1
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Ukraintsev AA, Kutuzov MM, Lavrik OI. Studying Structure and Functions of Nucleosomes with Atomic Force Microscopy. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:674-687. [PMID: 38831504 DOI: 10.1134/s0006297924040072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 02/19/2024] [Accepted: 02/22/2024] [Indexed: 06/05/2024]
Abstract
Chromatin is an epigenetic platform for implementation of DNA-dependent processes. Nucleosome, as a basic level of chromatin compaction, largely determines its properties and structure. In the study of nucleosomes structure and functions physicochemical tools are actively used, such as magnetic and optical "tweezers", "DNA curtains", nuclear magnetic resonance, X-ray crystallography, and cryogenic electron microscopy, as well as optical methods based on Förster resonance energy transfer. Despite the fact that these approaches make it possible to determine a wide range of structural and functional characteristics of chromatin and nucleosomes with high spatial and time resolution, atomic force microscopy (AFM) complements the capabilities of these methods. The results of structural studies of nucleosome focusing on the AFM method development are presented in this review. The possibilities of AFM are considered in the context of application of other physicochemical approaches.
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Affiliation(s)
- Alexander A Ukraintsev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Mikhail M Kutuzov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
- Novosibirsk State University, Novosibirsk, 630090, Russia
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2
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Karl LA, Galanti L, Bantele SC, Metzner F, Šafarić B, Rajappa L, Foster B, Pires VB, Bansal P, Chacin E, Basquin J, Duderstadt KE, Kurat CF, Bartke T, Hopfner KP, Pfander B. A SAM-key domain required for enzymatic activity of the Fun30 nucleosome remodeler. Life Sci Alliance 2023; 6:e202201790. [PMID: 37468166 PMCID: PMC10355287 DOI: 10.26508/lsa.202201790] [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: 10/31/2022] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 07/21/2023] Open
Abstract
Fun30 is the prototype of the Fun30-SMARCAD1-ETL subfamily of nucleosome remodelers involved in DNA repair and gene silencing. These proteins appear to act as single-subunit nucleosome remodelers, but their molecular mechanisms are, at this point, poorly understood. Using multiple sequence alignment and structure prediction, we identify an evolutionarily conserved domain that is modeled to contain a SAM-like fold with one long, protruding helix, which we term SAM-key. Deletion of the SAM-key within budding yeast Fun30 leads to a defect in DNA repair and gene silencing similar to that of the fun30Δ mutant. In vitro, Fun30 protein lacking the SAM-key is able to bind nucleosomes but is deficient in DNA-stimulated ATPase activity and nucleosome sliding and eviction. A structural model based on AlphaFold2 prediction and verified by crosslinking-MS indicates an interaction of the long SAM-key helix with protrusion I, a subdomain located between the two ATPase lobes that is critical for control of enzymatic activity. Mutation of the interaction interface phenocopies the domain deletion with a lack of DNA-stimulated ATPase activation and a nucleosome-remodeling defect, thereby confirming a role of the SAM-key helix in regulating ATPase activity. Our data thereby demonstrate a central role of the SAM-key domain in mediating the activation of Fun30 catalytic activity, thus highlighting the importance of allosteric activation for this class of enzymes.
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Affiliation(s)
- Leonhard A Karl
- DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Lorenzo Galanti
- DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
- Genome Maintenance Mechanisms in Health and Disease, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
- Genome Maintenance Mechanisms in Health and Disease, Institute of Genome Stability in Ageing and Disease, CECAD Research Center, University of Cologne, Cologne, Germany
| | - Susanne Cs Bantele
- DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Felix Metzner
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Barbara Šafarić
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Lional Rajappa
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Benjamin Foster
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, Neuherberg, Germany
| | - Vanessa Borges Pires
- Genome Maintenance Mechanisms in Health and Disease, Institute of Genome Stability in Ageing and Disease, CECAD Research Center, University of Cologne, Cologne, Germany
| | - Priyanka Bansal
- Biomedical Center Munich (BMC), Division of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Martinsried, Germany
| | - Erika Chacin
- Biomedical Center Munich (BMC), Division of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Martinsried, Germany
| | - Jerôme Basquin
- Crystallization Facility, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Karl E Duderstadt
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany
- Physik Department, Technische Universität München, Munich, Germany
| | - Christoph F Kurat
- Biomedical Center Munich (BMC), Division of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Martinsried, Germany
| | - Till Bartke
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, Neuherberg, Germany
| | - Karl-Peter Hopfner
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Boris Pfander
- DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
- Genome Maintenance Mechanisms in Health and Disease, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
- Genome Maintenance Mechanisms in Health and Disease, Institute of Genome Stability in Ageing and Disease, CECAD Research Center, University of Cologne, Cologne, Germany
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3
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Irvin EM, Wang H. Single-molecule imaging of genome maintenance proteins encountering specific DNA sequences and structures. DNA Repair (Amst) 2023; 128:103528. [PMID: 37392578 PMCID: PMC10989508 DOI: 10.1016/j.dnarep.2023.103528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 06/08/2023] [Accepted: 06/21/2023] [Indexed: 07/03/2023]
Abstract
DNA repair pathways are tightly regulated processes that recognize specific hallmarks of DNA damage and coordinate lesion repair through discrete mechanisms, all within the context of a three-dimensional chromatin landscape. Dysregulation or malfunction of any one of the protein constituents in these pathways can contribute to aging and a variety of diseases. While the collective action of these many proteins is what drives DNA repair on the organismal scale, it is the interactions between individual proteins and DNA that facilitate each step of these pathways. In much the same way that ensemble biochemical techniques have characterized the various steps of DNA repair pathways, single-molecule imaging (SMI) approaches zoom in further, characterizing the individual protein-DNA interactions that compose each pathway step. SMI techniques offer the high resolving power needed to characterize the molecular structure and functional dynamics of individual biological interactions on the nanoscale. In this review, we highlight how our lab has used SMI techniques - traditional atomic force microscopy (AFM) imaging in air, high-speed AFM (HS-AFM) in liquids, and the DNA tightrope assay - over the past decade to study protein-nucleic acid interactions involved in DNA repair, mitochondrial DNA replication, and telomere maintenance. We discuss how DNA substrates containing specific DNA sequences or structures that emulate DNA repair intermediates or telomeres were generated and validated. For each highlighted project, we discuss novel findings made possible by the spatial and temporal resolution offered by these SMI techniques and unique DNA substrates.
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Affiliation(s)
| | - Hong Wang
- Toxicology Program, North Carolina State University, Raleigh, NC, USA; Physics Department, North Carolina State University, Raleigh, NC, USA; Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.
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4
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Ryan BJ, Weaver TM, Spencer JJ, Freudenthal BD. Generation of Recombinant Nucleosomes Containing Site-Specific DNA Damage. Methods Mol Biol 2023; 2701:55-76. [PMID: 37574475 PMCID: PMC10794041 DOI: 10.1007/978-1-0716-3373-1_4] [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: 08/15/2023]
Abstract
Eukaryotic DNA exists in chromatin, where the genomic DNA is packaged into a fundamental repeating unit known as the nucleosome. In this chromatin environment, our genomic DNA is constantly under attack by exogenous and endogenous stressors that can lead to DNA damage. Importantly, this DNA damage must be repaired to prevent the accumulation of mutations and ensure normal cellular function. To date, most in-depth biochemical studies of DNA repair proteins have been performed in the context of free duplex DNA. However, chromatin can serve as a barrier that DNA repair enzymes must navigate in order find, access, and process DNA damage in the cell. To facilitate future studies of DNA repair in chromatin, we describe a protocol for generating nucleosome containing site-specific DNA damage that can be utilized for a variety of in vitro applications. This protocol describes several key steps including how to generate damaged DNA oligonucleotides, the expression and purification of recombinant histones, the refolding of histone complexes, and the reconstitution of nucleosomes containing site-specific DNA damage. These methods will enable researchers to generate nucleosomes containing site-specific DNA damage for extensive biochemical and structural studies of DNA repair in the nucleosome.
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Affiliation(s)
- Benjamin J Ryan
- Department of Biochemistry and Molecular Biology, Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Tyler M Weaver
- Department of Biochemistry and Molecular Biology, Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Jonah J Spencer
- Department of Biochemistry and Molecular Biology, Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Bret D Freudenthal
- Department of Biochemistry and Molecular Biology, Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS, USA.
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5
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Chen Z, Tyler JK. The Chromatin Landscape Channels DNA Double-Strand Breaks to Distinct Repair Pathways. Front Cell Dev Biol 2022; 10:909696. [PMID: 35757003 PMCID: PMC9213757 DOI: 10.3389/fcell.2022.909696] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/17/2022] [Indexed: 12/24/2022] Open
Abstract
DNA double-strand breaks (DSBs), the most deleterious DNA lesions, are primarily repaired by two pathways, namely homologous recombination (HR) and non-homologous end joining (NHEJ), the choice of which is largely dependent on cell cycle phase and the local chromatin landscape. Recent studies have revealed that post-translational modifications on histones play pivotal roles in regulating DSB repair pathways including repair pathway choice. In this review, we present our current understanding of how these DSB repair pathways are employed in various chromatin landscapes to safeguard genomic integrity. We place an emphasis on the impact of different histone post-translational modifications, characteristic of euchromatin or heterochromatin regions, on DSB repair pathway choice. We discuss the potential roles of damage-induced chromatin modifications in the maintenance of genome and epigenome integrity. Finally, we discuss how RNA transcripts from the vicinity of DSBs at actively transcribed regions also regulate DSB repair pathway choice.
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Affiliation(s)
- Zulong Chen
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York City, NY, United States
| | - Jessica K Tyler
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York City, NY, United States
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6
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Karl LA, Peritore M, Galanti L, Pfander B. DNA Double Strand Break Repair and Its Control by Nucleosome Remodeling. Front Genet 2022; 12:821543. [PMID: 35096025 PMCID: PMC8790285 DOI: 10.3389/fgene.2021.821543] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 12/23/2021] [Indexed: 12/12/2022] Open
Abstract
DNA double strand breaks (DSBs) are repaired in eukaryotes by one of several cellular mechanisms. The decision-making process controlling DSB repair takes place at the step of DNA end resection, the nucleolytic processing of DNA ends, which generates single-stranded DNA overhangs. Dependent on the length of the overhang, a corresponding DSB repair mechanism is engaged. Interestingly, nucleosomes-the fundamental unit of chromatin-influence the activity of resection nucleases and nucleosome remodelers have emerged as key regulators of DSB repair. Nucleosome remodelers share a common enzymatic mechanism, but for global genome organization specific remodelers have been shown to exert distinct activities. Specifically, different remodelers have been found to slide and evict, position or edit nucleosomes. It is an open question whether the same remodelers exert the same function also in the context of DSBs. Here, we will review recent advances in our understanding of nucleosome remodelers at DSBs: to what extent nucleosome sliding, eviction, positioning and editing can be observed at DSBs and how these activities affect the DSB repair decision.
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Affiliation(s)
- Leonhard Andreas Karl
- Resarch Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Martina Peritore
- Resarch Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Lorenzo Galanti
- Resarch Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Boris Pfander
- Resarch Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
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7
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Uruci S, Lo CSY, Wheeler D, Taneja N. R-Loops and Its Chro-Mates: The Strange Case of Dr. Jekyll and Mr. Hyde. Int J Mol Sci 2021; 22:ijms22168850. [PMID: 34445553 PMCID: PMC8396322 DOI: 10.3390/ijms22168850] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/04/2021] [Accepted: 08/12/2021] [Indexed: 12/22/2022] Open
Abstract
Since their discovery, R-loops have been associated with both physiological and pathological functions that are conserved across species. R-loops are a source of replication stress and genome instability, as seen in neurodegenerative disorders and cancer. In response, cells have evolved pathways to prevent R-loop accumulation as well as to resolve them. A growing body of evidence correlates R-loop accumulation with changes in the epigenetic landscape. However, the role of chromatin modification and remodeling in R-loops homeostasis remains unclear. This review covers various mechanisms precluding R-loop accumulation and highlights the role of chromatin modifiers and remodelers in facilitating timely R-loop resolution. We also discuss the enigmatic role of RNA:DNA hybrids in facilitating DNA repair, epigenetic landscape and the potential role of replication fork preservation pathways, active fork stability and stalled fork protection pathways, in avoiding replication-transcription conflicts. Finally, we discuss the potential role of several Chro-Mates (chromatin modifiers and remodelers) in the likely differentiation between persistent/detrimental R-loops and transient/benign R-loops that assist in various physiological processes relevant for therapeutic interventions.
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Affiliation(s)
- Sidrit Uruci
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands; (S.U.); (C.S.Y.L.)
| | - Calvin Shun Yu Lo
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands; (S.U.); (C.S.Y.L.)
| | - David Wheeler
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA;
| | - Nitika Taneja
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands; (S.U.); (C.S.Y.L.)
- Correspondence:
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8
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Peng H, Zhang S, Peng Y, Zhu S, Zhao X, Zhao X, Yang S, Liu G, Dong Y, Gan X, Li Q, Zhang X, Pei H, Chen X. Yeast Bromodomain Factor 1 and Its Human Homolog TAF1 Play Conserved Roles in Promoting Homologous Recombination. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2100753. [PMID: 34056863 PMCID: PMC8336524 DOI: 10.1002/advs.202100753] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/27/2021] [Indexed: 05/12/2023]
Abstract
Histone acetylation is a key histone post-translational modification that shapes chromatin structure, dynamics, and function. Bromodomain (BRD) proteins, the readers of acetyl-lysines, are located in the center of the histone acetylation-signaling network. How they regulate DNA repair and genome stability remains poorly understood. Here, a conserved function of the yeast Bromodomain Factor 1 (Bdf1) and its human counterpart TAF1 is reported in promoting DNA double-stranded break repair by homologous recombination (HR). Depletion of either yeast BDF1 or human TAF1, or disruption of their BRDs impairs DNA end resection, Replication Protein A (RPA) and Rad51 loading, and HR repair, causing genome instability and hypersensitivity to DNA damage. Mechanistically, it is shown that Bdf1 preferentially binds the DNA damage-induced histone H4 acetylation (H4Ac) via the BRD motifs, leading to its chromatin recruitment. Meanwhile, Bdf1 physically interacts with RPA, and this interaction facilitates RPA loading in the chromatin context and the subsequent HR repair. Similarly, TAF1 also interacts with H4Ac or RPA. Thus, Bdf1 and TAF1 appear to share a conserved mechanism in linking the HR repair to chromatin acetylation in preserving genome integrity.
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Affiliation(s)
- Haoyang Peng
- Hubei Key Laboratory of Cell HomeostasisCollege of Life Sciences and the Institute for Advanced StudiesWuhan UniversityWuhan430072China
| | - Simin Zhang
- Hubei Key Laboratory of Cell HomeostasisCollege of Life Sciences and the Institute for Advanced StudiesWuhan UniversityWuhan430072China
| | - Yihan Peng
- Department of Biochemistry and Molecular MedicineGeorge Washington University School of Medicine and Health ScienceWashingtonDC20037USA
| | - Shuangyi Zhu
- Hubei Key Laboratory of Cell HomeostasisCollege of Life Sciences and the Institute for Advanced StudiesWuhan UniversityWuhan430072China
| | - Xin Zhao
- Hubei Key Laboratory of Cell HomeostasisCollege of Life Sciences and the Institute for Advanced StudiesWuhan UniversityWuhan430072China
| | - Xiaocong Zhao
- Hubei Key Laboratory of Cell HomeostasisCollege of Life Sciences and the Institute for Advanced StudiesWuhan UniversityWuhan430072China
| | - Shuangshuang Yang
- State Key Laboratory of Protein and Plant Gene ResearchSchool of Life Sciences and Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijing100871China
| | - Guangxue Liu
- Hubei Key Laboratory of Cell HomeostasisCollege of Life Sciences and the Institute for Advanced StudiesWuhan UniversityWuhan430072China
| | - Yang Dong
- Hubei Key Laboratory of Cell HomeostasisCollege of Life Sciences and the Institute for Advanced StudiesWuhan UniversityWuhan430072China
| | - Xiaoli Gan
- Hubei Key Laboratory of Cell HomeostasisCollege of Life Sciences and the Institute for Advanced StudiesWuhan UniversityWuhan430072China
| | - Qing Li
- State Key Laboratory of Protein and Plant Gene ResearchSchool of Life Sciences and Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijing100871China
| | - Xinghua Zhang
- Hubei Key Laboratory of Cell HomeostasisCollege of Life Sciences and the Institute for Advanced StudiesWuhan UniversityWuhan430072China
| | - Huadong Pei
- Department of Biochemistry and Molecular MedicineGeorge Washington University School of Medicine and Health ScienceWashingtonDC20037USA
| | - Xuefeng Chen
- Hubei Key Laboratory of Cell HomeostasisCollege of Life Sciences and the Institute for Advanced StudiesWuhan UniversityWuhan430072China
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9
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DNA end resection during homologous recombination. Curr Opin Genet Dev 2021; 71:99-105. [PMID: 34329854 DOI: 10.1016/j.gde.2021.07.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/03/2021] [Accepted: 07/05/2021] [Indexed: 12/15/2022]
Abstract
Exposure to environmental mutagens but also cell-endogenous processes can create DNA double-strand breaks (DSBs) in a cell's genome. DSBs need to be repaired accurately and timely to ensure genomic integrity and cell survival. One major DSB repair mechanism, called homologous recombination, relies on the nucleolytic degradation of the 5'-terminated strands in a process termed end resection. Here, we review new insights into end resection with a focus on the mechanistic interplay of the nucleases, helicases, and accessory factors involved.
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10
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Abstract
The conformational dynamics of single-stranded DNA (ss-DNA) are implicated in the mechanisms of several key biological processes such as DNA replication and damage repair and have been modeled with those of semiflexible or flexible polymer. The high flexibility and customizability of ss-DNA also make it an excellent polymeric material for materials engineering. Polythymidine (poly(T)) is an excellent model ss-DNA as a flexible polymer since it does not form any secondary structure. However, only limited experimental results have been reported of poly(T) conformational dynamics with a very short length that is not relevant to the aforementioned processes and applications. Here, we provide the first experimental results of the conformational dynamics of poly(T) with lengths in the range of 130-170 nucleotides at the single-molecule level. Our experiments are based on single-molecule FRET and a DNA hairpin structure of which the folding kinetics are governed by the conformational dynamics of poly(T). We found that the folding kinetics deviate far from those of a flexible polymer model with a harmonic bending potential. To this end, we derived a simple model for the kinetics of DNA hairpin folding from the self-avoiding-walk (SAW). Our model describes the conformational dynamics of poly(T) very well and enables estimation of the conformational dimensionality. The estimated dimensionalities suggest that ss-DNA is completely flexible at 100 mM or a higher NaCl concentration, but not at 50 mM. These results will help understand the conformational dynamics of ss-DNA implicated in several key biological processes and maximize the utility of ss-DNA for materials engineering. Also, our system and model provide an excellent platform to investigate the conformational dynamics of ss-DNA.
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11
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Peritore M, Reusswig KU, Bantele SCS, Straub T, Pfander B. Strand-specific ChIP-seq at DNA breaks distinguishes ssDNA versus dsDNA binding and refutes single-stranded nucleosomes. Mol Cell 2021; 81:1841-1853.e4. [PMID: 33651987 DOI: 10.1016/j.molcel.2021.02.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 12/30/2020] [Accepted: 01/29/2021] [Indexed: 02/07/2023]
Abstract
In a first step of DNA double-strand break (DSB) repair by homologous recombination, DNA ends are resected such that single-stranded DNA (ssDNA) overhangs are generated. ssDNA is specifically bound by RPA and other factors, which constitutes a ssDNA-domain on damaged chromatin. The molecular organization of this ssDNA and the adjacent dsDNA domain is crucial during DSB signaling and repair. However, data regarding the presence of nucleosomes, the most basic chromatin components, in the ssDNA domain have been contradictory. Here, we use site-specific induction of DSBs and chromatin immunoprecipitation followed by strand-specific sequencing to analyze in vivo binding of key DSB repair and signaling proteins to either the ssDNA or dsDNA domain. In the case of nucleosomes, we show that recently proposed ssDNA nucleosomes are not a major, persistent species, but that nucleosome eviction and DNA end resection are intrinsically coupled. These results support a model of separated dsDNA-nucleosome and ssDNA-RPA domains during DSB repair.
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Affiliation(s)
- Martina Peritore
- Research Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Karl-Uwe Reusswig
- Research Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Susanne C S Bantele
- Research Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Tobias Straub
- Biomedizinisches Centrum, Core Facility Bioinformatics, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany
| | - Boris Pfander
- Research Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.
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12
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Tong ZB, Ai HS, Li JB. The Mechanism of Chromatin Remodeler SMARCAD1/Fun30 in Response to DNA Damage. Front Cell Dev Biol 2020; 8:560098. [PMID: 33102471 PMCID: PMC7545370 DOI: 10.3389/fcell.2020.560098] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 09/07/2020] [Indexed: 01/22/2023] Open
Abstract
DNA packs into highly condensed chromatin to organize the genome in eukaryotes but occludes many regulatory DNA elements. Access to DNA within nucleosomes is therefore required for a variety of biological processes in cells including transcription, replication, and DNA repair. To cope with this problem, cells employ a set of specialized ATP-dependent chromatin-remodeling protein complexes to enable dynamic access to packaged DNA. In the present review, we summarize the recent advances in the functional and mechanistic studies on a particular chromatin remodeler SMARCAD1Fun30 which has been demonstrated to play a key role in distinct cellular processes and gained much attention in recent years. Focus is given to how SMARCAD1Fun30 regulates various cellular processes through its chromatin remodeling activity, and especially the regulatory role of SMARCAD1Fun30 in gene expression control, maintenance and establishment of heterochromatin, and DNA damage repair. Moreover, we review the studies on the molecular mechanism of SMARCAD1Fun30 that promotes the DNA end-resection on double-strand break ends, including the mechanisms of recruitment, activity regulation and chromatin remodeling.
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Affiliation(s)
- Ze-Bin Tong
- College of Pharmaceutical Sciences, Soochow University, Suzhou, China.,Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Hua-Song Ai
- Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Jia-Bin Li
- College of Pharmaceutical Sciences, Soochow University, Suzhou, China
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13
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Aleksandrov R, Hristova R, Stoynov S, Gospodinov A. The Chromatin Response to Double-Strand DNA Breaks and Their Repair. Cells 2020; 9:cells9081853. [PMID: 32784607 PMCID: PMC7464352 DOI: 10.3390/cells9081853] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/03/2020] [Accepted: 08/04/2020] [Indexed: 02/07/2023] Open
Abstract
Cellular DNA is constantly being damaged by numerous internal and external mutagenic factors. Probably the most severe type of insults DNA could suffer are the double-strand DNA breaks (DSBs). They sever both DNA strands and compromise genomic stability, causing deleterious chromosomal aberrations that are implicated in numerous maladies, including cancer. Not surprisingly, cells have evolved several DSB repair pathways encompassing hundreds of different DNA repair proteins to cope with this challenge. In eukaryotic cells, DSB repair is fulfilled in the immensely complex environment of the chromatin. The chromatin is not just a passive background that accommodates the multitude of DNA repair proteins, but it is a highly dynamic and active participant in the repair process. Chromatin alterations, such as changing patterns of histone modifications shaped by numerous histone-modifying enzymes and chromatin remodeling, are pivotal for proficient DSB repair. Dynamic chromatin changes ensure accessibility to the damaged region, recruit DNA repair proteins, and regulate their association and activity, contributing to DSB repair pathway choice and coordination. Given the paramount importance of DSB repair in tumorigenesis and cancer progression, DSB repair has turned into an attractive target for the development of novel anticancer therapies, some of which have already entered the clinic.
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14
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Dynamic human MutSα-MutLα complexes compact mismatched DNA. Proc Natl Acad Sci U S A 2020; 117:16302-16312. [PMID: 32586954 DOI: 10.1073/pnas.1918519117] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
DNA mismatch repair (MMR) corrects errors that occur during DNA replication. In humans, mutations in the proteins MutSα and MutLα that initiate MMR cause Lynch syndrome, the most common hereditary cancer. MutSα surveilles the DNA, and upon recognition of a replication error it undergoes adenosine triphosphate-dependent conformational changes and recruits MutLα. Subsequently, proliferating cell nuclear antigen (PCNA) activates MutLα to nick the error-containing strand to allow excision and resynthesis. The structure-function properties of these obligate MutSα-MutLα complexes remain mostly unexplored in higher eukaryotes, and models are predominately based on studies of prokaryotic proteins. Here, we utilize atomic force microscopy (AFM) coupled with other methods to reveal time- and concentration-dependent stoichiometries and conformations of assembling human MutSα-MutLα-DNA complexes. We find that they assemble into multimeric complexes comprising three to eight proteins around a mismatch on DNA. On the timescale of a few minutes, these complexes rearrange, folding and compacting the DNA. These observations contrast with dominant models of MMR initiation that envision diffusive MutS-MutL complexes that move away from the mismatch. Our results suggest MutSα localizes MutLα near the mismatch and promotes DNA configurations that could enhance MMR efficiency by facilitating MutLα nicking the DNA at multiple sites around the mismatch. In addition, such complexes may also protect the mismatch region from nucleosome reassembly until repair occurs, and they could potentially remodel adjacent nucleosomes.
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15
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Hardy J, Dai D, Ait Saada A, Teixeira-Silva A, Dupoiron L, Mojallali F, Fréon K, Ochsenbein F, Hartmann B, Lambert S. Histone deposition promotes recombination-dependent replication at arrested forks. PLoS Genet 2019; 15:e1008441. [PMID: 31584934 PMCID: PMC6795475 DOI: 10.1371/journal.pgen.1008441] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 10/16/2019] [Accepted: 09/20/2019] [Indexed: 11/18/2022] Open
Abstract
Replication stress poses a serious threat to genome stability. Recombination-Dependent-Replication (RDR) promotes DNA synthesis resumption from arrested forks. Despite the identification of chromatin restoration pathways after DNA repair, crosstalk coupling RDR and chromatin assembly is largely unexplored. The fission yeast Chromatin Assembly Factor-1, CAF-1, is known to promote RDR. Here, we addressed the contribution of histone deposition to RDR. We expressed a mutated histone, H3-H113D, to genetically alter replication-dependent chromatin assembly by destabilizing (H3-H4)2 tetramer. We established that DNA synthesis-dependent histone deposition, by CAF-1 and Asf1, promotes RDR by preventing Rqh1-mediated disassembly of joint-molecules. The recombination factor Rad52 promotes CAF-1 binding to sites of recombination-dependent DNA synthesis, indicating that histone deposition occurs downstream Rad52. Histone deposition and Rqh1 activity act synergistically to promote cell resistance to camptothecin, a topoisomerase I inhibitor that induces replication stress. Moreover, histone deposition favors non conservative recombination events occurring spontaneously in the absence of Rqh1, indicating that the stabilization of joint-molecules by histone deposition also occurs independently of Rqh1 activity. These results indicate that histone deposition plays an active role in promoting RDR, a benefit counterbalanced by stabilizing at-risk joint-molecules for genome stability.
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Affiliation(s)
- Julien Hardy
- Institut Curie, PSL Research University, UMR3348, Orsay, France.,University Paris Sud, Paris-Saclay University, UMR3348, Orsay, France.,CNRS, UMR3348, Orsay France
| | - Dingli Dai
- Institut Curie, PSL Research University, UMR3348, Orsay, France.,University Paris Sud, Paris-Saclay University, UMR3348, Orsay, France.,CNRS, UMR3348, Orsay France
| | - Anissia Ait Saada
- Institut Curie, PSL Research University, UMR3348, Orsay, France.,University Paris Sud, Paris-Saclay University, UMR3348, Orsay, France.,CNRS, UMR3348, Orsay France
| | - Ana Teixeira-Silva
- Institut Curie, PSL Research University, UMR3348, Orsay, France.,University Paris Sud, Paris-Saclay University, UMR3348, Orsay, France.,CNRS, UMR3348, Orsay France
| | - Louise Dupoiron
- Institut Curie, PSL Research University, UMR3348, Orsay, France.,University Paris Sud, Paris-Saclay University, UMR3348, Orsay, France.,CNRS, UMR3348, Orsay France
| | - Fatemeh Mojallali
- Institut Curie, PSL Research University, UMR3348, Orsay, France.,University Paris Sud, Paris-Saclay University, UMR3348, Orsay, France.,CNRS, UMR3348, Orsay France
| | - Karine Fréon
- Institut Curie, PSL Research University, UMR3348, Orsay, France.,University Paris Sud, Paris-Saclay University, UMR3348, Orsay, France.,CNRS, UMR3348, Orsay France
| | - Francoise Ochsenbein
- CEA, DRF, SB2SM, Laboratoire de Biologie Structurale et Radiobiologie, Gif-sur-Yvette, France
| | - Brigitte Hartmann
- Laboratoire de Biologie et Pharmacologie Appliquée (LBPA) UMR 8113, CNRS / ENS de Cachan, Cachan cedex, France
| | - Sarah Lambert
- Institut Curie, PSL Research University, UMR3348, Orsay, France.,University Paris Sud, Paris-Saclay University, UMR3348, Orsay, France.,CNRS, UMR3348, Orsay France
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16
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Ait-Saada A, Khorosjutina O, Chen J, Kramarz K, Maksimov V, Svensson JP, Lambert S, Ekwall K. Chromatin remodeler Fft3 plays a dual role at blocked DNA replication forks. Life Sci Alliance 2019; 2:e201900433. [PMID: 31575705 PMCID: PMC6771652 DOI: 10.26508/lsa.201900433] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 09/23/2019] [Accepted: 09/24/2019] [Indexed: 01/26/2023] Open
Abstract
Here, we investigate the function of fission yeast Fun30/Smarcad1 family of SNF2 ATPase-dependent chromatin remodeling enzymes in DNA damage repair. There are three Fun30 homologues in fission yeast, Fft1, Fft2, and Fft3. We find that only Fft3 has a function in DNA repair and it is needed for single-strand annealing of an induced double-strand break. Furthermore, we use an inducible replication fork barrier system to show that Fft3 has two distinct roles at blocked DNA replication forks. First, Fft3 is needed for the resection of nascent strands, and second, it is required to restart the blocked forks. The latter function is independent of its ATPase activity.
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Affiliation(s)
- Anissia Ait-Saada
- Institut Curie, Paris-Saclay University, Centre National de la Recherche Scientifique, Unités Mixtes de Recherche 3348, F-91405, Orsay, France
| | - Olga Khorosjutina
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Jiang Chen
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Karol Kramarz
- Institut Curie, Paris-Saclay University, Centre National de la Recherche Scientifique, Unités Mixtes de Recherche 3348, F-91405, Orsay, France
| | - Vladimir Maksimov
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - J Peter Svensson
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Sarah Lambert
- Institut Curie, Paris-Saclay University, Centre National de la Recherche Scientifique, Unités Mixtes de Recherche 3348, F-91405, Orsay, France
| | - Karl Ekwall
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
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17
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Bantele SCS, Pfander B. Nucleosome Remodeling by Fun30 SMARCAD1 in the DNA Damage Response. Front Mol Biosci 2019; 6:78. [PMID: 31555662 PMCID: PMC6737033 DOI: 10.3389/fmolb.2019.00078] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 08/19/2019] [Indexed: 12/16/2022] Open
Abstract
Many cellular pathways are dedicated to maintain the integrity of the genome. In eukaryotes, the underlying DNA transactions occur in the context of chromatin. Cells utilize chromatin and its dynamic nature to regulate those genome integrity pathways. Accordingly, chromatin becomes restructured and modified around DNA damage sites. Here, we review the current knowledge of a chromatin remodeler Fun30SMARCAD1, which plays a key role in genome maintenance. Fun30SMARCAD1 promotes DNA end resection and the repair of DNA double-stranded breaks (DSBs). Notably, however, Fun30SMARCAD1 plays additional roles in maintaining heterochromatin and promoting transcription. Overall, Fun30SMARCAD1 is involved in distinct processes and the specific roles of Fun30SMARCAD1 at DSBs, replication forks and sites of transcription appear discordant at first view. Nonetheless, a picture emerges in which commonalities within these context-dependent roles of Fun30SMARCAD1 exist, which may help to gain a more global understanding of chromatin alterations induced by Fun30SMARCAD1.
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Affiliation(s)
- Susanne C S Bantele
- Max Planck Institute of Biochemistry, DNA Replication and Genome Integrity, Martinsried, Germany
| | - Boris Pfander
- Max Planck Institute of Biochemistry, DNA Replication and Genome Integrity, Martinsried, Germany
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18
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Densham RM, Morris JR. Moving Mountains-The BRCA1 Promotion of DNA Resection. Front Mol Biosci 2019; 6:79. [PMID: 31552267 PMCID: PMC6733915 DOI: 10.3389/fmolb.2019.00079] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 08/20/2019] [Indexed: 12/26/2022] Open
Abstract
DNA double-strand breaks (DSBs) occur in our cells in the context of chromatin. This type of lesion is toxic, entirely preventing genome continuity and causing cell death or terminal arrest. Several repair mechanisms can act on DNA surrounding a DSB, only some of which carry a low risk of mutation, so that which repair process is utilized is critical to the stability of genetic material of cells. A key component of repair outcome is the degree of DNA resection directed to either side of the break site. This in turn determines the subsequent forms of repair in which DNA homology plays a part. Here we will focus on chromatin and chromatin-bound complexes which constitute the "mountains" that block resection, with a particular focus on how the breast and ovarian cancer predisposition protein-1 (BRCA1) contributes to repair outcomes through overcoming these blocks.
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Affiliation(s)
| | - Joanna R. Morris
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, Medical and Dental Schools, University of Birmingham, Birmingham, United Kingdom
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19
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Chakraborty U, Mackenroth B, Shalloway D, Alani E. Chromatin Modifiers Alter Recombination Between Divergent DNA Sequences. Genetics 2019; 212:1147-1162. [PMID: 31221666 PMCID: PMC6707472 DOI: 10.1534/genetics.119.302395] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 06/18/2019] [Indexed: 02/07/2023] Open
Abstract
Recombination between divergent DNA sequences is actively prevented by heteroduplex rejection mechanisms. In baker's yeast, such antirecombination mechanisms can be initiated by the recognition of DNA mismatches in heteroduplex DNA by MSH proteins, followed by recruitment of the Sgs1-Top3-Rmi1 helicase-topoisomerase complex to unwind the recombination intermediate. We previously showed that the repair/rejection decision during single-strand annealing recombination is temporally regulated by MSH (MutShomolog) protein levels and by factors that excise nonhomologous single-stranded tails. These observations, coupled with recent studies indicating that mismatch repair (MMR) factors interact with components of the histone chaperone machinery, encouraged us to explore roles for epigenetic factors and chromatin conformation in regulating the decision to reject vs. repair recombination between divergent DNA substrates. This work involved the use of an inverted repeat recombination assay thought to measure sister chromatid repair during DNA replication. Our observations are consistent with the histone chaperones CAF-1 and Rtt106, and the histone deacetylase Sir2, acting to suppress heteroduplex rejection and the Rpd3, Hst3, and Hst4 deacetylases acting to promote heteroduplex rejection. These observations, and double-mutant analysis, have led to a model in which nucleosomes located at DNA lesions stabilize recombination intermediates and compete with MMR factors that mediate heteroduplex rejection.
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Affiliation(s)
- Ujani Chakraborty
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703
| | - Beata Mackenroth
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703
| | - David Shalloway
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703
| | - Eric Alani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703
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20
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Serag MF, Aikeremu A, Tsukamoto R, Piwoński H, Abadi M, Kaji N, Dwyer JR, Baba Y, Habuchi S. Geometry-Based Self-Assembly of Histone-DNA Nanostructures at Single-Nucleotide Resolution. ACS NANO 2019; 13:8155-8168. [PMID: 31244030 DOI: 10.1021/acsnano.9b03259] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Histones are basic protein monomers capable of interacting with DNA, providing the mechanism of DNA compaction inside the cell nucleus. The well-ordered assembly process of histone and DNA is a potential candidate as the approach for building DNA-protein nanostructures. Here, utilizing the sequence-independent histone-DNA interaction, we present an approach to self-assemble histones and single-stranded DNA (ssDNA) to form well-defined histone-DNA (sHD) nanoparticles and their multidimensional cross-linked complexes (cHD). By using various molecular biology and microscopy techniques, we elucidate the structure of these complexes, and we show that they are formed at carefully controlled conditions of temperature, ionic strength, concentration, and incubation time. We also demonstrate using a set of ssDNA molecular rulers and a geometric accommodation model that the assembly of sHD and cHD particles proceeds with precise geometry so that the number of ssDNA in these particles can be programmed by the length of ssDNA. We further show that the formation of cHD amplifies the effect of the length of ssDNA on the self-assembly, allowing for distinguishing ssDNA of different lengths at single nucleotide resolution. We envision that our geometry-directed approach of self-assembling histone-DNA nanostructures and the fundamental insights can serve as a structural platform to advance building precisely ordered DNA-protein nanostructures.
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Affiliation(s)
- Maged F Serag
- Biological and Environmental Science and Engineering Division , King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900 , Saudi Arabia
- Department of Biomolecular Engineering, Graduate School of Engineering , Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8603 , Japan
- ImPACT Research Center for Advanced Nanobiodevices , Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8603 , Japan
| | - Aimaiti Aikeremu
- Biological and Environmental Science and Engineering Division , King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900 , Saudi Arabia
| | - Ryoko Tsukamoto
- Department of Biomolecular Engineering, Graduate School of Engineering , Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8603 , Japan
- ImPACT Research Center for Advanced Nanobiodevices , Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8603 , Japan
| | - Hubert Piwoński
- Biological and Environmental Science and Engineering Division , King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900 , Saudi Arabia
| | - Maram Abadi
- Biological and Environmental Science and Engineering Division , King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900 , Saudi Arabia
| | - Noritada Kaji
- Department of Applied Chemistry, Graduate School of Engineering , Kyushu University , 744 Motooka , Nishi-ku, Fukuoka 819-0395 , Japan
- JST, PRESTO , 4-1-8 Honcho , Kawaguchi , Saitama 332-0012 , Japan
| | - Jason R Dwyer
- Department of Chemistry , University of Rhode Island , 140 Flagg Road , Kingston , Rhode Island 02881 , United States
| | - Yoshinobu Baba
- Department of Biomolecular Engineering, Graduate School of Engineering , Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8603 , Japan
- ImPACT Research Center for Advanced Nanobiodevices , Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8603 , Japan
- National Institute of Advanced Industrial Science and Technology (AIST) , Takamatsu 761-0395 , Japan
- School of Pharmacy , Kaohsiung Medical University , Kaohsiung 807 , Taiwan , R.O.C
| | - Satoshi Habuchi
- Biological and Environmental Science and Engineering Division , King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900 , Saudi Arabia
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21
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Zheng S, Li D, Lu Z, Liu G, Wang M, Xing P, Wang M, Dong Y, Wang X, Li J, Zhang S, Peng H, Ira G, Li G, Chen X. Bre1-dependent H2B ubiquitination promotes homologous recombination by stimulating histone eviction at DNA breaks. Nucleic Acids Res 2019; 46:11326-11339. [PMID: 30304473 PMCID: PMC6265479 DOI: 10.1093/nar/gky918] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 10/08/2018] [Indexed: 01/21/2023] Open
Abstract
Repair of DNA double-strand breaks (DSBs) requires eviction of the histones around DNA breaks to allow the loading of numerous repair and checkpoint proteins. However, the mechanism and regulation of this process remain poorly understood. Here, we show that histone H2B ubiquitination (uH2B) promotes histone eviction at DSBs independent of resection or ATP-dependent chromatin remodelers. Cells lacking uH2B or its E3 ubiquitin ligase Bre1 exhibit hyper-resection due to the loss of H3K79 methylation that recruits Rad9, a known negative regulator of resection. Unexpectedly, despite excessive single-strand DNA being produced, bre1Δ cells show defective RPA and Rad51 recruitment and impaired repair by homologous recombination and response to DNA damage. The HR defect in bre1Δ cells correlates with impaired histone loss at DSBs and can be largely rescued by depletion of CAF-1, a histone chaperone depositing histones H3-H4. Overexpression of Rad51 stimulates histone eviction and partially suppresses the recombination defects of bre1Δ mutant. Thus, we propose that Bre1 mediated-uH2B promotes DSB repair through facilitating histone eviction and subsequent loading of repair proteins.
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Affiliation(s)
- Sihao Zheng
- Hubei Key Laboratory of Cell Homeostasis, the Department of Genetics, College of Life Sciences and the Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 430072, China
| | - Dan Li
- Hubei Key Laboratory of Cell Homeostasis, the Department of Genetics, College of Life Sciences and the Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 430072, China
| | - Zhen Lu
- Hubei Key Laboratory of Cell Homeostasis, the Department of Genetics, College of Life Sciences and the Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 430072, China
| | - Guangxue Liu
- Hubei Key Laboratory of Cell Homeostasis, the Department of Genetics, College of Life Sciences and the Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 430072, China
| | - Meng Wang
- Hubei Key Laboratory of Cell Homeostasis, the Department of Genetics, College of Life Sciences and the Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 430072, China
| | - Poyuan Xing
- Hubei Key Laboratory of Cell Homeostasis, the Department of Genetics, College of Life Sciences and the Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 430072, China
| | - Min Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yang Dong
- Hubei Key Laboratory of Cell Homeostasis, the Department of Genetics, College of Life Sciences and the Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 430072, China
| | - Xuejie Wang
- Hubei Key Laboratory of Cell Homeostasis, the Department of Genetics, College of Life Sciences and the Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 430072, China
| | - Jingyao Li
- Hubei Key Laboratory of Cell Homeostasis, the Department of Genetics, College of Life Sciences and the Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 430072, China
| | - Simin Zhang
- Hubei Key Laboratory of Cell Homeostasis, the Department of Genetics, College of Life Sciences and the Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 430072, China
| | - Haoyang Peng
- Hubei Key Laboratory of Cell Homeostasis, the Department of Genetics, College of Life Sciences and the Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 430072, China
| | - Grzegorz Ira
- The Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Guohong Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xuefeng Chen
- Hubei Key Laboratory of Cell Homeostasis, the Department of Genetics, College of Life Sciences and the Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 430072, China
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22
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Kaur P, Longley MJ, Pan H, Wang H, Copeland WC. Single-molecule DREEM imaging reveals DNA wrapping around human mitochondrial single-stranded DNA binding protein. Nucleic Acids Res 2019; 46:11287-11302. [PMID: 30256971 PMCID: PMC6265486 DOI: 10.1093/nar/gky875] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 09/18/2018] [Indexed: 01/01/2023] Open
Abstract
Improper maintenance of the mitochondrial genome progressively disrupts cellular respiration and causes severe metabolic disorders commonly termed mitochondrial diseases. Mitochondrial single-stranded DNA binding protein (mtSSB) is an essential component of the mtDNA replication machinery. We utilized single-molecule methods to examine the modes by which human mtSSB binds DNA to help define protein interactions at the mtDNA replication fork. Direct visualization of individual mtSSB molecules by atomic force microscopy (AFM) revealed a random distribution of mtSSB tetramers bound to extended regions of single-stranded DNA (ssDNA), strongly suggesting non-cooperative binding by mtSSB. Selective binding to ssDNA was confirmed by AFM imaging of individual mtSSB tetramers bound to gapped plasmid DNA substrates bearing defined single-stranded regions. Shortening of the contour length of gapped DNA upon binding mtSSB was attributed to DNA wrapping around mtSSB. Tracing the DNA path in mtSSB–ssDNA complexes with Dual-Resonance-frequency-Enhanced Electrostatic force Microscopy established a predominant binding mode with one DNA strand winding once around each mtSSB tetramer at physiological salt conditions. Single-molecule imaging suggests mtSSB may not saturate or fully protect single-stranded replication intermediates during mtDNA synthesis, leaving the mitochondrial genome vulnerable to chemical mutagenesis, deletions driven by primer relocation or other actions consistent with clinically observed deletion biases.
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Affiliation(s)
- Parminder Kaur
- Physics Department, North Carolina State University, Raleigh, North Carolina, NC 27695, USA.,Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina, NC 27695, USA
| | - Matthew J Longley
- Genome Integrity and Structural Biology Laboratory, NIEHS, NIH, Research Triangle Park, NC 27709, USA
| | - Hai Pan
- Physics Department, North Carolina State University, Raleigh, North Carolina, NC 27695, USA
| | - Hong Wang
- Physics Department, North Carolina State University, Raleigh, North Carolina, NC 27695, USA.,Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina, NC 27695, USA
| | - William C Copeland
- Genome Integrity and Structural Biology Laboratory, NIEHS, NIH, Research Triangle Park, NC 27709, USA
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23
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Degtyareva NP, Saini N, Sterling JF, Placentra VC, Klimczak LJ, Gordenin DA, Doetsch PW. Mutational signatures of redox stress in yeast single-strand DNA and of aging in human mitochondrial DNA share a common feature. PLoS Biol 2019; 17:e3000263. [PMID: 31067233 PMCID: PMC6527239 DOI: 10.1371/journal.pbio.3000263] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 05/20/2019] [Accepted: 04/25/2019] [Indexed: 11/18/2022] Open
Abstract
Redox stress is a major hallmark of cancer. Analysis of thousands of sequenced cancer exomes and whole genomes revealed distinct mutational signatures that can be attributed to specific sources of DNA lesions. Clustered mutations discovered in several cancer genomes were linked to single-strand DNA (ssDNA) intermediates in various processes of DNA metabolism. Previously, only one clustered mutational signature had been clearly associated with a subclass of ssDNA-specific apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like (APOBEC) cytidine deaminases. Others remain to be elucidated. We report here deciphering of the mutational spectra and mutational signature of redox stress in ssDNA of budding yeast and the signature of aging in human mitochondrial DNA. We found that the predominance of C to T substitutions is a common feature of both signatures. Measurements of the frequencies of hydrogen peroxide-induced mutations in proofreading-defective yeast mutants supported the conclusion that hydrogen peroxide-induced mutagenesis is not the result of increased DNA polymerase misincorporation errors but rather is caused by direct damage to DNA. Proteins involved in modulation of chromatin status play a significant role in prevention of redox stress-induced mutagenesis, possibly by facilitating protection through modification of chromatin structure. These findings provide an opportunity for the search and identification of the mutational signature of redox stress in cancers and in other pathological conditions and could potentially be used for informing therapeutic decisions. In addition, the discovery of such signatures that may be present in related organisms should also advance our understanding of evolution.
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Affiliation(s)
- Natalya P. Degtyareva
- Mutagenesis and DNA Repair Regulation Group, Laboratory of Genome Integrity and Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina, United States of America
| | - Natalie Saini
- Mechanisms of Genome Dynamics Group, Laboratory of Genome Integrity and Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina, United States of America
| | - Joan F. Sterling
- Mechanisms of Genome Dynamics Group, Laboratory of Genome Integrity and Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina, United States of America
| | - Victoria C. Placentra
- Mutagenesis and DNA Repair Regulation Group, Laboratory of Genome Integrity and Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina, United States of America
| | - Leszek J. Klimczak
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina, United States of America
| | - Dmitry A. Gordenin
- Mechanisms of Genome Dynamics Group, Laboratory of Genome Integrity and Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina, United States of America
| | - Paul W. Doetsch
- Mutagenesis and DNA Repair Regulation Group, Laboratory of Genome Integrity and Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina, United States of America
- * E-mail:
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24
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Zong D, Adam S, Wang Y, Sasanuma H, Callén E, Murga M, Day A, Kruhlak MJ, Wong N, Munro M, Chaudhuri AR, Karim B, Xia B, Takeda S, Johnson N, Durocher D, Nussenzweig A. BRCA1 Haploinsufficiency Is Masked by RNF168-Mediated Chromatin Ubiquitylation. Mol Cell 2019; 73:1267-1281.e7. [PMID: 30704900 PMCID: PMC6430682 DOI: 10.1016/j.molcel.2018.12.010] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/22/2018] [Accepted: 12/13/2018] [Indexed: 12/22/2022]
Abstract
BRCA1 functions at two distinct steps during homologous recombination (HR). Initially, it promotes DNA end resection, and subsequently it recruits the PALB2 and BRCA2 mediator complex, which stabilizes RAD51-DNA nucleoprotein filaments. Loss of 53BP1 rescues the HR defect in BRCA1-deficient cells by increasing resection, suggesting that BRCA1's downstream role in RAD51 loading is dispensable when 53BP1 is absent. Here we show that the E3 ubiquitin ligase RNF168, in addition to its canonical role in inhibiting end resection, acts in a redundant manner with BRCA1 to load PALB2 onto damaged DNA. Loss of RNF168 negates the synthetic rescue of BRCA1 deficiency by 53BP1 deletion, and it predisposes BRCA1 heterozygous mice to cancer. BRCA1+/-RNF168-/- cells lack RAD51 foci and are hypersensitive to PARP inhibitor, whereas forced targeting of PALB2 to DNA breaks in mutant cells circumvents BRCA1 haploinsufficiency. Inhibiting the chromatin ubiquitin pathway may, therefore, be a synthetic lethality strategy for BRCA1-deficient cancers.
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Affiliation(s)
- Dali Zong
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Salomé Adam
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Yifan Wang
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Hiroyuki Sasanuma
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Elsa Callén
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Matilde Murga
- Genomic Instability Group, Spanish National Cancer Research Center, CNIO, Madrid, Spain
| | - Amanda Day
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Michael J. Kruhlak
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Nancy Wong
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Meagan Munro
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Arnab Ray Chaudhuri
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA.,Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Baktiar Karim
- Pathology/Histotechnology Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Bing Xia
- Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Neil Johnson
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Daniel Durocher
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA.
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25
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Clouaire T, Legube G. A Snapshot on the Cis Chromatin Response to DNA Double-Strand Breaks. Trends Genet 2019; 35:330-345. [PMID: 30898334 DOI: 10.1016/j.tig.2019.02.003] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/15/2019] [Accepted: 02/23/2019] [Indexed: 12/11/2022]
Abstract
In eukaryotes, detection and repair of DNA double-strand breaks (DSBs) operate within chromatin, an incredibly complex structure that tightly packages and regulates DNA metabolism. Chromatin participates in the repair of these lesions at multiple steps, from detection to genomic sequence recovery and chromatin is itself extensively modified during the repair process. In recent years, new methodologies and dedicated techniques have expanded the experimental toolbox, opening up a new era granting the high-resolution analysis of chromatin modifications at annotated DSBs in a genome-wide manner. A complex picture is starting to emerge whereby chromatin is altered at various scales around DSBs, in a manner that relates to the repair pathway used, hence defining a 'repair histone code'. Here, we review the recent advances regarding our knowledge of the chromatin landscape induced in cis around DSBs, with an emphasis on histone post-translational modifications and histone variants.
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Affiliation(s)
- Thomas Clouaire
- LBCMCP, Centre de Biologie Integrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
| | - Gaëlle Legube
- LBCMCP, Centre de Biologie Integrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France.
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26
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Huang TH, Fowler F, Chen CC, Shen ZJ, Sleckman B, Tyler JK. The Histone Chaperones ASF1 and CAF-1 Promote MMS22L-TONSL-Mediated Rad51 Loading onto ssDNA during Homologous Recombination in Human Cells. Mol Cell 2018; 69:879-892.e5. [PMID: 29478807 DOI: 10.1016/j.molcel.2018.01.031] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 11/27/2017] [Accepted: 01/23/2018] [Indexed: 10/18/2022]
Abstract
The access-repair-restore model for the role of chromatin in DNA repair infers that chromatin is a mere obstacle to DNA repair. However, here we show that blocking chromatin assembly, via knockdown of the histone chaperones ASF1 or CAF-1 or a mutation that prevents ASF1A binding to histones, hinders Rad51 loading onto ssDNA during homologous recombination. This is a consequence of reduced recruitment of the Rad51 loader MMS22L-TONSL to ssDNA, resulting in persistent RPA foci, extensive DNA end resection, persistent activation of the ATR-Chk1 pathway, and cell cycle arrest. In agreement, histones occupy ssDNA during DNA repair in yeast. We also uncovered DNA-PKcs-dependent DNA damage-induced ASF1A phosphorylation, which enhances chromatin assembly, promoting MMS22L-TONSL recruitment and, hence, Rad51 loading. We propose that transient assembly of newly synthesized histones onto ssDNA serves to recruit MMS22L-TONSL to efficiently form the Rad51 nucleofilament for strand invasion, suggesting an active role of chromatin assembly in homologous recombination.
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Affiliation(s)
- Ting-Hsiang Huang
- Weill Cornell Medicine, Department of Pathology and Laboratory Medicine, New York, NY 10065, USA
| | - Faith Fowler
- Weill Cornell Medicine, Department of Pathology and Laboratory Medicine, New York, NY 10065, USA
| | - Chin-Chuan Chen
- Graduate Institute of Natural Products, Chang Gung University, Taoyuan 333, Taiwan
| | - Zih-Jie Shen
- Weill Cornell Medicine, Department of Pathology and Laboratory Medicine, New York, NY 10065, USA
| | - Barry Sleckman
- Weill Cornell Medicine, Department of Pathology and Laboratory Medicine, New York, NY 10065, USA
| | - Jessica K Tyler
- Weill Cornell Medicine, Department of Pathology and Laboratory Medicine, New York, NY 10065, USA.
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27
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Ding D, Bergmaier P, Sachs P, Klangwart M, Rückert T, Bartels N, Demmers J, Dekker M, Poot RA, Mermoud JE. The CUE1 domain of the SNF2-like chromatin remodeler SMARCAD1 mediates its association with KRAB-associated protein 1 (KAP1) and KAP1 target genes. J Biol Chem 2017; 293:2711-2724. [PMID: 29284678 DOI: 10.1074/jbc.ra117.000959] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 12/13/2017] [Indexed: 12/13/2022] Open
Abstract
Chromatin in embryonic stem cells (ESCs) differs markedly from that in somatic cells, with ESCs exhibiting a more open chromatin configuration. Accordingly, ATP-dependent chromatin remodeling complexes are important regulators of ESC homeostasis. Depletion of the remodeler SMARCAD1, an ATPase of the SNF2 family, has been shown to affect stem cell state, but the mechanistic explanation for this effect is unknown. Here, we set out to gain further insights into the function of SMARCAD1 in mouse ESCs. We identified KRAB-associated protein 1 (KAP1) as the stoichiometric binding partner of SMARCAD1 in ESCs. We found that this interaction occurs on chromatin and that SMARCAD1 binds to different classes of KAP1 target genes, including zinc finger protein (ZFP) and imprinted genes. We also found that the RING B-box coiled-coil (RBCC) domain in KAP1 and the proximal coupling of ubiquitin conjugation to ER degradation (CUE) domain in SMARCAD1 mediate their direct interaction. Of note, retention of SMARCAD1 in the nucleus depended on KAP1 in both mouse ESCs and human somatic cells. Mutations in the CUE1 domain of SMARCAD1 perturbed the binding to KAP1 in vitro and in vivo Accordingly, an intact CUE1 domain was required for tethering this remodeler to the nucleus. Moreover, mutation of the CUE1 domain compromised SMARCAD1 binding to KAP1 target genes. Taken together, our results reveal a mechanism that localizes SMARCAD1 to genomic sites through the interaction of SMARCAD1's CUE1 motif with KAP1.
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Affiliation(s)
- Dong Ding
- Institute of Molecular Biology and Tumour Research, Philipps University Marburg, Marburg 35043, Germany
| | - Philipp Bergmaier
- Institute of Molecular Biology and Tumour Research, Philipps University Marburg, Marburg 35043, Germany
| | - Parysatis Sachs
- Institute of Molecular Biology and Tumour Research, Philipps University Marburg, Marburg 35043, Germany
| | - Marius Klangwart
- Institute of Molecular Biology and Tumour Research, Philipps University Marburg, Marburg 35043, Germany
| | - Tamina Rückert
- Institute of Molecular Biology and Tumour Research, Philipps University Marburg, Marburg 35043, Germany
| | - Nora Bartels
- Institute of Molecular Biology and Tumour Research, Philipps University Marburg, Marburg 35043, Germany
| | - Jeroen Demmers
- Center for Proteomics, Erasmus Medical Center, 3015 CN Rotterdam, The Netherlands
| | - Mike Dekker
- Department of Cell Biology, Erasmus Medical Center, 3015 CN Rotterdam, The Netherlands
| | - Raymond A Poot
- Department of Cell Biology, Erasmus Medical Center, 3015 CN Rotterdam, The Netherlands
| | - Jacqueline E Mermoud
- Institute of Molecular Biology and Tumour Research, Philipps University Marburg, Marburg 35043, Germany.
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28
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Beckwitt EC, Kong M, Van Houten B. Studying protein-DNA interactions using atomic force microscopy. Semin Cell Dev Biol 2017; 73:220-230. [PMID: 28673677 DOI: 10.1016/j.semcdb.2017.06.028] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 06/27/2017] [Accepted: 06/29/2017] [Indexed: 12/12/2022]
Abstract
Atomic force microscopy (AFM) has made significant contributions to the study of protein-DNA interactions by making it possible to topographically image biological samples. A single protein-DNA binding reaction imaged by AFM can reveal protein binding specificity and affinity, protein-induced DNA bending, and protein binding stoichiometry. Changes in DNA structure, complex conformation, and cooperativity, can also be analyzed. In this review we highlight some important examples in the literature and discuss the advantages and limitations of these measurements. We also discuss important advances in technology that will facilitate the progress of AFM in the future.
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Affiliation(s)
- Emily C Beckwitt
- Program in Molecular Biophysics and Structural Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA; The University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, PA 15213, USA
| | - Muwen Kong
- Program in Molecular Biophysics and Structural Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA; The University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, PA 15213, USA
| | - Bennett Van Houten
- Program in Molecular Biophysics and Structural Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA; The University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, PA 15213, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA.
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29
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The INO80 Complex Removes H2A.Z to Promote Presynaptic Filament Formation during Homologous Recombination. Cell Rep 2017; 19:1294-1303. [DOI: 10.1016/j.celrep.2017.04.051] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 03/27/2017] [Accepted: 04/18/2017] [Indexed: 02/08/2023] Open
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