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Osakabe A, Takizawa Y, Horikoshi N, Hatazawa S, Negishi L, Sato S, Berger F, Kakutani T, Kurumizaka H. Molecular and structural basis of the chromatin remodeling activity by Arabidopsis DDM1. Nat Commun 2024; 15:5187. [PMID: 38992002 PMCID: PMC11239853 DOI: 10.1038/s41467-024-49465-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: 07/10/2023] [Accepted: 06/05/2024] [Indexed: 07/13/2024] Open
Abstract
The histone H2A variant H2A.W occupies transposons and thus prevents access to them in Arabidopsis thaliana. H2A.W is deposited by the chromatin remodeler DDM1, which also promotes the accessibility of chromatin writers to heterochromatin by an unknown mechanism. To shed light on this question, we solve the cryo-EM structures of nucleosomes containing H2A and H2A.W, and the DDM1-H2A.W nucleosome complex. These structures show that the DNA end flexibility of the H2A nucleosome is higher than that of the H2A.W nucleosome. In the DDM1-H2A.W nucleosome complex, DDM1 binds to the N-terminal tail of H4 and the nucleosomal DNA and increases the DNA end flexibility of H2A.W nucleosomes. Based on these biochemical and structural results, we propose that DDM1 counters the low accessibility caused by nucleosomes containing H2A.W to enable the maintenance of repressive epigenetic marks on transposons and prevent their activity.
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Affiliation(s)
- Akihisa Osakabe
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan.
| | - Yoshimasa Takizawa
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Naoki Horikoshi
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Suguru Hatazawa
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Lumi Negishi
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Shoko Sato
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Frédéric Berger
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Tetsuji Kakutani
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
| | - Hitoshi Kurumizaka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan.
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2
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Li N, Ma J, Fu H, Yang Z, Xu C, Li H, Zhao Y, Zhao Y, Chen S, Gou L, Zhang X, Zhang S, Li M, Hou X, Zhang L, Lu Y. Four Parallel Pathways in T4 Ligase-Catalyzed Repair of Nicked DNA with Diverse Bending Angles. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2401150. [PMID: 38582512 PMCID: PMC11220639 DOI: 10.1002/advs.202401150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/08/2024] [Indexed: 04/08/2024]
Abstract
The structural diversity of biological macromolecules in different environments contributes complexity to enzymological processes vital for cellular functions. Fluorescence resonance energy transfer and electron microscopy are used to investigate the enzymatic reaction of T4 DNA ligase catalyzing the ligation of nicked DNA. The data show that both the ligase-AMP complex and the ligase-AMP-DNA complex can have four conformations. This finding suggests the parallel occurrence of four ligation reaction pathways, each characterized by specific conformations of the ligase-AMP complex that persist in the ligase-AMP-DNA complex. Notably, these complexes have DNA bending angles of ≈0°, 20°, 60°, or 100°. The mechanism of parallel reactions challenges the conventional notion of simple sequential reaction steps occurring among multiple conformations. The results provide insights into the dynamic conformational changes and the versatile attributes of T4 DNA ligase and suggest that the parallel multiple reaction pathways may correspond to diverse T4 DNA ligase functions. This mechanism may potentially have evolved as an adaptive strategy across evolutionary history to navigate complex environments.
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Affiliation(s)
- Na Li
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed MatterSchool of PhysicsXi'an Jiaotong UniversityXi'an710049China
| | - Jianbing Ma
- Beijing National Laboratory for Condensed Matter PhysicsInstitute of PhysicsChinese Academy of SciencesBeijing100190China
| | - Hang Fu
- Beijing National Laboratory for Condensed Matter PhysicsInstitute of PhysicsChinese Academy of SciencesBeijing100190China
- University of Chinese Academy of SciencesBeijing100049China
- Wenzhou InstituteUniversity of Chinese Academy of SciencesWenzhouZhejiang325011China
| | - Zhiwei Yang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed MatterSchool of PhysicsXi'an Jiaotong UniversityXi'an710049China
| | - Chunhua Xu
- Beijing National Laboratory for Condensed Matter PhysicsInstitute of PhysicsChinese Academy of SciencesBeijing100190China
| | - Haihong Li
- College of Life SciencesNorthwest A&F UniversityYangling712100China
| | - Yimin Zhao
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed MatterSchool of PhysicsXi'an Jiaotong UniversityXi'an710049China
| | - Yizhen Zhao
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed MatterSchool of PhysicsXi'an Jiaotong UniversityXi'an710049China
| | - Shuyu Chen
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed MatterSchool of PhysicsXi'an Jiaotong UniversityXi'an710049China
| | - Lu Gou
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed MatterSchool of PhysicsXi'an Jiaotong UniversityXi'an710049China
| | - Xinghua Zhang
- Hubei Key Laboratory of Cell HomeostasisCollege of Life SciencesWuhan UniversityWuhan430072China
| | - Shengli Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed MatterSchool of PhysicsXi'an Jiaotong UniversityXi'an710049China
| | - Ming Li
- Beijing National Laboratory for Condensed Matter PhysicsInstitute of PhysicsChinese Academy of SciencesBeijing100190China
- University of Chinese Academy of SciencesBeijing100049China
- Songshan Lake Materials LaboratoryDongguanGuangdong523808China
| | - Ximiao Hou
- College of Life SciencesNorthwest A&F UniversityYangling712100China
| | - Lei Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed MatterSchool of PhysicsXi'an Jiaotong UniversityXi'an710049China
| | - Ying Lu
- Beijing National Laboratory for Condensed Matter PhysicsInstitute of PhysicsChinese Academy of SciencesBeijing100190China
- University of Chinese Academy of SciencesBeijing100049China
- Songshan Lake Materials LaboratoryDongguanGuangdong523808China
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3
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Zhang H, Gu Z, Zeng Y, Zhang Y. Mechanism of heterochromatin remodeling revealed by the DDM1 bound nucleosome structures. Structure 2024:S0969-2126(24)00190-4. [PMID: 38870940 DOI: 10.1016/j.str.2024.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 04/07/2024] [Accepted: 05/17/2024] [Indexed: 06/15/2024]
Abstract
The SWI/SNF2 chromatin remodeling factor decreased DNA methylation 1 (DDM1) is essential for the silencing of transposable elements (TEs) in both euchromatic and heterochromatic regions. Here, we determined the cryo-EM structures of DDM1-nucleosomeH2A and DDM1-nucleosomeH2A.W complexes at near-atomic resolution in the presence of the ATP analog ADP-BeFx. The structures show that nucleosomal DNA is unwrapped more on the surface of the histone octamer containing histone H2A than that containing histone H2A.W. DDM1 embraces one DNA gyre of the nucleosome and interacts with the N-terminal tails of histone H4. Although we did not observe DDM1-H2A.W interactions in our structures, the results of the pull-down experiments suggest a direct interaction between DDM1 and the core region of histone H2A.W. Our work provides mechanistic insights into the heterochromatin remodeling process driven by DDM1 in plants.
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Affiliation(s)
- Hongwei Zhang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
| | - Zhanxi Gu
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuan Zeng
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yu Zhang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
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4
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Khatua P, Tang PK, Moulick AG, Patel R, Manandhar A, Loverde SM. Sequence Dependence in Nucleosome Dynamics. J Phys Chem B 2024; 128:3090-3101. [PMID: 38530903 PMCID: PMC11181342 DOI: 10.1021/acs.jpcb.3c07363] [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] [Indexed: 03/28/2024]
Abstract
The basic packaging unit of eukaryotic chromatin is the nucleosome that contains 145-147 base pair duplex DNA wrapped around an octameric histone protein. While the DNA sequence plays a crucial role in controlling the positioning of the nucleosome, the molecular details behind the interplay between DNA sequence and nucleosome dynamics remain relatively unexplored. This study analyzes this interplay in detail by performing all-atom molecular dynamics simulations of nucleosomes, comparing the human α-satellite palindromic (ASP) and the strong positioning "Widom-601" DNA sequence at time scales of 12 μs. The simulations are performed at salt concentrations 10-20 times higher than physiological salt concentrations to screen the electrostatic interactions and promote unwrapping. These microsecond-long simulations give insight into the molecular-level sequence-dependent events that dictate the pathway of DNA unwrapping. We find that the "ASP" sequence forms a loop around SHL ± 5 for three sets of simulations. Coincident with loop formation is a cooperative increase in contacts with the neighboring N-terminal H2B tail and C-terminal H2A tail and the release of neighboring counterions. We find that the Widom-601 sequence exhibits a strong breathing motion of the nucleic acid ends. Coincident with the breathing motion is the collapse of the full N-terminal H3 tail and formation of an α-helix that interacts with the H3 histone core. We postulate that the dynamics of these histone tails and their modification with post-translational modifications (PTMs) may play a key role in governing this dynamics.
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Affiliation(s)
- Prabir Khatua
- Department of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, New York, 10314, United States
- Present Address: Department of Chemistry, GITAM School of Science, GITAM (Deemed to be University), Bengaluru, 562163, INDIA
| | - Phu K. Tang
- Department of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, New York, 10314, United States
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, NY, 10016, United States
- Present Address: Flatiron Institute, New York, NY, 10010, United States
- These authors contributed equally: Phu K. Tang, Abhik Ghosh Moulick, and Rutika Patel
| | - Abhik Ghosh Moulick
- Department of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, New York, 10314, United States
- These authors contributed equally: Phu K. Tang, Abhik Ghosh Moulick, and Rutika Patel
| | - Rutika Patel
- Department of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, New York, 10314, United States
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, NY, 10016, United States
- These authors contributed equally: Phu K. Tang, Abhik Ghosh Moulick, and Rutika Patel
| | - Anjela Manandhar
- Department of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, New York, 10314, United States
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, NY, 10016, United States
- Present Address: Takeda Pharmaceuticals, Boston, MA, 02139, United States
| | - Sharon M. Loverde
- Department of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, New York, 10314, United States
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, NY, 10016, United States
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY, 10016, United States
- Ph.D. Program in Physics, The Graduate Center of the City University of New York, New York, NY, 10016, United States
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5
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Eustermann S, Patel AB, Hopfner KP, He Y, Korber P. Energy-driven genome regulation by ATP-dependent chromatin remodellers. Nat Rev Mol Cell Biol 2024; 25:309-332. [PMID: 38081975 DOI: 10.1038/s41580-023-00683-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2023] [Indexed: 03/28/2024]
Abstract
The packaging of DNA into chromatin in eukaryotes regulates gene transcription, DNA replication and DNA repair. ATP-dependent chromatin remodelling enzymes (re)arrange nucleosomes at the first level of chromatin organization. Their Snf2-type motor ATPases alter histone-DNA interactions through a common DNA translocation mechanism. Whether remodeller activities mainly catalyse nucleosome dynamics or accurately co-determine nucleosome organization remained unclear. In this Review, we discuss the emerging mechanisms of chromatin remodelling: dynamic remodeller architectures and their interactions, the inner workings of the ATPase cycle, allosteric regulation and pathological dysregulation. Recent mechanistic insights argue for a decisive role of remodellers in the energy-driven self-organization of chromatin, which enables both stability and plasticity of genome regulation - for example, during development and stress. Different remodellers, such as members of the SWI/SNF, ISWI, CHD and INO80 families, process (epi)genetic information through specific mechanisms into distinct functional outputs. Combinatorial assembly of remodellers and their interplay with histone modifications, histone variants, DNA sequence or DNA-bound transcription factors regulate nucleosome mobilization or eviction or histone exchange. Such input-output relationships determine specific nucleosome positions and compositions with distinct DNA accessibilities and mediate differential genome regulation. Finally, remodeller genes are often mutated in diseases characterized by genome dysregulation, notably in cancer, and we discuss their physiological relevance.
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Affiliation(s)
- Sebastian Eustermann
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Avinash B Patel
- Department of Molecular Biosciences, Robert H. Lurie Comprehensive Cancer Center, Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
| | - Karl-Peter Hopfner
- Gene Center and Department of Biochemistry, Faculty of Chemistry and Pharmacy, LMU Munich, Munich, Germany
| | - Yuan He
- Department of Molecular Biosciences, Robert H. Lurie Comprehensive Cancer Center, Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA.
| | - Philipp Korber
- Biomedical Center (BMC), Molecular Biology, Faculty of Medicine, LMU Munich, Martinsried, Germany.
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6
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Chio US, Palovcak E, Smith AAA, Autzen H, Muñoz EN, Yu Z, Wang F, Agard DA, Armache JP, Narlikar GJ, Cheng Y. Functionalized graphene-oxide grids enable high-resolution cryo-EM structures of the SNF2h-nucleosome complex without crosslinking. Nat Commun 2024; 15:2225. [PMID: 38472177 PMCID: PMC10933330 DOI: 10.1038/s41467-024-46178-y] [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: 05/19/2023] [Accepted: 02/15/2024] [Indexed: 03/14/2024] Open
Abstract
Single-particle cryo-EM is widely used to determine enzyme-nucleosome complex structures. However, cryo-EM sample preparation remains challenging and inconsistent due to complex denaturation at the air-water interface (AWI). Here, to address this issue, we develop graphene-oxide-coated EM grids functionalized with either single-stranded DNA (ssDNA) or thiol-poly(acrylic acid-co-styrene) (TAASTY) co-polymer. These grids protect complexes between the chromatin remodeler SNF2h and nucleosomes from the AWI and facilitate collection of high-quality micrographs of intact SNF2h-nucleosome complexes in the absence of crosslinking. The data yields maps ranging from 2.3 to 3 Å in resolution. 3D variability analysis reveals nucleotide-state linked conformational changes in SNF2h bound to a nucleosome. In addition, the analysis provides structural evidence for asymmetric coordination between two SNF2h protomers acting on the same nucleosome. We envision these grids will enable similar detailed structural analyses for other enzyme-nucleosome complexes and possibly other protein-nucleic acid complexes in general.
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Affiliation(s)
- Un Seng Chio
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Eugene Palovcak
- Biophysics Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Anton A A Smith
- Department of Materials Science & Engineering, Stanford University, Stanford, CA, USA
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Henriette Autzen
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
- Linderstrom-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, København, Denmark
| | - Elise N Muñoz
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Zanlin Yu
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Feng Wang
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - David A Agard
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Jean-Paul Armache
- Department of Biochemistry and Molecular Biology and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA.
| | - Geeta J Narlikar
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
| | - Yifan Cheng
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA.
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7
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Liu Y, Zhang Z, Hu H, Chen W, Zhang F, Wang Q, Wang C, Yan K, Du J. Molecular basis of chromatin remodelling by DDM1 involved in plant DNA methylation. NATURE PLANTS 2024; 10:374-380. [PMID: 38413824 DOI: 10.1038/s41477-024-01640-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 01/31/2024] [Indexed: 02/29/2024]
Abstract
Eukaryotic gene regulation occurs at the chromatin level, which requires changing the chromatin structure by a group of ATP-dependent DNA translocases-namely, the chromatin remodellers1. In plants, chromatin remodellers function in various biological processes and possess both conserved and plant-specific components2-5. DECREASE IN DNA METHYLATION 1 (DDM1) is a plant chromatin remodeller that plays a key role in the maintenance DNA methylation6-11. Here we determined the structures of Arabidopsis DDM1 in complex with nucleosome in ADP-BeFx-bound, ADP-bound and nucleotide-free conformations. We show that DDM1 specifically recognizes the H4 tail and nucleosomal DNA. The conformational differences between ADP-BeFx-bound, ADP-bound and nucleotide-free DDM1 suggest a chromatin remodelling cycle coupled to ATP binding, hydrolysis and ADP release. This, in turn, triggers conformational changes in the DDM1-bound nucleosomal DNA, which alters the nucleosome structure and promotes DNA sliding. Together, our data reveal the molecular basis of chromatin remodelling by DDM1.
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Affiliation(s)
- Yue Liu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Zhihui Zhang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Hongmiao Hu
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Wei Chen
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Fan Zhang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Qian Wang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Changshi Wang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Kaige Yan
- Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.
- Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, China.
| | - Jiamu Du
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.
- Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, China.
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8
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Yu J, Sui F, Gu F, Li W, Yu Z, Wang Q, He S, Wang L, Xu Y. Structural insights into histone exchange by human SRCAP complex. Cell Discov 2024; 10:15. [PMID: 38331872 PMCID: PMC10853557 DOI: 10.1038/s41421-023-00640-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 12/18/2023] [Indexed: 02/10/2024] Open
Abstract
Histone variant H2A.Z is found at promoters and regulates transcription. The ATP-dependent chromatin remodeler SRCAP complex (SRCAP-C) promotes the replacement of canonical histone H2A-H2B dimer with H2A.Z-H2B dimer. Here, we determined structures of human SRCAP-C bound to H2A-containing nucleosome at near-atomic resolution. The SRCAP subunit integrates a 6-subunit actin-related protein (ARP) module and an ATPase-containing motor module. The ATPase-associated ARP module encircles half of the nucleosome along the DNA and may restrain net DNA translocation, a unique feature of SRCAP-C. The motor module adopts distinct nucleosome binding modes in the apo (nucleotide-free), ADP-bound, and ADP-BeFx-bound states, suggesting that ATPase-driven movement destabilizes H2A-H2B by unwrapping the entry DNA and pulls H2A-H2B out of nucleosome through the ZNHIT1 subunit. Structure-guided chromatin immunoprecipitation sequencing analysis confirmed the requirement of H2A-contacting ZNHIT1 in maintaining H2A.Z occupancy on the genome. Our study provides structural insights into the mechanism of H2A-H2A.Z exchange mediated by SRCAP-C.
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Affiliation(s)
- Jiali Yu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, China
- The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology of China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
| | - Fengrui Sui
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, China
| | - Feng Gu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, China
| | - Wanjun Li
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, China
| | - Zishuo Yu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, China
| | - Qianmin Wang
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, China
| | - Shuang He
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, China
| | - Li Wang
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, China.
- Greater Bay Area Institute of Precision Medicine, Fudan University, Nansha District, Guangzhou, Guangdong, China.
| | - Yanhui Xu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, China.
- The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology of China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, China.
- Greater Bay Area Institute of Precision Medicine, Fudan University, Nansha District, Guangzhou, Guangdong, China.
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9
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Bacic L, Gaullier G, Mohapatra J, Mao G, Brackmann K, Panfilov M, Liszczak G, Sabantsev A, Deindl S. Asymmetric nucleosome PARylation at DNA breaks mediates directional nucleosome sliding by ALC1. Nat Commun 2024; 15:1000. [PMID: 38307862 PMCID: PMC10837151 DOI: 10.1038/s41467-024-45237-8] [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: 03/09/2023] [Accepted: 01/16/2024] [Indexed: 02/04/2024] Open
Abstract
The chromatin remodeler ALC1 is activated by DNA damage-induced poly(ADP-ribose) deposited by PARP1/PARP2 and their co-factor HPF1. ALC1 has emerged as a cancer drug target, but how it is recruited to ADP-ribosylated nucleosomes to affect their positioning near DNA breaks is unknown. Here we find that PARP1/HPF1 preferentially initiates ADP-ribosylation on the histone H2B tail closest to the DNA break. To dissect the consequences of such asymmetry, we generate nucleosomes with a defined ADP-ribosylated H2B tail on one side only. The cryo-electron microscopy structure of ALC1 bound to such an asymmetric nucleosome indicates preferential engagement on one side. Using single-molecule FRET, we demonstrate that this asymmetric recruitment gives rise to directed sliding away from the DNA linker closest to the ADP-ribosylation site. Our data suggest a mechanism by which ALC1 slides nucleosomes away from a DNA break to render it more accessible to repair factors.
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Affiliation(s)
- Luka Bacic
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124, Uppsala, Sweden
| | - Guillaume Gaullier
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124, Uppsala, Sweden
- Department of Chemistry - Ångström, Uppsala University, 75120, Uppsala, Sweden
| | - Jugal Mohapatra
- Department of Biochemistry, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390, USA
| | - Guanzhong Mao
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124, Uppsala, Sweden
| | - Klaus Brackmann
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124, Uppsala, Sweden
| | - Mikhail Panfilov
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124, Uppsala, Sweden
| | - Glen Liszczak
- Department of Biochemistry, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390, USA
| | - Anton Sabantsev
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124, Uppsala, Sweden.
| | - Sebastian Deindl
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124, Uppsala, Sweden.
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10
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Ahmad K, Brahma S, Henikoff S. Epigenetic pioneering by SWI/SNF family remodelers. Mol Cell 2024; 84:194-201. [PMID: 38016477 PMCID: PMC10842064 DOI: 10.1016/j.molcel.2023.10.045] [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: 07/06/2023] [Revised: 09/20/2023] [Accepted: 10/31/2023] [Indexed: 11/30/2023]
Abstract
In eukaryotic genomes, transcriptional machinery and nucleosomes compete for binding to DNA sequences; thus, a crucial aspect of gene regulatory element function is to modulate chromatin accessibility for transcription factor (TF) and RNA polymerase binding. Recent structural studies have revealed multiple modes of TF engagement with nucleosomes, but how initial "pioneering" results in steady-state DNA accessibility for further TF binding and RNA polymerase II (RNAPII) engagement has been unclear. Even less well understood is how distant sites of open chromatin interact with one another, such as when developmental enhancers activate promoters to release RNAPII for productive elongation. Here, we review evidence for the centrality of the conserved SWI/SNF family of nucleosome remodeling complexes, both in pioneering and in mediating enhancer-promoter contacts. Consideration of the nucleosome unwrapping and ATP hydrolysis activities of SWI/SNF complexes, together with their architectural features, may reconcile steady-state TF occupancy with rapid TF dynamics observed by live imaging.
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Affiliation(s)
- Kami Ahmad
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Sandipan Brahma
- University of Nebraska Medical Center, Department of Genetics, Cell Biology & Anatomy, Omaha, NE, USA
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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11
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Duan W, Hao Z, Pang H, Peng Y, Xu Y, Zhang Y, Zhang Y, Kang Z, Zhao J. Novel stripe rust effector boosts the transcription of a host susceptibility factor through affecting histone modification to promote infection in wheat. THE NEW PHYTOLOGIST 2024; 241:378-393. [PMID: 37828684 DOI: 10.1111/nph.19312] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 09/18/2023] [Indexed: 10/14/2023]
Abstract
Regulation of host gene expression to promote disease is a common strategy for plant pathogens. However, it remains unclear whether or not fungal pathogens manipulate host gene expression directly through secreted effectors with transcriptional activity. Here, we identified a fungal effector PstGTA1 from Puccinia striiformis f. sp. tritici (Pst), which has partial homology to the subunit of global transcriptional activator SNF2 from oyster. The transcriptional activating activity of PstGTA1 was validated in yeast, and the potential role of PstGTA1 in pathogenicity was assessed using gene silenced and overexpression transgenic wheat plants. Candidate targets regulated by PstGTA1 were screened by transcriptomic analysis, and the specific promoter region binding to PstGTA1 was further determined. PstGTA1 can be delivered to the wheat cell nucleus and contributes to the full virulence of Pst by targeting the promoter of TaSIG, a gene negatively regulating wheat immunity, and possibly activates its transcription by affecting the histone H3K4 acetylation level. Our study provides the first direct evidence for a fungal effector with transactivation activity modulating the transcription of a host specific susceptibility gene through promoter binding and histone acetylation.
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Affiliation(s)
- Wanlu Duan
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zhenkai Hao
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Huihui Pang
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yuxi Peng
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yiwen Xu
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yanfei Zhang
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Ying Zhang
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zhensheng Kang
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jing Zhao
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, 712100, China
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12
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Park S, Brandani GB, Ha T, Bowman G. Bi-directional nucleosome sliding by the Chd1 chromatin remodeler integrates intrinsic sequence-dependent and ATP-dependent nucleosome positioning. Nucleic Acids Res 2023; 51:10326-10343. [PMID: 37738162 PMCID: PMC10602870 DOI: 10.1093/nar/gkad738] [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: 03/11/2022] [Revised: 08/02/2023] [Accepted: 08/26/2023] [Indexed: 09/24/2023] Open
Abstract
Chromatin remodelers use a helicase-type ATPase motor to shift DNA around the histone core. Although not directly reading out the DNA sequence, some chromatin remodelers exhibit a sequence-dependent bias in nucleosome positioning, which presumably reflects properties of the DNA duplex. Here, we show how nucleosome positioning by the Chd1 remodeler is influenced by local DNA perturbations throughout the nucleosome footprint. Using site-specific DNA cleavage coupled with next-generation sequencing, we show that nucleosomes shifted by Chd1 can preferentially localize DNA perturbations - poly(dA:dT) tracts, DNA mismatches, and single-nucleotide insertions - about a helical turn outside the Chd1 motor domain binding site, super helix location 2 (SHL2). This phenomenon occurs with both the Widom 601 positioning sequence and the natural +1 nucleosome sequence from the Saccharomyces cerevisiae SWH1 gene. Our modeling indicates that localization of DNA perturbations about a helical turn outward from SHL2 results from back-and-forth sliding due to remodeler action on both sides of the nucleosome. Our results also show that barrier effects from DNA perturbations can be extended by the strong phasing of nucleosome positioning sequences.
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Affiliation(s)
- Sangwoo Park
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Giovanni B Brandani
- Department of Biophysics, Graduate School of Science, Kyoto University, Japan
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Baltimore, MD 21205, USA
- TC Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Gregory D Bowman
- TC Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
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13
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Lee SC, Adams DW, Ipsaro JJ, Cahn J, Lynn J, Kim HS, Berube B, Major V, Calarco JP, LeBlanc C, Bhattacharjee S, Ramu U, Grimanelli D, Jacob Y, Voigt P, Joshua-Tor L, Martienssen RA. Chromatin remodeling of histone H3 variants by DDM1 underlies epigenetic inheritance of DNA methylation. Cell 2023; 186:4100-4116.e15. [PMID: 37643610 PMCID: PMC10529913 DOI: 10.1016/j.cell.2023.08.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/19/2023] [Accepted: 08/01/2023] [Indexed: 08/31/2023]
Abstract
Nucleosomes block access to DNA methyltransferase, unless they are remodeled by DECREASE in DNA METHYLATION 1 (DDM1LSH/HELLS), a Snf2-like master regulator of epigenetic inheritance. We show that DDM1 promotes replacement of histone variant H3.3 by H3.1. In ddm1 mutants, DNA methylation is partly restored by loss of the H3.3 chaperone HIRA, while the H3.1 chaperone CAF-1 becomes essential. The single-particle cryo-EM structure at 3.2 Å of DDM1 with a variant nucleosome reveals engagement with histone H3.3 near residues required for assembly and with the unmodified H4 tail. An N-terminal autoinhibitory domain inhibits activity, while a disulfide bond in the helicase domain supports activity. DDM1 co-localizes with H3.1 and H3.3 during the cell cycle, and with the DNA methyltransferase MET1Dnmt1, but is blocked by H4K16 acetylation. The male germline H3.3 variant MGH3/HTR10 is resistant to remodeling by DDM1 and acts as a placeholder nucleosome in sperm cells for epigenetic inheritance.
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Affiliation(s)
- Seung Cho Lee
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Dexter W Adams
- W. M. Keck Structural Biology Laboratory, Howard Hughes Medical Institute, Cold Spring Harbor, NY 11724, USA; Graduate Program in Genetics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Jonathan J Ipsaro
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA; W. M. Keck Structural Biology Laboratory, Howard Hughes Medical Institute, Cold Spring Harbor, NY 11724, USA
| | - Jonathan Cahn
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Jason Lynn
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Hyun-Soo Kim
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Benjamin Berube
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA; Cold Spring Harbor Laboratory School of Biological Sciences, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA
| | - Viktoria Major
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Joseph P Calarco
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA; Cold Spring Harbor Laboratory School of Biological Sciences, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA
| | - Chantal LeBlanc
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Sonali Bhattacharjee
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Umamaheswari Ramu
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Daniel Grimanelli
- Institut de Recherche pour le Développement, 911Avenue Agropolis, 34394 Montpelier, France
| | - Yannick Jacob
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Philipp Voigt
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Leemor Joshua-Tor
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA; W. M. Keck Structural Biology Laboratory, Howard Hughes Medical Institute, Cold Spring Harbor, NY 11724, USA.
| | - Robert A Martienssen
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.
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14
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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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15
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Lee SC, Adams DW, Ipsaro JJ, Cahn J, Lynn J, Kim HS, Berube B, Major V, Calarco JP, LeBlanc C, Bhattacharjee S, Ramu U, Grimanelli D, Jacob Y, Voigt P, Joshua-Tor L, Martienssen RA. Chromatin remodeling of histone H3 variants underlies epigenetic inheritance of DNA methylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.11.548598. [PMID: 37503143 PMCID: PMC10369972 DOI: 10.1101/2023.07.11.548598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Epigenetic inheritance refers to the faithful replication of DNA methylation and histone modification independent of DNA sequence. Nucleosomes block access to DNA methyltransferases, unless they are remodeled by DECREASE IN DNA METHYLATION1 (DDM1 Lsh/HELLS ), a Snf2-like master regulator of epigenetic inheritance. We show that DDM1 activity results in replacement of the transcriptional histone variant H3.3 for the replicative variant H3.1 during the cell cycle. In ddm1 mutants, DNA methylation can be restored by loss of the H3.3 chaperone HIRA, while the H3.1 chaperone CAF-1 becomes essential. The single-particle cryo-EM structure at 3.2 Å of DDM1 with a variant nucleosome reveals direct engagement at SHL2 with histone H3.3 at or near variant residues required for assembly, as well as with the deacetylated H4 tail. An N-terminal autoinhibitory domain binds H2A variants to allow remodeling, while a disulfide bond in the helicase domain is essential for activity in vivo and in vitro . We show that differential remodeling of H3 and H2A variants in vitro reflects preferential deposition in vivo . DDM1 co-localizes with H3.1 and H3.3 during the cell cycle, and with the DNA methyltransferase MET1 Dnmt1 . DDM1 localization to the chromosome is blocked by H4K16 acetylation, which accumulates at DDM1 targets in ddm1 mutants, as does the sperm cell specific H3.3 variant MGH3 in pollen, which acts as a placeholder nucleosome in the germline and contributes to epigenetic inheritance.
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Affiliation(s)
- Seung Cho Lee
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory; 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Dexter W. Adams
- W. M. Keck Structural Biology Laboratory, Howard Hughes Medical Institute; Cold Spring Harbor, NY 11724, USA
- Graduate Program in Genetics, Stony Brook University; Stony Brook, NY 11794, USA
| | - Jonathan J. Ipsaro
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory; 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
- W. M. Keck Structural Biology Laboratory, Howard Hughes Medical Institute; Cold Spring Harbor, NY 11724, USA
| | - Jonathan Cahn
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory; 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Jason Lynn
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory; 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Hyun-Soo Kim
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory; 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Benjamin Berube
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory; 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
- Cold Spring Harbor Laboratory School of Biological Sciences; 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA
| | - Viktoria Major
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh; Edinburgh EH9 3BF, United Kingdom
| | - Joseph P. Calarco
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory; 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
- Cold Spring Harbor Laboratory School of Biological Sciences; 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA
| | - Chantal LeBlanc
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory; 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
- Present address: Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University; 260 Whitney Ave., New Haven, CT, 06511, USA
| | - Sonali Bhattacharjee
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory; 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Umamaheswari Ramu
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory; 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Daniel Grimanelli
- Institut de Recherche pour le Développement; 911 Avenue Agropolis, 34394 Montpellier, France
| | - Yannick Jacob
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory; 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
- Present address: Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University; 260 Whitney Ave., New Haven, CT, 06511, USA
| | - Philipp Voigt
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh; Edinburgh EH9 3BF, United Kingdom
- Present address: Epigenetics Programme, Babraham Institute; Cambridge CB22 3AT, United Kingdom
| | - Leemor Joshua-Tor
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory; 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
- W. M. Keck Structural Biology Laboratory, Howard Hughes Medical Institute; Cold Spring Harbor, NY 11724, USA
| | - Robert A. Martienssen
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory; 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
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16
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Valencia AM, Sankar A, van der Sluijs PJ, Satterstrom FK, Fu J, Talkowski ME, Vergano SAS, Santen GWE, Kadoch C. Landscape of mSWI/SNF chromatin remodeling complex perturbations in neurodevelopmental disorders. Nat Genet 2023; 55:1400-1412. [PMID: 37500730 PMCID: PMC10412456 DOI: 10.1038/s41588-023-01451-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 06/20/2023] [Indexed: 07/29/2023]
Abstract
DNA sequencing-based studies of neurodevelopmental disorders (NDDs) have identified a wide range of genetic determinants. However, a comprehensive analysis of these data, in aggregate, has not to date been performed. Here, we find that genes encoding the mammalian SWI/SNF (mSWI/SNF or BAF) family of ATP-dependent chromatin remodeling protein complexes harbor the greatest number of de novo missense and protein-truncating variants among nuclear protein complexes. Non-truncating NDD-associated protein variants predominantly disrupt the cBAF subcomplex and cluster in four key structural regions associated with high disease severity, including mSWI/SNF-nucleosome interfaces, the ATPase-core ARID-armadillo repeat (ARM) module insertion site, the Arp module and DNA-binding domains. Although over 70% of the residues perturbed in NDDs overlap with those mutated in cancer, ~60% of amino acid changes are NDD-specific. These findings provide a foundation to functionally group variants and link complex aberrancies to phenotypic severity, serving as a resource for the chromatin, clinical genetics and neurodevelopment communities.
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Affiliation(s)
- Alfredo M Valencia
- Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Chemical Biology Program, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Stanford Brain Organogenesis, Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Akshay Sankar
- Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - F Kyle Satterstrom
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital, Boston, MA, USA
| | - Jack Fu
- Massachusetts General Hospital, Boston, MA, USA
| | - Michael E Talkowski
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital, Boston, MA, USA
| | - Samantha A Schrier Vergano
- Children's Hospital of the King's Daughters, Norfolk, Virginia, USA
- Department of Pediatrics, Eastern Virginia Medical School, Norfolk, Virginia, USA
| | - Gijs W E Santen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Cigall Kadoch
- Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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17
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Kim J, Li CL, Chen X, Cui Y, Golebiowski FM, Wang H, Hanaoka F, Sugasawa K, Yang W. Lesion recognition by XPC, TFIIH and XPA in DNA excision repair. Nature 2023; 617:170-175. [PMID: 37076618 PMCID: PMC10416759 DOI: 10.1038/s41586-023-05959-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 03/15/2023] [Indexed: 04/21/2023]
Abstract
Nucleotide excision repair removes DNA lesions caused by ultraviolet light, cisplatin-like compounds and bulky adducts1. After initial recognition by XPC in global genome repair or a stalled RNA polymerase in transcription-coupled repair, damaged DNA is transferred to the seven-subunit TFIIH core complex (Core7) for verification and dual incisions by the XPF and XPG nucleases2. Structures capturing lesion recognition by the yeast XPC homologue Rad4 and TFIIH in transcription initiation or DNA repair have been separately reported3-7. How two different lesion recognition pathways converge and how the XPB and XPD helicases of Core7 move the DNA lesion for verification are unclear. Here we report on structures revealing DNA lesion recognition by human XPC and DNA lesion hand-off from XPC to Core7 and XPA. XPA, which binds between XPB and XPD, kinks the DNA duplex and shifts XPC and the DNA lesion by nearly a helical turn relative to Core7. The DNA lesion is thus positioned outside of Core7, as would occur with RNA polymerase. XPB and XPD, which track the lesion-containing strand but translocate DNA in opposite directions, push and pull the lesion-containing strand into XPD for verification.
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Affiliation(s)
- Jinseok Kim
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD, USA
| | - Chia-Lung Li
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD, USA
| | - Xuemin Chen
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD, USA
- School of Life Sciences, Anhui University, Hefei, China
| | - Yanxiang Cui
- Laboratory of Cell and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD, USA
| | - Filip M Golebiowski
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD, USA
- Roche Polska, Warsaw, Poland
| | - Huaibin Wang
- Laboratory of Cell and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD, USA
| | - Fumio Hanaoka
- National Institute of Genetics, Research Organization of Information and Systems, Mishima, Japan
| | - Kaoru Sugasawa
- Biosignal Research Center and Graduate School of Science, Kobe University, Kobe, Japan.
| | - Wei Yang
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD, USA.
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18
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Woike S, Eustermann S, Jung J, Wenzl SJ, Hagemann G, Bartho J, Lammens K, Butryn A, Herzog F, Hopfner KP. Structural basis for TBP displacement from TATA box DNA by the Swi2/Snf2 ATPase Mot1. Nat Struct Mol Biol 2023; 30:640-649. [PMID: 37106137 PMCID: PMC7615866 DOI: 10.1038/s41594-023-00966-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 03/13/2023] [Indexed: 04/29/2023]
Abstract
The Swi2/Snf2 family transcription regulator Modifier of Transcription 1 (Mot1) uses adenosine triphosphate (ATP) to dissociate and reallocate the TATA box-binding protein (TBP) from and between promoters. To reveal how Mot1 removes TBP from TATA box DNA, we determined cryogenic electron microscopy structures that capture different states of the remodeling reaction. The resulting molecular video reveals how Mot1 dissociates TBP in a process that, intriguingly, does not require DNA groove tracking. Instead, the motor grips DNA in the presence of ATP and swings back after ATP hydrolysis, moving TBP to a thermodynamically less stable position on DNA. Dislodged TBP is trapped by a chaperone element that blocks TBP's DNA binding site. Our results show how Swi2/Snf2 proteins can remodel protein-DNA complexes through DNA bending without processive DNA tracking and reveal mechanistic similarities to RNA gripping DEAD box helicases and RIG-I-like immune sensors.
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Affiliation(s)
- Stephan Woike
- Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
- Gene Center, Ludwig-Maximilians-Universität, Munich, Germany
| | - Sebastian Eustermann
- Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
- Gene Center, Ludwig-Maximilians-Universität, Munich, Germany
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany
| | - James Jung
- Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
- Gene Center, Ludwig-Maximilians-Universität, Munich, Germany
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Simon Josef Wenzl
- Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
- Gene Center, Ludwig-Maximilians-Universität, Munich, Germany
| | - Götz Hagemann
- Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
- Gene Center, Ludwig-Maximilians-Universität, Munich, Germany
| | - Joseph Bartho
- Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
- Gene Center, Ludwig-Maximilians-Universität, Munich, Germany
| | - Katja Lammens
- Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
- Gene Center, Ludwig-Maximilians-Universität, Munich, Germany
| | - Agata Butryn
- Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
- Gene Center, Ludwig-Maximilians-Universität, Munich, Germany
- Macromolecular Machines Laboratory, Francis Crick Institute, London, UK
| | - Franz Herzog
- Gene Center, Ludwig-Maximilians-Universität, Munich, Germany
- Institute Krems Bioanalytics, IMC University of Applied Sciences, Krems, Austria
| | - Karl-Peter Hopfner
- Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany.
- Gene Center, Ludwig-Maximilians-Universität, Munich, Germany.
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19
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Morse K, Swerdlow S, Ünal E. Swi/Snf Chromatin Remodeling Regulates Transcriptional Interference and Gene Repression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.27.538572. [PMID: 37162931 PMCID: PMC10168381 DOI: 10.1101/2023.04.27.538572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Alternative transcription start sites can affect transcript isoform diversity and translation levels. In a recently described form of gene regulation, coordinated transcriptional and translational interference results in transcript isoform-dependent changes in protein expression. Specifically, a long undecoded transcript isoform (LUTI) is transcribed from a gene-distal promoter, interfering with expression of the gene-proximal promoter. While transcriptional and chromatin features associated with LUTI expression have been described, the mechanism underlying LUTI-based transcriptional interference is not well understood. Using an unbiased genetic approach followed by integrated genomic analysis, we uncovered that the Swi/Snf chromatin remodeling complex is required for co-transcriptional nucleosome remodeling that leads to LUTI-based repression. We identified genes with tandem promoters that rely on Swi/Snf function for transcriptional interference during protein folding stress, including LUTI-regulated genes. To our knowledge, this study is the first to observe Swi/Snf's direct involvement in gene repression via a cis transcriptional interference mechanism.
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Affiliation(s)
- Kaitlin Morse
- Department of Molecular and Cell Biology, Barker Hall, University of California, Berkeley, CA, USA, 94720
| | - Sarah Swerdlow
- Department of Molecular and Cell Biology, Barker Hall, University of California, Berkeley, CA, USA, 94720
| | - Elçin Ünal
- Department of Molecular and Cell Biology, Barker Hall, University of California, Berkeley, CA, USA, 94720
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20
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Wang L, Yu J, Yu Z, Wang Q, Li W, Ren Y, Chen Z, He S, Xu Y. Structure of nucleosome-bound human PBAF complex. Nat Commun 2022; 13:7644. [PMID: 36496390 PMCID: PMC9741621 DOI: 10.1038/s41467-022-34859-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 11/09/2022] [Indexed: 12/13/2022] Open
Abstract
BAF and PBAF are mammalian SWI/SNF family chromatin remodeling complexes that possess multiple histone/DNA-binding subunits and create nucleosome-depleted/free regions for transcription activation. Despite previous structural studies and recent advance of SWI/SNF family complexes, it remains incompletely understood how PBAF-nucleosome complex is organized. Here we determined structure of 13-subunit human PBAF in complex with acetylated nucleosome in ADP-BeF3-bound state. Four PBAF-specific subunits work together with nine BAF/PBAF-shared subunits to generate PBAF-specific modular organization, distinct from that of BAF at various regions. PBAF-nucleosome structure reveals six histone-binding domains and four DNA-binding domains/modules, the majority of which directly bind histone/DNA. This multivalent nucleosome-binding pattern, not observed in previous studies, suggests that PBAF may integrate comprehensive chromatin information to target genomic loci for function. Our study reveals molecular organization of subunits and histone/DNA-binding domains/modules in PBAF-nucleosome complex and provides structural insights into PBAF-mediated nucleosome association complimentary to the recently reported PBAF-nucleosome structure.
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Affiliation(s)
- Li Wang
- grid.11841.3d0000 0004 0619 8943Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032 China ,grid.11841.3d0000 0004 0619 8943The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032 China ,grid.8547.e0000 0001 0125 2443Human Phenome Institute, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433 China
| | - Jiali Yu
- grid.11841.3d0000 0004 0619 8943Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032 China
| | - Zishuo Yu
- grid.11841.3d0000 0004 0619 8943Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032 China
| | - Qianmin Wang
- grid.11841.3d0000 0004 0619 8943Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032 China
| | - Wanjun Li
- grid.11841.3d0000 0004 0619 8943Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032 China
| | - Yulei Ren
- grid.11841.3d0000 0004 0619 8943Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032 China
| | - Zhenguo Chen
- grid.11841.3d0000 0004 0619 8943Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032 China ,grid.8547.e0000 0001 0125 2443The Fifth People’s Hospital of Shanghai, Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Key Laboratory of Medical Epigenetics, and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032 China
| | - Shuang He
- grid.11841.3d0000 0004 0619 8943Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032 China
| | - Yanhui Xu
- grid.11841.3d0000 0004 0619 8943Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032 China ,grid.11841.3d0000 0004 0619 8943The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032 China ,grid.8547.e0000 0001 0125 2443Human Phenome Institute, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433 China
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21
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Ding T, Zhang H. Novel biological insights revealed from the investigation of multiscale genome architecture. Comput Struct Biotechnol J 2022; 21:312-325. [PMID: 36582436 PMCID: PMC9791078 DOI: 10.1016/j.csbj.2022.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 12/06/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
Gene expression and cell fate determination require precise and coordinated epigenetic regulation. The complex three-dimensional (3D) genome organization plays a critical role in transcription in myriad biological processes. A wide range of architectural features of the 3D genome, including chromatin loops, topologically associated domains (TADs), chromatin compartments, and phase separation, together regulate the chromatin state and transcriptional activity at multiple levels. With the help of 3D genome informatics, recent biochemistry and imaging approaches based on different strategies have revealed functional interactions among biomacromolecules, even at the single-cell level. Here, we review the occurrence, mechanistic basis, and functional implications of dynamic genome organization, and outline recent experimental and computational approaches for profiling multiscale genome architecture to provide robust tools for studying the 3D genome.
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Affiliation(s)
| | - He Zhang
- Corresponding author at: School of Life Science and Technology, Tongji University, Shanghai 200092, PR China.
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22
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Kunert F, Metzner FJ, Jung J, Höpfler M, Woike S, Schall K, Kostrewa D, Moldt M, Chen JX, Bantele S, Pfander B, Eustermann S, Hopfner KP. Structural mechanism of extranucleosomal DNA readout by the INO80 complex. SCIENCE ADVANCES 2022; 8:eadd3189. [PMID: 36490333 PMCID: PMC9733932 DOI: 10.1126/sciadv.add3189] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The nucleosomal landscape of chromatin depends on the concerted action of chromatin remodelers. The INO80 remodeler specifically places nucleosomes at the boundary of gene regulatory elements, which is proposed to be the result of an ATP-dependent nucleosome sliding activity that is regulated by extranucleosomal DNA features. Here, we use cryo-electron microscopy and functional assays to reveal how INO80 binds and is regulated by extranucleosomal DNA. Structures of the regulatory A-module bound to DNA clarify the mechanism of linker DNA binding. The A-module is connected to the motor unit via an HSA/post-HSA lever element to chemomechanically couple the motor and linker DNA sensing. Two notable sites of curved DNA recognition by coordinated action of the four actin/actin-related proteins and the motor suggest how sliding by INO80 can be regulated by extranucleosomal DNA features. Last, the structures clarify the recruitment of YY1/Ies4 subunits and reveal deep architectural similarities between the regulatory modules of INO80 and SWI/SNF complexes.
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Affiliation(s)
- Franziska Kunert
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Felix J. Metzner
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - James Jung
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Markus Höpfler
- DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Stephan Woike
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Kevin Schall
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Dirk Kostrewa
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Manuela Moldt
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jia-Xuan Chen
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Susanne Bantele
- DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Boris Pfander
- DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Sebastian Eustermann
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Karl-Peter Hopfner
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
- Corresponding author.
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23
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Zhong Y, Moghaddas Sani H, Paudel BP, Low JKK, Silva APG, Mueller S, Deshpande C, Panjikar S, Reid XJ, Bedward MJ, van Oijen AM, Mackay JP. The role of auxiliary domains in modulating CHD4 activity suggests mechanistic commonality between enzyme families. Nat Commun 2022; 13:7524. [PMID: 36473839 PMCID: PMC9726900 DOI: 10.1038/s41467-022-35002-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022] Open
Abstract
CHD4 is an essential, widely conserved ATP-dependent translocase that is also a broad tumour dependency. In common with other SF2-family chromatin remodelling enzymes, it alters chromatin accessibility by repositioning histone octamers. Besides the helicase and adjacent tandem chromodomains and PHD domains, CHD4 features 1000 residues of N- and C-terminal sequence with unknown structure and function. We demonstrate that these regions regulate CHD4 activity through different mechanisms. An N-terminal intrinsically disordered region (IDR) promotes remodelling integrity in a manner that depends on the composition but not sequence of the IDR. The C-terminal region harbours an auto-inhibitory region that contacts the helicase domain. Auto-inhibition is relieved by a previously unrecognized C-terminal SANT-SLIDE domain split by ~150 residues of disordered sequence, most likely by binding of this domain to substrate DNA. Our data shed light on CHD4 regulation and reveal strong mechanistic commonality between CHD family members, as well as with ISWI-family remodellers.
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Affiliation(s)
- Yichen Zhong
- grid.1013.30000 0004 1936 834XSchool of Life and Environmental Sciences, University of Sydney, The University of Sydney, NSW 2006 Australia
| | - Hakimeh Moghaddas Sani
- grid.1013.30000 0004 1936 834XSchool of Life and Environmental Sciences, University of Sydney, The University of Sydney, NSW 2006 Australia
| | - Bishnu P. Paudel
- grid.1007.60000 0004 0486 528XMolecular Horizons, School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522 Australia ,grid.510958.0Illawarra Health and Medical Research Institute, Wollongong, NSW 2522 Australia
| | - Jason K. K. Low
- grid.1013.30000 0004 1936 834XSchool of Life and Environmental Sciences, University of Sydney, The University of Sydney, NSW 2006 Australia
| | - Ana P. G. Silva
- grid.1013.30000 0004 1936 834XSchool of Life and Environmental Sciences, University of Sydney, The University of Sydney, NSW 2006 Australia
| | - Stefan Mueller
- grid.1007.60000 0004 0486 528XMolecular Horizons, School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522 Australia ,grid.510958.0Illawarra Health and Medical Research Institute, Wollongong, NSW 2522 Australia
| | - Chandrika Deshpande
- grid.1013.30000 0004 1936 834XSchool of Life and Environmental Sciences, University of Sydney, The University of Sydney, NSW 2006 Australia
| | - Santosh Panjikar
- grid.248753.f0000 0004 0562 0567Australian Synchrotron, Clayton, VIC 3168 Australia ,grid.1002.30000 0004 1936 7857Department of Molecular Biology and Biochemistry, Monash University, Clayton, VIC 3800 Australia
| | - Xavier J. Reid
- grid.1013.30000 0004 1936 834XSchool of Life and Environmental Sciences, University of Sydney, The University of Sydney, NSW 2006 Australia
| | - Max J. Bedward
- grid.1013.30000 0004 1936 834XSchool of Life and Environmental Sciences, University of Sydney, The University of Sydney, NSW 2006 Australia
| | - Antoine M. van Oijen
- grid.1007.60000 0004 0486 528XMolecular Horizons, School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522 Australia ,grid.510958.0Illawarra Health and Medical Research Institute, Wollongong, NSW 2522 Australia
| | - Joel P. Mackay
- grid.1013.30000 0004 1936 834XSchool of Life and Environmental Sciences, University of Sydney, The University of Sydney, NSW 2006 Australia
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24
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Fan J, Moreno AT, Baier AS, Loparo JJ, Peterson CL. H2A.Z deposition by SWR1C involves multiple ATP-dependent steps. Nat Commun 2022; 13:7052. [PMID: 36396651 PMCID: PMC9672302 DOI: 10.1038/s41467-022-34861-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 11/09/2022] [Indexed: 11/18/2022] Open
Abstract
Histone variant H2A.Z is a conserved feature of nucleosomes flanking protein-coding genes. Deposition of H2A.Z requires ATP-dependent replacement of nucleosomal H2A by a chromatin remodeler related to the multi-subunit enzyme, yeast SWR1C. How these enzymes use ATP to promote this nucleosome editing reaction remains unclear. Here we use single-molecule and ensemble methodologies to identify three ATP-dependent phases in the H2A.Z deposition reaction. Real-time analysis of single nucleosome remodeling events reveals an initial priming step that occurs after ATP addition that involves a combination of both transient DNA unwrapping from the nucleosome and histone octamer deformations. Priming is followed by rapid loss of histone H2A, which is subsequently released from the H2A.Z nucleosomal product. Surprisingly, rates of both priming and the release of the H2A/H2B dimer are sensitive to ATP concentration. This complex reaction pathway provides multiple opportunities to regulate timely and accurate deposition of H2A.Z at key genomic locations.
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Affiliation(s)
- Jiayi Fan
- grid.168645.80000 0001 0742 0364Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605 USA ,grid.168645.80000 0001 0742 0364Interdisciplinary Graduate Program, University of Massachusetts Chan Medical School, Worcester, MA 01605 USA
| | - Andrew T. Moreno
- grid.38142.3c000000041936754XDepartment of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115 USA
| | - Alexander S. Baier
- grid.168645.80000 0001 0742 0364Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605 USA ,grid.168645.80000 0001 0742 0364Medical Scientist Training Program, University of Massachusetts Chan Medical School, Worcester, MA 01605 USA
| | - Joseph J. Loparo
- grid.38142.3c000000041936754XDepartment of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115 USA
| | - Craig L. Peterson
- grid.168645.80000 0001 0742 0364Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605 USA
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25
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Zuiddam M, Shakiba B, Schiessel H. Multiplexing mechanical and translational cues on genes. Biophys J 2022; 121:4311-4324. [PMID: 36230003 PMCID: PMC9703045 DOI: 10.1016/j.bpj.2022.10.011] [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: 03/04/2022] [Revised: 07/06/2022] [Accepted: 10/07/2022] [Indexed: 12/14/2022] Open
Abstract
The genetic code gives precise instructions on how to translate codons into amino acids. Due to the degeneracy of the genetic code-18 out of 20 amino acids are encoded for by more than one codon-more information can be stored in a basepair sequence. Indeed, various types of additional information have been discussed in the literature, e.g., the positioning of nucleosomes along eukaryotic genomes and the modulation of the translating efficiency in ribosomes to influence cotranslational protein folding. The purpose of this study is to show that it is indeed possible to carry more than one additional layer of information on top of a gene. In particular, we show how much translation efficiency and nucleosome positioning can be adjusted simultaneously without changing the encoded protein. We achieve this by mapping genes on weighted graphs that contain all synonymous genes, and then finding shortest paths through these graphs. This enables us, for example, to readjust the disrupted translational efficiency profile after a gene has been introduced from one organism (e.g., human) into another (e.g., yeast) without greatly changing the nucleosome landscape intrinsically encoded by the DNA molecule.
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Affiliation(s)
- Martijn Zuiddam
- Institute Lorentz for Theoretical Physics, Leiden University, Leiden, the Netherlands
| | - Bahareh Shakiba
- Institute Lorentz for Theoretical Physics, Leiden University, Leiden, the Netherlands
| | - Helmut Schiessel
- Cluster of Excellence Physics of Life, TU Dresden, Dresden, Germany.
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26
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Partitioned usage of chromatin remodelers by nucleosome-displacing factors. Cell Rep 2022; 40:111250. [PMID: 36001970 PMCID: PMC9422437 DOI: 10.1016/j.celrep.2022.111250] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 06/29/2022] [Accepted: 08/01/2022] [Indexed: 11/22/2022] Open
Abstract
Nucleosome-displacing-factors (NDFs) in yeast, similar to pioneer factors in higher eukaryotes, can open closed chromatin and generate nucleosome-depleted regions (NDRs). NDRs in yeast are also affected by ATP-dependent chromatin remodelers (CRs). However, how NDFs and CRs coordinate in nucleosome invasion and NDR formation is still unclear. Here, we design a high-throughput method to systematically study the interplay between NDFs and CRs. By combining an integrated synthetic oligonucleotide library with DNA methyltransferase-based, single-molecule nucleosome mapping, we measure the impact of CRs on NDRs generated by individual NDFs. We find that CRs are dispensable for nucleosome invasion by NDFs, and they function downstream of NDF binding to modulate the NDR length. A few CRs show high specificity toward certain NDFs; however, in most cases, CRs are recruited in a factor-nonspecific and NDR length-dependent manner. Overall, our study provides a framework to investigate how NDFs and CRs cooperate to regulate chromatin opening. Chromatin accessibility in yeast is regulated by nucleosome-displacing-factors (NDFs) and chromatin remodelers (CRs). Chen et al. show that NDFs first invade into nucleosomes and then recruit CRs to modulate the NDR length. NDF-specific and NDR length-dependent recruitment of CRs allow partitioned usage of CRs by NDFs.
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27
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Adebayo IA, Habib MAH, Sarmiento ME, Acosta A, Yaacob NS, Ismail MN. Proteomic analysis of Malaysian Horseshoe crab (Tachypleus gigas) hemocytes gives insights into its innate immunity host defence system and other biological processes. PLoS One 2022; 17:e0272799. [PMID: 35947629 PMCID: PMC9365167 DOI: 10.1371/journal.pone.0272799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 07/26/2022] [Indexed: 11/18/2022] Open
Abstract
Horseshoe crabs are one of the most studied invertebrates due to their remarkable innate immunity mechanism and biological processes. In this work, the proteins of the lipopolysaccharides (LPS)-stimulated and non-stimulated hemocytes of Malaysian Tachypleus gigas were profiled using LC-MS/MS. A total of 154 proteins were identified in both types of samples. Additionally, seventy-seven proteins were commonly found in both conditions, while 52 and 25 proteins were uniquely found in the LPS-stimulated and non-stimulated hemocytes, respectively. ATP-dependent energy-generating proteins such as actins and BLTX actin-related proteins were detected in both stimulated and non-stimulated T. gigas hemocytes, but more of such proteins were found in the former type. Proteins such as tachylectin-2, coagulogen, c-reactive proteins, histones, hemocyanin, and DNA polymerase, which play key roles in the organism’s innate immunity, were differentially expressed in the hemocytes following LPS challenge. In conclusion, the proteins identified in the hemolymph of T. gigas are vital for the organism’s molecular functions, biological processes, and activation of innate immunity.
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Affiliation(s)
- Ismail Abiola Adebayo
- Faculty of Biomedical Sciences, Department of Microbiology and Immunology, Kampala International University, Ishaka, Bushenyi, Uganda
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Bayan Lepas, Pulau Pinang, Malaysia
- Department of Clinical Biology, School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
| | - Mohd Afiq Hazlami Habib
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Bayan Lepas, Pulau Pinang, Malaysia
| | - Maria E. Sarmiento
- School of Health Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Armando Acosta
- School of Health Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Nik Soriani Yaacob
- Department of Chemical Pathology, School of Medical Sciences, Universiti Sains Malaysia (USM), Kelantan, Malaysia
| | - Mohd Nazri Ismail
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Bayan Lepas, Pulau Pinang, Malaysia
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, USM, Pulau Pinang, Malaysia
- * E-mail:
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28
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Cui S, Walker JR, Batenburg NL, Zhu XD. Cockayne syndrome group B protein uses its DNA translocase activity to promote mitotic DNA synthesis. DNA Repair (Amst) 2022; 116:103354. [PMID: 35738143 DOI: 10.1016/j.dnarep.2022.103354] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/30/2022] [Accepted: 06/07/2022] [Indexed: 11/24/2022]
Abstract
Mitotic DNA synthesis, also known as MiDAS, has been suggested to be a form of RAD52-dependent break-induced replication (BIR) that repairs under-replicated DNA regions of the genome in mitosis prior to chromosome segregation. Cockayne syndrome group B (CSB) protein, a chromatin remodeler of the SNF2 family, has been implicated in RAD52-dependent BIR repair of stalled replication forks. However, whether CSB plays a role in MiDAS has not been characterized. Here, we report that CSB functions epistatically with RAD52 to promote MiDAS at common fragile sites in response to replication stress, and prevents genomic instability associated with defects in MiDAS. We show that CSB is dependent upon the conserved phenylalanine at position 796 (F796), which lies in the recently-reported pulling pin that is required for CSB's translocase activity, to mediate MiDAS, suggesting that CSB uses its DNA translocase activity to promote MiDAS. Structural analysis reveals that CSB shares with a subset of SNF2 family proteins a translocase regulatory region (TRR), which is important for CSB's function in MiDAS. We further demonstrate that phosphorylation of S1013 in the TRR regulates the function of CSB in MiDAS and restart of stalled forks but not in fork degradation in BRCA2-deficient cells and UV repair. Taken together, these results suggest that the DNA translocase activity of CSB in vivo is likely to be highly regulated by post-translational modification in a context-specific manner.
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Affiliation(s)
- Shixin Cui
- Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - John R Walker
- Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Nicole L Batenburg
- Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Xu-Dong Zhu
- Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada.
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29
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Johnson SL, Narlikar GJ. ATP hydrolysis coordinates the activities of two motors in a dimeric chromatin remodeling enzyme. J Mol Biol 2022; 434:167653. [PMID: 35659534 DOI: 10.1016/j.jmb.2022.167653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 05/12/2022] [Accepted: 05/23/2022] [Indexed: 11/17/2022]
Abstract
ATP-dependent chromatin remodelers are essential enzymes that restructure eukaryotic genomes to enable all DNA-based processes. The diversity and complexity of these processes are matched by the complexity of the enzymes that carry them out, making remodelers a challenging class of molecular motors to study by conventional methods. Here we use a single molecule biophysical assay to overcome some of these challenges, enabling a detailed mechanistic dissection of a paradigmatic remodeler reaction, that of sliding a nucleosome towards the longer DNA linker. We focus on how two motors of a dimeric remodeler coordinate to accomplish such directional sliding. We find that ATP hydrolysis by both motors promotes coordination, suggesting a role for ATP in resolving the competition for directional commitment. Furthermore, we show an artificially constitutive dimer is no more or less coordinated, but is more processive, suggesting a cell could modulate a remodeler's oligomeric state to modulate local chromatin dynamics.
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Affiliation(s)
- Stephanie L Johnson
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA. https://twitter.com/StephL_Johnson
| | - Geeta J Narlikar
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
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30
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Structure of human chromatin-remodelling PBAF complex bound to a nucleosome. Nature 2022; 605:166-171. [PMID: 35477757 DOI: 10.1038/s41586-022-04658-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 03/16/2022] [Indexed: 12/17/2022]
Abstract
DNA wraps around the histone octamer to form nucleosomes1, the repeating unit of chromatin, which create barriers for accessing genetic information. Snf2-like chromatin remodellers couple the energy of ATP binding and hydrolysis to reposition and recompose the nucleosome, and have vital roles in various chromatin-based transactions2,3. Here we report the cryo-electron microscopy structure of the 12-subunit human chromatin-remodelling polybromo-associated BRG1-associated factor (PBAF) complex bound to the nucleosome. The motor subunit SMARCA4 engages the nucleosome in the active conformation, which reveals clustering of multiple disease-associated mutations at the interfaces that are essential for chromatin-remodelling activity. SMARCA4 recognizes the H2A-H2B acidic pocket of the nucleosome through three arginine anchors of the Snf2 ATP coupling (SnAc) domain. PBAF shows notable functional modularity, and most of the auxiliary subunits are interwoven into three lobe-like submodules for nucleosome recognition. The PBAF-specific auxiliary subunit ARID2 acts as the structural core for assembly of the DNA-binding lobe, whereas PBRM1, PHF10 and BRD7 are collectively incorporated into the lobe for histone tail binding. Together, our findings provide mechanistic insights into nucleosome recognition by PBAF and a structural basis for understanding SMARCA4-related human diseases.
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31
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Nodelman IM, Das S, Faustino AM, Fried SD, Bowman GD, Armache JP. Nucleosome recognition and DNA distortion by the Chd1 remodeler in a nucleotide-free state. Nat Struct Mol Biol 2022; 29:121-129. [PMID: 35173352 DOI: 10.1038/s41594-021-00719-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 12/23/2021] [Indexed: 12/12/2022]
Abstract
Chromatin remodelers are ATP-dependent enzymes that reorganize nucleosomes within all eukaryotic genomes. Here we report a complex of the Chd1 remodeler bound to a nucleosome in a nucleotide-free state, determined by cryo-EM to 2.3 Å resolution. The remodeler stimulates the nucleosome to absorb an additional nucleotide on each strand at two different locations: on the tracking strand within the ATPase binding site and on the guide strand one helical turn from the ATPase motor. Remarkably, the additional nucleotide on the tracking strand is associated with a local transformation toward an A-form geometry, explaining how sequential ratcheting of each DNA strand occurs. The structure also reveals a histone-binding motif, ChEx, which can block opposing remodelers on the nucleosome and may allow Chd1 to participate in histone reorganization during transcription.
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Affiliation(s)
- Ilana M Nodelman
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Sayan Das
- Department of Biochemistry and Molecular Biology and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | | | - Stephen D Fried
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA.,Department of Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - Gregory D Bowman
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA.
| | - Jean-Paul Armache
- Department of Biochemistry and Molecular Biology and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA.
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32
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Wang X, Meng C, Zhang H, Xing W, Cao K, Zhu B, Zhang C, Sun F, Gao Z. Transcriptomic and Proteomic Characterizations of the Molecular Response to Blue Light and Salicylic Acid in Haematococcus pluvialis. Mar Drugs 2021; 20:md20010001. [PMID: 35049856 PMCID: PMC8780009 DOI: 10.3390/md20010001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 12/17/2021] [Accepted: 12/17/2021] [Indexed: 12/13/2022] Open
Abstract
Haematococcus pluvialis accumulates a large amount of astaxanthin under various stresses, e.g., blue light and salicylic acid (SA). However, the metabolic response of H. pluvialis to blue light and SA is still unclear. We investigate the effects of blue light and SA on the metabolic response in H. pluvialis using both transcriptomic and proteomic sequencing analyses. The largest numbers of differentially expressed proteins (DEPs; 324) and differentially expressed genes (DEGs; 13,555) were identified on day 2 and day 7 of the treatment with blue light irradiation (150 μmol photons m−2s−1), respectively. With the addition of SA (2.5 mg/L), a total of 63 DEPs and 11,638 DEGs were revealed on day 2 and day 7, respectively. We further analyzed the molecular response in five metabolic pathways related to astaxanthin synthesis, including the astaxanthin synthesis pathway, the fatty acid synthesis pathway, the heme synthesis pathway, the reactive oxygen species (ROS) clearance pathway, and the cell wall biosynthesis pathway. Results show that blue light causes a significant down-regulation of the expression of key genes involved in astaxanthin synthesis and significantly increases the expression of heme oxygenase, which shows decreased expression by the treatment with SA. Our study provides novel insights into the production of astaxanthin by H. pluvialis treated with blue light and SA.
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Affiliation(s)
- Xiaodong Wang
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255049, China; (X.W.); (C.M.); (W.X.); (K.C.); (B.Z.); (C.Z.)
| | - Chunxiao Meng
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255049, China; (X.W.); (C.M.); (W.X.); (K.C.); (B.Z.); (C.Z.)
| | - Hao Zhang
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China;
| | - Wei Xing
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255049, China; (X.W.); (C.M.); (W.X.); (K.C.); (B.Z.); (C.Z.)
| | - Kai Cao
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255049, China; (X.W.); (C.M.); (W.X.); (K.C.); (B.Z.); (C.Z.)
| | - Bingkui Zhu
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255049, China; (X.W.); (C.M.); (W.X.); (K.C.); (B.Z.); (C.Z.)
| | - Chengsong Zhang
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255049, China; (X.W.); (C.M.); (W.X.); (K.C.); (B.Z.); (C.Z.)
| | - Fengjie Sun
- School of Science and Technology, Georgia Gwinnett College, 1000 University Center Lane, Lawrenceville, GA 30043, USA
- Correspondence: (F.S.); (Z.G.)
| | - Zhengquan Gao
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China;
- Correspondence: (F.S.); (Z.G.)
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33
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Yan C, Dodd T, Yu J, Leung B, Xu J, Oh J, Wang D, Ivanov I. Mechanism of Rad26-assisted rescue of stalled RNA polymerase II in transcription-coupled repair. Nat Commun 2021; 12:7001. [PMID: 34853308 PMCID: PMC8636621 DOI: 10.1038/s41467-021-27295-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 11/10/2021] [Indexed: 12/22/2022] Open
Abstract
Transcription-coupled repair is essential for the removal of DNA lesions from the transcribed genome. The pathway is initiated by CSB protein binding to stalled RNA polymerase II. Mutations impairing CSB function cause severe genetic disease. Yet, the ATP-dependent mechanism by which CSB powers RNA polymerase to bypass certain lesions while triggering excision of others is incompletely understood. Here we build structural models of RNA polymerase II bound to the yeast CSB ortholog Rad26 in nucleotide-free and bound states. This enables simulations and graph-theoretical analyses to define partitioning of this complex into dynamic communities and delineate how its structural elements function together to remodel DNA. We identify an allosteric pathway coupling motions of the Rad26 ATPase modules to changes in RNA polymerase and DNA to unveil a structural mechanism for CSB-assisted progression past less bulky lesions. Our models allow functional interpretation of the effects of Cockayne syndrome disease mutations.
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Affiliation(s)
- Chunli Yan
- grid.256304.60000 0004 1936 7400Department of Chemistry, Georgia State University, Atlanta, GA USA ,grid.256304.60000 0004 1936 7400Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA USA
| | - Thomas Dodd
- grid.256304.60000 0004 1936 7400Department of Chemistry, Georgia State University, Atlanta, GA USA ,grid.256304.60000 0004 1936 7400Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA USA
| | - Jina Yu
- grid.256304.60000 0004 1936 7400Department of Chemistry, Georgia State University, Atlanta, GA USA ,grid.256304.60000 0004 1936 7400Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA USA
| | - Bernice Leung
- grid.266100.30000 0001 2107 4242Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093 USA
| | - Jun Xu
- grid.266100.30000 0001 2107 4242Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093 USA
| | - Juntaek Oh
- grid.266100.30000 0001 2107 4242Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093 USA
| | - Dong Wang
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA. .,Department of Cellular & Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA. .,Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA.
| | - Ivaylo Ivanov
- Department of Chemistry, Georgia State University, Atlanta, GA, USA. .,Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA.
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34
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Bacic L, Gaullier G, Sabantsev A, Lehmann LC, Brackmann K, Dimakou D, Halic M, Hewitt G, Boulton SJ, Deindl S. Structure and dynamics of the chromatin remodeler ALC1 bound to a PARylated nucleosome. eLife 2021; 10:e71420. [PMID: 34486521 PMCID: PMC8463071 DOI: 10.7554/elife.71420] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 09/05/2021] [Indexed: 12/21/2022] Open
Abstract
The chromatin remodeler ALC1 is recruited to and activated by DNA damage-induced poly(ADP-ribose) (PAR) chains deposited by PARP1/PARP2/HPF1 upon detection of DNA lesions. ALC1 has emerged as a candidate drug target for cancer therapy as its loss confers synthetic lethality in homologous recombination-deficient cells. However, structure-based drug design and molecular analysis of ALC1 have been hindered by the requirement for PARylation and the highly heterogeneous nature of this post-translational modification. Here, we reconstituted an ALC1 and PARylated nucleosome complex modified in vitro using PARP2 and HPF1. This complex was amenable to cryo-EM structure determination without cross-linking, which enabled visualization of several intermediate states of ALC1 from the recognition of the PARylated nucleosome to the tight binding and activation of the remodeler. Functional biochemical assays with PARylated nucleosomes highlight the importance of nucleosomal epitopes for productive remodeling and suggest that ALC1 preferentially slides nucleosomes away from DNA breaks.
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Affiliation(s)
- Luka Bacic
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala UniversityUppsalaSweden
| | - Guillaume Gaullier
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala UniversityUppsalaSweden
| | - Anton Sabantsev
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala UniversityUppsalaSweden
| | - Laura C Lehmann
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala UniversityUppsalaSweden
| | - Klaus Brackmann
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala UniversityUppsalaSweden
| | - Despoina Dimakou
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala UniversityUppsalaSweden
| | - Mario Halic
- Department of Structural Biology, St Jude Children's Research HospitalMemphisUnited States
| | | | | | - Sebastian Deindl
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala UniversityUppsalaSweden
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35
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Nodelman IM, Patel A, Levendosky RF, Bowman GD. Reconstitution and Purification of Nucleosomes with Recombinant Histones and Purified DNA. ACTA ACUST UNITED AC 2021; 133:e130. [PMID: 33305911 DOI: 10.1002/cpmb.130] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nucleosomes are substrates for a broad range of factors, including those involved in transcription or chromosome maintenance/reorganization and enzymes that covalently modify histones. Given the heterogeneous nature of nucleosomes in vivo (i.e., varying histone composition, post-translational modifications, DNA sequence register), understanding the specificity and activities of chromatin-interacting factors has required in vitro studies using well-defined nucleosome substrates. Here, we provide detailed methods for large-scale PCR preparation of DNA, assembly of nucleosomes from purified DNA and histones, and purification of DNA and mononucleosomes. Such production of well-defined nucleosomes for biochemical and biophysical studies is key for studying numerous proteins and protein complexes that bind and/or alter nucleosomes and for revealing inherent characteristics of nucleosomes. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Large-scale PCR amplification of DNA Basic Protocol 2: DNA and nucleosome purification using a Bio-Rad Mini Prep Cell/Prep Cell Basic Protocol 3: Nucleosome reconstitution via linear gradient salt dialysis.
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Affiliation(s)
- Ilana M Nodelman
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland
| | - Ashok Patel
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
| | - Robert F Levendosky
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland.,Present address: Catalent Cell and Gene Therapy, Baltimore, Maryland
| | - Gregory D Bowman
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland
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36
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Structure and Function of Chromatin Remodelers. J Mol Biol 2021; 433:166929. [PMID: 33711345 PMCID: PMC8184634 DOI: 10.1016/j.jmb.2021.166929] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/27/2021] [Accepted: 03/04/2021] [Indexed: 12/25/2022]
Abstract
Chromatin remodelers act to regulate multiple cellular processes, such as transcription and DNA repair, by controlling access to genomic DNA. Four families of chromatin remodelers have been identified in yeast, each with non-redundant roles within the cell. There has been a recent surge in structural models of chromatin remodelers in complex with their nucleosomal substrate. These structural studies provide new insight into the mechanism of action for individual chromatin remodelers. In this review, we summarize available data for the structure and mechanism of action of the four chromatin remodeling complex families.
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37
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Surprising Twists in Nucleosomal DNA with Implication for Higher-order Folding. J Mol Biol 2021; 433:167121. [PMID: 34192585 DOI: 10.1016/j.jmb.2021.167121] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 06/19/2021] [Accepted: 06/21/2021] [Indexed: 11/21/2022]
Abstract
While nucleosomes are dynamic entities that must undergo structural deformations to perform their functions, the general view from available high-resolution structures is a largely static one. Even though numerous examples of twist defects have been documented, the DNA wrapped around the histone core is generally thought to be overtwisted. Analysis of available high-resolution structures from the Protein Data Bank reveals a heterogeneous distribution of twist along the nucleosomal DNA, with clear patterns that are consistent with the literature, and a significant fraction of structures that are undertwisted. The subtle differences in nucleosomal DNA folding, which extend beyond twist, have implications for nucleosome disassembly and modeled higher-order structures. Simulations of oligonucleosome arrays built with undertwisted models behave very differently from those constructed from overtwisted models, in terms of compaction and inter-nucleosome contacts, introducing configurational changes equivalent to those associated with 2-3 base-pair changes in nucleosome spacing. Differences in the nucleosomal DNA pathway, which underlie the way that DNA enters and exits the nucleosome, give rise to different nucleosome-decorated minicircles and affect the topological mix of configurational states.
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38
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Autoinhibitory elements of the Chd1 remodeler block initiation of twist defects by destabilizing the ATPase motor on the nucleosome. Proc Natl Acad Sci U S A 2021; 118:2014498118. [PMID: 33468676 DOI: 10.1073/pnas.2014498118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chromatin remodelers are ATP (adenosine triphosphate)-powered motors that reposition nucleosomes throughout eukaryotic chromosomes. Remodelers possess autoinhibitory elements that control the direction of nucleosome sliding, but underlying mechanisms of inhibition have been unclear. Here, we show that autoinhibitory elements of the yeast Chd1 remodeler block nucleosome sliding by preventing initiation of twist defects. We show that two autoinhibitory elements-the chromodomains and bridge-reinforce each other to block sliding when the DNA-binding domain is not bound to entry-side DNA. Our data support a model where the chromodomains and bridge target nucleotide-free and ADP-bound states of the ATPase motor, favoring a partially disengaged state of the ATPase motor on the nucleosome. By bypassing distortions of nucleosomal DNA prior to ATP binding, we propose that autoinhibitory elements uncouple the ATP binding/hydrolysis cycle from DNA translocation around the histone core.
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39
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Clapier CR. Sophisticated Conversations between Chromatin and Chromatin Remodelers, and Dissonances in Cancer. Int J Mol Sci 2021; 22:5578. [PMID: 34070411 PMCID: PMC8197500 DOI: 10.3390/ijms22115578] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/18/2021] [Accepted: 05/18/2021] [Indexed: 01/13/2023] Open
Abstract
The establishment and maintenance of genome packaging into chromatin contribute to define specific cellular identity and function. Dynamic regulation of chromatin organization and nucleosome positioning are critical to all DNA transactions-in particular, the regulation of gene expression-and involve the cooperative action of sequence-specific DNA-binding factors, histone modifying enzymes, and remodelers. Remodelers are molecular machines that generate various chromatin landscapes, adjust nucleosome positioning, and alter DNA accessibility by using ATP binding and hydrolysis to perform DNA translocation, which is highly regulated through sophisticated structural and functional conversations with nucleosomes. In this review, I first present the functional and structural diversity of remodelers, while emphasizing the basic mechanism of DNA translocation, the common regulatory aspects, and the hand-in-hand progressive increase in complexity of the regulatory conversations between remodelers and nucleosomes that accompanies the increase in challenges of remodeling processes. Next, I examine how, through nucleosome positioning, remodelers guide the regulation of gene expression. Finally, I explore various aspects of how alterations/mutations in remodelers introduce dissonance into the conversations between remodelers and nucleosomes, modify chromatin organization, and contribute to oncogenesis.
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Affiliation(s)
- Cedric R Clapier
- Department of Oncological Sciences & Howard Hughes Medical Institute, Huntsman Cancer Institute, University of Utah School of Medicine, 2000 Circle of Hope, Salt Lake City, UT 84112, USA
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40
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Structure of the SWI/SNF complex bound to the nucleosome and insights into the functional modularity. Cell Discov 2021; 7:28. [PMID: 33907182 PMCID: PMC8079448 DOI: 10.1038/s41421-021-00262-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 03/22/2021] [Indexed: 11/08/2022] Open
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41
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Aibara S, Schilbach S, Cramer P. Structures of mammalian RNA polymerase II pre-initiation complexes. Nature 2021; 594:124-128. [DOI: 10.1038/s41586-021-03554-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/14/2021] [Indexed: 01/24/2023]
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42
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Histone dynamics mediate DNA unwrapping and sliding in nucleosomes. Nat Commun 2021; 12:2387. [PMID: 33888707 PMCID: PMC8062685 DOI: 10.1038/s41467-021-22636-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/23/2021] [Indexed: 02/06/2023] Open
Abstract
Nucleosomes are elementary building blocks of chromatin in eukaryotes. They tightly wrap ∼147 DNA base pairs around an octamer of histone proteins. How nucleosome structural dynamics affect genome functioning is not completely clear. Here we report all-atom molecular dynamics simulations of nucleosome core particles at a timescale of 15 microseconds. At this timescale, functional modes of nucleosome dynamics such as spontaneous nucleosomal DNA breathing, unwrapping, twisting, and sliding were observed. We identified atomistic mechanisms of these processes by analyzing the accompanying structural rearrangements of the histone octamer and histone-DNA contacts. Octamer dynamics and plasticity were found to enable DNA unwrapping and sliding. Through multi-scale modeling, we showed that nucleosomal DNA dynamics contribute to significant conformational variability of the chromatin fiber at the supranucleosomal level. Our study further supports mechanistic coupling between fine details of histone dynamics and chromatin functioning, provides a framework for understanding the effects of various chromatin modifications.
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43
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Gamarra N, Narlikar GJ. Collaboration through chromatin: motors of transcription and chromatin structure. J Mol Biol 2021; 433:166876. [PMID: 33556407 DOI: 10.1016/j.jmb.2021.166876] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 01/09/2023]
Abstract
Packaging of the eukaryotic genome into chromatin places fundamental physical constraints on transcription. Clarifying how transcription operates within these constraints is essential to understand how eukaryotic gene expression programs are established and maintained. Here we review what is known about the mechanisms of transcription on chromatin templates. Current models indicate that transcription through chromatin is accomplished by the combination of an inherent nucleosome disrupting activity of RNA polymerase and the action of ATP-dependent chromatin remodeling motors. Collaboration between these two types of molecular motors is proposed to occur at all stages of transcription through diverse mechanisms. Further investigation of how these two motors combine their basic activities is essential to clarify the interdependent relationship between genome structure and transcription.
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Affiliation(s)
- Nathan Gamarra
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States; TETRAD Graduate Program, University of California, San Francisco, San Francisco, United States
| | - Geeta J Narlikar
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States.
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44
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Abstract
As primary carriers of epigenetic information and gatekeepers of genomic DNA, nucleosomes are essential for proper growth and development of all eukaryotic cells. Although they are intrinsically dynamic, nucleosomes are actively reorganized by ATP-dependent chromatin remodelers. Chromatin remodelers contain helicase-like ATPase motor domains that can translocate along DNA, and a long-standing question in the field is how this activity is used to reposition or slide nucleosomes. In addition to ratcheting along DNA like their helicase ancestors, remodeler ATPases appear to dictate specific alternating geometries of the DNA duplex, providing an unexpected means for moving DNA past the histone core. Emerging evidence supports twist-based mechanisms for ATP-driven repositioning of nucleosomes along DNA. In this review, we discuss core experimental findings and ideas that have shaped the view of how nucleosome sliding may be achieved.
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Affiliation(s)
- Ilana M Nodelman
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA;
| | - Gregory D Bowman
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA;
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45
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Lee JH, Bollschweiler D, Schäfer T, Huber R. Structural basis for the regulation of nucleosome recognition and HDAC activity by histone deacetylase assemblies. SCIENCE ADVANCES 2021; 7:7/2/eabd4413. [PMID: 33523989 PMCID: PMC7793584 DOI: 10.1126/sciadv.abd4413] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 11/11/2020] [Indexed: 05/12/2023]
Abstract
The chromatin-modifying histone deacetylases (HDACs) remove acetyl groups from acetyl-lysine residues in histone amino-terminal tails, thereby mediating transcriptional repression. Structural makeup and mechanisms by which multisubunit HDAC complexes recognize nucleosomes remain elusive. Our cryo-electron microscopy structures of the yeast class II HDAC ensembles show that the HDAC protomer comprises a triangle-shaped assembly of stoichiometry Hda12-Hda2-Hda3, in which the active sites of the Hda1 dimer are freely accessible. We also observe a tetramer of protomers, where the nucleosome binding modules are inaccessible. Structural analysis of the nucleosome-bound complexes indicates how positioning of Hda1 adjacent to histone H2B affords HDAC catalysis. Moreover, it reveals how an intricate network of multiple contacts between a dimer of protomers and the nucleosome creates a platform for expansion of the HDAC activities. Our study provides comprehensive insight into the structural plasticity of the HDAC complex and its functional mechanism of chromatin modification.
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Affiliation(s)
- Jung-Hoon Lee
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
- Proteros biostructures GmbH, Bunsenstr 7a, 82152 Martinsried, Germany
| | - Daniel Bollschweiler
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Tillman Schäfer
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Robert Huber
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
- Proteros biostructures GmbH, Bunsenstr 7a, 82152 Martinsried, Germany
- Zentrum für Medizinische Biotechnologie, Universität Duisburg-Essen, 45117 Essen, Germany
- Fakultät für Chemie, Technische Universität München, 85747 Garching, Germany
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Morgan A, LeGresley S, Fischer C. Remodeler Catalyzed Nucleosome Repositioning: Influence of Structure and Stability. Int J Mol Sci 2020; 22:ijms22010076. [PMID: 33374740 PMCID: PMC7793527 DOI: 10.3390/ijms22010076] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/04/2020] [Accepted: 12/16/2020] [Indexed: 02/06/2023] Open
Abstract
The packaging of the eukaryotic genome into chromatin regulates the storage of genetic information, including the access of the cell’s DNA metabolism machinery. Indeed, since the processes of DNA replication, translation, and repair require access to the underlying DNA, several mechanisms, both active and passive, have evolved by which chromatin structure can be regulated and modified. One mechanism relies upon the function of chromatin remodeling enzymes which couple the free energy obtained from the binding and hydrolysis of ATP to the mechanical work of repositioning and rearranging nucleosomes. Here, we review recent work on the nucleosome mobilization activity of this essential family of molecular machines.
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Baker RW, Reimer JM, Carman PJ, Turegun B, Arakawa T, Dominguez R, Leschziner AE. Structural insights into assembly and function of the RSC chromatin remodeling complex. Nat Struct Mol Biol 2020; 28:71-80. [PMID: 33288924 PMCID: PMC7855068 DOI: 10.1038/s41594-020-00528-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 09/28/2020] [Indexed: 12/30/2022]
Abstract
SWI/SNF chromatin remodelers modify the position and spacing of nucleosomes and, in humans, are linked to cancer. To provide insights into the assembly and regulation of this protein family, we focused on a subcomplex of S. cerevisiae RSC comprising its ATPase (Sth1), the essential actin-related proteins (ARPs) Arp7 and Arp9, and the ARP-binding protein Rtt102. Cryo-EM and biochemical analysis of this subcomplex shows that ARP binding induces a helical conformation in the HSA domain of Sth1. Surprisingly, the ARP module is rotated 120° relative to full RSC, about a pivot point previously identified as a regulatory hub in Sth1, suggesting that large conformational changes are part of Sth1 regulation and RSC assembly. We also show that a conserved interaction between Sth1 and the nucleosome acidic patch enhances remodeling. As some cancer-associated mutations dysregulate rather than inactivate SWI/SNF remodelers, our insights into RSC complex regulation advance a mechanistic understanding of chromatin remodeling in disease states.
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Affiliation(s)
- Richard W Baker
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA, USA.,Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Janice M Reimer
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Peter J Carman
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Bengi Turegun
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Foghorn Therapeutics, Cambridge, MA, USA
| | - Tsutomu Arakawa
- Alliance Protein Laboratories, a Division of KBI BioPharma, San Diego, CA, USA
| | - Roberto Dominguez
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Andres E Leschziner
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA, USA. .,Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA.
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48
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Fernando TM, Piskol R, Bainer R, Sokol ES, Trabucco SE, Zhang Q, Trinh H, Maund S, Kschonsak M, Chaudhuri S, Modrusan Z, Januario T, Yauch RL. Functional characterization of SMARCA4 variants identified by targeted exome-sequencing of 131,668 cancer patients. Nat Commun 2020; 11:5551. [PMID: 33144586 PMCID: PMC7609548 DOI: 10.1038/s41467-020-19402-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 10/09/2020] [Indexed: 02/06/2023] Open
Abstract
Genomic studies performed in cancer patients and tumor-derived cell lines have identified a high frequency of alterations in components of the mammalian switch/sucrose non-fermentable (mSWI/SNF or BAF) chromatin remodeling complex, including its core catalytic subunit, SMARCA4. Cells exhibiting loss of SMARCA4 rely on its paralog, SMARCA2, making SMARCA2 an attractive therapeutic target. Here we report the genomic profiling of solid tumors from 131,668 cancer patients, identifying 9434 patients with one or more SMARCA4 gene alterations. Homozygous SMARCA4 mutations were highly prevalent in certain tumor types, notably non-small cell lung cancer (NSCLC), and associated with reduced survival. The large sample size revealed previously uncharacterized hotspot missense mutations within the SMARCA4 helicase domain. Functional characterization of these mutations demonstrated markedly reduced remodeling activity. Surprisingly, a few SMARCA4 missense variants partially or fully rescued paralog dependency, underscoring that careful selection criteria must be employed to identify patients with inactivating, homozygous SMARCA4 missense mutations who may benefit from SMARCA2-targeted therapy.
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Affiliation(s)
- Tharu M Fernando
- Discovery Oncology, Genentech, South San Francisco, CA, 94080, USA
| | - Robert Piskol
- Bioinformatics and Computational Biology, Genentech, South San Francisco, CA, 94080, USA
| | - Russell Bainer
- Bioinformatics and Computational Biology, Genentech, South San Francisco, CA, 94080, USA
| | - Ethan S Sokol
- Cancer Genomics Research, Foundation Medicine, Cambridge, MA, 02141, USA
| | - Sally E Trabucco
- Cancer Genomics Research, Foundation Medicine, Cambridge, MA, 02141, USA
| | - Qing Zhang
- Product Development Personalized Healthcare Data Science, Genentech, South San Francisco, CA, 94080, USA
| | - Huong Trinh
- Product Development Personalized Healthcare Data Science, Genentech, South San Francisco, CA, 94080, USA
| | - Sophia Maund
- Oncology Biomarker Development, Genentech, South San Francisco, CA, 94080, USA
| | - Marc Kschonsak
- Structural Biology, Genentech, South San Francisco, CA, 94080, USA
| | - Subhra Chaudhuri
- Molecular Biology, Genentech, South San Francisco, CA, 94080, USA
| | - Zora Modrusan
- Molecular Biology, Genentech, South San Francisco, CA, 94080, USA
| | - Thomas Januario
- Discovery Oncology, Genentech, South San Francisco, CA, 94080, USA
| | - Robert L Yauch
- Discovery Oncology, Genentech, South San Francisco, CA, 94080, USA.
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Cappuccio G, Sayou C, Tanno PL, Tisserant E, Bruel AL, Kennani SE, Sá J, Low KJ, Dias C, Havlovicová M, Hančárová M, Eichler EE, Devillard F, Moutton S, Van-Gils J, Dubourg C, Odent S, Gerard B, Piton A, Yamamoto T, Okamoto N, Firth H, Metcalfe K, Moh A, Chapman KA, Aref-Eshghi E, Kerkhof J, Torella A, Nigro V, Perrin L, Piard J, Le Guyader G, Jouan T, Thauvin-Robinet C, Duffourd Y, George-Abraham JK, Buchanan CA, Williams D, Kini U, Wilson K, Sousa SB, Hennekam RCM, Sadikovic B, Thevenon J, Govin J, Vitobello A, Brunetti-Pierri N. De novo SMARCA2 variants clustered outside the helicase domain cause a new recognizable syndrome with intellectual disability and blepharophimosis distinct from Nicolaides-Baraitser syndrome. Genet Med 2020; 22:1838-1850. [PMID: 32694869 DOI: 10.1038/s41436-020-0898-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 06/25/2020] [Accepted: 06/26/2020] [Indexed: 12/12/2022] Open
Abstract
PURPOSE Nontruncating variants in SMARCA2, encoding a catalytic subunit of SWI/SNF chromatin remodeling complex, cause Nicolaides-Baraitser syndrome (NCBRS), a condition with intellectual disability and multiple congenital anomalies. Other disorders due to SMARCA2 are unknown. METHODS By next-generation sequencing, we identified candidate variants in SMARCA2 in 20 individuals from 18 families with a syndromic neurodevelopmental disorder not consistent with NCBRS. To stratify variant interpretation, we functionally analyzed SMARCA2 variants in yeasts and performed transcriptomic and genome methylation analyses on blood leukocytes. RESULTS Of 20 individuals, 14 showed a recognizable phenotype with recurrent features including epicanthal folds, blepharophimosis, and downturned nasal tip along with variable degree of intellectual disability (or blepharophimosis intellectual disability syndrome [BIS]). In contrast to most NCBRS variants, all SMARCA2 variants associated with BIS are localized outside the helicase domains. Yeast phenotype assays differentiated NCBRS from non-NCBRS SMARCA2 variants. Transcriptomic and DNA methylation signatures differentiated NCBRS from BIS and those with nonspecific phenotype. In the remaining six individuals with nonspecific dysmorphic features, clinical and molecular data did not permit variant reclassification. CONCLUSION We identified a novel recognizable syndrome named BIS associated with clustered de novo SMARCA2 variants outside the helicase domains, phenotypically and molecularly distinct from NCBRS.
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Affiliation(s)
- Gerarda Cappuccio
- Department of Translational Medicine, Federico II University, Naples, Italy
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Camille Sayou
- Inserm U1209, CNRS UMR 5309, Univ. Grenoble Alpes, Institute for Advanced Biosciences, Grenoble, France
| | - Pauline Le Tanno
- Department of Genetics and Reproduction, Centre Hospitalo-Universitaire Grenoble-Alpes, Grenoble, France
| | - Emilie Tisserant
- Inserm UMR 1231 GAD, Genetics of Developmental disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
| | - Ange-Line Bruel
- Inserm UMR 1231 GAD, Genetics of Developmental disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
| | - Sara El Kennani
- Inserm U1209, CNRS UMR 5309, Univ. Grenoble Alpes, Institute for Advanced Biosciences, Grenoble, France
| | - Joaquim Sá
- Medical Genetics Unit, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Karen J Low
- University Hospitals Bristol NHS Foundation Trust, University of Bristol, Bristol, UK
| | - Cristina Dias
- Department of Medical and Molecular Genetics, King's College, London, UK
- The Francis Crick Institute, London, UK
- Clinical Genetics, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Markéta Havlovicová
- Department of Biology and Medical Genetics, Charles University Prague 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Miroslava Hančárová
- Department of Biology and Medical Genetics, Charles University Prague 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Françoise Devillard
- Department of Genetics and Reproduction, Centre Hospitalo-Universitaire Grenoble-Alpes, Grenoble, France
| | - Sébastien Moutton
- CPDPN, Pôle mère enfant, Maison de Santé Protestante Bordeaux Bagatelle, Talence, France
| | - Julien Van-Gils
- Reference Center for Developmental Anomalies, Department of Medical Genetics, Bordeaux University Hospital, Bordeaux, France
| | - Christèle Dubourg
- Service de Génétique Moléculaire et Génomique, BMT-HC « Jean Dausset », Rennes, France
| | - Sylvie Odent
- Service de Génétique clinique, CHU de Rennes, Univ. Rennes, Institut de Génétique et Développement de Rennes (IGDR) UMR 6290, Rennes, France
| | - Bénédicte Gerard
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Amélie Piton
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Toshiyuki Yamamoto
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
- Tokyo Women's Medical University Institute of Integrated Medical Sciences, Tokyo, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Helen Firth
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK
| | - Kay Metcalfe
- Manchester Centre for Genomic Medicine, Manchester, UK
| | - Anna Moh
- Department of Genetics and Metabolism, Children's National Medical Center, Washington, DC, USA
| | - Kimberly A Chapman
- Department of Genetics and Metabolism, Children's National Medical Center, Washington, DC, USA
| | - Erfan Aref-Eshghi
- Molecular Genetics Laboratory, Victoria Hospital, London Health Sciences Centre, London, ON, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, Canada
| | - Jennifer Kerkhof
- Molecular Genetics Laboratory, Victoria Hospital, London Health Sciences Centre, London, ON, Canada
| | - Annalaura Torella
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Vincenzo Nigro
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Laurence Perrin
- Department of Genetics, Robert Debré Hospital, AP-HP, Paris, France
| | - Juliette Piard
- Centre de génétique humaine, Université de Franche-Comté, Besançon, France
| | - Gwenaël Le Guyader
- Department of Medical Genetics, Poitiers University Hospital, Poitiers, France
| | - Thibaud Jouan
- Inserm UMR 1231 GAD, Genetics of Developmental disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
| | - Christel Thauvin-Robinet
- Inserm UMR 1231 GAD, Genetics of Developmental disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
- Centre de Référence Déficiences Intellectuelles de Causes Rares, CHU Dijon, Dijon, France
- UF Innovation en diagnostic génomique des maladies rares, CHU Dijon, Dijon, France
| | - Yannis Duffourd
- Inserm UMR 1231 GAD, Genetics of Developmental disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
| | - Jaya K George-Abraham
- Dell Children's Medical Group, Austin, TX, USA
- Department of Pediatrics, The University of Texas at Austin Dell Medical School, Austin, TX, USA
| | | | | | - Usha Kini
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Kate Wilson
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Sérgio B Sousa
- Medical Genetics Unit, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
- University Clinic of Genetics, Faculty of Medicine, Universidade de Coimbra, Coimbra, Portugal
| | - Raoul C M Hennekam
- Department of Pediatrics and Translational Genetics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Bekim Sadikovic
- Molecular Genetics Laboratory, Victoria Hospital, London Health Sciences Centre, London, ON, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, Canada
| | - Julien Thevenon
- Department of Genetics and Reproduction, Centre Hospitalo-Universitaire Grenoble-Alpes, Grenoble, France
| | - Jérôme Govin
- Inserm U1209, CNRS UMR 5309, Univ. Grenoble Alpes, Institute for Advanced Biosciences, Grenoble, France.
| | - Antonio Vitobello
- Inserm UMR 1231 GAD, Genetics of Developmental disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France.
- UF Innovation en diagnostic génomique des maladies rares, CHU Dijon, Dijon, France.
| | - Nicola Brunetti-Pierri
- Department of Translational Medicine, Federico II University, Naples, Italy.
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy.
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50
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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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