream of actively transcribed genes. This review compares the mechanism of replication initiation in yeast and mammalian cells, summarizes the sequencing-based technologies used for the identification of initiation sites/zones, and proposes a possible mechanism of initiation-site/zone selection in mammalian cells. Future directions and challenges in this field are also discussed.
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Affiliation(s)
- Xiaoxuan Zhu
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Yata 1111, Shizuoka, Mishima 411-8540, Japan.
| | - Masato T Kanemaki
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Yata 1111, Shizuoka, Mishima 411-8540, Japan; Graduate Institute for Advanced Studies, SOKENDAI, Yata 1111, Shizuoka, Mishima 411-8540, Japan; Department of Biological Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan.
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2
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Goehring L, Keegan S, Lahiri S, Xia W, Kong M, Jimenez-Sainz J, Gupta D, Drapkin R, Jensen RB, Smith DJ, Rothenberg E, Fenyö D, Huang TT. Dormant origin firing promotes head-on transcription-replication conflicts at transcription termination sites in response to BRCA2 deficiency. Nat Commun 2024; 15:4716. [PMID: 38830843 PMCID: PMC11148086 DOI: 10.1038/s41467-024-48286-1] [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: 08/19/2023] [Accepted: 04/24/2024] [Indexed: 06/05/2024] Open
Abstract
BRCA2 is a tumor suppressor protein responsible for safeguarding the cellular genome from replication stress and genotoxicity, but the specific mechanism(s) by which this is achieved to prevent early oncogenesis remains unclear. Here, we provide evidence that BRCA2 acts as a critical suppressor of head-on transcription-replication conflicts (HO-TRCs). Using Okazaki-fragment sequencing (Ok-seq) and computational analysis, we identified origins (dormant origins) that are activated near the transcription termination sites (TTS) of highly expressed, long genes in response to replication stress. Dormant origins are a source for HO-TRCs, and drug treatments that inhibit dormant origin firing led to a reduction in HO-TRCs, R-loop formation, and DNA damage. Using super-resolution microscopy, we showed that HO-TRC events track with elongating RNA polymerase II, but not with transcription initiation. Importantly, RNase H2 is recruited to sites of HO-TRCs in a BRCA2-dependent manner to help alleviate toxic R-loops associated with HO-TRCs. Collectively, our results provide a mechanistic basis for how BRCA2 shields against genomic instability by preventing HO-TRCs through both direct and indirect means occurring at predetermined genomic sites based on the pre-cancer transcriptome.
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Affiliation(s)
- Liana Goehring
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Sarah Keegan
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
- Institute for Systems Genetics, New York University School of Medicine, New York University School of Medicine, New York, NY, USA
| | - Sudipta Lahiri
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
- Department of Therapeutic Radiology, Yale University, New Haven, CT, USA
| | - Wenxin Xia
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Michael Kong
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | | | - Dipika Gupta
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Ronny Drapkin
- Penn Ovarian Cancer Research Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Basser Center for BRCA, Abramson Cancer Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Ryan B Jensen
- Department of Therapeutic Radiology, Yale University, New Haven, CT, USA
| | - Duncan J Smith
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Eli Rothenberg
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - David Fenyö
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
- Institute for Systems Genetics, New York University School of Medicine, New York University School of Medicine, New York, NY, USA
| | - Tony T Huang
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, USA.
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3
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Duardo RC, Marinello J, Russo M, Morelli S, Pepe S, Guerra F, Gómez-González B, Aguilera A, Capranico G. Human DNA topoisomerase I poisoning causes R loop-mediated genome instability attenuated by transcription factor IIS. SCIENCE ADVANCES 2024; 10:eadm8196. [PMID: 38787953 PMCID: PMC11122683 DOI: 10.1126/sciadv.adm8196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 04/18/2024] [Indexed: 05/26/2024]
Abstract
DNA topoisomerase I can contribute to cancer genome instability. During catalytic activity, topoisomerase I forms a transient intermediate, topoisomerase I-DNA cleavage complex (Top1cc) to allow strand rotation and duplex relaxation, which can lead to elevated levels of DNA-RNA hybrids and micronuclei. To comprehend the underlying mechanisms, we have integrated genomic data of Top1cc-triggered hybrids and DNA double-strand breaks (DSBs) shortly after Top1cc induction, revealing that Top1ccs increase hybrid levels with different mechanisms. DSBs are at highly transcribed genes in early replicating initiation zones and overlap with hybrids downstream of accumulated RNA polymerase II (RNAPII) at gene 5'-ends. A transcription factor IIS mutant impairing transcription elongation further increased RNAPII accumulation likely due to backtracking. Moreover, Top1ccs can trigger micronuclei when occurring during late G1 or early/mid S, but not during late S. As micronuclei and transcription-replication conflicts are attenuated by transcription factor IIS, our results support a role of RNAPII arrest in Top1cc-induced transcription-replication conflicts leading to DSBs and micronuclei.
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Affiliation(s)
- Renée C. Duardo
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum–University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Jessica Marinello
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum–University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Marco Russo
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum–University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Sara Morelli
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum–University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Simona Pepe
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum–University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Federico Guerra
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum–University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Belén Gómez-González
- Centro Andaluz de Biología Molecular y Medicina Regenerativa—CABIMER, Universidad de Sevilla–CSIC, Calle Américo Vespucio 24, 41092 Seville, Spain
- Departamento de Genetica, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa—CABIMER, Universidad de Sevilla–CSIC, Calle Américo Vespucio 24, 41092 Seville, Spain
- Departamento de Genetica, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - Giovanni Capranico
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum–University of Bologna, via Selmi 3, 40126, Bologna, Italy
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4
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Kobayashi W, Sappler AH, Bollschweiler D, Kümmecke M, Basquin J, Arslantas EN, Ruangroengkulrith S, Hornberger R, Duderstadt K, Tachibana K. Nucleosome-bound NR5A2 structure reveals pioneer factor mechanism by DNA minor groove anchor competition. Nat Struct Mol Biol 2024; 31:757-766. [PMID: 38409506 PMCID: PMC11102866 DOI: 10.1038/s41594-024-01239-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 01/31/2024] [Indexed: 02/28/2024]
Abstract
Gene expression during natural and induced reprogramming is controlled by pioneer transcription factors that initiate transcription from closed chromatin. Nr5a2 is a key pioneer factor that regulates zygotic genome activation in totipotent embryos, pluripotency in embryonic stem cells and metabolism in adult tissues, but the mechanism of its pioneer activity remains poorly understood. Here, we present a cryo-electron microscopy structure of human NR5A2 bound to a nucleosome. The structure shows that the conserved carboxy-terminal extension (CTE) loop of the NR5A2 DNA-binding domain competes with a DNA minor groove anchor of the nucleosome and releases entry-exit site DNA. Mutational analysis showed that NR5A2 D159 of the CTE is dispensable for DNA binding but required for stable nucleosome association and persistent DNA 'unwrapping'. These findings suggest that NR5A2 belongs to an emerging class of pioneer factors that can use DNA minor groove anchor competition to destabilize nucleosomes and facilitate gene expression during reprogramming.
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Affiliation(s)
- Wataru Kobayashi
- Department of Totipotency, Max Planck Institute of Biochemistry (MPIB), Munich, Germany
| | - Anna H Sappler
- Structure and Dynamics of Molecular Machines, MPIB, Munich, Germany
| | | | - Maximilian Kümmecke
- Department of Totipotency, Max Planck Institute of Biochemistry (MPIB), Munich, Germany
| | - Jérôme Basquin
- Department of Structural Cell Biology, Crystallization Facility, MPIB, Munich, Germany
| | - Eda Nur Arslantas
- Department of Totipotency, Max Planck Institute of Biochemistry (MPIB), Munich, Germany
| | | | - Renate Hornberger
- Department of Totipotency, Max Planck Institute of Biochemistry (MPIB), Munich, Germany
| | - Karl Duderstadt
- Structure and Dynamics of Molecular Machines, MPIB, Munich, Germany
- Department of Bioscience, Technical University of Munich, Garching, Germany
| | - Kikuë Tachibana
- Department of Totipotency, Max Planck Institute of Biochemistry (MPIB), Munich, Germany.
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5
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Rankin BD, Rankin S. The MCM2-7 Complex: Roles beyond DNA Unwinding. BIOLOGY 2024; 13:258. [PMID: 38666870 PMCID: PMC11048021 DOI: 10.3390/biology13040258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 04/07/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024]
Abstract
The MCM2-7 complex is a hexameric protein complex that serves as a DNA helicase. It unwinds the DNA double helix during DNA replication, thereby providing the single-stranded replication template. In recent years, it has become clear that the MCM2-7 complex has additional functions that extend well beyond its role in DNA replication. Through physical and functional interactions with different pathways, it impacts other nuclear events and activities, including folding of the genome, histone inheritance, chromosome segregation, DNA damage sensing and repair, and gene transcription. Collectively, the diverse roles of the MCM2-7 complex suggest it plays a critical role in maintaining genome integrity by integrating the regulation of DNA replication with other pathways in the nucleus.
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Affiliation(s)
- Brooke D. Rankin
- Cell Cycle and Cancer Biology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA;
- Cell Biology Department, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Susannah Rankin
- Cell Cycle and Cancer Biology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA;
- Cell Biology Department, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
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6
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Yadav AK, Polasek-Sedlackova H. Quantity and quality of minichromosome maintenance protein complexes couple replication licensing to genome integrity. Commun Biol 2024; 7:167. [PMID: 38336851 PMCID: PMC10858283 DOI: 10.1038/s42003-024-05855-w] [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: 10/05/2023] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Accurate and complete replication of genetic information is a fundamental process of every cell division. The replication licensing is the first essential step that lays the foundation for error-free genome duplication. During licensing, minichromosome maintenance protein complexes, the molecular motors of DNA replication, are loaded to genomic sites called replication origins. The correct quantity and functioning of licensed origins are necessary to prevent genome instability associated with severe diseases, including cancer. Here, we delve into recent discoveries that shed light on the novel functions of licensed origins, the pathways necessary for their proper maintenance, and their implications for cancer therapies.
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Affiliation(s)
- Anoop Kumar Yadav
- Department of Cell Biology and Epigenetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Hana Polasek-Sedlackova
- Department of Cell Biology and Epigenetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic.
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7
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Fenstermaker TK, Petruk S, Mazo A. An emerging paradigm in epigenetic marking: coordination of transcription and replication. Transcription 2024; 15:22-37. [PMID: 38378467 DOI: 10.1080/21541264.2024.2316965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 02/06/2024] [Indexed: 02/22/2024] Open
Abstract
DNA replication and RNA transcription both utilize DNA as a template and therefore need to coordinate their activities. The predominant theory in the field is that in order for the replication fork to proceed, transcription machinery has to be evicted from DNA until replication is complete. If that does not occur, these machineries collide, and these collisions elicit various repair mechanisms which require displacement of one of the enzymes, often RNA polymerase, in order for replication to proceed. This model is also at the heart of the epigenetic bookmarking theory, which implies that displacement of RNA polymerase during replication requires gradual re-building of chromatin structure, which guides recruitment of transcriptional proteins and resumption of transcription. We discuss these theories but also bring to light newer data that suggest that these two processes may not be as detrimental to one another as previously thought. This includes findings suggesting that these processes can occur without fork collapse and that RNA polymerase may only be transiently displaced during DNA replication. We discuss potential mechanisms by which RNA polymerase may be retained at the replication fork and quickly rebind to DNA post-replication. These discoveries are important, not only as new evidence as to how these two processes are able to occur harmoniously but also because they have implications on how transcriptional programs are maintained through DNA replication. To this end, we also discuss the coordination of replication and transcription in light of revising the current epigenetic bookmarking theory of how the active gene status can be transmitted through S phase.
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Affiliation(s)
- Tyler K Fenstermaker
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Svetlana Petruk
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Alexander Mazo
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
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8
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Ramírez Montero D, Liu Z, Dekker NH. De novo fabrication of custom-sequence plasmids for the synthesis of long DNA constructs with extrahelical features. Biophys J 2024; 123:31-41. [PMID: 37968907 PMCID: PMC10808024 DOI: 10.1016/j.bpj.2023.11.008] [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: 08/28/2023] [Revised: 10/06/2023] [Accepted: 11/13/2023] [Indexed: 11/17/2023] Open
Abstract
DNA constructs for single-molecule experiments often require specific sequences and/or extrahelical/noncanonical structures to study DNA-processing mechanisms. The precise introduction of such structures requires extensive control of the sequence of the initial DNA substrate. A commonly used substrate in the synthesis of DNA constructs is plasmid DNA. Nevertheless, the controlled introduction of specific sequences and extrahelical/noncanonical structures into plasmids often requires several rounds of cloning on pre-existing plasmids whose sequence one cannot fully control. Here, we describe a simple and efficient way to synthesize 10.1-kb plasmids de novo using synthetic gBlocks that provides full control of the sequence. Using these plasmids, we developed a 1.5-day protocol to assemble 10.1-kb linear DNA constructs with end and internal modifications. As a proof of principle, we synthesize two different DNA constructs with biotinylated ends and one or two internal 3' single-stranded DNA flaps, characterize them using single-molecule force and fluorescence spectroscopy, and functionally validate them by showing that the eukaryotic replicative helicase Cdc45/Mcm2-7/GINS (CMG) binds the 3' single-stranded DNA flap and translocates in the expected direction. We anticipate that our approach can be used to synthesize custom-sequence DNA constructs for a variety of force and fluorescence single-molecule spectroscopy experiments to interrogate DNA replication, DNA repair, and transcription.
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Affiliation(s)
- Daniel Ramírez Montero
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Zhaowei Liu
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Nynke H Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands.
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9
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Lewis JS, van Oijen AM, Spenkelink LM. Embracing Heterogeneity: Challenging the Paradigm of Replisomes as Deterministic Machines. Chem Rev 2023; 123:13419-13440. [PMID: 37971892 PMCID: PMC10790245 DOI: 10.1021/acs.chemrev.3c00436] [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: 06/25/2023] [Revised: 10/15/2023] [Accepted: 10/20/2023] [Indexed: 11/19/2023]
Abstract
The paradigm of cellular systems as deterministic machines has long guided our understanding of biology. Advancements in technology and methodology, however, have revealed a world of stochasticity, challenging the notion of determinism. Here, we explore the stochastic behavior of multi-protein complexes, using the DNA replication system (replisome) as a prime example. The faithful and timely copying of DNA depends on the simultaneous action of a large set of enzymes and scaffolding factors. This fundamental cellular process is underpinned by dynamic protein-nucleic acid assemblies that must transition between distinct conformations and compositional states. Traditionally viewed as a well-orchestrated molecular machine, recent experimental evidence has unveiled significant variability and heterogeneity in the replication process. In this review, we discuss recent advances in single-molecule approaches and single-particle cryo-EM, which have provided insights into the dynamic processes of DNA replication. We comment on the new challenges faced by structural biologists and biophysicists as they attempt to describe the dynamic cascade of events leading to replisome assembly, activation, and progression. The fundamental principles uncovered and yet to be discovered through the study of DNA replication will inform on similar operating principles for other multi-protein complexes.
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Affiliation(s)
- Jacob S. Lewis
- Macromolecular
Machines Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Antoine M. van Oijen
- Molecular
Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Lisanne M. Spenkelink
- Molecular
Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
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10
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Malzl D, Peycheva M, Rahjouei A, Gnan S, Klein KN, Nazarova M, Schoeberl UE, Gilbert DM, Buonomo SCB, Di Virgilio M, Neumann T, Pavri R. RIF1 regulates early replication timing in murine B cells. Nat Commun 2023; 14:8049. [PMID: 38081811 PMCID: PMC10713614 DOI: 10.1038/s41467-023-43778-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
The mammalian DNA replication timing (RT) program is crucial for the proper functioning and integrity of the genome. The best-known mechanism for controlling RT is the suppression of late origins of replication in heterochromatin by RIF1. Here, we report that in antigen-activated, hypermutating murine B lymphocytes, RIF1 binds predominantly to early-replicating active chromatin and promotes early replication, but plays a minor role in regulating replication origin activity, gene expression and genome organization in B cells. Furthermore, we find that RIF1 functions in a complementary and non-epistatic manner with minichromosome maintenance (MCM) proteins to establish early RT signatures genome-wide and, specifically, to ensure the early replication of highly transcribed genes. These findings reveal additional layers of regulation within the B cell RT program, driven by the coordinated activity of RIF1 and MCM proteins.
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Affiliation(s)
- Daniel Malzl
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030, Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Lazarettgasse 14, Vienna, Austria
| | - Mihaela Peycheva
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030, Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Lazarettgasse 14, Vienna, Austria
| | - Ali Rahjouei
- Max-Delbruck Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Stefano Gnan
- School of Biological Sciences, Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3FF, UK
| | - Kyle N Klein
- San Diego Biomedical Research Institute, San Diego, CA, 92121, USA
| | - Mariia Nazarova
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030, Vienna, Austria
| | - Ursula E Schoeberl
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030, Vienna, Austria
| | - David M Gilbert
- San Diego Biomedical Research Institute, San Diego, CA, 92121, USA
| | - Sara C B Buonomo
- School of Biological Sciences, Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3FF, UK
| | - Michela Di Virgilio
- Max-Delbruck Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Tobias Neumann
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030, Vienna, Austria.
- Quantro Therapeutics, Vienna Biocenter, 1030, Vienna, Austria.
| | - Rushad Pavri
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030, Vienna, Austria.
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11
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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: 5] [Impact Index Per Article: 5.0] [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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12
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Abstract
Transcription and replication both require large macromolecular complexes to act on a DNA template, yet these machineries cannot simultaneously act on the same DNA sequence. Conflicts between the replication and transcription machineries (transcription-replication conflicts, or TRCs) are widespread in both prokaryotes and eukaryotes and have the capacity to both cause DNA damage and compromise complete, faithful replication of the genome. This review will highlight recent studies investigating the genomic locations of TRCs and the mechanisms by which they may be prevented, mitigated, or resolved. We address work from both model organisms and mammalian systems but predominantly focus on multicellular eukaryotes owing to the additional complexities inherent in the coordination of replication and transcription in the context of cell type-specific gene expression and higher-order chromatin organization.
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Affiliation(s)
- Liana Goehring
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, USA;
| | - Tony T Huang
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, USA;
| | - Duncan J Smith
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA;
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13
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Bellani MA, Shaik A, Majumdar I, Ling C, Seidman MM. The Response of the Replication Apparatus to Leading Template Strand Blocks. Cells 2023; 12:2607. [PMID: 37998342 PMCID: PMC10670059 DOI: 10.3390/cells12222607] [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: 10/23/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 11/25/2023] Open
Abstract
Duplication of the genome requires the replication apparatus to overcome a variety of impediments, including covalent DNA adducts, the most challenging of which is on the leading template strand. Replisomes consist of two functional units, a helicase to unwind DNA and polymerases to synthesize it. The helicase is a multi-protein complex that encircles the leading template strand and makes the first contact with a leading strand adduct. The size of the channel in the helicase would appear to preclude transit by large adducts such as DNA: protein complexes (DPC). Here we discuss some of the extensively studied pathways that support replication restart after replisome encounters with leading template strand adducts. We also call attention to recent work that highlights the tolerance of the helicase for adducts ostensibly too large to pass through the central channel.
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Affiliation(s)
| | | | | | | | - Michael M. Seidman
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA; (M.A.B.)
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14
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Zhang A, Friedman LJ, Gelles J, Bell SP. Changing protein-DNA interactions promote ORC binding site exchange during replication origin licensing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.16.545300. [PMID: 37398123 PMCID: PMC10312730 DOI: 10.1101/2023.06.16.545300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
During origin licensing, the eukaryotic replicative helicase Mcm2-7 forms head-to-head double hexamers to prime origins for bidirectional replication. Recent single-molecule and structural studies revealed that one molecule of the helicase loader ORC can sequentially load two Mcm2-7 hexamers to ensure proper head-to-head helicase alignment. To perform this task, ORC must release from its initial high-affinity DNA binding site and "flip" to bind a weaker, inverted DNA site. However, the mechanism of this binding-site switch remains unclear. In this study, we used single-molecule Förster resonance energy transfer (sm-FRET) to study the changing interactions between DNA and ORC or Mcm2-7. We found that the loss of DNA bending that occurs during DNA deposition into the Mcm2-7 central channel increases the rate of ORC dissociation from DNA. Further studies revealed temporally-controlled DNA sliding of helicase-loading intermediates, and that the first sliding complex includes ORC, Mcm2-7, and Cdt1. We demonstrate that sequential events of DNA unbending, Cdc6 release, and sliding lead to a stepwise decrease in ORC stability on DNA, facilitating ORC dissociation from its strong binding site during site switching. In addition, the controlled sliding we observed provides insight into how ORC accesses secondary DNA binding sites at different locations relative to the initial binding site. Our study highlights the importance of dynamic protein-DNA interactions in the loading of two oppositely-oriented Mcm2-7 helicases to ensure bidirectional DNA replication. Significance Statement Bidirectional DNA replication, in which two replication forks travel in opposite directions from each origin of replication, is required for complete genome duplication. To prepare for this event, two copies of the Mcm2-7 replicative helicase are loaded at each origin in opposite orientations. Using single-molecule assays, we studied the sequence of changing protein-DNA interactions involved in this process. These stepwise changes gradually reduce the DNA-binding strength of ORC, the primary DNA binding protein involved in this event. This reduced affinity promotes ORC dissociation and rebinding in the opposite orientation on the DNA, facilitating the sequential assembly of two Mcm2-7 molecules in opposite orientations. Our findings identify a coordinated series of events that drive proper DNA replication initiation.
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Affiliation(s)
- Annie Zhang
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Larry J. Friedman
- Department of Biochemistry, Brandeis University, Waltham, MA 02454, USA
| | - Jeff Gelles
- Department of Biochemistry, Brandeis University, Waltham, MA 02454, USA
| | - Stephen P Bell
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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15
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Hu Y, Stillman B. Origins of DNA replication in eukaryotes. Mol Cell 2023; 83:352-372. [PMID: 36640769 PMCID: PMC9898300 DOI: 10.1016/j.molcel.2022.12.024] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 01/15/2023]
Abstract
Errors occurring during DNA replication can result in inaccurate replication, incomplete replication, or re-replication, resulting in genome instability that can lead to diseases such as cancer or disorders such as autism. A great deal of progress has been made toward understanding the entire process of DNA replication in eukaryotes, including the mechanism of initiation and its control. This review focuses on the current understanding of how the origin recognition complex (ORC) contributes to determining the location of replication initiation in the multiple chromosomes within eukaryotic cells, as well as methods for mapping the location and temporal patterning of DNA replication. Origin specification and configuration vary substantially between eukaryotic species and in some cases co-evolved with gene-silencing mechanisms. We discuss the possibility that centromeres and origins of DNA replication were originally derived from a common element and later separated during evolution.
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Affiliation(s)
- Yixin Hu
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA; Program in Molecular and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Bruce Stillman
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.
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16
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Huisjes NM, Retzer TM, Scherr MJ, Agarwal R, Rajappa L, Safaric B, Minnen A, Duderstadt KE. Mars, a molecule archive suite for reproducible analysis and reporting of single-molecule properties from bioimages. eLife 2022; 11:e75899. [PMID: 36098381 PMCID: PMC9470159 DOI: 10.7554/elife.75899] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 08/19/2022] [Indexed: 11/16/2022] Open
Abstract
The rapid development of new imaging approaches is generating larger and more complex datasets, revealing the time evolution of individual cells and biomolecules. Single-molecule techniques, in particular, provide access to rare intermediates in complex, multistage molecular pathways. However, few standards exist for processing these information-rich datasets, posing challenges for wider dissemination. Here, we present Mars, an open-source platform for storing and processing image-derived properties of biomolecules. Mars provides Fiji/ImageJ2 commands written in Java for common single-molecule analysis tasks using a Molecule Archive architecture that is easily adapted to complex, multistep analysis workflows. Three diverse workflows involving molecule tracking, multichannel fluorescence imaging, and force spectroscopy, demonstrate the range of analysis applications. A comprehensive graphical user interface written in JavaFX enhances biomolecule feature exploration by providing charting, tagging, region highlighting, scriptable dashboards, and interactive image views. The interoperability of ImageJ2 ensures Molecule Archives can easily be opened in multiple environments, including those written in Python using PyImageJ, for interactive scripting and visualization. Mars provides a flexible solution for reproducible analysis of image-derived properties, facilitating the discovery and quantitative classification of new biological phenomena with an open data format accessible to everyone.
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Affiliation(s)
- Nadia M Huisjes
- Structure and Dynamics of Molecular Machines, Max Planck Institute of BiochemistryMartinsriedGermany
| | - Thomas M Retzer
- Structure and Dynamics of Molecular Machines, Max Planck Institute of BiochemistryMartinsriedGermany
- Physik Department, Technische Universität MünchenGarchingGermany
| | - Matthias J Scherr
- Structure and Dynamics of Molecular Machines, Max Planck Institute of BiochemistryMartinsriedGermany
| | - Rohit Agarwal
- Structure and Dynamics of Molecular Machines, Max Planck Institute of BiochemistryMartinsriedGermany
- Physik Department, Technische Universität MünchenGarchingGermany
| | - Lional Rajappa
- Structure and Dynamics of Molecular Machines, Max Planck Institute of BiochemistryMartinsriedGermany
| | - Barbara Safaric
- Structure and Dynamics of Molecular Machines, Max Planck Institute of BiochemistryMartinsriedGermany
| | - Anita Minnen
- Structure and Dynamics of Molecular Machines, Max Planck Institute of BiochemistryMartinsriedGermany
| | - Karl E Duderstadt
- Structure and Dynamics of Molecular Machines, Max Planck Institute of BiochemistryMartinsriedGermany
- Physik Department, Technische Universität MünchenGarchingGermany
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17
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Nucleosome-directed replication origin licensing independent of a consensus DNA sequence. Nat Commun 2022; 13:4947. [PMID: 35999198 PMCID: PMC9399094 DOI: 10.1038/s41467-022-32657-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 08/09/2022] [Indexed: 02/08/2023] Open
Abstract
The numerous enzymes and cofactors involved in eukaryotic DNA replication are conserved from yeast to human, and the budding yeast Saccharomyces cerevisiae (S.c.) has been a useful model organism for these studies. However, there is a gap in our knowledge of why replication origins in higher eukaryotes do not use a consensus DNA sequence as found in S.c. Using in vitro reconstitution and single-molecule visualization, we show here that S.c. origin recognition complex (ORC) stably binds nucleosomes and that ORC-nucleosome complexes have the intrinsic ability to load the replicative helicase MCM double hexamers onto adjacent nucleosome-free DNA regardless of sequence. Furthermore, we find that Xenopus laevis nucleosomes can substitute for yeast ones in engaging with ORC. Combined with re-analyses of genome-wide ORC binding data, our results lead us to propose that the yeast origin recognition machinery contains the cryptic capacity to bind nucleosomes near a nucleosome-free region and license origins, and that this nucleosome-directed origin licensing paradigm generalizes to all eukaryotes. Most eukaryotes do not use a consensus DNA sequence as binding sites for the origin recognition complex (ORC) to initiate DNA replication, however budding yeast do. Here the authors show S. cerevisiae ORC can bind nucleosomes near nucleosome-free regions and recruit replicative helicases to form a pre-replication complex independent of the DNA sequence.
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18
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Dequeker BJH, Scherr MJ, Brandão HB, Gassler J, Powell S, Gaspar I, Flyamer IM, Lalic A, Tang W, Stocsits R, Davidson IF, Peters JM, Duderstadt KE, Mirny LA, Tachibana K. MCM complexes are barriers that restrict cohesin-mediated loop extrusion. Nature 2022; 606:197-203. [PMID: 35585235 PMCID: PMC9159944 DOI: 10.1038/s41586-022-04730-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 04/06/2022] [Indexed: 12/23/2022]
Abstract
Eukaryotic genomes are compacted into loops and topologically associating domains (TADs)1-3, which contribute to transcription, recombination and genomic stability4,5. Cohesin extrudes DNA into loops that are thought to lengthen until CTCF boundaries are encountered6-12. Little is known about whether loop extrusion is impeded by DNA-bound machines. Here we show that the minichromosome maintenance (MCM) complex is a barrier that restricts loop extrusion in G1 phase. Single-nucleus Hi-C (high-resolution chromosome conformation capture) of mouse zygotes reveals that MCM loading reduces CTCF-anchored loops and decreases TAD boundary insulation, which suggests that loop extrusion is impeded before reaching CTCF. This effect extends to HCT116 cells, in which MCMs affect the number of CTCF-anchored loops and gene expression. Simulations suggest that MCMs are abundant, randomly positioned and partially permeable barriers. Single-molecule imaging shows that MCMs are physical barriers that frequently constrain cohesin translocation in vitro. Notably, chimeric yeast MCMs that contain a cohesin-interaction motif from human MCM3 induce cohesin pausing, indicating that MCMs are 'active' barriers with binding sites. These findings raise the possibility that cohesin can arrive by loop extrusion at MCMs, which determine the genomic sites at which sister chromatid cohesion is established. On the basis of in vivo, in silico and in vitro data, we conclude that distinct loop extrusion barriers shape the three-dimensional genome.
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Affiliation(s)
- Bart J H Dequeker
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Matthias J Scherr
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry (MPIB), Martinsried, Germany
| | - Hugo B Brandão
- Harvard Program in Biophysics, Harvard University, Cambridge, MA, USA
- Illumina Inc., San Diego, CA, USA
| | - Johanna Gassler
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Department of Totipotency, Max Planck Institute of Biochemistry (MPIB), Martinsried, Germany
| | - Sean Powell
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Imre Gaspar
- Department of Totipotency, Max Planck Institute of Biochemistry (MPIB), Martinsried, Germany
| | - Ilya M Flyamer
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Edinburgh, UK
| | - Aleksandar Lalic
- Department of Totipotency, Max Planck Institute of Biochemistry (MPIB), Martinsried, Germany
| | - Wen Tang
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Roman Stocsits
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Iain F Davidson
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Karl E Duderstadt
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry (MPIB), Martinsried, Germany.
- Department of Physics, Technical University of Munich, Garching, Germany.
| | - Leonid A Mirny
- Department of Physics, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA.
| | - Kikuë Tachibana
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria.
- Department of Totipotency, Max Planck Institute of Biochemistry (MPIB), Martinsried, Germany.
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