1
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Li Z, Schlick T. Hi-BDiSCO: folding 3D mesoscale genome structures from Hi-C data using brownian dynamics. Nucleic Acids Res 2024; 52:583-599. [PMID: 38015443 PMCID: PMC10810283 DOI: 10.1093/nar/gkad1121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 10/12/2023] [Accepted: 11/22/2023] [Indexed: 11/29/2023] Open
Abstract
The structure and dynamics of the eukaryotic genome are intimately linked to gene regulation and transcriptional activity. Many chromosome conformation capture experiments like Hi-C have been developed to detect genome-wide contact frequencies and quantify loop/compartment structures for different cellular contexts and time-dependent processes. However, a full understanding of these events requires explicit descriptions of representative chromatin and chromosome configurations. With the exponentially growing amount of data from Hi-C experiments, many methods for deriving 3D structures from contact frequency data have been developed. Yet, most reconstruction methods use polymer models with low resolution to predict overall genome structure. Here we present a Brownian Dynamics (BD) approach termed Hi-BDiSCO for producing 3D genome structures from Hi-C and Micro-C data using our mesoscale-resolution chromatin model based on the Discrete Surface Charge Optimization (DiSCO) model. Our approach integrates reconstruction with chromatin simulations at nucleosome resolution with appropriate biophysical parameters. Following a description of our protocol, we present applications to the NXN, HOXC, HOXA and Fbn2 mouse genes ranging in size from 50 to 100 kb. Such nucleosome-resolution genome structures pave the way for pursuing many biomedical applications related to the epigenomic regulation of chromatin and control of human disease.
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Affiliation(s)
- Zilong Li
- Department of Chemistry, 100 Washington Square East, Silver Building, New York University, New York, NY 10003, USA
- Simons Center for Computational Physical Chemistry, 24 Waverly Place, Silver Building, New York University, New York, NY 10003, USA
| | - Tamar Schlick
- Department of Chemistry, 100 Washington Square East, Silver Building, New York University, New York, NY 10003, USA
- Courant Institute of Mathematical Sciences, New York University, 251 Mercer St., New York, NY 10012, USA
- New York University-East China Normal University Center for Computational Chemistry, New York University Shanghai, Shanghai 200122, China
- Simons Center for Computational Physical Chemistry, 24 Waverly Place, Silver Building, New York University, New York, NY 10003, USA
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2
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Portillo-Ledesma S, Chung S, Hoffman J, Schlick T. Regulation of chromatin architecture by transcription factor binding. eLife 2024; 12:RP91320. [PMID: 38241351 PMCID: PMC10945602 DOI: 10.7554/elife.91320] [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: 01/21/2024] Open
Abstract
Transcription factors (TF) bind to chromatin and regulate the expression of genes. The pair Myc:Max binds to E-box regulatory DNA elements throughout the genome to control the transcription of a large group of specific genes. We introduce an implicit modeling protocol for Myc:Max binding to mesoscale chromatin fibers at nucleosome resolution to determine TF effect on chromatin architecture and shed light into its mechanism of gene regulation. We first bind Myc:Max to different chromatin locations and show how it can direct fiber folding and formation of microdomains, and how this depends on the linker DNA length. Second, by simulating increasing concentrations of Myc:Max binding to fibers that differ in the DNA linker length, linker histone density, and acetylation levels, we assess the interplay between Myc:Max and other chromatin internal parameters. Third, we study the mechanism of gene silencing by Myc:Max binding to the Eed gene loci. Overall, our results show how chromatin architecture can be regulated by TF binding. The position of TF binding dictates the formation of microdomains that appear visible only at the ensemble level. At the same time, the level of linker histone and tail acetylation, or different linker DNA lengths, regulates the concentration-dependent effect of TF binding. Furthermore, we show how TF binding can repress gene expression by increasing fiber folding motifs that help compact and occlude the promoter region. Importantly, this effect can be reversed by increasing linker histone density. Overall, these results shed light on the epigenetic control of the genome dictated by TF binding.
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Affiliation(s)
- Stephanie Portillo-Ledesma
- Department of Chemistry, 100 Washington Square East, Silver Building, New York UniversityNew YorkUnited States
- Simons Center for Computational Physical Chemistry, 24 Waverly Place, Silver Building, New York UniversityNew YorkUnited States
| | - Suckwoo Chung
- Department of Chemistry, 100 Washington Square East, Silver Building, New York UniversityNew YorkUnited States
| | - Jill Hoffman
- Department of Chemistry, 100 Washington Square East, Silver Building, New York UniversityNew YorkUnited States
| | - Tamar Schlick
- Department of Chemistry, 100 Washington Square East, Silver Building, New York UniversityNew YorkUnited States
- Simons Center for Computational Physical Chemistry, 24 Waverly Place, Silver Building, New York UniversityNew YorkUnited States
- Courant Institute of Mathematical Sciences, New York UniversityNew YorkUnited States
- New York University-East China Normal University Center for Computational Chemistry, New York University ShanghaiShanghaiChina
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3
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Portillo-Ledesma S, Chung S, Hoffman J, Schlick T. Regulation of Chromatin Architecture by Transcription Factor Binding. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.26.559535. [PMID: 37808867 PMCID: PMC10557667 DOI: 10.1101/2023.09.26.559535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Transcription factors (TF) bind to chromatin and regulate the expression of genes. The pair Myc:Max binds to E-box regulatory DNA elements throughout the genome, controlling transcription of a large group of specific genes. We introduce an implicit modeling protocol for Myc:Max binding to mesoscale chromatin fibers to determine TF effect on chromatin architecture and shed light on its mechanism of gene regulation. We first bind Myc:Max to different chromatin locations and show how it can direct fiber folding and formation of microdomains, and how this depends on the linker DNA length. Second, by simulating increasing concentrations of Myc:Max binding to fibers that differ in the DNA linker length, linker histone density, and acetylation levels, we assess the interplay between Myc:Max and other chromatin internal parameters. Third, we study the mechanism of gene silencing by Myc:Max binding to the Eed gene loci. Overall, our results show how chromatin architecture can be regulated by TF binding. The position of TF binding dictates the formation of microdomains that appear visible only at the ensemble level. On the other hand, the presence of linker histone, acetylations, or different linker DNA lengths regulates the concentration-dependent effect of TF binding. Furthermore, we show how TF binding can repress gene expression by increasing fiber folding motifs that help compact and occlude the promoter region. Importantly, this effect can be reversed by increasing linker histone density. Overall, these results shed light on the epigenetic control of the genome dictated by TF binding.
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Affiliation(s)
- Stephanie Portillo-Ledesma
- Department of Chemistry, 100 Washington Square East, Silver Building, New York University, New York, NY 10003 U.S.A
- Simons Center for Computational Physical Chemistry, 24 Waverly Place, Silver Building, New York University, New York, NY 10003 U.S.A
| | - Suckwoo Chung
- Department of Chemistry, 100 Washington Square East, Silver Building, New York University, New York, NY 10003 U.S.A
| | - Jill Hoffman
- Department of Chemistry, 100 Washington Square East, Silver Building, New York University, New York, NY 10003 U.S.A
| | - Tamar Schlick
- Department of Chemistry, 100 Washington Square East, Silver Building, New York University, New York, NY 10003 U.S.A
- Courant Institute of Mathematical Sciences, New York University, 251 Mercer St., New York, NY 10012 U.S.A
- New York University-East China Normal University Center for Computational Chemistry, New York University Shanghai, Shanghai 200122 China
- Simons Center for Computational Physical Chemistry, 24 Waverly Place, Silver Building, New York University, New York, NY 10003 U.S.A
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4
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Hou Z, Nightingale F, Zhu Y, MacGregor-Chatwin C, Zhang P. Structure of native chromatin fibres revealed by Cryo-ET in situ. Nat Commun 2023; 14:6324. [PMID: 37816746 PMCID: PMC10564948 DOI: 10.1038/s41467-023-42072-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 09/28/2023] [Indexed: 10/12/2023] Open
Abstract
The structure of chromatin plays pivotal roles in regulating gene transcription, DNA replication and repair, and chromosome segregation. This structure, however, remains elusive. Here, using cryo-FIB and cryo-ET, we delineate the 3D architecture of native chromatin fibres in intact interphase human T-lymphoblasts and determine the in situ structures of nucleosomes in different conformations. These chromatin fibres are not structured as uniform 30 nm one-start or two-start filaments but are composed of relaxed, variable zigzag organizations of nucleosomes connected by straight linker DNA. Nucleosomes with little H1 and linker DNA density are distributed randomly without any spatial preference. This work will inspire future high-resolution investigations on native chromatin structures in situ at both a single-nucleosome level and a population level under many different cellular conditions in health and disease.
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Affiliation(s)
- Zhen Hou
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Frank Nightingale
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Yanan Zhu
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Peijun Zhang
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK.
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK.
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5
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Li Y, Zhang H, Li X, Wu W, Zhu P. Cryo-ET study from in vitro to in vivo revealed a general folding mode of chromatin with two-start helical architecture. Cell Rep 2023; 42:113134. [PMID: 37708029 DOI: 10.1016/j.celrep.2023.113134] [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: 07/07/2022] [Revised: 07/19/2023] [Accepted: 08/30/2023] [Indexed: 09/16/2023] Open
Abstract
The organization and dynamics of chromatin fiber play crucial roles in regulating DNA accessibility for gene expression. Here we combine cryoelectron tomography (cryo-ET), sub-volume averaging, and 3D segmentation to visualize the in vitro and in vivo chromatin fibers folding by linker histone. We discover that an increased nucleosome repeat length and prolonged fiber length do not change the two-start helical architecture in reconstituted chromatin of homogeneous composition. Additionally, an isolated chromatin fiber with heterogeneous composition was observed, which includes short-range regions compatible with two-start helix. In vivo, sub-volume averaging reveals similar subunits of two-start helical architecture in transcriptionally inactive chromatin in frog erythrocyte nuclei. Strikingly, unambiguous DNA trajectories that displayed a zigzag pattern universally between alternate N/N+2 nucleosomes were further determined by cryo-ET with voltage phase plate. Therefore, these structural similarities suggest a general folding mode of chromatin induced by linker histone, and heterogeneous compositions mainly affect local conformation rather than changing the overall architecture.
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Affiliation(s)
- Yan Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Epigenetic Regulation and Intervention, Chinese Academy of Sciences, Beijing 100101, China
| | - Haonan Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Epigenetic Regulation and Intervention, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaomin 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
| | - Wanyu Wu
- 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 Zhu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Epigenetic Regulation and Intervention, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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6
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Jentink N, Purnell C, Kable B, Swulius MT, Grigoryev SA. Cryoelectron tomography reveals the multiplex anatomy of condensed native chromatin and its unfolding by histone citrullination. Mol Cell 2023; 83:3236-3252.e7. [PMID: 37683647 PMCID: PMC10566567 DOI: 10.1016/j.molcel.2023.08.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 05/31/2023] [Accepted: 08/16/2023] [Indexed: 09/10/2023]
Abstract
Nucleosome chains fold and self-associate to form higher-order structures whose internal organization is unknown. Here, cryoelectron tomography (cryo-ET) of native human chromatin reveals intrinsic folding motifs such as (1) non-uniform nucleosome stacking, (2) intermittent parallel and perpendicular orientations of adjacent nucleosome planes, and (3) a regressive nucleosome chain path, which deviates from the direct zigzag topology seen in reconstituted nucleosomal arrays. By examining the self-associated structures, we observed prominent nucleosome stacking in cis and anti-parallel nucleosome interactions, which are consistent with partial nucleosome interdigitation in trans. Histone citrullination strongly inhibits nucleosome stacking and self-association with a modest effect on chromatin folding, whereas the reconstituted arrays undergo a dramatic unfolding into open zigzag chains induced by histone citrullination. This study sheds light on the internal structure of compact chromatin nanoparticles and suggests a mechanism for how epigenetic changes in chromatin folding are retained across both open and condensed forms.
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Affiliation(s)
- Nathan Jentink
- Penn State University College of Medicine, Department of Biochemistry & Molecular Biology, H171, Milton S. Hershey Medical Center, P.O. Box 850, 500 University Drive, Hershey, PA 17033, USA
| | - Carson Purnell
- Penn State University College of Medicine, Department of Biochemistry & Molecular Biology, H171, Milton S. Hershey Medical Center, P.O. Box 850, 500 University Drive, Hershey, PA 17033, USA
| | - Brianna Kable
- Penn State University College of Medicine, Department of Biochemistry & Molecular Biology, H171, Milton S. Hershey Medical Center, P.O. Box 850, 500 University Drive, Hershey, PA 17033, USA
| | - Matthew T Swulius
- Penn State University College of Medicine, Department of Biochemistry & Molecular Biology, H171, Milton S. Hershey Medical Center, P.O. Box 850, 500 University Drive, Hershey, PA 17033, USA.
| | - Sergei A Grigoryev
- Penn State University College of Medicine, Department of Biochemistry & Molecular Biology, H171, Milton S. Hershey Medical Center, P.O. Box 850, 500 University Drive, Hershey, PA 17033, USA.
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7
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Tan ZY, Cai S, Noble AJ, Chen JK, Shi J, Gan L. Heterogeneous non-canonical nucleosomes predominate in yeast cells in situ. eLife 2023; 12:RP87672. [PMID: 37503920 PMCID: PMC10382156 DOI: 10.7554/elife.87672] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023] Open
Abstract
Nuclear processes depend on the organization of chromatin, whose basic units are cylinder-shaped complexes called nucleosomes. A subset of mammalian nucleosomes in situ (inside cells) resembles the canonical structure determined in vitro 25 years ago. Nucleosome structure in situ is otherwise poorly understood. Using cryo-electron tomography (cryo-ET) and 3D classification analysis of budding yeast cells, here we find that canonical nucleosomes account for less than 10% of total nucleosomes expected in situ. In a strain in which H2A-GFP is the sole source of histone H2A, class averages that resemble canonical nucleosomes both with and without GFP densities are found ex vivo (in nuclear lysates), but not in situ. These data suggest that the budding yeast intranuclear environment favors multiple non-canonical nucleosome conformations. Using the structural observations here and the results of previous genomics and biochemical studies, we propose a model in which the average budding yeast nucleosome's DNA is partially detached in situ.
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Affiliation(s)
- Zhi Yang Tan
- Department of Biological Sciences and Center for BioImaging Sciences, National University of Singapore, Singapore, Singapore
| | - Shujun Cai
- Department of Biological Sciences and Center for BioImaging Sciences, National University of Singapore, Singapore, Singapore
| | - Alex J Noble
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, United States
| | - Jon K Chen
- Department of Biological Sciences and Center for BioImaging Sciences, National University of Singapore, Singapore, Singapore
| | - Jian Shi
- Department of Biological Sciences and Center for BioImaging Sciences, National University of Singapore, Singapore, Singapore
| | - Lu Gan
- Department of Biological Sciences and Center for BioImaging Sciences, National University of Singapore, Singapore, Singapore
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8
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Kadam S, Kumari K, Manivannan V, Dutta S, Mitra MK, Padinhateeri R. Predicting scale-dependent chromatin polymer properties from systematic coarse-graining. Nat Commun 2023; 14:4108. [PMID: 37433821 PMCID: PMC10336007 DOI: 10.1038/s41467-023-39907-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 06/30/2023] [Indexed: 07/13/2023] Open
Abstract
Simulating chromatin is crucial for predicting genome organization and dynamics. Although coarse-grained bead-spring polymer models are commonly used to describe chromatin, the relevant bead dimensions, elastic properties, and the nature of inter-bead potentials are unknown. Using nucleosome-resolution contact probability (Micro-C) data, we systematically coarse-grain chromatin and predict quantities essential for polymer representation of chromatin. We compute size distributions of chromatin beads for different coarse-graining scales, quantify fluctuations and distributions of bond lengths between neighboring regions, and derive effective spring constant values. Unlike the prevalent notion, our findings argue that coarse-grained chromatin beads must be considered as soft particles that can overlap, and we derive an effective inter-bead soft potential and quantify an overlap parameter. We also compute angle distributions giving insights into intrinsic folding and local bendability of chromatin. While the nucleosome-linker DNA bond angle naturally emerges from our work, we show two populations of local structural states. The bead sizes, bond lengths, and bond angles show different mean behavior at Topologically Associating Domain (TAD) boundaries and TAD interiors. We integrate our findings into a coarse-grained polymer model and provide quantitative estimates of all model parameters, which can serve as a foundational basis for all future coarse-grained chromatin simulations.
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Affiliation(s)
- Sangram Kadam
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076, India.
| | - Kiran Kumari
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Vinoth Manivannan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Shuvadip Dutta
- Department of Physics, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Mithun K Mitra
- Department of Physics, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Ranjith Padinhateeri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076, India.
- Sunita Sanghi Centre of Aging and Neurodegenerative Diseases, Indian Institute of Technology Bombay, Mumbai, 400076, India.
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9
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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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10
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Smrt ST, Gonzalez Salguero N, Thomas JK, Zandian M, Poirier MG, Jaroniec CP. Histone H3 core domain in chromatin with different DNA linker lengths studied by 1H-Detected solid-state NMR spectroscopy. Front Mol Biosci 2023; 9:1106588. [PMID: 36660422 PMCID: PMC9846530 DOI: 10.3389/fmolb.2022.1106588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 12/20/2022] [Indexed: 01/06/2023] Open
Abstract
Chromatin, a dynamic protein-DNA complex that regulates eukaryotic genome accessibility and essential functions, is composed of nucleosomes connected by linker DNA with each nucleosome consisting of DNA wrapped around an octamer of histones H2A, H2B, H3 and H4. Magic angle spinning solid-state nuclear magnetic resonance (NMR) spectroscopy can yield unique insights into histone structure and dynamics in condensed nucleosomes and nucleosome arrays representative of chromatin at physiological concentrations. Recently we used J-coupling-based solid-state NMR methods to investigate with residue-specific resolution the conformational dynamics of histone H3 N-terminal tails in 16-mer nucleosome arrays containing 15, 30 or 60 bp DNA linkers. Here, we probe the H3 core domain in the 16-mer arrays as a function of DNA linker length via dipolar coupling-based 1H-detected solid-state NMR techniques. Specifically, we established nearly complete assignments of backbone chemical shifts for H3 core residues in arrays with 15-60 bp DNA linkers reconstituted with 2H,13C,15N-labeled H3. Overall, these chemical shifts were similar irrespective of the DNA linker length indicating no major changes in H3 core conformation. Notably, however, multiple residues at the H3-nucleosomal DNA interface in arrays with 15 bp DNA linkers exhibited relatively pronounced differences in chemical shifts and line broadening compared to arrays with 30 and 60 bp linkers. These findings are consistent with increased heterogeneity in nucleosome packing and structural strain within arrays containing short DNA linkers that likely leads to side-chains of these interfacial residues experiencing alternate conformations or shifts in their rotamer populations relative to arrays with the longer DNA linkers.
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Affiliation(s)
- Sean T. Smrt
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, United States
| | - Nicole Gonzalez Salguero
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, United States
| | - Justin K. Thomas
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, United States
| | - Mohamad Zandian
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, United States
| | - Michael G. Poirier
- Department of Physics, The Ohio State University, Columbus, OH, United States
| | - Christopher P. Jaroniec
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, United States,*Correspondence: Christopher P. Jaroniec,
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11
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Zhu H, Narita M, Joseph JA, Krainer G, Arter WE, Olan I, Saar KL, Ermann N, Espinosa JR, Shen Y, Kuri MA, Qi R, Welsh TJ, Collepardo‐Guevara R, Narita M, Knowles TPJ. The Chromatin Regulator HMGA1a Undergoes Phase Separation in the Nucleus. Chembiochem 2023; 24:e202200450. [PMID: 36336658 PMCID: PMC10098602 DOI: 10.1002/cbic.202200450] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/20/2022] [Indexed: 11/09/2022]
Abstract
The protein high mobility group A1 (HMGA1) is an important regulator of chromatin organization and function. However, the mechanisms by which it exerts its biological function are not fully understood. Here, we report that the HMGA isoform, HMGA1a, nucleates into foci that display liquid-like properties in the nucleus, and that the protein readily undergoes phase separation to form liquid condensates in vitro. By bringing together machine-leaning modelling, cellular and biophysical experiments and multiscale simulations, we demonstrate that phase separation of HMGA1a is promoted by protein-DNA interactions, and has the potential to be modulated by post-transcriptional effects such as phosphorylation. We further show that the intrinsically disordered C-terminal tail of HMGA1a significantly contributes to its phase separation through electrostatic interactions via AT hooks 2 and 3. Our work sheds light on HMGA1 phase separation as an emergent biophysical factor in regulating chromatin structure.
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Affiliation(s)
- Hongjia Zhu
- Centre for Misfolding DiseasesYusuf Hamied Department of ChemistryUniversity of CambridgeCambridgeUK
| | - Masako Narita
- Cancer Research UK Cambridge InstituteLi Ka Shing CentreUniversity of CambridgeCambridgeUK
| | - Jerelle A. Joseph
- Department of GeneticsUniversity of CambridgeCambridgeUK
- Cavendish LaboratoryDepartment of PhysicsUniversity of CambridgeJJ Thomson AvenueCambridgeUK
- Yusuf Hamied Department of ChemistryUniversity of CambridgeCambridgeUK
| | - Georg Krainer
- Centre for Misfolding DiseasesYusuf Hamied Department of ChemistryUniversity of CambridgeCambridgeUK
| | - William E. Arter
- Centre for Misfolding DiseasesYusuf Hamied Department of ChemistryUniversity of CambridgeCambridgeUK
- Transition Bio Ltd., Maxwell CentreJJ Thomson AvenueCambridgeUK
| | - Ioana Olan
- Cancer Research UK Cambridge InstituteLi Ka Shing CentreUniversity of CambridgeCambridgeUK
| | - Kadi L. Saar
- Centre for Misfolding DiseasesYusuf Hamied Department of ChemistryUniversity of CambridgeCambridgeUK
- Transition Bio Ltd., Maxwell CentreJJ Thomson AvenueCambridgeUK
| | - Niklas Ermann
- Transition Bio Ltd., Maxwell CentreJJ Thomson AvenueCambridgeUK
| | - Jorge R. Espinosa
- Cavendish LaboratoryDepartment of PhysicsUniversity of CambridgeJJ Thomson AvenueCambridgeUK
| | - Yi Shen
- School of Chemical and Biomolecular EngineeringThe University of SydneySydneyAustralia
| | - Masami Ando Kuri
- Cancer Research UK Cambridge InstituteLi Ka Shing CentreUniversity of CambridgeCambridgeUK
| | - Runzhang Qi
- Centre for Misfolding DiseasesYusuf Hamied Department of ChemistryUniversity of CambridgeCambridgeUK
| | - Timothy J. Welsh
- Centre for Misfolding DiseasesYusuf Hamied Department of ChemistryUniversity of CambridgeCambridgeUK
| | - Rosana Collepardo‐Guevara
- Department of GeneticsUniversity of CambridgeCambridgeUK
- Cavendish LaboratoryDepartment of PhysicsUniversity of CambridgeJJ Thomson AvenueCambridgeUK
- Yusuf Hamied Department of ChemistryUniversity of CambridgeCambridgeUK
| | - Masashi Narita
- Cancer Research UK Cambridge InstituteLi Ka Shing CentreUniversity of CambridgeCambridgeUK
| | - Tuomas P. J. Knowles
- Centre for Misfolding DiseasesYusuf Hamied Department of ChemistryUniversity of CambridgeCambridgeUK
- Cavendish LaboratoryDepartment of PhysicsUniversity of CambridgeJJ Thomson AvenueCambridgeUK
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12
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DNA Sequence-Dependent Properties of Nucleosome Positioning in Regions of Distinct Chromatin States in Mouse Embryonic Stem Cells. Int J Mol Sci 2022; 23:ijms232214488. [PMID: 36430966 PMCID: PMC9693356 DOI: 10.3390/ijms232214488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/18/2022] [Accepted: 11/19/2022] [Indexed: 11/23/2022] Open
Abstract
Chromatin architecture is orchestrated, and plays crucial roles during the developmental process by regulating gene expression. In embryonic stem cells (ESCs), three types of chromatin states, including active, repressive and poised states, were previously identified and characterized with specific chromatin modification marks and different transcription activity, but it is largely unknown how nucleosomes are organized in these chromatin states. In this study, by using a DNA deformation energy model, we investigated the sequence-dependent nucleosome organization within the chromatin states in mouse ESCs. The results revealed that: (1) compared with poised genes, active genes are characterized with a higher level of nucleosome occupancy around their transcription start sites (TSS) and transcription termination sites (TTS), and both types of genes do not have a nucleosome-depleted region at their TTS, contrasting with the MNase-seq based result; (2) based on our previous DNA bending energy model, we developed an improved model capable of predicting both rotational positioning and nucleosome occupancy determined by a chemical mapping approach; (3) DNA bending-energy-based analyses demonstrated that the fragile nucleosomes positioned at both gene ends could be explained largely by enhanced rotational positioning signals encoded in DNA, but nucleosome phasing around the TSS of active genes was not determined by sequence preference; (4) the nucleosome occupancy landscape around the binding sites of some developmentally important transcription factors known to bind with different chromatin contexts, was also successfully predicted; (5) the difference of nucleosome occupancy around the TSS between CpG-rich and CpG-poor promoters was partly captured by our sequence-dependent model. Taken together, by developing an improved deformation-energy-based model, we revealed some sequence-dependent properties of the nucleosome arrangements in regions of distinct chromatin states in mouse ESCs.
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Iida S, Shinkai S, Itoh Y, Tamura S, Kanemaki MT, Onami S, Maeshima K. Single-nucleosome imaging reveals steady-state motion of interphase chromatin in living human cells. SCIENCE ADVANCES 2022; 8:eabn5626. [PMID: 35658044 PMCID: PMC9166292 DOI: 10.1126/sciadv.abn5626] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Dynamic chromatin behavior plays a critical role in various genome functions. However, it remains unclear how chromatin behavior changes during interphase, where the nucleus enlarges and genomic DNA doubles. While the previously reported chromatin movements varied during interphase when measured using a minute or longer time scale, we unveil that local chromatin motion captured by single-nucleosome imaging/tracking on a second time scale remained steady throughout G1, S, and G2 phases in live human cells. This motion mode appeared to change beyond this time scale. A defined genomic region also behaved similarly. Combined with Brownian dynamics modeling, our results suggest that this steady-state chromatin motion was mainly driven by thermal fluctuations. Steady-state motion temporarily increased following a DNA damage response. Our findings support the viscoelastic properties of chromatin. We propose that the observed steady-state chromatin motion allows cells to conduct housekeeping functions, such as transcription and DNA replication, under similar environments during interphase.
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Affiliation(s)
- Shiori Iida
- Genome Dynamics Laboratory, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Mishima, Japan
- Department of Genetics, School of Life Science, SOKENDAI, Mishima, Japan
| | - Soya Shinkai
- Laboratory for Developmental Dynamics, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Yuji Itoh
- Genome Dynamics Laboratory, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Mishima, Japan
| | - Sachiko Tamura
- Genome Dynamics Laboratory, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Mishima, Japan
| | - Masato T. Kanemaki
- Department of Genetics, School of Life Science, SOKENDAI, Mishima, Japan
- Molecular Cell Engineering Laboratory, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Mishima, Japan
| | - Shuichi Onami
- Laboratory for Developmental Dynamics, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Mishima, Japan
- Department of Genetics, School of Life Science, SOKENDAI, Mishima, Japan
- Corresponding author.
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Ide S, Tamura S, Maeshima K. Chromatin behavior in living cells: Lessons from single‐nucleosome imaging and tracking. Bioessays 2022; 44:e2200043. [DOI: 10.1002/bies.202200043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/24/2022] [Accepted: 04/26/2022] [Indexed: 11/05/2022]
Affiliation(s)
- Satoru Ide
- Genome Dynamics Laboratory National Institute of Genetics, ROIS Mishima Shizuoka Japan
- Department of Genetics School of Life Science SOKENDAI Mishima Shizuoka Japan
| | - Sachiko Tamura
- Genome Dynamics Laboratory National Institute of Genetics, ROIS Mishima Shizuoka Japan
| | - Kazuhiro Maeshima
- Genome Dynamics Laboratory National Institute of Genetics, ROIS Mishima Shizuoka Japan
- Department of Genetics School of Life Science SOKENDAI Mishima Shizuoka Japan
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15
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Mozo-Villarías A, Cedano JA, Querol E. The use of vector formalism in the analysis of hydrophobic and electric driving forces in biological assemblies. Q Rev Biophys 2022; 55:1-50. [PMID: 35400352 DOI: 10.1017/s0033583522000038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Abstract
Hydrophobic forces are known to have a crucial part not only in the conformation of the three-dimensional structure of proteins, but also in the build-up of DNA–protein complexes. Electric forces also play an important role both in the tertiary as well in the quaternary structure of macromolecular associations. Sometimes both hydrophobic and electric interactions add up their strengths to accomplish these structures but in most cases they act in opposite directions. This fact, together with being overall interactions with different ranges, provides a nuanced equilibrium also modulated by the need to comply with steric hindrances and geometric frustration effects. This review focuses on the utility of using the hydrophobic and electrical dipole moment vectors to describe the interactions that give rise to the structures of biological macromolecules. Although different definitions of both electric dipole and hydrophobic moments have been described in the literature, results obtained in biological assemblies demonstrate the principle of the biological membrane model. According to this model, postulated by our group, biological macromolecules tend to associate by aligning their hydrophobic moments in a similar manner to phospholipids in a membrane. Examples of both closed and open structures are used to assess the predictability of our model. We seek agreement between our results with those described in the current literature. The review ends with possible future projections using this formalism.
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Affiliation(s)
- Angel Mozo-Villarías
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Campus de Bellaterra, Universitat Autónoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Juan A Cedano
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Campus de Bellaterra, Universitat Autónoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Enrique Querol
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Campus de Bellaterra, Universitat Autónoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
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16
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Huertas J, Woods EJ, Collepardo-Guevara R. Multiscale modelling of chromatin organisation: Resolving nucleosomes at near-atomistic resolution inside genes. Curr Opin Cell Biol 2022; 75:102067. [DOI: 10.1016/j.ceb.2022.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/24/2022] [Accepted: 02/04/2022] [Indexed: 12/15/2022]
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17
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Brandstetter K, Zülske T, Ragoczy T, Hörl D, Guirao-Ortiz M, Steinek C, Barnes T, Stumberger G, Schwach J, Haugen E, Rynes E, Korber P, Stamatoyannopoulos JA, Leonhardt H, Wedemann G, Harz H. Differences in nanoscale organization of regulatory active and inactive human chromatin. Biophys J 2022; 121:977-990. [PMID: 35150617 PMCID: PMC8943813 DOI: 10.1016/j.bpj.2022.02.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 12/11/2021] [Accepted: 02/07/2022] [Indexed: 11/25/2022] Open
Abstract
Methodological advances in conformation capture techniques have fundamentally changed our understanding of chromatin architecture. However, the nanoscale organization of chromatin and its cell-to-cell variance are less studied. Analyzing genome-wide data from 733 human cell and tissue samples, we identified 2 prototypical regions that exhibit high or absent hypersensitivity to deoxyribonuclease I, respectively. These regulatory active or inactive regions were examined in the lymphoblast cell line K562 by using high-throughput super-resolution microscopy. In both regions, we systematically measured the physical distance of 2 fluorescence in situ hybridization spots spaced by only 5 kb of DNA. Unexpectedly, the resulting distance distributions range from very compact to almost elongated configurations of more than 200-nm length for both the active and inactive regions. Monte Carlo simulations of a coarse-grained model of these chromatin regions based on published data of nucleosome occupancy in K562 cells were performed to understand the underlying mechanisms. There was no parameter set for the simulation model that can explain the microscopically measured distance distributions. Obviously, the chromatin state given by the strength of internucleosomal interaction, nucleosome occupancy, or amount of histone H1 differs from cell to cell, which results in the observed broad distance distributions. This large variability was not expected, especially in inactive regions. The results for the mechanisms for different distance distributions on this scale are important for understanding the contacts that mediate gene regulation. Microscopic measurements show that the inactive region investigated here is expected to be embedded in a more compact chromatin environment. The simulation results of this region require an increase in the strength of internucleosomal interactions. It may be speculated that the higher density of chromatin is caused by the increased internucleosomal interaction strength.
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Affiliation(s)
- Katharina Brandstetter
- Human Biology & BioImaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Tilo Zülske
- Competence Center Bioinformatics, Institute for Applied Computer Science, Hochschule Stralsund, Stralsund, Germany
| | - Tobias Ragoczy
- Altius Institute for Biomedical Sciences, Seattle, Washington
| | - David Hörl
- Human Biology & BioImaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Miguel Guirao-Ortiz
- Human Biology & BioImaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Clemens Steinek
- Human Biology & BioImaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Toby Barnes
- Biomedical Center (BMC), Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Gabriela Stumberger
- Human Biology & BioImaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jonathan Schwach
- Human Biology & BioImaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Eric Haugen
- Altius Institute for Biomedical Sciences, Seattle, Washington
| | - Eric Rynes
- Altius Institute for Biomedical Sciences, Seattle, Washington
| | - Philipp Korber
- Biomedical Center (BMC), Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - John A Stamatoyannopoulos
- Altius Institute for Biomedical Sciences, Seattle, Washington; Department of Genome Sciences, University of Washington, Seattle, Washington; Department of Medicine, Division of Oncology, University of Washington, Seattle, Washington
| | - Heinrich Leonhardt
- Human Biology & BioImaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Gero Wedemann
- Competence Center Bioinformatics, Institute for Applied Computer Science, Hochschule Stralsund, Stralsund, Germany.
| | - Hartmann Harz
- Human Biology & BioImaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany.
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18
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Watson GD, Chan EW, Leake MC, Noy A. Structural interplay between DNA-shape protein recognition and supercoiling: The case of IHF. Comput Struct Biotechnol J 2022; 20:5264-5274. [PMID: 36212531 PMCID: PMC9519438 DOI: 10.1016/j.csbj.2022.09.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 09/12/2022] [Accepted: 09/12/2022] [Indexed: 11/03/2022] Open
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19
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Swygert SG, Lin D, Portillo-Ledesma S, Lin PY, Hunt DR, Kao CF, Schlick T, Noble WS, Tsukiyama T. Local chromatin fiber folding represses transcription and loop extrusion in quiescent cells. eLife 2021; 10:e72062. [PMID: 34734806 PMCID: PMC8598167 DOI: 10.7554/elife.72062] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 11/03/2021] [Indexed: 12/16/2022] Open
Abstract
A longstanding hypothesis is that chromatin fiber folding mediated by interactions between nearby nucleosomes represses transcription. However, it has been difficult to determine the relationship between local chromatin fiber compaction and transcription in cells. Further, global changes in fiber diameters have not been observed, even between interphase and mitotic chromosomes. We show that an increase in the range of local inter-nucleosomal contacts in quiescent yeast drives the compaction of chromatin fibers genome-wide. Unlike actively dividing cells, inter-nucleosomal interactions in quiescent cells require a basic patch in the histone H4 tail. This quiescence-specific fiber folding globally represses transcription and inhibits chromatin loop extrusion by condensin. These results reveal that global changes in chromatin fiber compaction can occur during cell state transitions, and establish physiological roles for local chromatin fiber folding in regulating transcription and chromatin domain formation.
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Affiliation(s)
- Sarah G Swygert
- Basic Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Dejun Lin
- Department of Genome Sciences, University of WashingtonSeattleUnited States
| | | | - Po-Yen Lin
- Institute of Cellular and Organismic Biology, Academia SinicaTaipeiTaiwan
| | - Dakota R Hunt
- Basic Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Cheng-Fu Kao
- Institute of Cellular and Organismic Biology, Academia SinicaTaipeiTaiwan
| | - Tamar Schlick
- Department of Chemistry, New York UniversityNew YorkUnited States
- Courant Institute of Mathematical Sciences, New York UniversityNew YorkUnited States
- New York University-East China Normal University Center for Computational Chemistry at New York University ShanghaiShanghaiChina
| | - William S Noble
- Department of Genome Sciences, University of WashingtonSeattleUnited States
- Paul G. Allen School of Computer Science and Engineering, University of WashingtonSeattleUnited States
| | - Toshio Tsukiyama
- Basic Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
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20
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Forte G, Michieletto D, Marenduzzo D, Orlandini E. Investigating site-selection mechanisms of retroviral integration in supercoiled DNA braids. J R Soc Interface 2021; 18:20210229. [PMID: 34428944 PMCID: PMC8385341 DOI: 10.1098/rsif.2021.0229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
We theoretically study the integration of short viral DNA in a DNA braid made up by two entwined double-stranded DNA molecules. We show that the statistics of single integration events substantially differ in the straight and buckled, or plectonemic, phase of the braid and are more likely in the latter. We further discover that integration is most likely close to plectoneme tips, where the larger bending energy helps overcome the associated energy barrier and that successive integration events are spatio-temporally correlated, suggesting a potential mechanistic explanation of clustered integration sites in host genomes. The braid geometry we consider provides a novel experimental set-up to quantify integration in a supercoiled substrate in vitro, and to better understand the role of double-stranded DNA topology during this process.
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Affiliation(s)
- G Forte
- SUPA, School of Physics and Astronomy, Peter Guthrie Tait Road, University of Edinburgh, Edinburgh EH9 3FD, UK.,MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - D Michieletto
- SUPA, School of Physics and Astronomy, Peter Guthrie Tait Road, University of Edinburgh, Edinburgh EH9 3FD, UK.,MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - D Marenduzzo
- SUPA, School of Physics and Astronomy, Peter Guthrie Tait Road, University of Edinburgh, Edinburgh EH9 3FD, UK
| | - E Orlandini
- Dipartimento di Fisica e Astronomia and Sezione INFN, Universitá degli Studi di Padova, 35131 Padova, Italy
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21
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Bjarnason S, Ruidiaz SF, McIvor J, Mercadante D, Heidarsson PO. Protein intrinsic disorder on a dynamic nucleosomal landscape. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 183:295-354. [PMID: 34656332 DOI: 10.1016/bs.pmbts.2021.06.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The complex nucleoprotein landscape of the eukaryotic cell nucleus is rich in dynamic proteins that lack a stable three-dimensional structure. Many of these intrinsically disordered proteins operate directly on the first fundamental level of genome compaction: the nucleosome. Here we give an overview of how disordered interactions with and within nucleosomes shape the dynamics, architecture, and epigenetic regulation of the genetic material, controlling cellular transcription patterns. We highlight experimental and computational challenges in the study of protein disorder and illustrate how integrative approaches are increasingly unveiling the fine details of nuclear interaction networks. We finally dissect sequence properties encoded in disordered regions and assess common features of disordered nucleosome-binding proteins. As drivers of many critical biological processes, disordered proteins are integral to a comprehensive molecular view of the dynamic nuclear milieu.
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Affiliation(s)
- Sveinn Bjarnason
- Department of Biochemistry, Science Institute, University of Iceland, Reykjavík, Iceland
| | - Sarah F Ruidiaz
- Department of Biochemistry, Science Institute, University of Iceland, Reykjavík, Iceland
| | - Jordan McIvor
- School of Chemical Science, University of Auckland, Auckland, New Zealand
| | - Davide Mercadante
- School of Chemical Science, University of Auckland, Auckland, New Zealand.
| | - Pétur O Heidarsson
- Department of Biochemistry, Science Institute, University of Iceland, Reykjavík, Iceland.
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22
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Itoh Y, Woods EJ, Minami K, Maeshima K, Collepardo-Guevara R. Liquid-like chromatin in the cell: What can we learn from imaging and computational modeling? Curr Opin Struct Biol 2021; 71:123-135. [PMID: 34303931 DOI: 10.1016/j.sbi.2021.06.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 06/08/2021] [Indexed: 12/23/2022]
Abstract
Chromatin in eukaryotic cells is a negatively charged long polymer consisting of DNA, histones, and various associated proteins. With its highly charged and heterogeneous nature, chromatin structure varies greatly depending on various factors (e.g. chemical modifications and protein enrichment) and the surrounding environment (e.g. cations): from a 10-nm fiber, a folded 30-nm fiber, to chromatin condensates/droplets. Recent advanced imaging has observed that chromatin exhibits a dynamic liquid-like behavior and undergoes structural variations within the cell. Current computational modeling has made it possible to reconstruct the liquid-like chromatin in the cell by dealing with a number of nucleosomes on multiscale levels and has become a powerful technique to inspect the molecular mechanisms giving rise to the observed behavior, which imaging methods cannot do on their own. Based on new findings from both imaging and modeling studies, we discuss the dynamic aspect of chromatin in living cells and its functional relevance.
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Affiliation(s)
- Yuji Itoh
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Esmae J Woods
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge CB3 0HE, UK
| | - Katsuhiko Minami
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan; Department of Genetics, School of Life Science, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan
| | - Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan; Department of Genetics, School of Life Science, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan.
| | - Rosana Collepardo-Guevara
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge CB3 0HE, UK; Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK; Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK.
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23
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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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24
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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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25
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Farr SE, Woods EJ, Joseph JA, Garaizar A, Collepardo-Guevara R. Nucleosome plasticity is a critical element of chromatin liquid-liquid phase separation and multivalent nucleosome interactions. Nat Commun 2021; 12:2883. [PMID: 34001913 PMCID: PMC8129070 DOI: 10.1038/s41467-021-23090-3] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/23/2021] [Indexed: 12/19/2022] Open
Abstract
Liquid-liquid phase separation (LLPS) is an important mechanism that helps explain the membraneless compartmentalization of the nucleus. Because chromatin compaction and LLPS are collective phenomena, linking their modulation to the physicochemical features of nucleosomes is challenging. Here, we develop an advanced multiscale chromatin model-integrating atomistic representations, a chemically-specific coarse-grained model, and a minimal model-to resolve individual nucleosomes within sub-Mb chromatin domains and phase-separated systems. To overcome the difficulty of sampling chromatin at high resolution, we devise a transferable enhanced-sampling Debye-length replica-exchange molecular dynamics approach. We find that nucleosome thermal fluctuations become significant at physiological salt concentrations and destabilize the 30-nm fiber. Our simulations show that nucleosome breathing favors stochastic folding of chromatin and promotes LLPS by simultaneously boosting the transient nature and heterogeneity of nucleosome-nucleosome contacts, and the effective nucleosome valency. Our work puts forward the intrinsic plasticity of nucleosomes as a key element in the liquid-like behavior of nucleosomes within chromatin, and the regulation of chromatin LLPS.
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Affiliation(s)
- Stephen E Farr
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK
| | - Esmae J Woods
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK
| | - Jerelle A Joseph
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Adiran Garaizar
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK
| | - Rosana Collepardo-Guevara
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK.
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
- Department of Genetics, University of Cambridge, Cambridge, UK.
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26
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Abstract
Genomic information is encoded on long strands of DNA, which are folded into chromatin and stored in a tiny nucleus. Nuclear chromatin is a negatively charged polymer composed of DNA, histones, and various nonhistone proteins. Because of its highly charged nature, chromatin structure varies greatly depending on the surrounding environment (e.g., cations, molecular crowding, etc.). New technologies to capture chromatin in living cells have been developed over the past 10 years. Our view on chromatin organization has drastically shifted from a regular and static one to a more variable and dynamic one. Chromatin forms numerous compact dynamic domains that act as functional units of the genome in higher eukaryotic cells and locally appear liquid-like. By changing DNA accessibility, these domains can govern various functions. Based on new evidences from versatile genomics and advanced imaging studies, we discuss the physical nature of chromatin in the crowded nuclear environment and how it is regulated.
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Affiliation(s)
- Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan
| | - Shiori Iida
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan
| | - Sachiko Tamura
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
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27
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Woods DC, Rodríguez-Ropero F, Wereszczynski J. The Dynamic Influence of Linker Histone Saturation within the Poly-Nucleosome Array. J Mol Biol 2021; 433:166902. [PMID: 33667509 DOI: 10.1016/j.jmb.2021.166902] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 02/15/2021] [Accepted: 02/20/2021] [Indexed: 02/08/2023]
Abstract
Linker histones bind to nucleosomes and modify chromatin structure and dynamics as a means of epigenetic regulation. Biophysical studies have shown that chromatin fibers can adopt a plethora of conformations with varying levels of compaction. Linker histone condensation, and its specific binding disposition, has been associated with directly tuning this ensemble of states. However, the atomistic dynamics and quantification of this mechanism remains poorly understood. Here, we present molecular dynamics simulations of octa-nucleosome arrays, based on a cryo-EM structure of the 30-nm chromatin fiber, with and without the globular domains of the H1 linker histone to determine how they influence fiber structures and dynamics. Results show that when bound, linker histones inhibit DNA flexibility and stabilize repeating tetra-nucleosomal units, giving rise to increased chromatin compaction. Furthermore, upon the removal of H1, there is a significant destabilization of this compact structure as the fiber adopts less strained and untwisted states. Interestingly, linker DNA sampling in the octa-nucleosome is exaggerated compared to its mono-nucleosome counterparts, suggesting that chromatin architecture plays a significant role in DNA strain even in the absence of linker histones. Moreover, H1-bound states are shown to have increased stiffness within tetra-nucleosomes, but not between them. This increased stiffness leads to stronger long-range correlations within the fiber, which may result in the propagation of epigenetic signals over longer spatial ranges. These simulations highlight the effects of linker histone binding on the internal dynamics and global structure of poly-nucleosome arrays, while providing physical insight into a mechanism of chromatin compaction.
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Affiliation(s)
- Dustin C Woods
- Department of Chemistry and the Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, IL 60616, United States
| | - Francisco Rodríguez-Ropero
- Department of Physics and the Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, IL 60616, United States
| | - Jeff Wereszczynski
- Department of Physics and the Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, IL 60616, United States.
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28
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Zhurkin VB, Norouzi D. Topological polymorphism of nucleosome fibers and folding of chromatin. Biophys J 2021; 120:577-585. [PMID: 33460599 PMCID: PMC7896024 DOI: 10.1016/j.bpj.2021.01.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 12/28/2020] [Accepted: 01/07/2021] [Indexed: 01/19/2023] Open
Abstract
We discuss recent observations of polymorphic chromatin packaging at the oligonucleosomal level and compare them with computer simulations. Our computations reveal two topologically different families of two-start 30-nm fiber conformations distinguished by the linker length L; fibers with L ≈ 10n and L ≈ 10n+5 basepairs have DNA linking numbers per nucleosome of ΔLk ≈ -1.5 and -1.0, respectively (where n is a natural number). Although fibers with ΔLk ≈ -1.5 were observed earlier, the topoisomer with ΔLk ≈ -1.0 is novel. These predictions were confirmed experimentally for circular nucleosome arrays with precisely positioned nucleosomes. We suggest that topological polymorphism of chromatin may play a role in transcription, with the {10n+5} fibers producing transcriptionally competent chromatin structures. This hypothesis is consistent with available data for yeast and, partially, for fly. We show that both fiber topoisomers (with ΔLk ≈ -1.5 and -1.0) have to be taken into account to interpret experimental data obtained using new techniques: genome-wide Micro-C, Hi-CO, and RICC-seq, as well as self-association of nucleosome arrays in vitro. The relative stability of these topoisomers is likely to depend on epigenetic histone modifications modulating the strength of internucleosome interactions. Potentially, our findings may reflect a general tendency of functionally distinct parts of the genome to retain topologically different higher-order structures.
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Affiliation(s)
- Victor B Zhurkin
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.
| | - Davood Norouzi
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.
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29
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Gómez-García PA, Portillo-Ledesma S, Neguembor MV, Pesaresi M, Oweis W, Rohrlich T, Wieser S, Meshorer E, Schlick T, Cosma MP, Lakadamyali M. Mesoscale Modeling and Single-Nucleosome Tracking Reveal Remodeling of Clutch Folding and Dynamics in Stem Cell Differentiation. Cell Rep 2021; 34:108614. [PMID: 33440158 PMCID: PMC7842188 DOI: 10.1016/j.celrep.2020.108614] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 10/29/2020] [Accepted: 12/16/2020] [Indexed: 01/01/2023] Open
Abstract
Nucleosomes form heterogeneous groups in vivo, named clutches. Clutches are smaller and less dense in mouse embryonic stem cells (ESCs) compared to neural progenitor cells (NPCs). Using coarse-grained modeling of the pluripotency Pou5f1 gene, we show that the genome-wide clutch differences between ESCs and NPCs can be reproduced at a single gene locus. Larger clutch formation in NPCs is associated with changes in the compaction and internucleosome contact probability of the Pou5f1 fiber. Using single-molecule tracking (SMT), we further show that the core histone protein H2B is dynamic, and its local mobility relates to the structural features of the chromatin fiber. H2B is less stable and explores larger areas in ESCs compared to NPCs. The amount of linker histone H1 critically affects local H2B dynamics. Our results have important implications for how nucleosome organization and H2B dynamics contribute to regulate gene activity and cell identity.
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Affiliation(s)
- Pablo Aurelio Gómez-García
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain; Institute of Photonic Sciences (ICFO), The Barcelona Institute of Science and Technology (BIST), Castelldefels, 08860 Barcelona, Spain
| | - Stephanie Portillo-Ledesma
- Department of Chemistry, 1021 Silver Center, 100 Washington Square East, New York University, New York, NY 10003, USA
| | - Maria Victoria Neguembor
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain
| | - Martina Pesaresi
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain
| | - Walaa Oweis
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel
| | - Talia Rohrlich
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel
| | - Stefan Wieser
- Institute of Photonic Sciences (ICFO), The Barcelona Institute of Science and Technology (BIST), Castelldefels, 08860 Barcelona, Spain
| | - Eran Meshorer
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel; The Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel
| | - Tamar Schlick
- Department of Chemistry, 1021 Silver Center, 100 Washington Square East, New York University, New York, NY 10003, USA; Courant Institute of Mathematical Sciences, 251 Mercer Street, New York University, New York, NY 10012, USA; NYU-ECNU Center for Computational Chemistry at New York University Shanghai, 340 Geography Building, 3663 North Zhongshan Road, Shanghai 3663, China
| | - Maria Pia Cosma
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain; Bioland Laboratory, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China; CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.
| | - Melike Lakadamyali
- Perelman School of Medicine, Department of Physiology, University of Pennsylvania, Clinical Research Building, 415 Curie Boulevard, Philadelphia, PA 19104, USA; Perelman School of Medicine, Department of Cell and Developmental Biology, University of Pennsylvania, Biomedical Research Building, 421 Curie Boulevard, Philadelphia, PA 19104, USA.
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30
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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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31
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Huertas J, Cojocaru V. Breaths, Twists, and Turns of Atomistic Nucleosomes. J Mol Biol 2020; 433:166744. [PMID: 33309853 DOI: 10.1016/j.jmb.2020.166744] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/02/2020] [Accepted: 12/02/2020] [Indexed: 02/07/2023]
Abstract
Gene regulation programs establish cellular identity and rely on dynamic changes in the structural packaging of genomic DNA. The DNA is packaged in chromatin, which is formed from arrays of nucleosomes displaying different degree of compaction and different lengths of inter-nucleosomal linker DNA. The nucleosome represents the repetitive unit of chromatin and is formed by wrapping 145-147 basepairs of DNA around an octamer of histone proteins. Each of the four histones is present twice and has a structured core and intrinsically disordered terminal tails. Chromatin dynamics are triggered by inter- and intra-nucleosome motions that are controlled by the DNA sequence, the interactions between the histone core and the DNA, and the conformations, positions, and DNA interactions of the histone tails. Understanding chromatin dynamics requires studying all these features at the highest possible resolution. For this, molecular dynamics simulations can be used as a powerful complement or alternative to experimental approaches, from which it is often very challenging to characterize the structural features and atomic interactions controlling nucleosome motions. Molecular dynamics simulations can be performed at different resolutions, by coarse graining the molecular system with varying levels of details. Here we review the successes and the remaining challenges of the application of atomic resolution simulations to study the structure and dynamics of nucleosomes and their complexes with interacting partners.
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Affiliation(s)
- Jan Huertas
- In Silico Biomolecular Structure and Dynamics Group, Hubrecht Institute, Utrecht, the Netherlands; Department of Cellular and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany; Center for Multiscale Theory and Computation, Westfälische Wilhelms University, Münster, Germany
| | - Vlad Cojocaru
- In Silico Biomolecular Structure and Dynamics Group, Hubrecht Institute, Utrecht, the Netherlands; Department of Cellular and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany; Center for Multiscale Theory and Computation, Westfälische Wilhelms University, Münster, Germany.
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32
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Shabane PS, Onufriev AV. Significant compaction of H4 histone tail upon charge neutralization by acetylation and its mimics, possible effects on chromatin structure. J Mol Biol 2020; 433:166683. [PMID: 33096105 DOI: 10.1016/j.jmb.2020.10.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/30/2020] [Accepted: 10/13/2020] [Indexed: 10/23/2022]
Abstract
The intrinsically disordered, positively charged H4 histone tail is important for chromatin structure and function. We have explored conformational ensembles of human H4 tail in solution, with varying levels of charge neutralization via acetylation or amino-acid substitutions such as K→Q. We have employed an explicit water model shown recently to be well suited for simulations of intrinsically disordered proteins. Upon progressive neutralization of the H4, its radius of gyration decreases linearly with the tail charge q, the trend is explained using a simple polymer model. While the wild type state (q=+8) is essentially a random coil, hyper-acetylated H4 (q=+3) is virtually as compact and stable as a globular protein of the same number of amino-acids. Conformational ensembles of acetylated H4 match the corresponding K→X substitutions only approximately: based on the ensemble similarity, we propose K→M as a possible alternative to the commonly used K→Q. Possible effects of the H4 tail compaction on chromatin structure are discussed within a qualitative model in which the chromatin is highly heterogeneous, easily inter-converting between various structural forms. We predict that upon progressive charge neutralization of the H4 tail, the least compact sub-states of chromatin de-condense first, followed by de-condensation of more compact structures, e.g. those that harbor a high fraction of stacked di-nucleosomes. The predicted hierarchy of DNA accessibility increase upon progressive acetylation of H4 might be utilized by the cell for selective DNA accessibility control.
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Affiliation(s)
| | - Alexey V Onufriev
- Departments of Computer Science, Virginia Tech, Blacksburg, VA 24060, United States; Department of Physics, Virginia Tech, Blacksburg, VA 24060, United States; Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA 24061, USA.
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33
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Bendandi A, Patelli AS, Diaspro A, Rocchia W. The role of histone tails in nucleosome stability: An electrostatic perspective. Comput Struct Biotechnol J 2020; 18:2799-2809. [PMID: 33133421 PMCID: PMC7575852 DOI: 10.1016/j.csbj.2020.09.034] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 09/23/2020] [Accepted: 09/24/2020] [Indexed: 01/20/2023] Open
Abstract
We propose a methodology for the study of protein-DNA electrostatic interactions and apply it to clarify the effect of histone tails in nucleosomes. This method can be used to correlate electrostatic interactions to structural and functional features of protein-DNA systems, and can be combined with coarse-grained representations. In particular, we focus on the electrostatic field and resulting forces acting on the DNA. We investigate the electrostatic origins of effects such as different stages in DNA unwrapping, nucleosome destabilization upon histone tail truncation, and the role of specific arginines and lysines undergoing Post-Translational Modifications. We find that the positioning of the histone tails can oppose the attractive pull of the histone core, locally deform the DNA, and tune DNA unwrapping. Small conformational variations in the often overlooked H2A C-terminal tails had significant electrostatic repercussions near the DNA entry and exit sites. The H2A N-terminal tail exerts attractive electrostatic forces towards the histone core in positions where Polymerase II halts its progress. We validate our results with comparisons to previous experimental and computational observations.
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Affiliation(s)
- Artemi Bendandi
- DIFILAB, Department of Physics, University of Genoa, Via Dodecaneso 33, 16149 Genoa, Italy.,CHT Erzelli, Nanoscopy, Istituto Italiano di Tecnologia, Via Enrico Melen 83, 16152 Genoa, Italy
| | - Alessandro S Patelli
- LCVMM, Institute of Mathematics, Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland
| | - Alberto Diaspro
- DIFILAB, Department of Physics, University of Genoa, Via Dodecaneso 33, 16149 Genoa, Italy.,CHT Erzelli, Nanoscopy, Istituto Italiano di Tecnologia, Via Enrico Melen 83, 16152 Genoa, Italy
| | - Walter Rocchia
- Concept Lab, Istituto Italiano di Tecnologia, Via Enrico Melen 83, 16152 Genoa, Italy
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34
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Li F, Wang D, Song R, Cao C, Zhang Z, Wang Y, Li X, Huang J, Liu Q, Hou N, Xu B, Li X, Gao X, Jia Y, Zhao J, Wang Y. The asynchronous establishment of chromatin 3D architecture between in vitro fertilized and uniparental preimplantation pig embryos. Genome Biol 2020; 21:203. [PMID: 32778155 PMCID: PMC7418210 DOI: 10.1186/s13059-020-02095-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 07/07/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Pigs are important animals for agricultural and biomedical research, and improvement is needed for use of the assisted reproductive technologies. Determining underlying mechanisms of epigenetic reprogramming in the early stage of preimplantation embryos derived from in vitro fertilization (IVF), parthenogenesis, and androgenesis will not only contribute to assisted reproductive technologies of pigs but also will shed light into early human development. However, the reprogramming of three-dimensional architecture of chromatin in this process in pigs is poorly understood. RESULTS We generate three-dimensional chromatin profiles for pig somatic cells, IVF, parthenogenesis, and androgenesis preimplantation embryos. We find that the chromosomes in the pig preimplantation embryos are enriched for superdomains, which are more rare in mice. However, p(s) curves, compartments, and topologically associated domains (TADs) are largely conserved in somatic cells and are gradually established during preimplantation embryogenesis in both mammals. In the uniparental pig embryos, the establishment of chromatin architecture is highly asynchronized at all levels from IVF embryos, and a remarkably strong decompartmentalization is observed during zygotic genome activation (ZGA). Finally, chromosomes originating from oocytes always establish TADs faster than chromosomes originating from sperm, both before and during ZGA. CONCLUSIONS Our data highlight a potential unique 3D chromatin pattern of enriched superdomains in pig preimplantation embryos, an unusual decompartmentalization process during ZGA in the uniparental embryos, and an asynchronized TAD reprogramming between maternal and paternal genomes, implying a severe dysregulation of ZGA in the uniparental embryos in pigs.
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Affiliation(s)
- Feifei Li
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, 100101 China
| | - Danyang Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Ruigao Song
- University of Chinese Academy of Sciences, Beijing, 100049 China
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Chunwei Cao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120 China
| | - Zhihua Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Yu Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Xiaoli Li
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Jiaojiao Huang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Qiang Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Naipeng Hou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Bingxiang Xu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Xiao Li
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Xiaomeng Gao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Yan Jia
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, 100101 China
| | - Jianguo Zhao
- University of Chinese Academy of Sciences, Beijing, 100049 China
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yanfang Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
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35
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Parmar JJ, Padinhateeri R. Nucleosome positioning and chromatin organization. Curr Opin Struct Biol 2020; 64:111-118. [PMID: 32731156 DOI: 10.1016/j.sbi.2020.06.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 05/31/2020] [Accepted: 06/23/2020] [Indexed: 11/24/2022]
Abstract
In our cells, DNA is folded and packed with the help of many proteins into chromatin whose basic unit is a nucleosome-DNA wrapped around octamer of histone proteins. The chain of nucleosomes is further folded and arranged into many layers and has a dynamic organization. How does the complex chromatin organization emerge from interactions among DNA, histones, and non-histone proteins have been a question of great interest. Here we review recent literature that investigated how nucleosome positioning and nucleosome-mediated interactions drive chromatin organization. Unlike our earlier understanding, chromatin is organized into 3D domains of various sizes having irregularly organized nucleosomes. These domains emerge due to heterogeneous nucleosome positioning and diverse inter-nucleosome interactions that vary in space and time.
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Affiliation(s)
- Jyotsana J Parmar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400 076, India
| | - Ranjith Padinhateeri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400 076, India.
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36
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Boopathi R, Dimitrov S, Hamiche A, Petosa C, Bednar J. Cryo-electron microscopy of the chromatin fiber. Curr Opin Struct Biol 2020; 64:97-103. [PMID: 32717688 DOI: 10.1016/j.sbi.2020.06.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 06/16/2020] [Accepted: 06/22/2020] [Indexed: 01/10/2023]
Abstract
The three-dimensional (3D) organization of chromatin plays a crucial role in the regulation of gene expression. Chromatin conformation is strongly affected by the composition, structural features and dynamic properties of the nucleosome, which in turn determine the nature and geometry of interactions that can occur between neighboring nucleosomes. Understanding how chromatin is spatially organized above the nucleosome level is thus essential for understanding how gene regulation is achieved. Towards this end, great effort has been made to understand how an array of nucleosomes folds into a regular chromatin fiber. This review summarizes new insights into the 3D structure of the chromatin fiber that were made possible by recent advances in cryo-electron microscopy.
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Affiliation(s)
- Ramachandran Boopathi
- Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences (IAB), Site Sante´ - Allée des Alpes, 38700 La Tronche, France; Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 38000 Grenoble, France
| | - Stefan Dimitrov
- Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences (IAB), Site Sante´ - Allée des Alpes, 38700 La Tronche, France; Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Balcova, Izmir 35330, Turkey
| | - Ali Hamiche
- Département de Génomique Fonctionnelle et Cancer, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC)/Université de Strasbourg/CNRS/INSERM, 67404 Illkirch Cedex, France
| | - Carlo Petosa
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 38000 Grenoble, France
| | - Jan Bednar
- Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences (IAB), Site Sante´ - Allée des Alpes, 38700 La Tronche, France; Laboratory of the Biology and Pathology of the Eye, Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, 128 00 Prague 2, Czech Republic.
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37
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Myers CG, Olins DE, Olins AL, Schlick T. Mesoscale Modeling of Nucleosome-Binding Antibody PL2-6: Mono- versus Bivalent Chromatin Complexes. Biophys J 2020; 118:2066-2076. [PMID: 31668748 PMCID: PMC7202932 DOI: 10.1016/j.bpj.2019.08.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 07/25/2019] [Accepted: 08/15/2019] [Indexed: 12/28/2022] Open
Abstract
Interactions of chromatin with bivalent immunoglobin nucleosome-binding antibodies and their monovalent (papain-derived) antigen-binding fragment analogs are useful probes for examining chromatin conformational states. To help interpret antibody-chromatin interactions and explore how antibodies might compete for interactions with chromatin components, we incorporate coarse-grained PL2-6 antibody modeling into our mesoscale chromatin model. We analyze interactions and fiber structures for the antibody-chromatin complexes in open and condensed chromatin, with and without H1 linker histone (LH). Despite minimal and transient interactions at physiological salt, we capture significant differences in antibody-chromatin complex configurations in open fibers, with more intense interactions between the bivalent antibody and chromatin compared to monovalent antigen-binding fragments. For these open chromatin fiber morphologies, antibody binding to histone tails is increased and compaction is greater for bivalent compared to monovalent and antibody-free systems. Differences between monovalent and bivalent binding result from antibody competition with internal chromatin fiber components (nucleosome core and linker DNA) for histone tail (H3, H4, H2A, H2B) interactions. This antibody competition for tail contacts reduces tail-core and tail-linker interactions and increases tail-antibody interactions. Such internal structural changes in open fibers resemble mechanisms of LH condensation, driven by charge screening and entropy changes. For condensed fibers at physiological salt, the three systems are much more similar overall, but some subtle tail interaction differences can be noted. Adding LH results in less-dramatic changes for all systems, except that the bivalent complex at physiological salt shows cooperative effects between LH and the antibodies in condensing chromatin fibers. Such dynamic interactions that depend on the internal structure and complex-stabilizing interactions within the chromatin fiber have implications for gene regulation and other chromatin complexes such as with LH, remodeling proteins, and small molecular chaperones that bind and modulate chromatin structure.
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Affiliation(s)
| | - Donald E Olins
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New England, Portland, Maine
| | - Ada L Olins
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New England, Portland, Maine
| | - Tamar Schlick
- Department of Chemistry, New York University, New York, New York; Courant Institute of Mathematical Sciences, New York University, New York, New York; New York University-East China Normal University Center for Computational Chemistry at New York University Shanghai, Shanghai, China.
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Maeshima K, Tamura S, Hansen JC, Itoh Y. Fluid-like chromatin: Toward understanding the real chromatin organization present in the cell. Curr Opin Cell Biol 2020; 64:77-89. [PMID: 32283330 DOI: 10.1016/j.ceb.2020.02.016] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 02/16/2020] [Accepted: 02/22/2020] [Indexed: 12/23/2022]
Abstract
Eukaryotic chromatin is a negatively charged polymer consisting of genomic DNA, histones, and various nonhistone proteins. Because of its highly charged character, the structure of chromatin varies greatly depending on the surrounding environment (i.e. cations etc.): from an extended 10-nm fiber, to a folded 30-nm fiber, to chromatin condensates/liquid-droplets. Over the last ten years, newly developed technologies have drastically shifted our view on chromatin from a static regular structure to a more irregular and dynamic one, locally like a fluid. Since no single imaging (or genomics) method can tell us everything and beautiful images (or models) can fool our minds, comprehensive analyses based on many technical approaches are important to capture actual chromatin organization inside the cell. Here we critically discuss our current view on chromatin and methodology used to support the view.
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Affiliation(s)
- Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan; Department of Genetics, School of Life Science, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka, 411-8540, Japan.
| | - Sachiko Tamura
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Jeffrey C Hansen
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Yuji Itoh
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
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Emergence of chromatin hierarchical loops from protein disorder and nucleosome asymmetry. Proc Natl Acad Sci U S A 2020; 117:7216-7224. [PMID: 32165536 DOI: 10.1073/pnas.1910044117] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Protein flexibility and disorder is emerging as a crucial modulator of chromatin structure. Histone tail disorder enables transient binding of different molecules to the nucleosomes, thereby promoting heterogeneous and dynamic internucleosome interactions and making possible recruitment of a wide-range of regulatory and remodeling proteins. On the basis of extensive multiscale modeling we reveal the importance of linker histone H1 protein disorder for chromatin hierarchical looping. Our multiscale approach bridges microsecond-long bias-exchange metadynamics molecular dynamics simulations of atomistic 211-bp nucleosomes with coarse-grained Monte Carlo simulations of 100-nucleosome systems. We show that the long C-terminal domain (CTD) of H1-a ubiquitous nucleosome-binding protein-remains disordered when bound to the nucleosome. Notably, such CTD disorder leads to an asymmetric and dynamical nucleosome conformation that promotes chromatin structural flexibility and establishes long-range hierarchical loops. Furthermore, the degree of condensation and flexibility of H1 can be fine-tuned, explaining chromosomal differences of interphase versus metaphase states that correspond to partial and hyperphosphorylated H1, respectively. This important role of H1 protein disorder in large-scale chromatin organization has a wide range of biological implications.
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40
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Bendandi A, Dante S, Zia SR, Diaspro A, Rocchia W. Chromatin Compaction Multiscale Modeling: A Complex Synergy Between Theory, Simulation, and Experiment. Front Mol Biosci 2020; 7:15. [PMID: 32158765 PMCID: PMC7051991 DOI: 10.3389/fmolb.2020.00015] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 01/27/2020] [Indexed: 12/24/2022] Open
Abstract
Understanding the mechanisms that trigger chromatin compaction, its patterns, and the factors they depend on, is a fundamental and still open question in Biology. Chromatin compacts and reinforces DNA and is a stable but dynamic structure, to make DNA accessible to proteins. In recent years, computational advances have provided larger amounts of data and have made large-scale simulations more viable. Experimental techniques for the extraction and reconstitution of chromatin fibers have improved, reinvigorating theoretical and experimental interest in the topic and stimulating debate on points previously considered as certainties regarding chromatin. A great assortment of approaches has emerged, from all-atom single-nucleosome or oligonucleosome simulations to various degrees of coarse graining, to polymer models, to fractal-like structures and purely topological models. Different fiber-start patterns have been studied in theory and experiment, as well as different linker DNA lengths. DNA is a highly charged macromolecule, making ionic and electrostatic interactions extremely important for chromatin topology and dynamics. Indeed, the repercussions of varying ionic concentration have been extensively examined at the computational level, using all-atom, coarse-grained, and continuum techniques. The presence of high-curvature AT-rich segments in DNA can cause conformational variations, attesting to the fact that the role of DNA is both structural and electrostatic. There have been some tentative attempts to describe the force fields governing chromatin conformational changes and the energy landscapes of these transitions, but the intricacy of the system has hampered reaching a consensus. The study of chromatin conformations is an intrinsically multiscale topic, influenced by a wide range of biological and physical interactions, spanning from the atomic to the chromosome level. Therefore, powerful modeling techniques and carefully planned experiments are required for an overview of the most relevant phenomena and interactions. The topic provides fertile ground for interdisciplinary studies featuring a synergy between theoretical and experimental scientists from different fields and the cross-validation of respective results, with a multi-scale perspective. Here, we summarize some of the most representative approaches, and focus on the importance of electrostatics and solvation, often overlooked aspects of chromatin modeling.
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Affiliation(s)
- Artemi Bendandi
- Physics Department, University of Genoa, Genoa, Italy
- Nanophysics & NIC@IIT, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Silvia Dante
- Nanophysics & NIC@IIT, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Syeda Rehana Zia
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Alberto Diaspro
- Physics Department, University of Genoa, Genoa, Italy
- Nanophysics & NIC@IIT, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Walter Rocchia
- Concept Lab, Istituto Italiano di Tecnologia, Genoa, Italy
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Abstract
Chromosome organisation is increasingly recognised as an essential component of genome regulation, cell fate and cell health. Within the realm of transposable elements (TEs) however, the spatial information of how genomes are folded is still only rarely integrated in experimental studies or accounted for in modelling. Whilst polymer physics is recognised as an important tool to understand the mechanisms of genome folding, in this commentary we discuss its potential applicability to aspects of TE biology. Based on recent works on the relationship between genome organisation and TE integration, we argue that existing polymer models may be extended to create a predictive framework for the study of TE integration patterns. We suggest that these models may offer orthogonal and generic insights into the integration profiles (or "topography") of TEs across organisms. In addition, we provide simple polymer physics arguments and preliminary molecular dynamics simulations of TEs inserting into heterogeneously flexible polymers. By considering this simple model, we show how polymer folding and local flexibility may generically affect TE integration patterns. The preliminary discussion reported in this commentary is aimed to lay the foundations for a large-scale analysis of TE integration dynamics and topography as a function of the three-dimensional host genome.
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42
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Öztürk MA, De M, Cojocaru V, Wade RC. Chromatosome Structure and Dynamics from Molecular Simulations. Annu Rev Phys Chem 2020; 71:101-119. [PMID: 32017651 DOI: 10.1146/annurev-physchem-071119-040043] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Chromatosomes are fundamental units of chromatin structure that are formed when a linker histone protein binds to a nucleosome. The positioning of the linker histone on the nucleosome influences the packing of chromatin. Recent simulations and experiments have shown that chromatosomes adopt an ensemble of structures that differ in the geometry of the linker histone-nucleosome interaction. In this article we review the application of Brownian, Monte Carlo, and molecular dynamics simulations to predict the structure of linker histone-nucleosome complexes, to study the binding mechanisms involved, and to predict how this binding affects chromatin fiber structure. These simulations have revealed the sensitivityof the chromatosome structure to variations in DNA and linker histone sequence, as well as to posttranslational modifications, thereby explaining the structural variability observed in experiments. We propose that a concerted application of experimental and computational approaches will reveal the determinants of chromatosome structural variability and how it impacts chromatin packing.
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Affiliation(s)
- Mehmet Ali Öztürk
- Centre for Biological Signalling Studies (BIOSS) and Centre for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, 79104 Freiburg, Germany;
| | - Madhura De
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Germany; .,Department of Biophysics of Macromolecules, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; .,Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Vlad Cojocaru
- In Silico Biomolecular Structure and Dynamics, Hubrecht Institute, 3584 CT Utrecht, The Netherlands; .,Computational Structural Biology Group, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany
| | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Germany; .,Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany.,Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, 69120 Heidelberg, Germany.,Interdisciplinary Center for Scientific Computing (IWR), 69120 Heidelberg, Germany
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43
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Perišić O, Portillo-Ledesma S, Schlick T. Sensitive effect of linker histone binding mode and subtype on chromatin condensation. Nucleic Acids Res 2019; 47:4948-4957. [PMID: 30968131 PMCID: PMC6547455 DOI: 10.1093/nar/gkz234] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 03/19/2019] [Accepted: 03/22/2019] [Indexed: 12/14/2022] Open
Abstract
The complex role of linker histone (LH) on chromatin compaction regulation has been highlighted by recent discoveries of the effect of LH binding variability and isoforms on genome structure and function. Here we examine the effect of two LH variants and variable binding modes on the structure of chromatin fibers. Our mesoscale modeling considers oligonucleosomes with H1C and H1E, bound in three different on and off-dyad modes, and spanning different LH densities (0.5–1.6 per nucleosome), over a wide range of physiologically relevant nucleosome repeat lengths (NRLs). Our studies reveal an LH-variant and binding-mode dependent heterogeneous ensemble of fiber structures with variable packing ratios, sedimentation coefficients, and persistence lengths. For maximal compaction, besides dominantly interacting with parental DNA, LHs must have strong interactions with nonparental DNA and promote tail/nonparental core interactions. An off-dyad binding of H1E enables both; others compromise compaction for bendability. We also find that an increase of LH density beyond 1 is best accommodated in chromatosomes with one on-dyad and one off-dyad LH. We suggest that variable LH binding modes and concentrations are advantageous, allowing tunable levels of chromatin condensation and DNA accessibility/interactions. Thus, LHs add another level of epigenetic regulation of chromatin.
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Affiliation(s)
- Ognjen Perišić
- Department of Chemistry, New York University, 1001 Silver, 100 Washington Square East, New York, NY 10003, USA
| | - Stephanie Portillo-Ledesma
- Department of Chemistry, New York University, 1001 Silver, 100 Washington Square East, New York, NY 10003, USA
| | - Tamar Schlick
- Department of Chemistry, New York University, 1001 Silver, 100 Washington Square East, New York, NY 10003, USA.,Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, NY 10012, USA.,New York University ECNU - Center for Computational Chemistry at NYU Shanghai, 3663 North Zhongshan Road, Shanghai, 200062, China
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44
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Fiorillo L, Bianco S, Esposito A, Conte M, Sciarretta R, Musella F, Chiariello AM. A modern challenge of polymer physics: Novel ways to study, interpret, and reconstruct chromatin structure. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2019. [DOI: 10.1002/wcms.1454] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Luca Fiorillo
- Dipartimento di Fisica Università di Napoli Federico II, and INFN Napoli Complesso Universitario di Monte Sant'Angelo Naples Italy
| | - Simona Bianco
- Dipartimento di Fisica Università di Napoli Federico II, and INFN Napoli Complesso Universitario di Monte Sant'Angelo Naples Italy
| | - Andrea Esposito
- Dipartimento di Fisica Università di Napoli Federico II, and INFN Napoli Complesso Universitario di Monte Sant'Angelo Naples Italy
| | - Mattia Conte
- Dipartimento di Fisica Università di Napoli Federico II, and INFN Napoli Complesso Universitario di Monte Sant'Angelo Naples Italy
| | - Renato Sciarretta
- Dipartimento di Fisica Università di Napoli Federico II, and INFN Napoli Complesso Universitario di Monte Sant'Angelo Naples Italy
| | - Francesco Musella
- Dipartimento di Fisica Università di Napoli Federico II, and INFN Napoli Complesso Universitario di Monte Sant'Angelo Naples Italy
| | - Andrea M. Chiariello
- Dipartimento di Fisica Università di Napoli Federico II, and INFN Napoli Complesso Universitario di Monte Sant'Angelo Naples Italy
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45
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Beltran B, Kannan D, MacPherson Q, Spakowitz AJ. Geometrical Heterogeneity Dominates Thermal Fluctuations in Facilitating Chromatin Contacts. PHYSICAL REVIEW LETTERS 2019; 123:208103. [PMID: 31809067 DOI: 10.1103/physrevlett.123.208103] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Indexed: 06/10/2023]
Abstract
Within a living cell, the myriad of proteins that bind DNA introduce heterogeneously spaced kinks into an otherwise semiflexible DNA double helix. To investigate the effects of heterogeneous nucleosome binding on chromatin organization, we extend the wormlike chain model to include statistically spaced, rigid kinks. On timescales where nucleosome positions are fixed, we find that the probability of chromatin loop formation can vary by up to six orders of magnitude between two sets of nucleosome positions drawn from the same distribution. On longer timescales, we show that continuous rerandomization due to nucleosome turnover results in chromatin tracing out an effective WLC with a dramatically smaller Kuhn length than bare DNA. Together, these observations demonstrate that nucleosome spacing acts as the primary source of the structural heterogeneity that dominates local and global chromatin organization.
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Affiliation(s)
- Bruno Beltran
- Biophysics Program, Stanford University, Stanford, California 94305, USA
| | - Deepti Kannan
- Department of Physics, Stanford University, Stanford, California 94305, USA
| | - Quinn MacPherson
- Department of Physics, Stanford University, Stanford, California 94305, USA
| | - Andrew J Spakowitz
- Chemical Engineering Department, Stanford University, Stanford, California 94305, USA
- Department of Materials Science and Engineering, Stanford University Stanford, California 94305, USA
- Department of Applied Physics, Stanford University, Stanford, California 94305, USA
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46
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Bajpai G, Padinhateeri R. Irregular Chromatin: Packing Density, Fiber Width, and Occurrence of Heterogeneous Clusters. Biophys J 2019; 118:207-218. [PMID: 31810656 DOI: 10.1016/j.bpj.2019.11.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 10/12/2019] [Accepted: 11/05/2019] [Indexed: 12/12/2022] Open
Abstract
How chromatin is folded on the length scale of a gene is an open question. Recent experiments have suggested that, in vivo, chromatin is folded in an irregular manner and not as an ordered fiber with a width of 30 nm that is expected from theories of higher order packaging. Using computational methods, we examine how the interplay between DNA-bending nonhistone proteins, histone tails, intrachromatin electrostatic, and other interactions decide the nature of the packaging of chromatin. We show that although the DNA-bending nonhistone proteins make the chromatin irregular, they may not alter the packing density and size of the fiber. We find that the length of the interacting region and intrachromatin electrostatic interactions influence the packing density, clustering of nucleosomes, and the width of the chromatin fiber. Our results suggest that the heterogeneity in the interaction pattern will play an important role in deciding the nature of the packaging of chromatin.
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Affiliation(s)
- Gaurav Bajpai
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Ranjith Padinhateeri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India.
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47
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Portillo-Ledesma S, Schlick T. Bridging chromatin structure and function over a range of experimental spatial and temporal scales by molecular modeling. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2019; 10. [PMID: 34046090 DOI: 10.1002/wcms.1434] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Chromatin structure, dynamics, and function are being intensely investigated by a variety of methods, including microscopy, X-ray diffraction, nuclear magnetic resonance, biochemical crosslinking, chromosome conformation capture, and computation. A range of experimental techniques combined with modeling is clearly valuable to help interpret experimental data and, importantly, generate configurations and mechanisms related to the 3D organization and function of the genome. Contact maps, in particular, as obtained by a variety of chromosome conformation capture methods, are of increasing interest due to their implications on genome structure and regulation on many levels. In this perspective, using seven examples from our group's studies, we illustrate how molecular modeling can help interpret such experimental data. Specifically, we show how computed contact maps related to experimental systems can be used to explain structures of nucleosomes, chromatin higher-order folding, domain segregation mechanisms, gene organization, and the effect on chromatin structure of external and internal fiber parameters, such as nucleosome positioning, presence of nucleosome free regions, histone posttranslational modifications, and linker histone binding. We argue that such computations on multiple spatial and temporal scales will be increasingly important for the integration of genomic, epigenomic, and biophysical data on chromatin structure and related cellular processes.
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Affiliation(s)
- Stephanie Portillo-Ledesma
- Department of Chemistry, New York University, 1001 Silver, 100 Washington Square East, New York, New York, 10003, USA
| | - Tamar Schlick
- Department of Chemistry, New York University, 1001 Silver, 100 Washington Square East, New York, New York, 10003, USA.,Courant Institute of Mathematical Sciences, New York University, 251 Mercer St, New York, New York, 10012, USA.,New York University-East China Normal University Center for Computational Chemistry at New York University Shanghai, Room 340, Geography Building, 3663 North Zhongshan Road, Shanghai, 200062, China
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48
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Abstract
Physical access to DNA is a highly dynamic property of chromatin that plays an essential role in establishing and maintaining cellular identity. The organization of accessible chromatin across the genome reflects a network of permissible physical interactions through which enhancers, promoters, insulators and chromatin-binding factors cooperatively regulate gene expression. This landscape of accessibility changes dynamically in response to both external stimuli and developmental cues, and emerging evidence suggests that homeostatic maintenance of accessibility is itself dynamically regulated through a competitive interplay between chromatin-binding factors and nucleosomes. In this Review, we examine how the accessible genome is measured and explore the role of transcription factors in initiating accessibility remodelling; our goal is to illustrate how chromatin accessibility defines regulatory elements within the genome and how these epigenetic features are dynamically established to control gene expression.
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Affiliation(s)
- Sandy L Klemm
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Zohar Shipony
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, CA, USA. .,Department of Applied Physics, Stanford University, Stanford, CA, USA. .,Chan Zuckerberg BioHub, San Francisco, CA, USA.
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49
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Maeshima K, Ide S, Babokhov M. Dynamic chromatin organization without the 30-nm fiber. Curr Opin Cell Biol 2019; 58:95-104. [DOI: 10.1016/j.ceb.2019.02.003] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 02/08/2019] [Accepted: 02/14/2019] [Indexed: 12/24/2022]
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50
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Onufriev AV, Schiessel H. The nucleosome: from structure to function through physics. Curr Opin Struct Biol 2019; 56:119-130. [DOI: 10.1016/j.sbi.2018.11.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 11/07/2018] [Accepted: 11/13/2018] [Indexed: 02/07/2023]
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