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Zhang M, Celis CD, Liu J, Bustamante C, Ren G. Conformational Change of Nucleosome Arrays prior to Phase Separation. RESEARCH SQUARE 2023:rs.3.rs-2460504. [PMID: 36711774 PMCID: PMC9882673 DOI: 10.21203/rs.3.rs-2460504/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Chromatin phase transition serves as a regulatory mechanism for eukaryotic transcription. Understanding this process requires the characterization of the nucleosome array structure in response to external stimuli prior to phase separation. However, the intrinsic flexibility and heterogeneity hinders the arrays' structure determination. Here we exploit advances in cryogenic electron tomography (cryo-ET) to determine the three-dimensional (3D) structure of each individual particle of mono-, di-, tri-, and tetranucleosome arrays. Statistical analysis reveals the ionic strength changes the angle between the DNA linker and nucleosome core particle (NCP), which regulate the overall morphology of nucleosome arrays. The finding that one-third of the arrays in the presence of H1 contain an NCP invaded by foreign DNA suggests an alternative function of H1 in constructing nucleosomal networks. The new insights into the nucleosome conformational changes prior to the intermolecular interaction stage extends our understanding of chromatin phase separation regulation.
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Affiliation(s)
- Meng Zhang
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, USA
- Applied Science and Technology Graduate Group, University of California, Berkeley, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, USA
| | - César-Díaz Celis
- California Institute for Quantitative Biosciences, University of California, Berkeley, USA
- Howard Hughes Medical Institute, University of California, Berkeley, USA
| | - Jianfang Liu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, USA
| | - Carlos Bustamante
- Applied Science and Technology Graduate Group, University of California, Berkeley, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, USA
- Howard Hughes Medical Institute, University of California, Berkeley, USA
- Department of Chemistry, University of California, Berkeley, USA
- Department of Physics, University of California, Berkeley, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, USA
- Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, USA
- Kavli Energy Nanoscience Institute, University of California, Berkeley, USA
| | - Gang Ren
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, USA
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2
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Zhao H, Guo M, Zhang F, Shao X, Liu G, Xing Y, Zhao X, Luo L, Cai L. Nucleosome Assembly and Disassembly in vitro Are Governed by Chemical Kinetic Principles. Front Cell Dev Biol 2021; 9:762571. [PMID: 34692710 PMCID: PMC8529108 DOI: 10.3389/fcell.2021.762571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 09/17/2021] [Indexed: 12/05/2022] Open
Abstract
As the elementary unit of eukaryotic chromatin, nucleosomes in vivo are highly dynamic in many biological processes, such as DNA replication, repair, recombination, or transcription, to allow the necessary factors to gain access to their substrate. The dynamic mechanism of nucleosome assembly and disassembly has not been well described thus far. We proposed a chemical kinetic model of nucleosome assembly and disassembly in vitro. In the model, the efficiency of nucleosome assembly was positively correlated with the total concentration of histone octamer, reaction rate constant and reaction time. All the corollaries of the model were well verified for the Widom 601 sequence and the six artificially synthesized DNA sequences, named CS1–CS6, by using the salt dialysis method in vitro. The reaction rate constant in the model may be used as a new parameter to evaluate the nucleosome reconstitution ability with DNAs. Nucleosome disassembly experiments for the Widom 601 sequence detected by Förster resonance energy transfer (FRET) and fluorescence thermal shift (FTS) assays demonstrated that nucleosome disassembly is the inverse process of assembly and can be described as three distinct stages: opening phase of the (H2A–H2B) dimer/(H3–H4)2 tetramer interface, release phase of the H2A–H2B dimers from (H3–H4)2 tetramer/DNA and removal phase of the (H3–H4)2 tetramer from DNA. Our kinetic model of nucleosome assembly and disassembly allows to confirm that nucleosome assembly and disassembly in vitro are governed by chemical kinetic principles.
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Affiliation(s)
- Hongyu Zhao
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, China.,Inner Mongolia Key Laboratory of Functional Genome Bioinformatics, Inner Mongolia University of Science and Technology, Baotou, China
| | - Mingxin Guo
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, China.,Inner Mongolia Key Laboratory of Functional Genome Bioinformatics, Inner Mongolia University of Science and Technology, Baotou, China
| | - Fenghui Zhang
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, China.,Inner Mongolia Key Laboratory of Functional Genome Bioinformatics, Inner Mongolia University of Science and Technology, Baotou, China
| | - Xueqin Shao
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, China.,Inner Mongolia Key Laboratory of Functional Genome Bioinformatics, Inner Mongolia University of Science and Technology, Baotou, China
| | - Guoqing Liu
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, China.,Inner Mongolia Key Laboratory of Functional Genome Bioinformatics, Inner Mongolia University of Science and Technology, Baotou, China
| | - Yongqiang Xing
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, China.,Inner Mongolia Key Laboratory of Functional Genome Bioinformatics, Inner Mongolia University of Science and Technology, Baotou, China
| | - Xiujuan Zhao
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, China.,Inner Mongolia Key Laboratory of Functional Genome Bioinformatics, Inner Mongolia University of Science and Technology, Baotou, China
| | - Liaofu Luo
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, China.,Inner Mongolia Key Laboratory of Functional Genome Bioinformatics, Inner Mongolia University of Science and Technology, Baotou, China
| | - Lu Cai
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, China.,Inner Mongolia Key Laboratory of Functional Genome Bioinformatics, Inner Mongolia University of Science and Technology, Baotou, China
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3
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Liu G, Zhao H, Meng H, Xing Y, Cai L. A deformation energy model reveals sequence-dependent property of nucleosome positioning. Chromosoma 2021; 130:27-40. [PMID: 33452566 PMCID: PMC7889546 DOI: 10.1007/s00412-020-00750-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 12/24/2020] [Accepted: 12/29/2020] [Indexed: 11/18/2022]
Abstract
We present a deformation energy model for predicting nucleosome positioning, in which a position-dependent structural parameter set derived from crystal structures of nucleosomes was used to calculate the DNA deformation energy. The model is successful in predicting nucleosome occupancy genome-wide in budding yeast, nucleosome free energy, and rotational positioning of nucleosomes. Our model also indicates that the genomic regions underlying the MNase-sensitive nucleosomes in budding yeast have high deformation energy and, consequently, low nucleosome-forming ability, while the MNase-sensitive non-histone particles are characterized by much lower DNA deformation energy and high nucleosome preference. In addition, we also revealed that remodelers, SNF2 and RSC8, are likely to act in chromatin remodeling by binding to broad nucleosome-depleted regions that are intrinsically favorable for nucleosome positioning. Our data support the important role of position-dependent physical properties of DNA in nucleosome positioning.
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Affiliation(s)
- Guoqing Liu
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China.
- Inner Mongolia Key Lab of Functional Genome Bioinformatics, Inner Mongolia University of Science and Technology, Baotou, 014010, China.
| | - Hongyu Zhao
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China
- Inner Mongolia Key Lab of Functional Genome Bioinformatics, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Hu Meng
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China
- Inner Mongolia Key Lab of Functional Genome Bioinformatics, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Yongqiang Xing
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China
- Inner Mongolia Key Lab of Functional Genome Bioinformatics, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Lu Cai
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China
- Inner Mongolia Key Lab of Functional Genome Bioinformatics, Inner Mongolia University of Science and Technology, Baotou, 014010, China
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4
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Liu G, Zhao H, Meng H, Xing Y, Yang H, Lin H. Deform-nu: A DNA Deformation Energy-Based Predictor for Nucleosome Positioning. Front Cell Dev Biol 2021; 8:596341. [PMID: 33425904 PMCID: PMC7785812 DOI: 10.3389/fcell.2020.596341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 11/26/2020] [Indexed: 12/01/2022] Open
Abstract
The structure and function of chromatin can be regulated through positioning patterns of nucleosomes. DNA-based processes are regulated via nucleosomes. Therefore, it is significant to determine nucleosome positions in DNA-based processes. A deformation energy model was proposed to predict nucleosome positions in our previous study. A free web server based on the model (http://lin-group.cn/server/deform-nu/) was firstly established to estimate the occupancy and rotational positioning of nucleosomes in the study. Then, the performance of the model was verified by several examples. The results indicated that nucleosome positioning relied on the physical properties of DNA, such as deformation energy.
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Affiliation(s)
- Guoqing Liu
- School of Life Sciences and Technology, Inner Mongolia University of Science and Technology, Baotou, China
| | - Hongyu Zhao
- School of Life Sciences and Technology, Inner Mongolia University of Science and Technology, Baotou, China
| | - Hu Meng
- School of Life Sciences and Technology, Inner Mongolia University of Science and Technology, Baotou, China
| | - Yongqiang Xing
- School of Life Sciences and Technology, Inner Mongolia University of Science and Technology, Baotou, China
| | - Hui Yang
- School of Life Sciences and Technology, Inner Mongolia University of Science and Technology, Baotou, China
| | - Hao Lin
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
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Kenzaki H, Takada S. Linker DNA Length is a Key to Tri-nucleosome Folding. J Mol Biol 2020; 433:166792. [PMID: 33383034 DOI: 10.1016/j.jmb.2020.166792] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 12/07/2020] [Accepted: 12/22/2020] [Indexed: 01/18/2023]
Abstract
The folding of a nucleosome array has long been one of the fundamental and unsolved problems in chromatin biology. In this study, we address how nucleosome array folding depends on the length of linker DNA. We performed molecular dynamics simulations of a tri-nucleosome, a minimal model of chromatin folding, with various linker lengths (LLs) ranging from 20 to 40 base pairs (bps). We found that the tri-nucleosome folding strongly depends on LLs, and classified the structure ensemble into five classes, named from trinuc-1 to trinuc-5. As a function of LL, the different classes appear, on average, every 2 bps with a period of 10 bps, and are characterized by distinct inter-nucleosome interactions. The trinuc-1 conformation corresponds to LL ~ 10n, where n is an integer, and is stabilized by the tight packing between the first and the third nucleosomes, consistent with a zigzag fiber form. Structures of the other four classes are more diverse and distributed continuously in the space of possible configurations. Histone-DNA electrostatic interactions in the tri-nucleosome are further analyzed.
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Affiliation(s)
- Hiroo Kenzaki
- Information Systems Division, Head Office for Information Systems and Cybersecurity, RIKEN, Hirosawa, Wako, Saitama 351-0198, Japan.
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kitashirakawa, Sakyo, Kyoto 606-8502, Japan.
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Liu G, Liu GJ, Tan JX, Lin H. DNA physical properties outperform sequence compositional information in classifying nucleosome-enriched and -depleted regions. Genomics 2018; 111:1167-1175. [PMID: 30055231 DOI: 10.1016/j.ygeno.2018.07.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 07/07/2018] [Accepted: 07/15/2018] [Indexed: 12/15/2022]
Abstract
The nucleosome is the fundamental structural unit of eukaryotic chromatin and plays an essential role in the epigenetic regulation of cellular processes, such as DNA replication, recombination, and transcription. Hence, it is important to identify nucleosome positions in the genome. Our previous model based on DNA deformation energy, in which a set of DNA physical descriptors was used, performed well in predicting nucleosome dyad positions and occupancy. In this study, we established a machine-learning model for predicting nucleosome occupancy in order to further verify the physical descriptors. Results showed that (1) our model outperformed several other sequence compositional information-based models, indicating a stronger dependence of nucleosome positioning on DNA physical properties; (2) nucleosome-enriched and -depleted regions have distinct features in terms of DNA physical descriptors like sequence-dependent flexibility and equilibrium structure parameters; (3) gene transcription start sites and termination sites can be well characterized with the distribution patterns of the physical descriptors, indicating the regulatory role of DNA physical properties in gene transcription. In addition, we developed a web server for the model, which is freely accessible at http://lin-group.cn/server/iNuc-force/.
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Affiliation(s)
- Guoqing Liu
- The School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou 014010, China.
| | - Guo-Jun Liu
- School of Natural Sciences and Mathematics, Ural Federal University, Ekaterinburg 620000, Russia
| | - Jiu-Xin Tan
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Hao Lin
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.
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