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Chen P, Li G, Li W. Nucleosome Dynamics Derived at the Single-Molecule Level Bridges Its Structures and Functions. JACS AU 2024; 4:866-876. [PMID: 38559720 PMCID: PMC10976579 DOI: 10.1021/jacsau.3c00658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 04/04/2024]
Abstract
Nucleosome, the building block of chromatin, plays pivotal roles in all DNA-related processes. While cryogenic-electron microscopy (cryo-EM) has significantly advanced our understanding of nucleosome structures, the emerging field of single-molecule force spectroscopy is illuminating their dynamic properties. This technique is crucial for revealing how nucleosome behavior is influenced by chaperones, remodelers, histone variants, and post-translational modifications, particularly in their folding and unfolding mechanisms under tension. Such insights are vital for deciphering the complex interplay in nucleosome assembly and structural regulation, highlighting the nucleosome's versatility in response to DNA activities. In this Perspective, we aim to consolidate the latest advancements in nucleosome dynamics, with a special focus on the revelations brought forth by single-molecule manipulation. Our objective is to highlight the insights gained from studying nucleosome dynamics through this innovative approach, emphasizing the transformative impact of single-molecule manipulation techniques in the field of chromatin research.
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Affiliation(s)
- Ping Chen
- National
Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation
and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P. R. China
- Department
of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory
for Tumor Invasion and Metastasis, Capital
Medical University, Beijing 100069, P. R. China
| | - Guohong Li
- National
Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation
and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P. R. China
- University
of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Wei Li
- National
Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation
and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P. R. China
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2
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Lei ZC, Wang X, Yang L, Qu H, Sun Y, Yang Y, Li W, Zhang WB, Cao XY, Fan C, Li G, Wu J, Tian ZQ. What can molecular assembly learn from catalysed assembly in living organisms? Chem Soc Rev 2024; 53:1892-1914. [PMID: 38230701 DOI: 10.1039/d3cs00634d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
Molecular assembly is the process of organizing individual molecules into larger structures and complex systems. The self-assembly approach is predominantly utilized in creating artificial molecular assemblies, and was believed to be the primary mode of molecular assembly in living organisms as well. However, it has been shown that the assembly of many biological complexes is "catalysed" by other molecules, rather than relying solely on self-assembly. In this review, we summarize these catalysed-assembly (catassembly) phenomena in living organisms and systematically analyse their mechanisms. We then expand on these phenomena and discuss related concepts, including catalysed-disassembly and catalysed-reassembly. Catassembly proves to be an efficient and highly selective strategy for synergistically controlling and manipulating various noncovalent interactions, especially in hierarchical molecular assemblies. Overreliance on self-assembly may, to some extent, hinder the advancement of artificial molecular assembly with powerful features. Furthermore, inspired by the biological catassembly phenomena, we propose guidelines for designing artificial catassembly systems and developing characterization and theoretical methods, and review pioneering works along this new direction. Overall, this approach may broaden and deepen our understanding of molecular assembly, enabling the construction and control of intelligent assembly systems with advanced functionality.
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Affiliation(s)
- Zhi-Chao Lei
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China.
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Xinchang Wang
- School of Electronic Science and Engineering, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, P. R. China
| | - Liulin Yang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China.
| | - Hang Qu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China.
| | - Yibin Sun
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Yang Yang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China.
| | - Wei Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Wen-Bin Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Xiao-Yu Cao
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China.
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science, Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Guohong Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Jiarui Wu
- Key Laboratory of Systems Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, P. R. China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, P. R. China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, 310024, P. R. China
| | - Zhong-Qun Tian
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China.
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3
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Ji D, Shao C, Yu J, Hou Y, Gao X, Wu Y, Wang L, Chen P. FOXA1 forms biomolecular condensates that unpack condensed chromatin to function as a pioneer factor. Mol Cell 2024; 84:244-260.e7. [PMID: 38101414 DOI: 10.1016/j.molcel.2023.11.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 09/14/2023] [Accepted: 11/15/2023] [Indexed: 12/17/2023]
Abstract
Eukaryotic DNA is packaged into chromatin in the nucleus, restricting the binding of transcription factors (TFs) to their target DNA sites. FOXA1 functions as a pioneer TF to bind condensed chromatin and initiate the opening of local chromatin for gene expression. However, the principles of FOXA1 recruitment and how it subsequently unpacks the condensed chromatin remain elusive. Here, we revealed that FOXA1 intrinsically forms submicron-sized condensates through its N- and C-terminal intrinsically disordered regions (IDRs). Notably, both IDRs enable FOXA1 to dissolve the condensed chromatin. In addition, the DNA-binding capacity of FOXA1 contributes to its ability to both form condensates and dissolve condensed chromatin. Further genome-wide investigation showed that IDRs enable FOXA1 to bind and unpack the condensed chromatin to regulate the proliferation and migration of breast cancer cells. This work provides a principle of how pioneer TFs function to initiate competent chromatin states using their IDRs.
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Affiliation(s)
- Dengyu Ji
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory for Tumor Invasion and Metastasis, Capital Medical University, Beijing 100069, China
| | - Changrong Shao
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory for Tumor Invasion and Metastasis, Capital Medical University, Beijing 100069, China
| | - Juan Yu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yaoyao Hou
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Xiao Gao
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory for Tumor Invasion and Metastasis, Capital Medical University, Beijing 100069, China
| | - Yichuan Wu
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory for Tumor Invasion and Metastasis, Capital Medical University, Beijing 100069, China
| | - Liang Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Ping Chen
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory for Tumor Invasion and Metastasis, Capital Medical University, Beijing 100069, China; National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
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4
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Wang M, Li J, Wang Y, Fu H, Qiu H, Li Y, Li M, Lu Y, Fu YV. Single-molecule study reveals Hmo1, not Hho1, promotes chromatin assembly in budding yeast. mBio 2023; 14:e0099323. [PMID: 37432033 PMCID: PMC10470511 DOI: 10.1128/mbio.00993-23] [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: 05/09/2023] [Accepted: 05/25/2023] [Indexed: 07/12/2023] Open
Abstract
Linker histone H1 plays a crucial role in various biological processes, including nucleosome stabilization, high-order chromatin structure organization, gene expression, and epigenetic regulation in eukaryotic cells. Unlike higher eukaryotes, little about the linker histone in Saccharomyces cerevisiae is known. Hho1 and Hmo1 are two long-standing controversial histone H1 candidates in budding yeast. In this study, we directly observed at the single-molecule level that Hmo1, but not Hho1, is involved in chromatin assembly in the yeast nucleoplasmic extracts (YNPE), which can replicate the physiological condition of the yeast nucleus. The presence of Hmo1 facilitates the assembly of nucleosomes on DNA in YNPE, as revealed by single-molecule force spectroscopy. Further single-molecule analysis showed that the lysine-rich C-terminal domain (CTD) of Hmo1 is essential for the function of chromatin compaction, while the second globular domain at the C-terminus of Hho1 impairs its ability. In addition, Hmo1, but not Hho1, forms condensates with double-stranded DNA via reversible phase separation. The phosphorylation fluctuation of Hmo1 coincides with metazoan H1 during the cell cycle. Our data suggest that Hmo1, but not Hho1, possesses some functionality similar to that of linker histone in Saccharomyces cerevisiae, even though some properties of Hmo1 differ from those of a canonical linker histone H1. Our study provides clues for the linker histone H1 in budding yeast and provides insights into the evolution and diversity of histone H1 across eukaryotes. IMPORTANCE There has been a long-standing debate regarding the identity of linker histone H1 in budding yeast. To address this issue, we utilized YNPE, which accurately replicate the physiological conditions in yeast nuclei, in combination with total internal reflection fluorescence microscopy and magnetic tweezers. Our findings demonstrated that Hmo1, rather than Hho1, is responsible for chromatin assembly in budding yeast. Additionally, we found that Hmo1 shares certain characteristics with histone H1, including phase separation and phosphorylation fluctuations throughout the cell cycle. Furthermore, we discovered that the lysine-rich domain of Hho1 is buried by its second globular domain at the C-terminus, resulting in the loss of function that is similar to histone H1. Our study provides compelling evidence to suggest that Hmo1 shares linker histone H1 function in budding yeast and contributes to our understanding of the evolution of linker histone H1 across eukaryotes.
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Affiliation(s)
- Mengxue Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jinghua Li
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Yong Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Hang Fu
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, China
- School of Physics, University of Chinese Academy of Sciences, Beijing, China
| | - Haoning Qiu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yanying Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ming Li
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
- School of Physics, University of Chinese Academy of Sciences, Beijing, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, China
| | - Ying Lu
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
- School of Physics, University of Chinese Academy of Sciences, Beijing, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, China
| | - Yu Vincent Fu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
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5
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Shan Z, Zhang Y, Bu J, Li H, Zhang Z, Xiong J, Zhu B. The patterns and participants of parental histone recycling during DNA replication in Saccharomyces cerevisiae. SCIENCE CHINA. LIFE SCIENCES 2023:10.1007/s11427-022-2267-6. [PMID: 36914923 DOI: 10.1007/s11427-022-2267-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 09/27/2022] [Indexed: 03/14/2023]
Abstract
Epigenetic information carried by histone modifications not only reflects the state of gene expression, but also participates in the maintenance of chromatin states and the regulation of gene expression. Recycling of parental histones to daughter chromatin after DNA replication is vital to mitotic inheritance of epigenetic information and the maintenance of cell identity, because the locus-specific modifications of the parental histones need to be maintained. To assess the precision of parental histone recycling, we developed a synthetic local label-chasing system in budding yeast Saccharomyces cerevisiae. Using this system, we observed that parental histone H3 can be recycled to their original position, thereby recovering their position information after DNA replication at all tested loci, including heterochromatin boundary, non-transcribed region, and actively transcribed regions. Moreover, the recycling rate appears to be affected by local chromatin environment. We surveyed a number of potential regulatory factors and observed that histone H3-H4 chaperon Asf1 contributed to parental histone recycling, while the eukaryotic replisome-associated components Mcm2 and Dpb3 displayed compounding effects in this process. In addition, the FACT complex also plays a role in the recycling of parental histones and helps to stabilize the nucleosomes.
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Affiliation(s)
- Zhongqing Shan
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yan Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jiachen Bu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Huizhi Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhuqiang Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jun Xiong
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Bing Zhu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. .,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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6
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Luo A, Kong J, Chen J, Xiao X, Lan J, Li X, Liu C, Wang PY, Li G, Li W, Chen P. H2B ubiquitination recruits FACT to maintain a stable altered nucleosome state for transcriptional activation. Nat Commun 2023; 14:741. [PMID: 36765085 PMCID: PMC9918737 DOI: 10.1038/s41467-023-36467-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 02/02/2023] [Indexed: 02/12/2023] Open
Abstract
Histone H2B mono-ubiquitination at lysine 120 (ubH2B) has been found to regulate transcriptional elongation by collaborating with the histone chaperone FACT (Facilitates Chromatin Transcription) and plays essential roles in chromatin-based transcriptional processes. However, the mechanism of how ubH2B directly collaborates with FACT at the nucleosome level still remains elusive. In this study, we demonstrate that ubH2B impairs the mechanical stability of the nucleosome and helps to recruit FACT by enhancing the binding of FACT on the nucleosome. FACT prefers to bind and deposit H2A-ubH2B dimers to form an intact nucleosome. Strikingly, the preferable binding of FACT on ubH2B-nucleosome greatly enhances nucleosome stability and maintains its integrity. The stable altered nucleosome state obtained by ubH2B and FACT provides a key platform for gene transcription, as revealed by genome-wide and time-course ChIP-qPCR analyses. Our findings provide mechanistic insights of how ubH2B directly collaborates with FACT to regulate nucleosome dynamics for gene transcription.
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Affiliation(s)
- Anfeng Luo
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory for Tumor Invasion and Metastasis, Capital Medical University, Beijing, 100069, China
| | - Jingwei Kong
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jun Chen
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory for Tumor Invasion and Metastasis, Capital Medical University, Beijing, 100069, China
| | - Xue Xiao
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
| | - Jie Lan
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaorong Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Cuifang Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Peng-Ye Wang
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Songshan Lake Materials Laboratory, Dongguan, Guangdong, 523808, China
| | - Guohong Li
- University of Chinese Academy of Sciences, Beijing, 100049, China.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wei Li
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China. .,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. .,Songshan Lake Materials Laboratory, Dongguan, Guangdong, 523808, China.
| | - Ping Chen
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory for Tumor Invasion and Metastasis, Capital Medical University, Beijing, 100069, China. .,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
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7
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Portillo-Ledesma S, Li Z, Schlick T. Genome modeling: From chromatin fibers to genes. Curr Opin Struct Biol 2023; 78:102506. [PMID: 36577295 PMCID: PMC9908845 DOI: 10.1016/j.sbi.2022.102506] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/01/2022] [Accepted: 11/06/2022] [Indexed: 12/27/2022]
Abstract
The intricacies of the 3D hierarchical organization of the genome have been approached by many creative modeling studies. The specific model/simulation technique combination defines and restricts the system and phenomena that can be investigated. We present the latest modeling developments and studies of the genome, involving models ranging from nucleosome systems and small polynucleosome arrays to chromatin fibers in the kb-range, chromosomes, and whole genomes, while emphasizing gene folding from first principles. Clever combinations allow the exploration of many interesting phenomena involved in gene regulation, such as nucleosome structure and dynamics, nucleosome-nucleosome stacking, polynucleosome array folding, protein regulation of chromatin architecture, mechanisms of gene folding, loop formation, compartmentalization, and structural transitions at the chromosome and genome levels. Gene-level modeling with full details on nucleosome positions, epigenetic factors, and protein binding, in particular, can in principle be scaled up to model chromosomes and cells to study fundamental biological regulation.
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Affiliation(s)
- Stephanie Portillo-Ledesma
- Department of Chemistry, New York University, 100 Washington Square East, Silver Building, New York, 10003, NY, USA
| | - Zilong Li
- Department of Chemistry, New York University, 100 Washington Square East, Silver Building, New York, 10003, NY, USA
| | - Tamar Schlick
- Department of Chemistry, New York University, 100 Washington Square East, Silver Building, New York, 10003, NY, USA; Courant Institute of Mathematical Sciences, New York University, 251 Mercer St., New York, 10012, NY, USA; New York University-East China Normal University Center for Computational Chemistry, New York University Shanghai, Room 340, Geography Building, 3663 North Zhongshan Road, Shanghai, 200122, China; Simons Center for Computational Physical Chemistry, 24 Waverly Place, Silver Building, New York University, New York, 10003, NY, USA.
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8
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Jiang Y, Huang J, Tian K, Yi X, Zheng H, Zhu Y, Guo T, Ji X. Cross-regulome profiling of RNA polymerases highlights the regulatory role of polymerase III on mRNA transcription by maintaining local chromatin architecture. Genome Biol 2022; 23:246. [PMID: 36443871 PMCID: PMC9703767 DOI: 10.1186/s13059-022-02812-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 11/07/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Mammalian cells have three types of RNA polymerases (Pols), Pol I, II, and III. However, the extent to which these polymerases are cross-regulated and the underlying mechanisms remain unclear. RESULTS We employ genome-wide profiling after acute depletion of Pol I, Pol II, or Pol III to assess cross-regulatory effects between these Pols. We find that these enzymes mainly affect the transcription of their own target genes, while certain genes are transcribed by the other polymerases. Importantly, the most active type of crosstalk is exemplified by the fact that Pol III depletion affects Pol II transcription. Pol II genes with transcription changes upon Pol III depletion are enriched in diverse cellular functions, and Pol III binding sites are found near their promoters. However, these Pol III binding sites do not correspond to transfer RNAs. Moreover, we demonstrate that Pol III regulates Pol II transcription and chromatin binding of the facilitates chromatin transcription (FACT) complex to alter local chromatin structures, which in turn affects the Pol II transcription rate. CONCLUSIONS Our results support a model suggesting that RNA polymerases show cross-regulatory effects: Pol III affects local chromatin structures and the FACT-Pol II axis to regulate the Pol II transcription rate at certain gene loci. This study provides a new perspective for understanding the dysregulation of Pol III in various tissues affected by developmental diseases.
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Affiliation(s)
- Yongpeng Jiang
- grid.452723.50000 0004 7887 9190Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871 China
| | - Jie Huang
- grid.452723.50000 0004 7887 9190Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871 China
| | - Kai Tian
- grid.452723.50000 0004 7887 9190Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871 China
| | - Xiao Yi
- grid.494629.40000 0004 8008 9315Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, 310024 Zhejiang Province China ,grid.494629.40000 0004 8008 9315Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024 Zhejiang Province China ,Westlake Omics (Hangzhou) Biotechnology Co., Ltd, Hangzhou, 310024 China
| | - Haonan Zheng
- grid.452723.50000 0004 7887 9190Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871 China
| | - Yi Zhu
- grid.494629.40000 0004 8008 9315Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, 310024 Zhejiang Province China ,grid.494629.40000 0004 8008 9315Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024 Zhejiang Province China ,Westlake Omics (Hangzhou) Biotechnology Co., Ltd, Hangzhou, 310024 China
| | - Tiannan Guo
- grid.494629.40000 0004 8008 9315Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, 310024 Zhejiang Province China ,grid.494629.40000 0004 8008 9315Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024 Zhejiang Province China ,Westlake Omics (Hangzhou) Biotechnology Co., Ltd, Hangzhou, 310024 China
| | - Xiong Ji
- grid.452723.50000 0004 7887 9190Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871 China
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9
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Sengupta B, Huynh M, Smith CB, McGinty RK, Krajewski W, Lee TH. The Effects of Histone H2B Ubiquitylations on the Nucleosome Structure and Internucleosomal Interactions. Biochemistry 2022; 61:2198-2205. [PMID: 36112542 PMCID: PMC9588709 DOI: 10.1021/acs.biochem.2c00422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Eukaryotic gene compaction takes place at multiple levels to package DNA to chromatin and chromosomes. Two of the most fundamental levels of DNA packaging are at the nucleosome and dinucleosome stacks. The nucleosome is the basic gene-packing unit and is composed of DNA wrapped around a histone core. Nucleosomes stack with one another for further compaction of DNA. The first stacking step leads to dinucleosome formation, which is driven by internucleosomal interactions between various parts of two nucleosomes. Histone proteins are rich targets for post-translational modifications, some of which affect the structure of the nucleosome and the interactions between nucleosomes. These effects are often implicated in the regulation of various genomic transactions. In particular, histone H2B ubiquitylation has been associated with facilitated transcription and hexasome formation. Here, we employed semi-synthetically ubiquitylated histone H2B and single-molecule FRET to investigate the effects of H2B ubiquitylations at lysine 34 (H2BK34) and lysine 120 (H2BK120) on the structure of the nucleosome and the interactions between two nucleosomes. Our results suggest that H2BK34 ubiquitylation widens the DNA gyre gap in the nucleosome and stabilizes long- and short-range internucleosomal interactions while H2BK120 ubiquitylation does not affect the nucleosome structure or internucleosomal interactions. These results suggest potential roles for H2B ubiquitylations in facilitated transcription and hexasome formation while maintaining the structural integrity of chromatin.
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Affiliation(s)
- Bhaswati Sengupta
- Department of Chemistry, Pennsylvania State University, PA 16802, USA
| | - Mai Huynh
- Department of Chemistry, Pennsylvania State University, PA 16802, USA
| | - Charlotte B. Smith
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Robert K McGinty
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Wladyslaw Krajewski
- N. K. Koltsov Institute of Developmental Biology of Russian Academy of Sciences, Vavilova str. 26, Moscow, 119334, Russia
| | - Tae-Hee Lee
- Department of Chemistry, Pennsylvania State University, PA 16802, USA
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10
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Liu S, Lin X, Zhang B. Chromatin fiber breaks into clutches under tension and crowding. Nucleic Acids Res 2022; 50:9738-9747. [PMID: 36029149 PMCID: PMC9508854 DOI: 10.1093/nar/gkac725] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 07/08/2022] [Accepted: 08/12/2022] [Indexed: 11/18/2022] Open
Abstract
The arrangement of nucleosomes inside chromatin is of extensive interest. While in vitro experiments have revealed the formation of 30 nm fibers, most in vivo studies have failed to confirm their presence in cell nuclei. To reconcile the diverging experimental findings, we characterized chromatin organization using a residue-level coarse-grained model. The computed force–extension curve matches well with measurements from single-molecule experiments. Notably, we found that a dodeca-nucleosome in the two-helix zigzag conformation breaks into structures with nucleosome clutches and a mix of trimers and tetramers under tension. Such unfolded configurations can also be stabilized through trans interactions with other chromatin chains. Our study suggests that unfolding from chromatin fibers could contribute to the irregularity of in vivo chromatin configurations. We further revealed that chromatin segments with fibril or clutch structures engaged in distinct binding modes and discussed the implications of these inter-chain interactions for a potential sol–gel phase transition.
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Affiliation(s)
- Shuming Liu
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Xingcheng Lin
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
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11
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Song Y, Ma Z, Zhang W. Manipulation of a Single Polymer Chain: From the Nanomechanical Properties to Dynamic Structure Evolution. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c00076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yu Song
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P. R. China
| | - Ziwen Ma
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P. R. China
| | - Wenke Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P. R. China
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12
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Jeronimo C, Robert F. The histone chaperone FACT: a guardian of chromatin structure integrity. Transcription 2022; 13:16-38. [PMID: 35485711 PMCID: PMC9467567 DOI: 10.1080/21541264.2022.2069995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The identification of FACT as a histone chaperone enabling transcription through chromatin in vitro has strongly shaped how its roles are envisioned. However, FACT has been implicated in essentially all aspects of chromatin biology, from transcription to DNA replication, DNA repair, and chromosome segregation. In this review, we focus on recent literature describing the role and mechanisms of FACT during transcription. We highlight the prime importance of FACT in preserving chromatin integrity during transcription and challenge its role as an elongation factor. We also review evidence for FACT's role as a cell-type/gene-specificregulator of gene expression and briefly summarize current efforts at using FACT inhibition as an anti-cancerstrategy.
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Affiliation(s)
- Célia Jeronimo
- Institut de recherches cliniques de Montréal, Montréal, Québec, Canada
| | - François Robert
- Institut de recherches cliniques de Montréal, Montréal, Québec, Canada.,Département de Médecine, Faculté de Médecine, Université de Montréal, Montréal, Québec, Canada.,Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec, Canada
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13
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Goswami I, Sandlesh P, Stablewski A, Toshkov I, Safina AF, Magnitov M, Wang J, Gurova K. FACT maintains nucleosomes during transcription and stem cell viability in adult mice. EMBO Rep 2022; 23:e53684. [PMID: 35179289 PMCID: PMC8982582 DOI: 10.15252/embr.202153684] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 01/20/2022] [Accepted: 01/28/2022] [Indexed: 12/14/2022] Open
Abstract
Preservation of nucleosomes during replication has been extensively studied, while the maintenance of nucleosomes during transcription has gotten less attention. The histone chaperone FACT has a role in transcription elongation, although whether it disassembles or assembles nucleosomes during this process is unclear. To elucidate the function of FACT in mammals, we deleted the Ssrp1 subunit of FACT in adult mice. FACT loss is lethal, possibly due to the loss of the earliest progenitors in bone marrow and intestine, while more differentiated cells are not affected. Using cells isolated from several tissues, we show that FACT loss reduces the viability of stem cells but not of cells differentiated in vitro. FACT depletion increases chromatin accessibility in a transcription-dependent manner in adipose mesenchymal stem cells, indicating that nucleosomes are lost in these cells during transcription in the absence of FACT. We also observe activation of interferon (IFN) signaling and the accumulation of immunocytes in organs sensitive to FACT loss. Our data indicate that FACT maintains chromatin integrity during transcription in mammalian adult stem cells, suggesting that chromatin transcription in stem cells and differentiated cells is different.
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Affiliation(s)
- Imon Goswami
- Department of Cell Stress BiologyRoswell Park Comprehensive Cancer CenterBuffaloNYUSA
| | - Poorva Sandlesh
- Department of Cell Stress BiologyRoswell Park Comprehensive Cancer CenterBuffaloNYUSA,Present address:
Department of Neurological SurgeryUniversity of PittsburghPittsburghPAUSA,Present address:
Department of NeurosurgeryUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Aimee Stablewski
- Transgenic Shared FacilityRoswell Park Comprehensive Cancer CenterBuffaloNYUSA
| | | | - Alfiya F Safina
- Department of Cell Stress BiologyRoswell Park Comprehensive Cancer CenterBuffaloNYUSA
| | - Mikhail Magnitov
- Institute of Gene BiologyRussian Academy of SciencesMoscowRussia
| | - Jianmin Wang
- Department of Biostatistics and BioinformaticsRoswell Park Comprehensive Cancer CenterBuffaloNYUSA
| | - Katerina Gurova
- Department of Cell Stress BiologyRoswell Park Comprehensive Cancer CenterBuffaloNYUSA
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14
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Zhang M, Seitz C, Chang G, Iqbal F, Lin H, Liu J. A guide for single-particle chromatin tracking in live cell nuclei. Cell Biol Int 2022; 46:683-700. [PMID: 35032142 PMCID: PMC9035067 DOI: 10.1002/cbin.11762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 12/29/2021] [Accepted: 01/08/2022] [Indexed: 11/09/2022]
Abstract
The emergence of labeling strategies and live cell imaging methods enables the imaging of chromatin in living cells at single digit nanometer resolution as well as milliseconds temporal resolution. These technical breakthroughs revolutionize our understanding of chromatin structure, dynamics and functions. Single molecule tracking algorithms are usually preferred to quantify the movement of these intranucleus elements to interpret the spatiotemporal evolution of the chromatin. In this review, we will first summarize the fluorescent labeling strategy of chromatin in live cells which will be followed by a sys-tematic comparison of live cell imaging instrumentation. With the proper microscope, we will discuss the image analysis pipelines to extract the biophysical properties of the chromatin. Finally, we expect to give practical suggestions to broad biologists on how to select methods and link to the model properly according to different investigation pur-poses. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Mengdi Zhang
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Clayton Seitz
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Garrick Chang
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Fadil Iqbal
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Hua Lin
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Jing Liu
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA.,Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN, USA.,Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA
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15
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Wang YZ, Liu C, Zhao J, Yu J, Luo A, Xiao X, Dou SX, Ma L, Wang PY, Li M, Li G, Yan J, Chen P, Li W. H2A mono-ubiquitination differentiates FACT's functions in nucleosome assembly and disassembly. Nucleic Acids Res 2021; 50:833-846. [PMID: 34951461 PMCID: PMC8789066 DOI: 10.1093/nar/gkab1271] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 12/06/2021] [Accepted: 12/14/2021] [Indexed: 11/26/2022] Open
Abstract
The histone chaperone FACT (FAcilitates Chromatin Transcription) plays an essential role in transcription and DNA replication by its dual functions on nucleosome assembly to maintain chromatin integrity and nucleosome disassembly to destabilize nucleosome and facilitate its accessibility simultaneously. Mono-ubiquitination at Lysine 119 of H2A (ubH2A) has been suggested to repress transcription by preventing the recruitment of FACT at early elongation process. However, up to date, how ubH2A directly affects FACT on nucleosome assembly and disassembly remains elusive. In this study, we demonstrated that the dual functions of FACT are differently regulated by ubH2A. The H2A ubiquitination does not affect FACT’s chaperone function in nucleosome assembly and FACT can deposit ubH2A–H2B dimer on tetrasome to form intact nucleosome. However, ubH2A greatly restricts FACT binding on nucleosome and inhibits its activity of nucleosome disassembly. Interestingly, deubiquitination of ubH2A rescues the nucleosome disassembly function of FACT to activate gene transcription. Our findings provide mechanistic insights of how H2A ubiquitination affects FACT in breaking nucleosome and maintaining its integrity, which sheds light on the biological function of ubH2A and various FACT’s activity under different chromatin states.
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Affiliation(s)
- Yi-Zhou Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Cuifang Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jicheng Zhao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Juan Yu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Anfeng Luo
- Department of Immunology, School of Basic Medical Sciences, Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing 100069, China
| | - Xue Xiao
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Shuo-Xing Dou
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lu Ma
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Peng-Ye Wang
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Ming Li
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Guohong Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianbin Yan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Ping Chen
- Department of Immunology, School of Basic Medical Sciences, Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing 100069, China.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Wei Li
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.,Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
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16
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Makasheva K, Bryan LC, Anders C, Panikulam S, Jinek M, Fierz B. Multiplexed Single-Molecule Experiments Reveal Nucleosome Invasion Dynamics of the Cas9 Genome Editor. J Am Chem Soc 2021; 143:16313-16319. [PMID: 34597515 PMCID: PMC8517959 DOI: 10.1021/jacs.1c06195] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
![]()
Single-molecule measurements
provide detailed mechanistic insights
into molecular processes, for example in genome regulation where DNA
access is controlled by nucleosomes and the chromatin machinery. However,
real-time single-molecule observations of nuclear factors acting on
defined chromatin substrates are challenging to perform quantitatively
and reproducibly. Here we present XSCAN (multiplexed single-molecule detection of chromatin association), a method to parallelize single-molecule experiments
by simultaneous imaging of a nucleosome library, where each nucleosome
type carries an identifiable DNA sequence within its nucleosomal DNA.
Parallel experiments are subsequently spatially decoded, via the detection
of specific binding of dye-labeled DNA probes. We use this method
to reveal how the Cas9 nuclease overcomes the nucleosome barrier when
invading chromatinized DNA as a function of PAM position.
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Affiliation(s)
- Kristina Makasheva
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne (EPFL), Station 6, 1015 Lausanne, Switzerland
| | - Louise C Bryan
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne (EPFL), Station 6, 1015 Lausanne, Switzerland
| | - Carolin Anders
- Department of Biochemistry, University of Zurich, Winterthurerstr. 190, 8057 Zurich, Switzerland
| | - Sherin Panikulam
- Department of Biochemistry, University of Zurich, Winterthurerstr. 190, 8057 Zurich, Switzerland
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Winterthurerstr. 190, 8057 Zurich, Switzerland
| | - Beat Fierz
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne (EPFL), Station 6, 1015 Lausanne, Switzerland
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17
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Choppakatla P, Dekker B, Cutts EE, Vannini A, Dekker J, Funabiki H. Linker histone H1.8 inhibits chromatin binding of condensins and DNA topoisomerase II to tune chromosome length and individualization. eLife 2021; 10:e68918. [PMID: 34406118 PMCID: PMC8416026 DOI: 10.7554/elife.68918] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 08/13/2021] [Indexed: 12/14/2022] Open
Abstract
DNA loop extrusion by condensins and decatenation by DNA topoisomerase II (topo II) are thought to drive mitotic chromosome compaction and individualization. Here, we reveal that the linker histone H1.8 antagonizes condensins and topo II to shape mitotic chromosome organization. In vitro chromatin reconstitution experiments demonstrate that H1.8 inhibits binding of condensins and topo II to nucleosome arrays. Accordingly, H1.8 depletion in Xenopus egg extracts increased condensins and topo II levels on mitotic chromatin. Chromosome morphology and Hi-C analyses suggest that H1.8 depletion makes chromosomes thinner and longer through shortening the average loop size and reducing the DNA amount in each layer of mitotic loops. Furthermore, excess loading of condensins and topo II to chromosomes by H1.8 depletion causes hyper-chromosome individualization and dispersion. We propose that condensins and topo II are essential for chromosome individualization, but their functions are tuned by the linker histone to keep chromosomes together until anaphase.
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Affiliation(s)
- Pavan Choppakatla
- Laboratory of Chromosome and Cell Biology, The Rockefeller UniversityNew YorkUnited States
| | - Bastiaan Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Erin E Cutts
- Division of Structural Biology, The Institute of Cancer ResearchLondonUnited Kingdom
| | - Alessandro Vannini
- Division of Structural Biology, The Institute of Cancer ResearchLondonUnited Kingdom
- Fondazione Human Technopole, Structural Biology Research Centre, 20157MilanItaly
| | - Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical SchoolWorcesterUnited States
- Howard Hughes Medical InstituteChevy ChaseUnited States
| | - Hironori Funabiki
- Laboratory of Chromosome and Cell Biology, The Rockefeller UniversityNew YorkUnited States
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18
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Zhang S, Xiao X, Kong J, Lu K, Dou SX, Wang PY, Ma L, Liu Y, Li G, Li W, Zhang H. DNA polymerase Gp90 activities and regulations on strand displacement DNA synthesis revealed at single-molecule level. FASEB J 2021; 35:e21607. [PMID: 33908664 DOI: 10.1096/fj.202100033rr] [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: 01/07/2021] [Revised: 03/18/2021] [Accepted: 04/05/2021] [Indexed: 11/11/2022]
Abstract
Strand displacement DNA synthesis (SDDS) is an essential step in DNA replication. With magnetic tweezers, we investigated SDDS kinetics of wild-type gp90 and its exonuclease-deficient polymerase gp90 exo- at single-molecule level. A novel binding state of gp90 to the fork flap was confirmed prior to SDDS, suggesting an intermediate in the initiation of SDDS. The rate and processivity of SDDS by gp90 exo- or wt-gp90 are increased with force and dNTP concentration. The rate and processivity of exonuclease by wt-gp90 are decreased with force. High GC content decreases SDDS and exonuclease processivity but increases exonuclease rate for wt-gp90. The high force and dNTP concentration and low GC content facilitate the successive SDDS but retard the successive exonuclease for wt-gp90. Furthermore, increasing GC content accelerates the transition from SDDS or exonuclease to exonuclease. This work reveals the kinetics of SDDS in detail and offers a broader cognition on the regulation of various factors on SDDS at single-polymerase level.
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Affiliation(s)
- Shuming Zhang
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health & West China Fourth Hospital, Sichuan University, Chengdu, China.,National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Xue Xiao
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jingwei Kong
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ke Lu
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Shuo-Xing Dou
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Peng-Ye Wang
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Songshan Lake Materials Laboratory, Dongguan, China
| | - Lu Ma
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Yuru Liu
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Guohong Li
- National Laboratory of Biomacromolecules, CAS Centre for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Wei Li
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China.,Songshan Lake Materials Laboratory, Dongguan, China
| | - Huidong Zhang
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health & West China Fourth Hospital, Sichuan University, Chengdu, China.,Research Center for Environment and Female Reproductive Health, the Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
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19
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Abstract
The field of epigenetics has exploded over the last two decades, revealing an astonishing level of complexity in the way genetic information is stored and accessed in eukaryotes. This expansion of knowledge, which is very much ongoing, has been made possible by the availability of evermore sensitive and precise molecular tools. This review focuses on the increasingly important role that chemistry plays in this burgeoning field. In an effort to make these contributions more accessible to the nonspecialist, we group available chemical approaches into those that allow the covalent structure of the protein and DNA components of chromatin to be manipulated, those that allow the activity of myriad factors that act on chromatin to be controlled, and those that allow the covalent structure and folding of chromatin to be characterized. The application of these tools is illustrated through a series of case studies that highlight how the molecular precision afforded by chemistry is being used to establish causal biochemical relationships at the heart of epigenetic regulation.
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Affiliation(s)
- John D Bagert
- Frick Chemistry Laboratory, Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA; ,
| | - Tom W Muir
- Frick Chemistry Laboratory, Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA; ,
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20
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Rudnizky S, Khamis H, Ginosar Y, Goren E, Melamed P, Kaplan A. Extended and dynamic linker histone-DNA Interactions control chromatosome compaction. Mol Cell 2021; 81:3410-3421.e4. [PMID: 34192510 DOI: 10.1016/j.molcel.2021.06.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 06/01/2021] [Accepted: 06/03/2021] [Indexed: 02/06/2023]
Abstract
Chromatosomes play a fundamental role in chromatin regulation, but a detailed understanding of their structure is lacking, partially due to their complex dynamics. Using single-molecule DNA unzipping with optical tweezers, we reveal that linker histone interactions with DNA are remarkably extended, with the C-terminal domain binding both DNA linkers as far as approximately ±140 bp from the dyad. In addition to a symmetrical compaction of the nucleosome core governed by globular domain contacts at the dyad, the C-terminal domain compacts the nucleosome's entry and exit. These interactions are dynamic, exhibit rapid binding and dissociation, are sensitive to phosphorylation of a specific residue, and are crucial to determining the symmetry of the chromatosome's core. Extensive unzipping of the linker DNA, which mimics its invasion by motor proteins, shifts H1 into an asymmetric, off-dyad configuration and triggers nucleosome decompaction, highlighting the plasticity of the chromatosome structure and its potential regulatory role.
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Affiliation(s)
- Sergei Rudnizky
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Hadeel Khamis
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel; Faculty of Physics, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Yuval Ginosar
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Efrat Goren
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Philippa Melamed
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel; Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Ariel Kaplan
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel; Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology, Haifa 32000, Israel.
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21
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Abstract
In eukaryotes, genomic DNA is packaged into chromatin in the nucleus. The accessibility of DNA is dependent on the chromatin structure and dynamics, which essentially control DNA-related processes, including transcription, DNA replication, and repair. All of the factors that affect the structure and dynamics of nucleosomes, the nucleosome-nucleosome interaction interfaces, and the binding of linker histones or other chromatin-binding proteins need to be considered to understand the organization and function of chromatin fibers. In this review, we provide a summary of recent progress on the structure of chromatin fibers in vitro and in the nucleus, highlight studies on the dynamic regulation of chromatin fibers, and discuss their related biological functions and abnormal organization in diseases.
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Affiliation(s)
- Ping Chen
- Department of Immunology, School of Basic Medical Sciences, Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing 100069, China; .,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China;
| | - Wei Li
- National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China; .,Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.,Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Guohong Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; .,University of Chinese Academy of Sciences, Beijing 100049, China
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22
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Yu J, Xiong C, Zhuo B, Wen Z, Shen J, Liu C, Chang L, Wang K, Wang M, Wu C, Wu X, Xu X, Ruan H, Li G. Analysis of Local Chromatin States Reveals Gene Transcription Potential during Mouse Neural Progenitor Cell Differentiation. Cell Rep 2021; 32:107953. [PMID: 32726618 DOI: 10.1016/j.celrep.2020.107953] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 05/25/2020] [Accepted: 07/02/2020] [Indexed: 01/23/2023] Open
Abstract
Chromatin dynamics play a critical role in cell fate determination and maintenance by regulating the expression of genes essential for development and differentiation. In mouse embryonic stem cells (mESCs), maintenance of pluripotency coincides with a poised chromatin state containing active and repressive histone modifications. However, the structural features of poised chromatin are largely uncharacterized. By adopting mild time-course MNase-seq with computational analysis, the low-compact chromatin in mESCs is featured in two groups: one in more open regions, corresponding to an active state, and the other enriched with bivalent histone modifications, considered the poised state. A parameter called the chromatin opening potential index (COPI) is also devised to quantify the transcription potential based on the dynamic changes of MNase-seq signals at promoter regions. Use of COPI provides effective prediction of gene activation potential and, more importantly, reveals a few developmental factors essential for mouse neural progenitor cell (NPC) differentiation.
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Affiliation(s)
- Juan Yu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Chaoyang Xiong
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Baowen Zhuo
- Baoan Maternal and Child Health Hospital, Jinan University, Shenzhen 518102, China
| | - Zengqi Wen
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jie Shen
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Cuifang Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Luyuan Chang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Kehui Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Min Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Chenyi Wu
- Molecular Biophysics Laboratories, School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK
| | - Xudong Wu
- Department of Cell Biology, Tianjin Medical University, Qixiangtai Road 22, Tianjin 300070, China
| | - Xueqing Xu
- Baoan Maternal and Child Health Hospital, Jinan University, Shenzhen 518102, China.
| | - Haihe Ruan
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Guohong Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of the Chinese Academy of Sciences, Beijing 100049, China.
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23
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Dai L, Xiao X, Pan L, Shi L, Xu N, Zhang Z, Feng X, Ma L, Dou S, Wang P, Zhu B, Li W, Zhou Z. Recognition of the inherently unstable H2A nucleosome by Swc2 is a major determinant for unidirectional H2A.Z exchange. Cell Rep 2021; 35:109183. [PMID: 34038732 DOI: 10.1016/j.celrep.2021.109183] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/29/2021] [Accepted: 05/05/2021] [Indexed: 12/24/2022] Open
Abstract
The multisubunit chromatin remodeler SWR1/SRCAP/p400 replaces the nucleosomal H2A-H2B dimer with the free-form H2A.Z-H2B dimer, but the mechanism governing the unidirectional H2A-to-H2A.Z exchange remains elusive. Here, we perform single-molecule force spectroscopy to dissect the disassembly/reassembly processes of the H2A nucleosome and H2A.Z nucleosome. We find that the N-terminal 1-135 residues of yeast SWR1 complex protein 2 (previously termed Swc2-Z) facilitate the disassembly of nucleosomes containing H2A but not H2A.Z. The Swc2-mediated nucleosome disassembly/reassembly requires the inherently unstable H2A nucleosome, whose instability is conferred by three H2A α2-helical residues, Gly47, Pro49, and Ile63, as they selectively weaken the structural rigidity of the H2A-H2B dimer. It also requires Swc2-ZN (residues 1-37) that directly anchors to the H2A nucleosome and functions in the SWR1-catalyzed H2A.Z replacement in vitro and yeast H2A.Z deposition in vivo. Our findings provide mechanistic insights into how the SWR1 complex discriminates between the H2A nucleosome and H2A.Z nucleosome, establishing a simple paradigm for the governance of unidirectional H2A.Z exchange.
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Affiliation(s)
- Linchang Dai
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xue Xiao
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lu Pan
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Liuxin Shi
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ning Xu
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhuqiang Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaoli Feng
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Lu Ma
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Shuoxing Dou
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pengye Wang
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China; Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Bing Zhu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Li
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China; Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China.
| | - Zheng Zhou
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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24
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Viktorovskaya O, Chuang J, Jain D, Reim NI, López-Rivera F, Murawska M, Spatt D, Churchman LS, Park PJ, Winston F. Essential histone chaperones collaborate to regulate transcription and chromatin integrity. Genes Dev 2021; 35:698-712. [PMID: 33888559 PMCID: PMC8091981 DOI: 10.1101/gad.348431.121] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 03/30/2021] [Indexed: 12/15/2022]
Abstract
Histone chaperones are critical for controlling chromatin integrity during transcription, DNA replication, and DNA repair. Three conserved and essential chaperones, Spt6, Spn1/Iws1, and FACT, associate with elongating RNA polymerase II and interact with each other physically and/or functionally; however, there is little understanding of their individual functions or their relationships with each other. In this study, we selected for suppressors of a temperature-sensitive spt6 mutation that disrupts the Spt6-Spn1 physical interaction and that also causes both transcription and chromatin defects. This selection identified novel mutations in FACT. Surprisingly, suppression by FACT did not restore the Spt6-Spn1 interaction, based on coimmunoprecipitation, ChIP, and mass spectrometry experiments. Furthermore, suppression by FACT bypassed the complete loss of Spn1. Interestingly, the FACT suppressor mutations cluster along the FACT-nucleosome interface, suggesting that they alter FACT-nucleosome interactions. In agreement with this observation, we showed that the spt6 mutation that disrupts the Spt6-Spn1 interaction caused an elevated level of FACT association with chromatin, while the FACT suppressors reduced the level of FACT-chromatin association, thereby restoring a normal Spt6-FACT balance on chromatin. Taken together, these studies reveal previously unknown regulation between histone chaperones that is critical for their essential in vivo functions.
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Affiliation(s)
- Olga Viktorovskaya
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - James Chuang
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Dhawal Jain
- Department of Biomedical Informatics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Natalia I Reim
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Francheska López-Rivera
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Magdalena Murawska
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Dan Spatt
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - L Stirling Churchman
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Peter J Park
- Department of Biomedical Informatics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Fred Winston
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
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25
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Nagpal H, Fierz B. The Elusive Structure of Centro-Chromatin: Molecular Order or Dynamic Heterogenetity? J Mol Biol 2021; 433:166676. [PMID: 33065112 DOI: 10.1016/j.jmb.2020.10.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/07/2020] [Accepted: 10/08/2020] [Indexed: 01/09/2023]
Abstract
The centromere is an essential chromatin domain required for kinetochore recruitment and chromosome segregation in eukaryotes. To perform this role, centro-chromatin adopts a unique structure that provides access to kinetochore proteins and maintains stability under tension during mitosis. This is achieved by the presence of nucleosomes containing the H3 variant CENP-A, which also acts as the epigenetic mark defining the centromere. In this review, we discuss the role of CENP-A on the structure and dynamics of centromeric chromatin. We further discuss the impact of the CENP-A binding proteins CENP-C, CENP-N, and CENP-B on modulating centro-chromatin structure. Based on these findings we provide an overview of the higher order structure of the centromere.
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Affiliation(s)
- Harsh Nagpal
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Beat Fierz
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
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26
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Formosa T, Winston F. The role of FACT in managing chromatin: disruption, assembly, or repair? Nucleic Acids Res 2020; 48:11929-11941. [PMID: 33104782 PMCID: PMC7708052 DOI: 10.1093/nar/gkaa912] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/01/2020] [Accepted: 10/05/2020] [Indexed: 12/20/2022] Open
Abstract
FACT (FAcilitates Chromatin Transcription) has long been considered to be a transcription elongation factor whose ability to destabilize nucleosomes promotes RNAPII progression on chromatin templates. However, this is just one function of this histone chaperone, as FACT also functions in DNA replication. While broadly conserved among eukaryotes and essential for viability in many organisms, dependence on FACT varies widely, with some differentiated cells proliferating normally in its absence. It is therefore unclear what the core functions of FACT are, whether they differ in different circumstances, and what makes FACT essential in some situations but not others. Here, we review recent advances and propose a unifying model for FACT activity. By analogy to DNA repair, we propose that the ability of FACT to both destabilize and assemble nucleosomes allows it to monitor and restore nucleosome integrity as part of a system of chromatin repair, in which disruptions in the packaging of DNA are sensed and returned to their normal state. The requirement for FACT then depends on the level of chromatin disruption occurring in the cell, and the cell's ability to tolerate packaging defects. The role of FACT in transcription would then be just one facet of a broader system for maintaining chromatin integrity.
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Affiliation(s)
- Tim Formosa
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Fred Winston
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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27
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Feng Y, Hashiya F, Hidaka K, Sugiyama H, Endo M. Direct Observation of Dynamic Interactions between Orientation-Controlled Nucleosomes in a DNA Origami Frame. Chemistry 2020; 26:15282-15289. [PMID: 32830347 DOI: 10.1002/chem.202003071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/30/2020] [Indexed: 11/12/2022]
Abstract
The nucleosome is one of the most fundamental units involved in gene expression and consequent cell development, differentiation, and expression of cell functions. We report here a method to place reconstituted nucleosomes into a DNA origami frame for direct observation using high-speed atomic-force microscopy (HS-AFM). By using this method, multiple nucleosomes can be incorporated into a DNA origami frame and real-time movement of nucleosomes can be visualized. The arrangement and conformation of nucleosomes and the distance between two nucleosomes can be designed and controlled. In addition, four nucleosomes can be placed in a DNA frame. Multiple nucleosomes were well accessible in each conformation. Dynamic movement of the individual nucleosomes were precisely monitored in the DNA frame, and their assembly and interaction were directly observed. Neither mica surface modification nor chemical fixation of nucleosomes is used in this method, meaning that the DNA frame not only holds nucleosomes, but also retains their natural state. This method offers a promising platform for investigating nucleosome interactions and for studying chromatin structure.
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Affiliation(s)
- Yihong Feng
- Department of Chemistry, Graduate School of Science, Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Fumitaka Hashiya
- Department of Chemistry, Graduate School of Science, Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan.,present address: Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Kumi Hidaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan.,Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto, 606-8501, Japan
| | - Masayuki Endo
- Department of Chemistry, Graduate School of Science, Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan.,Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto, 606-8501, Japan
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28
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Jing Y, Ding D, Tian G, Kwan KCJ, Liu Z, Ishibashi T, Li XD. Semisynthesis of site-specifically succinylated histone reveals that succinylation regulates nucleosome unwrapping rate and DNA accessibility. Nucleic Acids Res 2020; 48:9538-9549. [PMID: 32766790 PMCID: PMC7515725 DOI: 10.1093/nar/gkaa663] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/22/2020] [Accepted: 07/29/2020] [Indexed: 01/06/2023] Open
Abstract
Posttranslational modifications (PTMs) of histones represent a crucial regulatory mechanism of nucleosome and chromatin dynamics in various of DNA-based cellular processes, such as replication, transcription and DNA damage repair. Lysine succinylation (Ksucc) is a newly identified histone PTM, but its regulation and function in chromatin remain poorly understood. Here, we utilized an expressed protein ligation (EPL) strategy to synthesize histone H4 with site-specific succinylation at K77 residue (H4K77succ), an evolutionarily conserved succinylation site at the nucleosomal DNA-histone interface. We then assembled mononucleosomes with the semisynthetic H4K77succ in vitro. We demonstrated that this succinylation impacts nucleosome dynamics and promotes DNA unwrapping from the histone surface, which allows proteins such as transcription factors to rapidly access buried regions of the nucleosomal DNA. In budding yeast, a lysine-to-glutamic acid mutation, which mimics Ksucc, at the H4K77 site reduced nucleosome stability and led to defects in DNA damage repair and telomere silencing in vivo. Our findings revealed this uncharacterized histone modification has important roles in nucleosome and chromatin dynamics.
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Affiliation(s)
- Yihang Jing
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Dongbo Ding
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Gaofei Tian
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Ka Chun Jonathan Kwan
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Zheng Liu
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Toyotaka Ishibashi
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Xiang David Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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29
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Mechanistic and structural insights into histone H2A–H2B chaperone in chromatin regulation. Biochem J 2020; 477:3367-3386. [DOI: 10.1042/bcj20190852] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 08/15/2020] [Accepted: 08/21/2020] [Indexed: 11/17/2022]
Abstract
Histone chaperones include a wide variety of proteins which associate with histones and regulate chromatin structure. The classic H2A–H2B type of histone chaperones, and the chromatin remodeling complex components possessing H2A–H2B chaperone activity, show a broad range of structures and functions. Rapid progress in the structural and functional study of H2A–H2B chaperones extends our knowledge about the epigenetic regulation of chromatin. In this review, we summarize the most recent advances in the understanding of the structure and function of H2A–H2B chaperones that interact with either canonical or variant H2A–H2B dimers. We discuss the current knowledge of the H2A–H2B chaperones, which present no preference for canonical and variant H2A–H2B dimers, describing how they interact with H2A–H2B to fulfill their functions. We also review recent advances of H2A variant-specific chaperones, demarcating how they achieve specific recognition for histone variant H2A.Z and how these interactions regulate chromatin structure by nucleosome editing. We highlight the universal mechanism underlying H2A–H2B dimers recognition by a large variety of histone chaperones. These findings will shed insight into the biological impacts of histone chaperone, chromatin remodeling complex, and histone variants in chromatin regulation.
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30
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Abstract
Derivation of induced Pluripotent Stem Cells (iPSCs) by reprogramming somatic cells to a pluripotent state has revolutionized stem cell research. Ensuing this, various groups have used genetic and non-genetic approaches to generate iPSCs from numerous cell types. However, achieving a pluripotent state in most of the reprogramming studies is marred by serious limitations such as low reprogramming efficiency and slow kinetics. These limitations are mainly due to the presence of potent barriers that exist during reprogramming when a mature cell is coaxed to achieve a pluripotent state. Several studies have revealed that intrinsic factors such as non-optimal stoichiometry of reprogramming factors, specific signaling pathways, cellular senescence, pluripotency-inhibiting transcription factors and microRNAs act as a roadblock. In addition, the epigenetic state of somatic cells and specific epigenetic modifications that occur during reprogramming also remarkably impede the generation of iPSCs. In this review, we present a comprehensive overview of the barriers that inhibit reprogramming and the understanding of which will pave the way to develop safe strategies for efficient reprogramming.
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31
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32
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Le TT, Gao X, Park SH, Lee J, Inman JT, Lee JH, Killian JL, Badman RP, Berger JM, Wang MD. Synergistic Coordination of Chromatin Torsional Mechanics and Topoisomerase Activity. Cell 2020; 179:619-631.e15. [PMID: 31626768 PMCID: PMC6899335 DOI: 10.1016/j.cell.2019.09.034] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 06/16/2019] [Accepted: 09/24/2019] [Indexed: 12/23/2022]
Abstract
DNA replication in eukaryotes generates DNA supercoiling, which may intertwine (braid) daughter chromatin fibers to form precatenanes, posing topological challenges during chromosome segregation. The mechanisms that limit precatenane formation remain unclear. By making direct torque measurements, we demonstrate that the intrinsic mechanical properties of chromatin play a fundamental role in dictating precatenane formation and regulating chromatin topology. Whereas a single chromatin fiber is torsionally soft, a braided fiber is torsionally stiff, indicating that supercoiling on chromatin substrates is preferentially directed in front of the fork during replication. We further show that topoisomerase II relaxation displays a strong preference for a single chromatin fiber over a braided fiber. These results suggest a synergistic coordination-the mechanical properties of chromatin inherently suppress precatenane formation during replication elongation by driving DNA supercoiling ahead of the fork, where supercoiling is more efficiently removed by topoisomerase II. VIDEO ABSTRACT.
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Affiliation(s)
- Tung T Le
- Howard Hughes Medical Institute, Cornell University, Ithaca, NY 14853, USA; Physics Department & LASSP, Cornell University, Ithaca, NY 14853, USA
| | - Xiang Gao
- Howard Hughes Medical Institute, Cornell University, Ithaca, NY 14853, USA; Physics Department & LASSP, Cornell University, Ithaca, NY 14853, USA
| | - Seong Ha Park
- Biophysics Program, Cornell University, Ithaca, NY 14853, USA
| | - Jaeyoon Lee
- Physics Department & LASSP, Cornell University, Ithaca, NY 14853, USA
| | - James T Inman
- Howard Hughes Medical Institute, Cornell University, Ithaca, NY 14853, USA; Physics Department & LASSP, Cornell University, Ithaca, NY 14853, USA
| | - Joyce H Lee
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jessica L Killian
- Howard Hughes Medical Institute, Cornell University, Ithaca, NY 14853, USA; Physics Department & LASSP, Cornell University, Ithaca, NY 14853, USA
| | - Ryan P Badman
- Physics Department & LASSP, Cornell University, Ithaca, NY 14853, USA
| | - James M Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Michelle D Wang
- Howard Hughes Medical Institute, Cornell University, Ithaca, NY 14853, USA; Physics Department & LASSP, Cornell University, Ithaca, NY 14853, USA.
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33
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Mesoscale organization of the chromatin fiber. Curr Opin Genet Dev 2020; 61:32-36. [DOI: 10.1016/j.gde.2020.02.022] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 02/13/2020] [Accepted: 02/22/2020] [Indexed: 12/11/2022]
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34
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Zhang W, Feng J, Li Q. The replisome guides nucleosome assembly during DNA replication. Cell Biosci 2020; 10:37. [PMID: 32190287 PMCID: PMC7066812 DOI: 10.1186/s13578-020-00398-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 02/29/2020] [Indexed: 12/18/2022] Open
Abstract
Nucleosome assembly during DNA replication is tightly coupled to ongoing DNA synthesis. This process, termed DNA replication-coupled (RC) nucleosome assembly, is essential for chromatin replication and has a great impact on both genome stability maintenance and epigenetic inheritance. This review discusses a set of recent findings regarding the role of replisome components contributing to RC nucleosome assembly. Starting with a brief introduction to the factors involved in nucleosome assembly and some aspects of the architecture of the eukaryotic replisome, we discuss studies from yeast to mammalian cells and the interactions of replisome components with histones and histone chaperones. We describe the proposed functions of replisome components during RC nucleosome assembly and discuss their impacts on histone segregation and implications for epigenetic inheritance.
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Affiliation(s)
- Wenshuo Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871 China
| | - Jianxun Feng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871 China
| | - Qing Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871 China
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35
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Chikhirzhina EV, Starkova TY, Polyanichko AM. The Role of Linker Histones in Chromatin Structural Organization. 2. Interaction with DNA and Nuclear Proteins. Biophysics (Nagoya-shi) 2020. [DOI: 10.1134/s0006350920020049] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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36
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Rett syndrome-causing mutations compromise MeCP2-mediated liquid-liquid phase separation of chromatin. Cell Res 2020; 30:393-407. [PMID: 32111972 DOI: 10.1038/s41422-020-0288-7] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 02/05/2020] [Indexed: 01/09/2023] Open
Abstract
Rett syndrome (RTT), a severe postnatal neurodevelopmental disorder, is caused by mutations in the X-linked gene encoding methyl-CpG-binding protein 2 (MeCP2). MeCP2 is a chromatin organizer regulating gene expression. RTT-causing mutations have been shown to affect this function. However, the mechanism by which MeCP2 organizes chromatin is unclear. In this study, we found that MeCP2 can induce compaction and liquid-liquid phase separation of nucleosomal arrays in vitro, and DNA methylation further enhances formation of chromatin condensates by MeCP2. Interestingly, RTT-causing mutations compromise MeCP2-mediated chromatin phase separation, while benign variants have little effect on this process. Moreover, MeCP2 competes with linker histone H1 to form mutually exclusive chromatin condensates in vitro and distinct heterochromatin foci in vivo. RTT-causing mutations reduce or even abolish the ability of MeCP2 to compete with histone H1 and to form chromatin condensates. Together, our results identify a novel mechanism by which phase separation underlies MeCP2-mediated heterochromatin formation and reveal the potential link between this process and the pathology of RTT.
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Xiao X, Liu C, Pei Y, Wang YZ, Kong J, Lu K, Ma L, Dou SX, Wang PY, Li G, Chen P, Li W. Histone H2A Ubiquitination Reinforces Mechanical Stability and Asymmetry at the Single-Nucleosome Level. J Am Chem Soc 2020; 142:3340-3345. [DOI: 10.1021/jacs.9b12448] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Xue Xiao
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cuifang Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yingxin Pei
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi-Zhou Wang
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Synthetic Biology Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, China
| | - Jingwei Kong
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ke Lu
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lu Ma
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Shuo-Xing Dou
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peng-Ye Wang
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Guohong Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ping Chen
- School of Basic Medical Sciences, Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing 100054, China
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Wei Li
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
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Kaczmarczyk A, Meng H, Ordu O, Noort JV, Dekker NH. Chromatin fibers stabilize nucleosomes under torsional stress. Nat Commun 2020; 11:126. [PMID: 31913285 PMCID: PMC6949304 DOI: 10.1038/s41467-019-13891-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 11/25/2019] [Indexed: 01/11/2023] Open
Abstract
Torsional stress generated during DNA replication and transcription has been suggested to facilitate nucleosome unwrapping and thereby the progression of polymerases. However, the propagation of twist in condensed chromatin remains yet unresolved. Here, we measure how force and torque impact chromatin fibers with a nucleosome repeat length of 167 and 197. We find that both types of fibers fold into a left-handed superhelix that can be stabilized by positive torsion. We observe that the structural changes induced by twist were reversible, indicating that chromatin has a large degree of elasticity. Our direct measurements of torque confirmed the hypothesis of chromatin fibers as a twist buffer. Using a statistical mechanics-based torsional spring model, we extracted values of the chromatin twist modulus and the linking number per stacked nucleosome that were in good agreement with values measured here experimentally. Overall, our findings indicate that the supercoiling generated by DNA-processing enzymes, predicted by the twin-supercoiled domain model, can be largely accommodated by the higher-order structure of chromatin.
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Affiliation(s)
- Artur Kaczmarczyk
- Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, 2333 CA, Leiden, The Netherlands
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
- Faculty of Medicine, Imperial College London, Du Cane Road, W12 0NN, London, United Kingdom
| | - He Meng
- Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, 2333 CA, Leiden, The Netherlands
| | - Orkide Ordu
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - John van Noort
- Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, 2333 CA, Leiden, The Netherlands.
| | - Nynke H Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands.
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Mivelaz M, Cao AM, Kubik S, Zencir S, Hovius R, Boichenko I, Stachowicz AM, Kurat CF, Shore D, Fierz B. Chromatin Fiber Invasion and Nucleosome Displacement by the Rap1 Transcription Factor. Mol Cell 2019; 77:488-500.e9. [PMID: 31761495 PMCID: PMC7005674 DOI: 10.1016/j.molcel.2019.10.025] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 07/09/2019] [Accepted: 10/16/2019] [Indexed: 02/03/2023]
Abstract
Pioneer transcription factors (pTFs) bind to target sites within compact chromatin, initiating chromatin remodeling and controlling the recruitment of downstream factors. The mechanisms by which pTFs overcome the chromatin barrier are not well understood. Here, we reveal, using single-molecule fluorescence, how the yeast transcription factor Rap1 invades and remodels chromatin. Using a reconstituted chromatin system replicating yeast promoter architecture, we demonstrate that Rap1 can bind nucleosomal DNA within a chromatin fiber but with shortened dwell times compared to naked DNA. Moreover, we show that Rap1 binding opens chromatin fiber structure by inhibiting inter-nucleosome contacts. Finally, we reveal that Rap1 collaborates with the chromatin remodeler RSC to displace promoter nucleosomes, paving the way for long-lived bound states on newly exposed DNA. Together, our results provide a mechanistic view of how Rap1 gains access and opens chromatin, thereby establishing an active promoter architecture and controlling gene expression. The yeast transcription factor Rap1 can invade compact chromatin Rap1 directly opens chromatin structure by preventing nucleosome stacking Stable Rap1 binding requires collaboration with RSC to shift promoter nucleosomes
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Affiliation(s)
- Maxime Mivelaz
- École Polytechnique Fédérale de Lausanne (EPFL), SB ISIC LCBM, Station 6, 1015 Lausanne, Switzerland
| | - Anne-Marinette Cao
- École Polytechnique Fédérale de Lausanne (EPFL), SB ISIC LCBM, Station 6, 1015 Lausanne, Switzerland
| | - Slawomir Kubik
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), 1211 Geneva 4, Switzerland
| | - Sevil Zencir
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), 1211 Geneva 4, Switzerland
| | - Ruud Hovius
- École Polytechnique Fédérale de Lausanne (EPFL), SB ISIC LCBM, Station 6, 1015 Lausanne, Switzerland
| | - Iuliia Boichenko
- École Polytechnique Fédérale de Lausanne (EPFL), SB ISIC LCBM, Station 6, 1015 Lausanne, Switzerland
| | - Anna Maria Stachowicz
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), 1211 Geneva 4, Switzerland
| | - Christoph F Kurat
- Molecular Biology Division, Biomedical Center, Faculty of Medicine, LMU Munich, 82152 Planegg-Martinsried, Germany
| | - David Shore
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), 1211 Geneva 4, Switzerland
| | - Beat Fierz
- École Polytechnique Fédérale de Lausanne (EPFL), SB ISIC LCBM, Station 6, 1015 Lausanne, Switzerland.
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40
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Abstract
Nucleosomes and chromatin control eukaryotic genome accessibility and thereby regulate DNA processes, including transcription, replication, and repair. Conformational dynamics within the nucleosome and chromatin structure play a key role in this regulatory function. Structural fluctuations continuously expose internal DNA sequences and nucleosome surfaces, thereby providing transient access for the nuclear machinery. Progress in structural studies of nucleosomes and chromatin has provided detailed insight into local chromatin organization and has set the stage for recent in-depth investigations of the structural dynamics of nucleosomes and chromatin fibers. Here, we discuss the dynamic processes observed in chromatin over different length scales and timescales and review current knowledge about the biophysics of distinct structural transitions.
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Affiliation(s)
- Beat Fierz
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Michael G. Poirier
- Department of Physics, Biophysics Graduate Program, Ohio State Biochemistry Graduate Program, and Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210-1117, USA
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41
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Chromatin fiber structural motifs as regulatory hubs of genome function? Essays Biochem 2019; 63:123-132. [PMID: 30967476 PMCID: PMC6484786 DOI: 10.1042/ebc20180065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/13/2019] [Accepted: 03/13/2019] [Indexed: 02/07/2023]
Abstract
Nucleosomes cover eukaryotic genomes like beads on a string and play a central role in regulating genome function. Isolated strings of nucleosomes have the potential to compact and form higher order chromatin structures, such as the well-characterized 30-nm fiber. However, despite tremendous advances in observing chromatin fibers in situ it has not been possible to confirm that regularly ordered fibers represent a prevalent structural level in the folding of chromosomes. Instead, it appears that folding at a larger scale than the nucleosome involves a variety of random structures with fractal characteristics. Nevertheless, recent progress provides evidence for the existence of structural motifs in chromatin fibers, potentially localized to strategic sites in the genome. Here we review the current understanding of chromatin fiber folding and the emerging roles that oligonucleosomal motifs play in the regulation of genome function.
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42
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Chemical and biophysical methods to explore dynamic mechanisms of chromatin silencing. Curr Opin Chem Biol 2019; 51:1-10. [PMID: 30825740 DOI: 10.1016/j.cbpa.2019.01.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/15/2019] [Accepted: 01/25/2019] [Indexed: 12/19/2022]
Abstract
Chromatin, the nucleoprotein complex organizing the genome, is central in regulating gene expression and genome organization. Chromatin conformational dynamics, controlled by histone post-translational modifications (PTM) and effector proteins, play a key role in this regulatory function. Recent developments in chemical biology, cell biology, and biophysics sparked important new studies, which probe direct causal connections between histone PTMs, chromatin effector proteins that write or read these modifications, and the involved functional chromatin states. In particular, the mechanisms of heterochromatin silencing have been explored in great detail in recent years. These studies revealed the highly dynamic nature of this chromatin state, its conformational heterogeneity, and different mechanisms of its formation. Here, we review how chemical biology and biophysics shaped our current understanding of the dynamic processes observed in heterochromatin and discuss the emerging technologies to detect chromatin organization directly in the cellular environment.
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43
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de Jong BE, Brouwer TB, Kaczmarczyk A, Visscher B, van Noort J. Rigid Basepair Monte Carlo Simulations of One-Start and Two-Start Chromatin Fiber Unfolding by Force. Biophys J 2018; 115:1848-1859. [PMID: 30366627 PMCID: PMC6303278 DOI: 10.1016/j.bpj.2018.10.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 09/21/2018] [Accepted: 10/05/2018] [Indexed: 12/30/2022] Open
Abstract
The organization of chromatin in 30 nm fibers remains a topic of debate. Here, we quantify the mechanical properties of the linker DNA and evaluate the impact of these properties on chromatin fiber folding. We extended a rigid basepair DNA model to include (un)wrapping of nucleosomal DNA and (un)stacking of nucleosomes in one-start and two-start chromatin fibers. Monte Carlo simulations that mimic single-molecule force spectroscopy experiments of folded nucleosomal arrays reveal different stages of unfolding as a function of force and are largely consistent with a two-start folding for 167 and one-start folding for 197 nucleosome repeat length fibers. The major insight is that nucleosome unstacking and subsequent unwrapping is not necessary to obtain quantitative agreement with experimental force extension curves up to the overstretching plateau of folded chromatin fibers at 3-5 pN. Nucleosome stacking appears better accommodated in one-start than in two-start conformations, and we suggest that this difference can compensate the increased energy for bending the linker DNA. Overall, these simulations capture the dynamic structure of chromatin fibers while maintaining realistic physical properties of the linker DNA.
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Affiliation(s)
- Babette E de Jong
- Huygens-Kamerlingh Onnes Laboratory, Leiden Institute of Physics, Leiden University, Leiden, The Netherlands
| | - Thomas B Brouwer
- Huygens-Kamerlingh Onnes Laboratory, Leiden Institute of Physics, Leiden University, Leiden, The Netherlands
| | - Artur Kaczmarczyk
- Huygens-Kamerlingh Onnes Laboratory, Leiden Institute of Physics, Leiden University, Leiden, The Netherlands
| | - Bert Visscher
- Huygens-Kamerlingh Onnes Laboratory, Leiden Institute of Physics, Leiden University, Leiden, The Netherlands
| | - John van Noort
- Huygens-Kamerlingh Onnes Laboratory, Leiden Institute of Physics, Leiden University, Leiden, The Netherlands.
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44
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Dynamics of Chromatin Fibers: Comparison of Monte Carlo Simulations with Force Spectroscopy. Biophys J 2018; 115:1644-1655. [PMID: 30236784 PMCID: PMC6225046 DOI: 10.1016/j.bpj.2018.06.032] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 06/15/2018] [Accepted: 06/19/2018] [Indexed: 12/17/2022] Open
Abstract
To elucidate conformational dynamics of chromatin fibers, we compared available force-spectroscopy measurements with extensive Monte Carlo simulations of nucleosome arrays under external force. Our coarse-grained model of chromatin includes phenomenological energy terms for the DNA-histone adhesion and the internucleosome stacking interactions. We found that the Monte Carlo fiber ensembles simulated with increasing degrees of DNA unwrapping and the stacking energy 8 kT can account for the intricate force-extension response observed experimentally. Our analysis shows that at low external forces (F < 3.0 picoNewtons), the DNA ends in nucleosomes breathe by ∼10 bp. Importantly, under these conditions, the fiber is highly dynamic, exhibiting continuous unstacking-restacking transitions, allowing accessibility of transcription factors to DNA, while maintaining a relatively compact conformation. Of note, changing the stacking interaction by a few kT, an in silico way to mimic histone modifications, is sufficient to transform an open chromatin state into a compact fiber. The fibers are mostly two-start zigzag folds with rare occurrences of three- to five-start morphologies. The internucleosome stacking is lost during the linear response regime. At the higher forces exceeding 4 picoNewtons, the nucleosome unwrapping becomes stochastic and asymmetric, with one DNA arm opened by ∼55 bp and the other arm only by ∼10 bp. Importantly, this asymmetric unwrapping occurs for any kind of sequence, including the symmetric ones. Our analysis brings new, to our knowledge, insights in dynamics of chromatin modulated by histone epigenetic modifications and molecular motors such as RNA polymerase.
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45
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Dissection of structural dynamics of chromatin fibers by single-molecule magnetic tweezers. BIOPHYSICS REPORTS 2018; 4:222-232. [PMID: 30310859 PMCID: PMC6153500 DOI: 10.1007/s41048-018-0064-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 07/18/2018] [Indexed: 12/01/2022] Open
Abstract
The accessibility of genomic DNA, as a key determinant of gene-related processes, is dependent on the packing density and structural dynamics of chromatin fiber. However, due to the highly dynamic and heterogeneous properties of chromatin fiber, it is technically challenging to study these properties of chromatin. Here, we report a strategy for dissecting the dynamics of chromatin fibers based on single-molecule magnetic tweezers. Using magnetic tweezers, we can manipulate the chromatin fiber and trace its extension during the folding and unfolding process under tension to investigate the dynamic structural transitions at single-molecule level. The highly accurate and reliable in vitro single-molecule strategy provides a new research platform to dissect the structural dynamics of chromatin fiber and its regulation by different epigenetic factors during gene expression.
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46
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Gurova K, Chang HW, Valieva ME, Sandlesh P, Studitsky VM. Structure and function of the histone chaperone FACT - Resolving FACTual issues. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2018; 1861:S1874-9399(18)30159-7. [PMID: 30055319 PMCID: PMC6349528 DOI: 10.1016/j.bbagrm.2018.07.008] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 07/17/2018] [Accepted: 07/19/2018] [Indexed: 12/12/2022]
Abstract
FAcilitates Chromatin Transcription (FACT) has been considered essential for transcription through chromatin mostly based on cell-free experiments. However, FACT inactivation in cells does not cause a significant reduction in transcription. Moreover, not all mammalian cells require FACT for viability. Here we synthesize information from different organisms to reveal the core function(s) of FACT and propose a model that reconciles the cell-free and cell-based observations. We describe FACT structure and nucleosomal interactions, and their roles in FACT-dependent transcription, replication and repair. The variable requirements for FACT among different tumor and non-tumor cells suggest that various FACT-dependent processes have significantly different levels of relative importance in different eukaryotic cells. We propose that the stability of chromatin, which might vary among different cell types, dictates these diverse requirements for FACT to support cell viability. Since tumor cells are among the most sensitive to FACT inhibition, this vulnerability could be exploited for cancer treatment.
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Affiliation(s)
- Katerina Gurova
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA.
| | - Han-Wen Chang
- Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Maria E Valieva
- Biology Faculty, Lomonosov Moscow State University, Moscow, Russia
| | - Poorva Sandlesh
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA
| | - Vasily M Studitsky
- Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Biology Faculty, Lomonosov Moscow State University, Moscow, Russia.
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47
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Chen P, Dong L, Hu M, Wang YZ, Xiao X, Zhao Z, Yan J, Wang PY, Reinberg D, Li M, Li W, Li G. Functions of FACT in Breaking the Nucleosome and Maintaining Its Integrity at the Single-Nucleosome Level. Mol Cell 2018; 71:284-293.e4. [DOI: 10.1016/j.molcel.2018.06.020] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 05/01/2018] [Accepted: 06/13/2018] [Indexed: 12/12/2022]
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48
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Zhou BR, Jiang J, Ghirlando R, Norouzi D, Sathish Yadav KN, Feng H, Wang R, Zhang P, Zhurkin V, Bai Y. Revisit of Reconstituted 30-nm Nucleosome Arrays Reveals an Ensemble of Dynamic Structures. J Mol Biol 2018; 430:3093-3110. [PMID: 29959925 DOI: 10.1016/j.jmb.2018.06.020] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 06/05/2018] [Accepted: 06/05/2018] [Indexed: 01/23/2023]
Abstract
It has long been suggested that chromatin may form a fiber with a diameter of ~30 nm that suppresses transcription. Despite nearly four decades of study, the structural nature of the 30-nm chromatin fiber and conclusive evidence of its existence in vivo remain elusive. The key support for the existence of specific 30-nm chromatin fiber structures is based on the determination of the structures of reconstituted nucleosome arrays using X-ray crystallography and single-particle cryo-electron microscopy coupled with glutaraldehyde chemical cross-linking. Here we report the characterization of these nucleosome arrays in solution using analytical ultracentrifugation, NMR, and small-angle X-ray scattering. We found that the physical properties of these nucleosome arrays in solution are not consistent with formation of just a few discrete structures of nucleosome arrays. In addition, we obtained a crystal of the nucleosome in complex with the globular domain of linker histone H5 that shows a new form of nucleosome packing and suggests a plausible alternative compact conformation for nucleosome arrays. Taken together, our results challenge the key evidence for the existence of a limited number of structures of reconstituted nucleosome arrays in solution by revealing that the reconstituted nucleosome arrays are actually best described as an ensemble of various conformations with a zigzagged arrangement of nucleosomes. Our finding has implications for understanding the structure and function of chromatin in vivo.
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Affiliation(s)
- Bing-Rui Zhou
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jiansheng Jiang
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Davood Norouzi
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - K N Sathish Yadav
- Laboratory of Structural Biophysics, National Cancer Institute, Frederick, MD 21701, USA
| | - Hanqiao Feng
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rui Wang
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ping Zhang
- Laboratory of Structural Biophysics, National Cancer Institute, Frederick, MD 21701, USA
| | - Victor Zhurkin
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yawen Bai
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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49
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Kilic S, Boichenko I, Lechner CC, Fierz B. A bi-terminal protein ligation strategy to probe chromatin structure during DNA damage. Chem Sci 2018; 9:3704-3709. [PMID: 29780501 PMCID: PMC5935033 DOI: 10.1039/c8sc00681d] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 03/15/2018] [Indexed: 12/18/2022] Open
Abstract
The cellular response to DNA damage results in a signaling cascade that primes chromatin for repair. Combinatorial post-translational modifications (PTMs) play an important role in this process by altering the physical properties of chromatin and recruiting downstream factors. One key signal integrator is the histone variant H2A.X, which is phosphorylated at a C-terminal serine (S139ph), and ubiquitylated within its N-terminal tail at lysines 13 and 15 (K13/15ub). How these PTMs directly impact chromatin structure and thereby facilitate DNA repair is not well understood. Detailed studies require synthetic access to such N- and C-terminally modified proteins. This is complicated by the requirement for protecting groups allowing multi-fragment assembly. Here, we report a semi-synthetic route to generate simultaneously N- and C-terminally modified proteins using genetically encoded orthogonal masking groups. Applied to H2A.X, expression of a central protein fragment, containing a protected N-terminal cysteine and a C-terminal thioester masked as a split intein, enables sequential C- and N-terminal protein modification and results in the convergent production of H2A.X carrying K15ub and S139ph. Using single-molecule FRET between defined nucleosomes in synthetic chromatin fibers, we then show that K15 ubiquitylation (but not S139ph) impairs nucleosome stacking in tetranucleosome units, opening chromatin during DNA repair.
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Affiliation(s)
- Sinan Kilic
- Laboratory of Biophysical Chemistry of Macromolecules , Institute of Chemical Sciences and Engineering , Ecole Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland .
| | - Iuliia Boichenko
- Laboratory of Biophysical Chemistry of Macromolecules , Institute of Chemical Sciences and Engineering , Ecole Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland .
| | - Carolin C Lechner
- Laboratory of Biophysical Chemistry of Macromolecules , Institute of Chemical Sciences and Engineering , Ecole Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland .
| | - Beat Fierz
- Laboratory of Biophysical Chemistry of Macromolecules , Institute of Chemical Sciences and Engineering , Ecole Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland .
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50
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Nucleosome-level 3D organization of the genome. Biochem Soc Trans 2018; 46:491-501. [PMID: 29626147 DOI: 10.1042/bst20170388] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 02/26/2018] [Accepted: 03/01/2018] [Indexed: 01/19/2023]
Abstract
Nucleosomes are the unitary structures of chromosome folding, and their arrangements are intimately coupled to the regulation of genome activities. Conventionally, structural analyses using electron microscopy and X-ray crystallography have been used to study such spatial nucleosome arrangements. In contrast, recent improvements in the resolution of sequencing-based methods allowed investigation of nucleosome arrangements separately at each genomic locus, enabling exploration of gene-dependent regulation mechanisms. Here, we review recent studies on nucleosome folding in chromosomes from these two methodological perspectives: conventional structural analyses and DNA sequencing, and discuss their implications for future research.
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