1
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Sun LZ, Qian JL, Cai P, Xu X. Mutual effects between single-stranded DNA conformation and Na +-Mg 2+ ion competition in mixed salt solutions. Phys Chem Chem Phys 2022; 24:20867-20881. [PMID: 36043348 DOI: 10.1039/d2cp02737b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The ion-dependence of single-stranded DNA (ssDNA) conformational changes has attracted growing attention because of its biological and technological importance. Although single-species ion effects have been extensively explored, it is challenging to study the ssDNA conformational properties under mixed monovalent/divalent ion conditions due to the complications of ssDNA flexibility and ion-ion competition. In this study, we apply Langevin dynamics simulations to investigate mixed Na+/Mg2+ ion-dependent ssDNA conformations. The ssDNA structure is described using a coarse-grained model, in which the phosphate, base, and sugar of each nucleotide are represented by three different beads. A novel improvement in our simulation model is that mixed-salt-related electrostatic interactions are computed via combining Manning counterion condensation (MCC) theory with the Monte Carlo tightly bound ion (MCTBI) model. Based on this MCC-MCTBI combination, we report new empirical functions to describe the ion-concentration-dependent and ssDNA conformation/structure-dependent electrostatic effects. The calculation results relating to the ion binding properties and the simulation results relating to the ssDNA conformational properties are validated against experimental results. In addition, our simulation results suggest a quantitative relationship between the ssDNA conformation and Na+-Mg2+ competition; this in turn reveals their mutual impact in the ion atmosphere.
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Affiliation(s)
- Li-Zhen Sun
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China.
| | - Jun-Lin Qian
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China.
| | - Pinggen Cai
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China.
| | - Xiaojun Xu
- Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou, 213001, China
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2
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Tan ZW, Guarnera E, Berezovsky IN. Exploring chromatin hierarchical organization via Markov State Modelling. PLoS Comput Biol 2018; 14:e1006686. [PMID: 30596637 PMCID: PMC6355033 DOI: 10.1371/journal.pcbi.1006686] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 01/31/2019] [Accepted: 11/27/2018] [Indexed: 01/02/2023] Open
Abstract
We propose a new computational method for exploring chromatin structural organization based on Markov State Modelling of Hi-C data represented as an interaction network between genomic loci. A Markov process describes the random walk of a traveling probe in the corresponding energy landscape, mimicking the motion of a biomolecule involved in chromatin function. By studying the metastability of the associated Markov State Model upon annealing, the hierarchical structure of individual chromosomes is observed, and corresponding set of structural partitions is identified at each level of hierarchy. Then, the notion of effective interaction between partitions is derived, delineating the overall topology and architecture of chromosomes. Mapping epigenetic data on the graphs of intra-chromosomal effective interactions helps in understanding how chromosome organization facilitates its function. A sketch of whole-genome interactions obtained from the analysis of 539 partitions from all 23 chromosomes, complemented by distributions of gene expression regulators and epigenetic factors, sheds light on the structure-function relationships in chromatin, delineating chromosomal territories, as well as structural partitions analogous to topologically associating domains and active / passive epigenomic compartments. In addition to the overall genome architecture shown by effective interactions, the affinity between partitions of different chromosomes was analyzed as an indicator of the degree of association between partitions in functionally relevant genomic interactions. The overall static picture of whole-genome interactions obtained with the method presented in this work provides a foundation for chromatin structural reconstruction, for the modelling of chromatin dynamics, and for exploring the regulation of genome function. The algorithms used in this study are implemented in a freely available Python package ChromaWalker (https://bitbucket.org/ZhenWahTan/chromawalker).
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Affiliation(s)
- Zhen Wah Tan
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Matrix, Singapore
| | - Enrico Guarnera
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Matrix, Singapore
| | - Igor N. Berezovsky
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Matrix, Singapore
- Department of Biological Sciences (DBS), National University of Singapore (NUS), Singapore
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3
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Miller EL, Hargreaves DC, Kadoch C, Chang CY, Calarco JP, Hodges C, Buenrostro JD, Cui K, Greenleaf WJ, Zhao K, Crabtree GR. TOP2 synergizes with BAF chromatin remodeling for both resolution and formation of facultative heterochromatin. Nat Struct Mol Biol 2017; 24:344-352. [PMID: 28250416 PMCID: PMC5395302 DOI: 10.1038/nsmb.3384] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 02/01/2017] [Indexed: 12/19/2022]
Abstract
Resolution and formation of facultative heterochromatin is essential to development, reprogramming, and oncogenesis. The mechanisms underlying these changes are poorly understood due to the inability to study heterochromatin dynamics and structure in vivo. We devised an in vivo approach to investigate these mechanisms and found that topoisomerase II (TOP2), but not TOP1, synergizes with BAF (mSWI/SNF) ATP-dependent chromatin remodeling complexes genome-wide to resolve facultative heterochromatin to accessible chromatin independent of transcription, indicating that changes in DNA topology through (de-)catenation rather than release of torsional stress through swiveling is necessary for heterochromatin resolution. In turn, TOP2 and BAF cooperate to recruit pluripotency factors, explaining some of the instructive roles of BAF complexes. Unexpectedly, we found that TOP2, also plays a role in the reformation of facultative heterochromatin, suggesting that facultative heterochromatin and accessible chromatin exist at different states of catenation or other topologies, which may be critical to their structures.
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Affiliation(s)
- Erik L Miller
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA.,Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Diana C Hargreaves
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA.,Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Cigall Kadoch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Chiung-Ying Chang
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA.,Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Joseph P Calarco
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA.,Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Courtney Hodges
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA.,Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Jason D Buenrostro
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Harvard Society of Fellows, Harvard University, Cambridge, Massachusetts, USA
| | - Kairong Cui
- Systems Biology Center, National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, Maryland, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Keji Zhao
- Systems Biology Center, National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, Maryland, USA
| | - Gerald R Crabtree
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA.,Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
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4
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Muskhelishvili G, Travers A. The regulatory role of DNA supercoiling in nucleoprotein complex assembly and genetic activity. Biophys Rev 2016; 8:5-22. [PMID: 28510220 PMCID: PMC5425797 DOI: 10.1007/s12551-016-0237-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 10/21/2016] [Indexed: 01/06/2023] Open
Abstract
We argue that dynamic changes in DNA supercoiling in vivo determine both how DNA is packaged and how it is accessed for transcription and for other manipulations such as recombination. In both bacteria and eukaryotes, the principal generators of DNA superhelicity are DNA translocases, supplemented in bacteria by DNA gyrase. By generating gradients of superhelicity upstream and downstream of their site of activity, translocases enable the differential binding of proteins which preferentially interact with respectively more untwisted or more writhed DNA. Such preferences enable, in principle, the sequential binding of different classes of protein and so constitute an essential driver of chromatin organization.
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Affiliation(s)
| | - Andrew Travers
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK.
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK.
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5
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Feng YL, Xiang JF, Kong N, Cai XJ, Xie AY. Buried territories: heterochromatic response to DNA double-strand breaks. Acta Biochim Biophys Sin (Shanghai) 2016; 48:594-602. [PMID: 27151295 DOI: 10.1093/abbs/gmw033] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 03/28/2016] [Indexed: 12/22/2022] Open
Abstract
Cellular response to DNA double-strand breaks (DSBs), the most deleterious type of DNA damage, is highly influenced by higher-order chromatin structure in eukaryotic cells. Compared with euchromatin, the compacted structure of heterochromatin not only protects heterochromatic DNA from damage, but also adds an extra layer of control over the response to DSBs occurring in heterochromatin. One key step in this response is the decondensation of heterochromatin structure. This decondensation process facilitates the DNA damage signaling and promotes proper heterochromatic DSB repair, thus helping to prevent instability of heterochromatic regions of genomes. This review will focus on the functions of the ataxia telangiectasia mutated (ATM) signaling cascade involving ATM, heterochromatin protein 1 (HP1), Krüppel-associated box (KRAB)-associated protein-1 (KAP-1), tat-interacting protein 60 (Tip60), and many other protein factors in DSB-induced decondensation of heterochromatin and subsequent repair of heterochromatic DSBs. As some subsets of DSBs may be repaired in heterochromatin independently of the ATM signaling, a possible repair model is also proposed for ATM-independent repair of these heterochromatic DSBs.
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Affiliation(s)
- Yi-Li Feng
- Key Laboratory of Surgery of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou 310016, China Institute of Translational Medicine, Zhejiang University, Hangzhou 310029, China
| | - Ji-Feng Xiang
- Key Laboratory of Surgery of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou 310016, China Institute of Translational Medicine, Zhejiang University, Hangzhou 310029, China
| | - Na Kong
- Key Laboratory of Surgery of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou 310016, China Institute of Translational Medicine, Zhejiang University, Hangzhou 310029, China
| | - Xiu-Jun Cai
- Key Laboratory of Surgery of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou 310016, China
| | - An-Yong Xie
- Key Laboratory of Surgery of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou 310016, China Institute of Translational Medicine, Zhejiang University, Hangzhou 310029, China
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6
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Ghirlando R, Felsenfeld G. Physical chemistry of nucleic acids and their complexes. Biopolymers 2016; 99:910-5. [PMID: 23765314 DOI: 10.1002/bip.22311] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 05/30/2013] [Indexed: 01/12/2023]
Abstract
Studies of the physical properties of nucleic acids began almost immediately following the discovery of the DNA structure. Early investigations focused on the stability and specificity of multi-strand polynucleotide complexes, then gradually on their interaction with other molecules, particularly proteins. As molecular and structural biology expanded to provide detailed information about biochemical mechanisms, physical studies eventually acquired the additional constraint that they should be relevant to functioning biological systems. We describe work in our laboratory that began with investigations of relatively simple questions about the role of electrostatic interactions in the stabilization of multi-strand nucleic acid structures, and evolved to studies of chromatin structure in vitro and within the nucleus.
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Affiliation(s)
- Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892
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7
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Liquid-like behavior of chromatin. Curr Opin Genet Dev 2016; 37:36-45. [DOI: 10.1016/j.gde.2015.11.006] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 11/23/2015] [Accepted: 11/25/2015] [Indexed: 11/23/2022]
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8
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Hollar D. Epigenetic Significance of Chromatin Organization During Cellular Aging and Organismal Lifespan. EPIGENETICS, THE ENVIRONMENT, AND CHILDREN’S HEALTH ACROSS LIFESPANS 2016. [PMCID: PMC7153164 DOI: 10.1007/978-3-319-25325-1_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- David Hollar
- Pfeiffer University, Morrisville, North Carolina USA
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9
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Popken J, Brero A, Koehler D, Schmid VJ, Strauss A, Wuensch A, Guengoer T, Graf A, Krebs S, Blum H, Zakhartchenko V, Wolf E, Cremer T. Reprogramming of fibroblast nuclei in cloned bovine embryos involves major structural remodeling with both striking similarities and differences to nuclear phenotypes of in vitro fertilized embryos. Nucleus 2015; 5:555-89. [PMID: 25482066 PMCID: PMC4615760 DOI: 10.4161/19491034.2014.979712] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Nuclear landscapes were studied during preimplantation development of bovine embryos, generated either by in vitro fertilization (IVF), or generated as cloned embryos by somatic cell nuclear transfer (SCNT) of bovine fetal fibroblasts, using 3-dimensional confocal laser scanning microscopy (3D-CLSM) and structured illumination microscopy (3D-SIM). Nuclear landscapes of IVF and SCNT embryonic nuclei were compared with each other and with fibroblast nuclei. We demonstrate that reprogramming of fibroblast nuclei in cloned embryos requires changes of their landscapes similar to nuclei of IVF embryos. On the way toward the 8-cell stage, where major genome activation occurs, a major lacuna, enriched with splicing factors, was formed in the nuclear interior and chromosome territories (CTs) were shifted toward the nuclear periphery. During further development the major lacuna disappeared and CTs were redistributed throughout the nuclear interior forming a contiguous higher order chromatin network. At all stages of development CTs of IVF and SCNT embryonic nuclei were built up from chromatin domain clusters (CDCs) pervaded by interchromatin compartment (IC) channels. Quantitative analyses revealed a highly significant enrichment of RNA polymerase II and H3K4me3, a marker for transcriptionally competent chromatin, at the periphery of CDCs. In contrast, H3K9me3, a marker for silent chromatin, was enriched in the more compacted interior of CDCs. Despite these striking similarities, we also detected major differences between nuclear landscapes of IVF and cloned embryos. Possible implications of these differences for the developmental potential of cloned animals remain to be investigated. We present a model, which integrates generally applicable structural and functional features of the nuclear landscape.
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Key Words
- 3D-CLSM, 3-dimensional confocal laser scanning microscopy
- 3D-SIM, 3-dimensional structured illumination microscopy
- B23, nucleophosmin B23
- BTA, Bos taurus
- CDC, chromatin domain cluster
- CT, chromosome territory
- EM, electron microscopy
- ENC, embryonic nuclei with conventional nuclear architecture
- ENP, embryonic nuclei with peripheral CT distribution
- H3K4me3
- H3K4me3, histone H3 with tri-methylated lysine 4
- H3K9me3
- H3K9me3, histone H3 with tri-methylated lysine 9
- H3S10p, histone H3 with phosphorylated serine 10
- IC, interchromatin compartment
- IVF, in vitro fertilization
- MCB, major chromatin body
- PR, perichromatin region
- RNA polymerase II
- RNA polymerase II-S2p, RNA polymerase II with phosphorylated serine 2 of its CTD domain
- RNA polymerase II-S5p, RNA polymerase II with phosphorylated serine 5 of its CTD domain
- SC-35, splicing factor SC-35
- SCNT, somatic cell nuclear transfer.
- bovine preimplantation development
- chromatin domain
- chromosome territory
- embryonic genome activation
- in vitro fertilization (IVF)
- interchromatin compartment
- major EGA, major embryonic genome activation
- somatic cell nuclear transfer (SCNT)
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Affiliation(s)
- Jens Popken
- a Division of Anthropology and Human Genetics ; Biocenter; LMU Munich ; Munich , Germany
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10
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Risca VI, Greenleaf WJ. Unraveling the 3D genome: genomics tools for multiscale exploration. Trends Genet 2015; 31:357-72. [PMID: 25887733 DOI: 10.1016/j.tig.2015.03.010] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 03/16/2015] [Accepted: 03/24/2015] [Indexed: 12/15/2022]
Abstract
A decade of rapid method development has begun to yield exciting insights into the 3D architecture of the metazoan genome and the roles it may play in regulating transcription. Here we review core methods and new tools in the modern genomicist's toolbox at three length scales, ranging from single base pairs to megabase-scale chromosomal domains, and discuss the emerging picture of the 3D genome that these tools have revealed. Blind spots remain, especially at intermediate length scales spanning a few nucleosomes, but thanks in part to new technologies that permit targeted alteration of chromatin states and time-resolved studies, the next decade holds great promise for hypothesis-driven research into the mechanisms that drive genome architecture and transcriptional regulation.
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Affiliation(s)
- Viviana I Risca
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
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11
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Monte E, Vondriska TM. Epigenomes: the missing heritability in human cardiovascular disease? Proteomics Clin Appl 2015; 8:480-7. [PMID: 24957631 DOI: 10.1002/prca.201400031] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 05/20/2014] [Accepted: 06/16/2014] [Indexed: 12/24/2022]
Abstract
Cardiovascular disease is a tremendous burden on human health and results from malfunction of various networks of biological molecules in the context of environmental stress. Despite strong evidence of heritability, many common forms of heart disease (heart failure in particular) have not yielded to genome-wide association studies to identify causative mutations acting via the disruption of individual molecules. Increasing evidence suggests, however, that genetic variation in noncoding regions is strongly linked to disease susceptibility. We hypothesize that epigenomic variation may engender different chromatin environments in the absence of (or in parallel with) changes in protein or mRNA sequence and abundance. In this manner, distinct-genetically encoded-chromatin environments can exhibit distinct responses to environmental stresses that cause heart failure, explaining a significant portion of the altered susceptibility that is observed in human disease.
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Affiliation(s)
- Emma Monte
- Departments of Anesthesiology and Perioperative Medicine, Medicine and Physiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
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12
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Maffeo C, Ngo TT, Ha T, Aksimentiev A. A Coarse-Grained Model of Unstructured Single-Stranded DNA Derived from Atomistic Simulation and Single-Molecule Experiment. J Chem Theory Comput 2014; 10:2891-2896. [PMID: 25136266 PMCID: PMC4132850 DOI: 10.1021/ct500193u] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Indexed: 01/02/2023]
Abstract
A simple coarse-grained model of single-stranded DNA (ssDNA) was developed, featuring only two sites per nucleotide that represent the centers of mass of the backbone and sugar/base groups. In the model, the interactions between sites are described using tabulated bonded potentials optimized to reproduce the solution structure of DNA observed in atomistic molecular dynamics simulations. Isotropic potentials describe nonbonded interactions, implicitly taking into account the solvent conditions to match the experimentally determined radius of gyration of ssDNA. The model reproduces experimentally measured force-extension dependence of an unstructured DNA strand across 2 orders of magnitude of the applied force. The accuracy of the model was confirmed by measuring the end-to-end distance of a dT14 fragment via FRET while stretching the molecules using optical tweezers. The model offers straightforward generalization to systems containing double-stranded DNA and DNA binding proteins.
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Affiliation(s)
- Christopher Maffeo
- Department
of Physics, University of Illinois at Urbana−Champaign, Urbana, Illinois, United States
| | - Thuy T.
M. Ngo
- Center
for Biophysics and Computational Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois, United States
| | - Taekjip Ha
- Department
of Physics, University of Illinois at Urbana−Champaign, Urbana, Illinois, United States
- The
Howard Hughes Medical Institute, Chevy Chase, Maryland, United
States
| | - Aleksei Aksimentiev
- Department
of Physics, University of Illinois at Urbana−Champaign, Urbana, Illinois, United States
- Beckman
Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois, United States
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13
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Maeshima K, Imai R, Tamura S, Nozaki T. Chromatin as dynamic 10-nm fibers. Chromosoma 2014; 123:225-37. [PMID: 24737122 PMCID: PMC4031381 DOI: 10.1007/s00412-014-0460-2] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 03/18/2014] [Accepted: 03/20/2014] [Indexed: 01/01/2023]
Abstract
Since Flemming described a nuclear substance in the nineteenth century and named it “chromatin,” this substance has fascinated biologists. What is the structure of chromatin? DNA is wrapped around core histones, forming a nucleosome fiber (10-nm fiber). This fiber has long been assumed to fold into a 30-nm chromatin fiber and subsequently into helically folded larger fibers or radial loops. However, several recent studies, including our cryo-EM and X-ray scattering analyses, demonstrated that chromatin is composed of irregularly folded 10-nm fibers, without 30-nm chromatin fibers, in interphase chromatin and mitotic chromosomes. This irregular folding implies a chromatin state that is physically less constrained, which could be more dynamic compared with classical regular helical folding structures. Consistent with this, recently, we uncovered by single nucleosome imaging large nucleosome fluctuations in living mammalian cells (∼50 nm/30 ms). Subsequent computational modeling suggested that nucleosome fluctuation increases chromatin accessibility, which is advantageous for many “target searching” biological processes such as transcriptional regulation. Therefore, this review provides a novel view on chromatin structure in which chromatin consists of dynamic and disordered 10-nm fibers.
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Affiliation(s)
- Kazuhiro Maeshima
- Biological Macromolecules Laboratory, Structural Biology Center, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan,
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14
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Razin SV, Gavrilov AA. Chromatin without the 30-nm fiber: constrained disorder instead of hierarchical folding. Epigenetics 2014; 9:653-7. [PMID: 24561903 PMCID: PMC4063823 DOI: 10.4161/epi.28297] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Several hierarchical levels of DNA packaging are believed to exist in chromatin, starting from a 10-nm chromatin fiber that is further packed into a 30-nm fiber. Transitions between the 30-nm and 10-nm fibers are thought to be essential for the control of chromatin transcriptional status. However, recent studies demonstrate that in the nuclei, DNA is packed in tightly associated 10-nm fibers that are not compacted into 30-nm fibers. Additionally, the accessibility of DNA in chromatin depends on the local mobility of nucleosomes rather than on decompaction of chromosome regions. These findings argue for reconsidering the hierarchical model of chromatin packaging and some of the basic definitions of chromatin. In particular, chromatin domains should be considered as three-dimensional objects, which may include genomic regions that do not necessarily constitute a continuous domain on the DNA chain.
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Affiliation(s)
- Sergey V Razin
- Institute of Gene Biology of the Russian Academy of Sciences; Moscow, Russia; Faculty of Biology; M.V. Lomonosov Moscow State University; Moscow, Russia; LIA 1066 French-Russian Joint Cancer Research Laboratory; Moscow, Russia
| | - Alexey A Gavrilov
- Institute of Gene Biology of the Russian Academy of Sciences; Moscow, Russia; LIA 1066 French-Russian Joint Cancer Research Laboratory; Moscow, Russia
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15
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Belmont AS. Large-scale chromatin organization: the good, the surprising, and the still perplexing. Curr Opin Cell Biol 2013; 26:69-78. [PMID: 24529248 DOI: 10.1016/j.ceb.2013.10.002] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Revised: 10/07/2013] [Accepted: 10/15/2013] [Indexed: 11/19/2022]
Abstract
Traditionally large-scale chromatin structure has been studied by microscopic approaches, providing direct spatial information but limited sequence context. In contrast, newer 3C (chromosome capture conformation) methods provide rich sequence context but uncertain spatial context. Recent demonstration of large, topologically linked DNA domains, hundreds to thousands of kb in size, may now link 3C data to actual chromosome physical structures, as visualized directly by microscopic methods. Yet, new data suggesting that 3C may measure cytological rather than molecular proximity prompts a renewed focus on understanding the origin of 3C interactions and dissecting the biological significance of long-range genomic interactions.
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Affiliation(s)
- Andrew S Belmont
- Department of Cell and Developmental Biology, University of Illinois, Urbana-Champaign, B107 CLSL, 601 South Goodwin Avenue, Urbana, IL 61801, United States.
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