1
|
Schuette G, Ding X, Zhang B. Efficient Hi-C inversion facilitates chromatin folding mechanism discovery and structure prediction. Biophys J 2023; 122:3425-3438. [PMID: 37496267 PMCID: PMC10502442 DOI: 10.1016/j.bpj.2023.07.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 07/10/2023] [Accepted: 07/24/2023] [Indexed: 07/28/2023] Open
Abstract
Genome-wide chromosome conformation capture (Hi-C) experiments have revealed many structural features of chromatin across multiple length scales. Further understanding genome organization requires relating these discoveries to the mechanisms that establish chromatin structures and reconstructing these structures in three dimensions, but both objectives are difficult to achieve with existing algorithms that are often computationally expensive. To alleviate this challenge, we present an algorithm that efficiently converts Hi-C data into contact energies, which measure the interaction strength between genomic loci brought into proximity. Contact energies are local quantities unaffected by the topological constraints that correlate Hi-C contact probabilities. Thus, extracting contact energies from Hi-C contact probabilities distills the biologically unique information contained in the data. We show that contact energies reveal the location of chromatin loop anchors, support a phase separation mechanism for genome compartmentalization, and parameterize polymer simulations that predict three-dimensional chromatin structures. Therefore, we anticipate that contact energy extraction will unleash the full potential of Hi-C data and that our inversion algorithm will facilitate the widespread adoption of contact energy analysis.
Collapse
Affiliation(s)
- Greg Schuette
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Xinqiang Ding
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts.
| |
Collapse
|
2
|
Schuette G, Ding X, Zhang B. Efficient Hi-C inversion facilitates chromatin folding mechanism discovery and structure prediction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.17.533194. [PMID: 36993500 PMCID: PMC10055272 DOI: 10.1101/2023.03.17.533194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Genome-wide chromosome conformation capture (Hi-C) experiments have revealed many structural features of chromatin across multiple length scales. Further understanding genome organization requires relating these discoveries to the mechanisms that establish chromatin structures and reconstructing these structures in three dimensions, but both objectives are difficult to achieve with existing algorithms that are often computationally expensive. To alleviate this challenge, we present an algorithm that efficiently converts Hi-C data into contact energies, which measure the interaction strength between genomic loci brought into proximity. Contact energies are local quantities unaffected by the topological constraints that correlate Hi-C contact probabilities. Thus, extracting contact energies from Hi-C contact probabilities distills the biologically unique information contained in the data. We show that contact energies reveal the location of chromatin loop anchors, support a phase separation mechanism for genome compartmentalization, and parameterize polymer simulations that predict three-dimensional chromatin structures. Therefore, we anticipate that contact energy extraction will unleash the full potential of Hi-C data and that our inversion algorithm will facilitate the widespread adoption of contact energy analysis.
Collapse
Affiliation(s)
- Greg Schuette
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Xinqiang Ding
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| |
Collapse
|
3
|
Thuma J, Chung YC, Tu LC. Advances and challenges in CRISPR-based real-time imaging of dynamic genome organization. Front Mol Biosci 2023; 10:1173545. [PMID: 37065447 PMCID: PMC10102487 DOI: 10.3389/fmolb.2023.1173545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 03/23/2023] [Indexed: 04/03/2023] Open
Abstract
Nuclear chromosome compaction is non-random and dynamic. The spatial distance among genomic elements instantly modulates transcription. Visualization of the genome organization in the cell nucleus is essential to understand nuclear function. In addition to cell type-dependent organization, high-resolution 3D imaging shows heterogeneous compaction of chromatin organization among the same cell type. Questions remain to be answered if these structural variations were the snapshots of dynamic organization at different time points and if they are functionally different. Live-cell imaging has provided unique insights into dynamic genome organization at short (milliseconds) and long (hours) time scales. The recent development of CRISPR-based imaging opened windows for studying dynamic chromatin organization in single cells in real time. Here we highlight these CRISPR-based imaging techniques and discuss their advances and challenges as a powerful live-cell imaging method that poses high potential to generate paradigm-shifting discoveries and reveal functional implications of dynamic chromatin organization.
Collapse
Affiliation(s)
- Jenna Thuma
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, United States
- Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, OH, United States
| | - Yu-Chieh Chung
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, United States
| | - Li-Chun Tu
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, United States
- Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, OH, United States
- Center for RNA Biology, The Ohio State University, Columbus, OH, United States
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States
- *Correspondence: Li-Chun Tu,
| |
Collapse
|
4
|
Chung YC, Bisht M, Thuma J, Tu LC. Single-chromosome dynamics reveals locus-dependent dynamics and chromosome territory orientation. J Cell Sci 2023; 136:289470. [PMID: 36718642 PMCID: PMC10022681 DOI: 10.1242/jcs.260137] [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: 04/16/2022] [Accepted: 01/19/2023] [Indexed: 02/01/2023] Open
Abstract
Dynamic chromatin organization instantly influences DNA accessibility through modulating local macromolecular density and interactions, driving changes in transcription activities. Chromatin dynamics have been reported to be locally confined but contribute to coherent chromatin motion across the entire nucleus. However, the regulation of dynamics, nuclear orientation and compaction of subregions along a single chromosome are not well-understood. We used CRISPR-based real-time single-particle tracking and polymer models to characterize the dynamics of specific genomic loci and determine compaction levels of large human chromosomal domains. Our studies showed that chromosome compaction changed during interphase and that compactions of two arms on chromosome 19 were different. The dynamics of genomic loci were subdiffusive and dependent on chromosome regions and transcription states. Surprisingly, the correlation between locus-dependent nuclear localization and mobility was negligible. Strong tethering interactions detected at the pericentromeric region implies local condensation or associations with organelles within local nuclear microenvironments, such as chromatin-nuclear body association. Based on our findings, we propose a 'guided radial model' for the nuclear orientation of the long arm of chromosome 19.
Collapse
Affiliation(s)
- Yu-Chieh Chung
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
| | - Madhoolika Bisht
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Jenna Thuma
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
- Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
| | - Li-Chun Tu
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
- Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
- Author for correspondence ()
| |
Collapse
|
5
|
Yesbolatova AK, Arai R, Sakaue T, Kimura A. Formulation of Chromatin Mobility as a Function of Nuclear Size during C. elegans Embryogenesis Using Polymer Physics Theories. PHYSICAL REVIEW LETTERS 2022; 128:178101. [PMID: 35570447 DOI: 10.1103/physrevlett.128.178101] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 03/21/2022] [Indexed: 06/15/2023]
Abstract
During early embryogenesis of the nematode, Caenorhabditis elegans, the chromatin motion markedly decreases. Despite its biological implications, the underlying mechanism for this transition was unclear. By combining theory and experiment, we analyze the mean-square displacement (MSD) of the chromatin loci, and demonstrate that MSD-vs-time relationships in various nuclei collapse into a single master curve by normalizing them with the mesh size and the corresponding time scale. This enables us to identify the onset of the entangled dynamics with the size of tube diameter of chromatin polymer in the C. elegans embryo. Our dynamical scaling analysis predicts the transition between unentangled and entangled dynamics of chromatin polymers, the quantitative formula for MSD as a function of nuclear size and timescale, and provides testable hypotheses on chromatin mobility in other cell types and species.
Collapse
Affiliation(s)
- Aiya K Yesbolatova
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies, SOKENDAI, Mishima 411-8540, Japan
- Cell Architecture Laboratory, Department of Chromosome Science, National Institute of Genetics, Mishima 411-8540, Japan
| | - Ritsuko Arai
- Cell Architecture Laboratory, Department of Chromosome Science, National Institute of Genetics, Mishima 411-8540, Japan
| | - Takahiro Sakaue
- Department of Physical Sciences, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, Kanagawa 252-5258, Japan
| | - Akatsuki Kimura
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies, SOKENDAI, Mishima 411-8540, Japan
- Cell Architecture Laboratory, Department of Chromosome Science, National Institute of Genetics, Mishima 411-8540, Japan
| |
Collapse
|
6
|
Roy PK, Chaudhuri P, Vemparala S. Effect of ring stiffness and ambient pressure on the dynamical slowdown in ring polymers. SOFT MATTER 2022; 18:2959-2967. [PMID: 35348146 DOI: 10.1039/d1sm01754c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Using extensive molecular dynamics simulations, we investigate the slowdown of dynamics in a 3D system of ring polymers by varying the ambient pressure and the stiffness of the rings. Our study demonstrates that the stiffness of the rings determines the dynamics of the ring polymers, leading to glassiness at lower pressures for stiffer rings. The threading of the ring polymers, a unique feature that emerges only due to the topological nature of such polymers in three dimensions, is shown to be the determinant feature of dynamical slowdown, albeit only in a certain stiffness range. Our results suggest a possible framework for exploring the phase space spanned by ring stiffness and pressure to obtain spontaneously emerging topologically constrained polymer glasses.
Collapse
Affiliation(s)
- Projesh Kumar Roy
- The Institute of Mathematical Sciences, C. I. T. Campus, Taramani, Chennai 600113, India.
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Pinaki Chaudhuri
- The Institute of Mathematical Sciences, C. I. T. Campus, Taramani, Chennai 600113, India.
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Satyavani Vemparala
- The Institute of Mathematical Sciences, C. I. T. Campus, Taramani, Chennai 600113, India.
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| |
Collapse
|
7
|
Gravitational Force-Induced 3D Chromosomal Conformational Changes Are Associated with Rapid Transcriptional Response in Human T Cells. Int J Mol Sci 2021; 22:ijms22179426. [PMID: 34502336 PMCID: PMC8430767 DOI: 10.3390/ijms22179426] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 08/26/2021] [Accepted: 08/27/2021] [Indexed: 12/14/2022] Open
Abstract
The mechanisms underlying gravity perception in mammalian cells are unknown. We have recently discovered that the transcriptome of cells in the immune system, which is the most affected system during a spaceflight, responds rapidly and broadly to altered gravity. To pinpoint potential underlying mechanisms, we compared gene expression and three-dimensional (3D) chromosomal conformational changes in human Jurkat T cells during the short-term gravitational changes in parabolic flight and suborbital ballistic rocket flight experiments. We found that differential gene expression in gravity-responsive chromosomal regions, but not differentially regulated single genes, are highly conserved between different real altered gravity comparisons. These coupled gene expression effects in chromosomal regions could be explained by underlying chromatin structures. Based on a high-throughput chromatin conformation capture (Hi-C) analysis in altered gravity, we found that small chromosomes (chr16–22, with the exception of chr18) showed increased intra- and interchromosomal interactions in altered gravity, whereby large chromosomes showed decreased interactions. Finally, we detected a nonrandom overlap between Hi-C-identified chromosomal interacting regions and gravity-responsive chromosomal regions (GRCRs). We therefore demonstrate the first evidence that gravitational force-induced 3D chromosomal conformational changes are associated with rapid transcriptional response in human T cells. We propose a general model of cellular sensitivity to gravitational forces, where gravitational forces acting on the cellular membrane are rapidly and mechanically transduced through the cytoskeleton into the nucleus, moving chromosome territories to new conformation states and their genes into more expressive or repressive environments, finally resulting in region-specific differential gene expression.
Collapse
|
8
|
MacKay K, Kusalik A. Computational methods for predicting 3D genomic organization from high-resolution chromosome conformation capture data. Brief Funct Genomics 2021; 19:292-308. [PMID: 32353112 PMCID: PMC7388788 DOI: 10.1093/bfgp/elaa004] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 01/30/2020] [Accepted: 02/07/2020] [Indexed: 12/19/2022] Open
Abstract
The advent of high-resolution chromosome conformation capture assays (such as 5C, Hi-C and Pore-C) has allowed for unprecedented sequence-level investigations into the structure-function relationship of the genome. In order to comprehensively understand this relationship, computational tools are required that utilize data generated from these assays to predict 3D genome organization (the 3D genome reconstruction problem). Many computational tools have been developed that answer this need, but a comprehensive comparison of their underlying algorithmic approaches has not been conducted. This manuscript provides a comprehensive review of the existing computational tools (from November 2006 to September 2019, inclusive) that can be used to predict 3D genome organizations from high-resolution chromosome conformation capture data. Overall, existing tools were found to use a relatively small set of algorithms from one or more of the following categories: dimensionality reduction, graph/network theory, maximum likelihood estimation (MLE) and statistical modeling. Solutions in each category are far from maturity, and the breadth and depth of various algorithmic categories have not been fully explored. While the tools for predicting 3D structure for a genomic region or single chromosome are diverse, there is a general lack of algorithmic diversity among computational tools for predicting the complete 3D genome organization from high-resolution chromosome conformation capture data.
Collapse
|
9
|
Mamberti S, Cardoso MC. Are the processes of DNA replication and DNA repair reading a common structural chromatin unit? Nucleus 2020; 11:66-82. [PMID: 32275847 PMCID: PMC7289585 DOI: 10.1080/19491034.2020.1744415] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Decades of investigation on genomic DNA have brought us deeper insights into its organization within the nucleus and its metabolic mechanisms. This was fueled by the parallel development of experimental techniques and has stimulated model building to simulate genome conformation in agreement with the experimental data. Here, we will discuss our recent discoveries on the chromatin units of DNA replication and DNA damage response. We will highlight their remarkable structural similarities and how both revealed themselves as clusters of nanofocal structures each on the hundred thousand base pair size range corresponding well with chromatin loop sizes. We propose that the function of these two global genomic processes is determined by the loop level organization of chromatin structure with structure dictating function. Abbreviations: 3D-SIM: 3D-structured illumination microscopy; 3C: chromosome conformation capture; DDR: DNA damage response; FISH: fluorescent in situ hybridization; Hi-C: high conformation capture; HiP-HoP: highly predictive heteromorphic polymer model; IOD: inter-origin distance; LAD: lamina associated domain; STED: stimulated emission depletion microscopy; STORM: stochastic optical reconstruction microscopy; SBS: strings and binders switch model; TAD: topologically associated domain
Collapse
Affiliation(s)
- Stefania Mamberti
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - M Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| |
Collapse
|
10
|
Chromatin as an active polymeric material. Emerg Top Life Sci 2020; 4:111-118. [PMID: 32830859 DOI: 10.1042/etls20200010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/31/2020] [Accepted: 08/04/2020] [Indexed: 01/09/2023]
Abstract
The patterns of the large-scale spatial organization of chromatin in interphase human somatic cells are not random. Such patterns include the radial separation of euchromatin and heterochromatin, the territorial organization of individual chromosomes, the non-random locations of chromosome territories and the differential positioning of the two X chromosomes in female cells. These features of large-scale nuclear architecture follow naturally from the hypothesis that ATP-consuming non-equilibrium processes associated with highly transcribed regions of chromosomes are a source of 'active' forces. These forces are in excess of those that arise from Brownian motion. Simulations of model chromosomes that incorporate such activity recapitulate these features. In addition, they reproduce many other aspects of the spatial organization of chromatin at large scales that are known from experiments. Our results, reviewed here, suggest that the distribution of transcriptional activity across chromosomes underlies many aspects of large-scale nuclear architecture that were hitherto believed to be unrelated.
Collapse
|
11
|
Kwon S, Sung BJ. History-dependent nonequilibrium conformations of a highly confined polymer globule in a sphere. Phys Rev E 2020; 102:022501. [PMID: 32942375 DOI: 10.1103/physreve.102.022501] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 07/28/2020] [Indexed: 11/07/2022]
Abstract
Chromatin undergoes condensation-decondensation processes repeatedly during its cell lifetime. The spatial organization of chromatin in nucleus resembles the fractal globule, of which structure significantly differs from an equilibrium polymer globule. There have been efforts to develop a polymer globule model to describe the fractal globulelike structure of tightly packed chromatin in nucleus. However, the transition pathway of a polymer toward a globular state has been often ignored. Because biological systems are intrinsically in nonequilibrium states, the transition pathway that the chromatin would take before reaching the densely packaged globule should be of importance. In this study, by employing a simple polymer model and Langevin dynamics simulations, we investigate the conformational transition of a single polymer from a swollen coil to a compact globule. We aim to elucidate the effect of transition pathways on the final globular structure. We show that a fast collapse induces a nonequilibrium structure even without a specific intramolecular interaction and that its relaxation toward an equilibrium globule is extremely slow. Due to a strong confinement, the fractal globule never relaxes into an equilibrium state during our simulations such that the globular structure becomes dependent on the transition pathway.
Collapse
Affiliation(s)
- Seulki Kwon
- Department of Chemistry, Sogang University, Seoul 121-742, Republic of Korea
| | - Bong June Sung
- Department of Chemistry, Sogang University, Seoul 121-742, Republic of Korea
| |
Collapse
|
12
|
Tripathi K, Menon GI, Vemparala S. Confined crowded polymers near attractive surfaces. J Chem Phys 2019; 151:244901. [PMID: 31893876 DOI: 10.1063/1.5115284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present results from molecular dynamics simulations of a spherically confined neutral polymer in the presence of crowding particles, studying polymer shapes and conformations as a function of the strength of the attraction to the confining wall, solvent quality, and the density of crowders. The conformations of the polymer under good solvent conditions are weakly dependent on crowder particle density, even when the polymer is strongly confined. In contrast, under poor solvent conditions, when the polymer assumes a collapsed conformation when unconfined, it can exhibit transitions to two different adsorbed phases, when either the interaction with the wall or the density of crowder particles is changed. One such transition involves a desorbed collapsed phase change to an adsorbed extended phase as the attraction of the polymer towards the confining wall is increased. Such an adsorbed extended phase can exhibit a second transition to an ordered adsorbed collapsed phase as the crowder particle density is increased. The ordered adsorbed collapsed phase of the polymer differs significantly in its structure from the desorbed collapsed phase. We revisit the earlier understanding of the adsorption of confined polymers on attractive surfaces in light of our results.
Collapse
Affiliation(s)
- Kamal Tripathi
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113, India
| | - Gautam I Menon
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113, India
| | - Satyavani Vemparala
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113, India
| |
Collapse
|
13
|
Agrawal A, Ganai N, Sengupta S, Menon GI. Nonequilibrium Biophysical Processes Influence the Large-Scale Architecture of the Cell Nucleus. Biophys J 2019; 118:2229-2244. [PMID: 31818465 DOI: 10.1016/j.bpj.2019.11.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 10/30/2019] [Accepted: 11/11/2019] [Indexed: 10/25/2022] Open
Abstract
Model approaches to nuclear architecture have traditionally ignored the biophysical consequences of ATP-fueled active processes acting on chromatin. However, transcription-coupled activity is a source of stochastic forces that are substantially larger than the Brownian forces present at physiological temperatures. Here, we describe an approach to large-scale nuclear architecture in metazoans that incorporates cell-type-specific active processes. The model predicts the statistics of positional distributions, shapes, and overlaps of each chromosome. Simulations of the model reproduce common organizing principles underlying large-scale nuclear architecture across human cell nuclei in interphase. These include the differential positioning of euchromatin and heterochromatin, the territorial organization of chromosomes (including both gene-density-based and size-based chromosome radial positioning schemes), the nonrandom locations of chromosome territories, and the shape statistics of individual chromosomes. We propose that the biophysical consequences of the distribution of transcriptional activity across chromosomes should be central to any chromosome positioning code.
Collapse
Affiliation(s)
- Ankit Agrawal
- Computational Biology Group, The Institute of Mathematical Sciences, Taramani, Chennai, India; Homi Bhabha National Institute, Mumbai, India
| | - Nirmalendu Ganai
- Department of Physics, Nabadwip Vidyasagar College, Nabadwip, Nadia, India
| | - Surajit Sengupta
- TIFR Centre for Interdisciplinary Sciences, Serilingampally Mandal, Ranga Reddy District, Hyderabad, India
| | - Gautam I Menon
- Computational Biology Group, The Institute of Mathematical Sciences, Taramani, Chennai, India; Homi Bhabha National Institute, Mumbai, India; Department of Physics, Ashoka University, Rajiv Gandhi Education City, National Capital Region P.O.Rai, Sonepat, India.
| |
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
Fritz AJ, Sehgal N, Pliss A, Xu J, Berezney R. Chromosome territories and the global regulation of the genome. Genes Chromosomes Cancer 2019; 58:407-426. [PMID: 30664301 DOI: 10.1002/gcc.22732] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 01/11/2019] [Accepted: 01/12/2019] [Indexed: 12/29/2022] Open
Abstract
Spatial positioning is a fundamental principle governing nuclear processes. Chromatin is organized as a hierarchy from nucleosomes to Mbp chromatin domains (CD) or topologically associating domains (TADs) to higher level compartments culminating in chromosome territories (CT). Microscopic and sequencing techniques have substantiated chromatin organization as a critical factor regulating gene expression. For example, enhancers loop back to interact with their target genes almost exclusively within TADs, distally located coregulated genes reposition into common transcription factories upon activation, and Mbp CDs exhibit dynamic motion and configurational changes in vivo. A longstanding question in the nucleus field is whether an interactive nuclear matrix provides a direct link between structure and function. The findings of nonrandom radial positioning of CT within the nucleus suggest the possibility of preferential interaction patterns among populations of CT. Sequential labeling up to 10 CT followed by application of computer imaging and geometric graph mining algorithms revealed cell-type specific interchromosomal networks (ICN) of CT that are altered during the cell cycle, differentiation, and cancer progression. It is proposed that the ICN correlate with the global level of genome regulation. These approaches also demonstrated that the large scale 3-D topology of CT is specific for each CT. The cell-type specific proximity of certain chromosomal regions in normal cells may explain the propensity of distinct translocations in cancer subtypes. Understanding how genes are dysregulated upon disruption of the normal "wiring" of the nucleus by translocations, deletions, and amplifications that are hallmarks of cancer, should enable more targeted therapeutic strategies.
Collapse
Affiliation(s)
- Andrew J Fritz
- Department of Biochemistry and University of Vermont Cancer Center, The University of Vermont Larner College of Medicine, Burlington, Vermont
| | - Nitasha Sehgal
- Department of Biological Sciences, University at Buffalo, Buffalo, New York
| | - Artem Pliss
- Institute for Lasers, Photonics and Biophotonics and the Department of Chemistry, University at Buffalo, Buffalo, New York
| | - Jinhui Xu
- Department of Computer Science and Engineering, University at Buffalo, Buffalo, New York
| | - Ronald Berezney
- Department of Biological Sciences, University at Buffalo, Buffalo, New York
| |
Collapse
|
16
|
Understanding Chromatin Structure: Efficient Computational Implementation of Polymer Physics Models. LECTURE NOTES IN COMPUTER SCIENCE 2019. [DOI: 10.1007/978-3-030-10549-5_53] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
|
17
|
Abstract
Organisms display astonishing levels of cell and molecular diversity, including genome size, shape, and architecture. In this chapter, we review how the genome can be viewed as both a structural and an informational unit of biological diversity and explicitly define our intended meaning of genetic information. A brief overview of the characteristic features of bacterial, archaeal, and eukaryotic cell types and viruses sets the stage for a review of the differences in organization, size, and packaging strategies of their genomes. We include a detailed review of genetic elements found outside the primary chromosomal structures, as these provide insights into how genomes are sometimes viewed as incomplete informational entities. Lastly, we reassess the definition of the genome in light of recent advancements in our understanding of the diversity of genomic structures and the mechanisms by which genetic information is expressed within the cell. Collectively, these topics comprise a good introduction to genome biology for the newcomer to the field and provide a valuable reference for those developing new statistical or computation methods in genomics. This review also prepares the reader for anticipated transformations in thinking as the field of genome biology progresses.
Collapse
|
18
|
Osmanović D. Properties of Rouse polymers with actively driven regions. J Chem Phys 2018; 149:164911. [DOI: 10.1063/1.5045686] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Dino Osmanović
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| |
Collapse
|
19
|
Abstract
This article sets the stage for a genealogy of the postgenomic body. It starts with the current transformative views of epigenetics and microbiomics to offer a more pluralistic history in which the ethical problem of how to live with a permeable body - that is plasticity as a form of life - is pervasive in traditions pre-dating and coexisting with modern biomedicine (particularly humoralism in its several ramifications). To challenge universalizing narratives, I draw on genealogical method to illuminate the unequal distribution of plasticity across gender and ethnic groups. Finally, after analysing postgenomics as a different thought-style to genomics, I outline some of its implications for notions of plasticity. I argue that postgenomic plasticity is neither a modernistic plasticity of instrumental control of the body nor a postmodernist celebration of endless potentialities. It is instead closer to an alter-modernistic view that disrupts clear boundaries between openness and determination, individual and community.
Collapse
|
20
|
Erdel F, Rippe K. Formation of Chromatin Subcompartments by Phase Separation. Biophys J 2018; 114:2262-2270. [PMID: 29628210 DOI: 10.1016/j.bpj.2018.03.011] [Citation(s) in RCA: 234] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 02/19/2018] [Accepted: 03/06/2018] [Indexed: 10/17/2022] Open
Abstract
Chromatin is partitioned on multiple length scales into subcompartments that differ from each other with respect to their molecular composition and biological function. It is a key question how these compartments can form even though diffusion constantly mixes the nuclear interior and rapidly balances concentration gradients of soluble nuclear components. Different biophysical concepts are currently used to explain the formation of "chromatin bodies" in a self-organizing manner and without consuming energy. They rationalize how soluble protein factors that are dissolved in the liquid nuclear phase, the nucleoplasm, bind and organize transcriptionally active or silenced chromatin domains. In addition to cooperative binding of proteins to a preformed chromatin structure, two different mechanisms for the formation of phase-separated chromatin subcompartments have been proposed. One is based on bridging proteins that cross-link polymer segments with particular properties. Bridging can induce a collapse of the nucleosome chain and associated factors into an ordered globular phase. The other mechanism is based on multivalent interactions among soluble molecules that bind to chromatin. These interactions can induce liquid-liquid phase separation, which drives the assembly of liquid-like nuclear bodies around the respective binding sites on chromatin. Both phase separation mechanisms can explain that chromatin bodies are dynamic spherical structures, which can coalesce and are in constant and rapid exchange with the surrounding nucleoplasm. However, they make distinct predictions about how the size, density, and stability of chromatin bodies depends on the concentration and interaction behavior of the molecules involved. Here, we compare the different biophysical mechanisms for the assembly of chromatin bodies and discuss experimental strategies to distinguish them from each other. Furthermore, we outline the implications for the establishment and memory of functional chromatin state patterns.
Collapse
Affiliation(s)
- Fabian Erdel
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany.
| | - Karsten Rippe
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany.
| |
Collapse
|
21
|
Abstract
In recent years interest has grown on the applications of polymer physics to model chromatin folding in order to try to make sense of the complexity of experimental data emerging from new technologies such as Hi-C or GAM, in a principled way. Here we review the methods employed to efficiently implement Molecular Dynamics computer simulations of polymer models, focusing in particular on the String&Binders Switch (SBS) model. The constant improvement of such methods and computer power is returning increasingly more accurate insights on the structure and molecular mechanisms underlying the spatial organization of chromosomes in the cell nucleus. We aim to provide an account of the state of the art of computational techniques employed in this type of investigations and to review recent applications of such methods to the description of real genomic loci, such as the Sox9 locus in mESC.
Collapse
|
22
|
Ou HD, Phan S, Deerinck TJ, Thor A, Ellisman MH, O'Shea CC. ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells. Science 2018; 357:357/6349/eaag0025. [PMID: 28751582 DOI: 10.1126/science.aag0025] [Citation(s) in RCA: 505] [Impact Index Per Article: 84.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 01/11/2017] [Accepted: 06/08/2017] [Indexed: 12/30/2022]
Abstract
The chromatin structure of DNA determines genome compaction and activity in the nucleus. On the basis of in vitro structures and electron microscopy (EM) studies, the hierarchical model is that 11-nanometer DNA-nucleosome polymers fold into 30- and subsequently into 120- and 300- to 700-nanometer fibers and mitotic chromosomes. To visualize chromatin in situ, we identified a fluorescent dye that stains DNA with an osmiophilic polymer and selectively enhances its contrast in EM. Using ChromEMT (ChromEM tomography), we reveal the ultrastructure and three-dimensional (3D) organization of individual chromatin polymers, megabase domains, and mitotic chromosomes. We show that chromatin is a disordered 5- to 24-nanometer-diameter curvilinear chain that is packed together at different 3D concentration distributions in interphase and mitosis. Chromatin chains have many different particle arrangements and bend at various lengths to achieve structural compaction and high packing densities.
Collapse
Affiliation(s)
- Horng D Ou
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Sébastien Phan
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Thomas J Deerinck
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Andrea Thor
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Mark H Ellisman
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.,Department of Neurosciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Clodagh C O'Shea
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
| |
Collapse
|
23
|
Sugawara T, Kimura A. Physical properties of the chromosomes and implications for development. Dev Growth Differ 2017; 59:405-414. [PMID: 28573677 DOI: 10.1111/dgd.12363] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 04/13/2017] [Accepted: 04/13/2017] [Indexed: 01/15/2023]
Abstract
Remarkable progress has been made in understanding chromosome structures inside the cell nucleus. Recent advances in Hi-C technologies enable the detection of genome-wide chromatin interactions, providing insight into three-dimensional (3D) genome organization. Advancements in the spatial and temporal resolutions of imaging as well as in molecular biological techniques allow the tracking of specific chromosomal loci, improving our understanding of chromosome movements. From these data, we are beginning to understand how the intra-nuclear locations of chromatin loci and the 3D genome structure change during development and differentiation. This emerging field of genome structure and dynamics research requires an interdisciplinary approach including efficient collaborations between experimental biologists and physicists, informaticians, or engineers. Quantitative and mathematical analyses based on polymer physics are becoming increasingly important for processing and interpreting experimental data on 3D chromosome structures and dynamics. In this review, we aim to provide an overview of recent research on the physical aspects of chromosome structure and dynamics oriented for biologists. These studies have mainly focused on chromosomes at the cellular level, using unicellular organisms and cultured cells. However, physical parameters that change during development, such as nuclear size, may impact genome structure and dynamics. Here, we discuss how chromatin dynamics and genome structures in early embryos change during development, which we expect will be a hot topic in the field of chromatin dynamics in the near future. We hope this review helps developmental biologists to quantitatively investigate the physical natures of chromosomes in developmental biology research.
Collapse
Affiliation(s)
- Takeshi Sugawara
- Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD), Hiroshima University, Higashi-Hiroshima, 739-8530, Japan.,Cell Architecture Laboratory, Structural Biology Center, National Institute of Genetics, Mishima, 411-8540, Japan
| | - Akatsuki Kimura
- Cell Architecture Laboratory, Structural Biology Center, National Institute of Genetics, Mishima, 411-8540, Japan.,Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (Sokendai), Mishima, 411-8540, Japan
| |
Collapse
|
24
|
Bascom GD, Kim T, Schlick T. Kilobase Pair Chromatin Fiber Contacts Promoted by Living-System-Like DNA Linker Length Distributions and Nucleosome Depletion. J Phys Chem B 2017; 121:3882-3894. [PMID: 28299939 DOI: 10.1021/acs.jpcb.7b00998] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Nucleosome placement, or DNA linker length patterns, are believed to yield specific spatial features in chromatin fibers, but details are unknown. Here we examine by mesoscale modeling how kilobase (kb) range contacts and fiber looping depend on linker lengths ranging from 18 to 45 bp, with values modeled after living systems, including nucleosome free regions (NFRs) and gene encoding segments. We also compare artificial constructs with alternating versus randomly distributed linker lengths in the range of 18-72 bp. We show that nonuniform distributions with NFRs enhance flexibility and encourage kb-range contacts. NFRs between neighboring gene segments diminish short-range contacts between flanking nucleosomes, while enhancing kb-range contacts via hierarchical looping. We also demonstrate that variances in linker lengths enhance such contacts. In particular, moderate sized variations in fiber linker lengths (∼27 bp) encourage long-range contacts in randomly distributed linker length fibers. Our work underscores the importance of linker length patterns, alongside bound proteins, in biological regulation. Contacts formed by kb-range chromatin folding are crucial to gene activity. Because we find that special linker length distributions in living systems promote kb contacts, our work suggests ways to manipulate these patterns for regulation of gene activity.
Collapse
Affiliation(s)
- Gavin D Bascom
- Department of Chemistry, New York University , 100 Washington Square E, New York, New York 10003, United States
| | - Taejin Kim
- Department of Chemistry, New York University , 100 Washington Square E, New York, New York 10003, United States
| | - Tamar Schlick
- Department of Chemistry, New York University , 100 Washington Square E, New York, New York 10003, United States.,Courant Institute of Mathematical Sciences, New York University , 251 Mercer St, New York, New York 10012, United States.,New York University-East China Normal University Center for Computational Chemistry at New York University Shanghai , Room 340, Geography Building, North Zhongshan Road, 3663 Shanghai, China
| |
Collapse
|
25
|
Bascom G, Schlick T. Linking Chromatin Fibers to Gene Folding by Hierarchical Looping. Biophys J 2017; 112:434-445. [PMID: 28153411 DOI: 10.1016/j.bpj.2017.01.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 01/05/2017] [Accepted: 01/06/2017] [Indexed: 12/16/2022] Open
Abstract
While much is known about DNA structure on the basepair level, this scale represents only a fraction of the structural levels involved in folding the genomic material. With recent advances in experimental and theoretical techniques, a variety of structures have been observed on the fiber, gene, and chromosome levels of genome organization. Here we view chromatin architecture from nucleosomes and fibers to genes and chromosomes, highlighting the rich structural diversity and fiber fluidity emerging from both experimental and theoretical techniques. In this context, we discuss our recently proposed folding mechanism, which we call "hierarchical looping", similar to rope flaking used in mountain climbing, where 10-nm zigzag chromatin fibers are compacted laterally into self-associating loops which then stack and fold in space. We propose that hierarchical looping may act as a bridge between fibers and genes as well as provide a mechanism to relate key features of interphase and metaphase chromosome architecture to genome structural changes. This motif emerged by analysis of ultrastructural internucleosome contact data by electron microscopy-assisted nucleosome interaction capture cross-linking experiments, in combination with mesoscale modeling. We suggest that while the local folding of chromatin can be regulated at the fiber level by adjustment of internal factors such as linker-histone binding affinities, linker DNA lengths, and divalent ion levels, hierarchical looping on the gene level can additionally be controlled by posttranslational modifications and external factors such as polycomb group proteins. From a combination of 3C data and mesoscale modeling, we suggest that hierarchical looping could also play a role in epigenetic gene silencing, as stacked loops may occlude access to transcription start sites. With advances in crystallography, single-molecule in vitro biochemistry, in vivo imaging techniques, and genome-wide contact data experiments, various modeling approaches are allowing for previously unavailable structural interpretation of these data at multiple spatial and temporal scales. An unprecedented level of productivity and opportunity is on the horizon for the chromatin structure field.
Collapse
Affiliation(s)
- Gavin Bascom
- Department of Chemistry, New York University, New York, New York
| | - 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.
| |
Collapse
|
26
|
Computational inference of physical spatial organization of eukaryotic genomes. QUANTITATIVE BIOLOGY 2016. [DOI: 10.1007/s40484-016-0082-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
27
|
Annunziatella C, Chiariello AM, Bianco S, Nicodemi M. Polymer models of the hierarchical folding of the Hox-B chromosomal locus. Phys Rev E 2016; 94:042402. [PMID: 27841585 DOI: 10.1103/physreve.94.042402] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Indexed: 06/06/2023]
Abstract
As revealed by novel technologies, chromosomes in the nucleus of mammalian cells have a complex spatial organization that serves vital functional purposes. Here we use models from polymer physics to identify the mechanisms that control their three-dimensional spatial organization. In particular, we investigate a model of the Hox-B locus, an important genomic region involved in embryo development, to expose the principles regulating chromatin folding and its complex behaviors in mouse embryonic stem cells. We reconstruct with high accuracy the pairwise contact matrix of the Hox-B locus as derived by Hi-C experiments and investigate its hierarchical folding dynamics. We trace back the observed behaviors to general scaling properties of polymer physics.
Collapse
Affiliation(s)
- Carlo Annunziatella
- Dipartimento di Fisica, Universitá di Napoli Federico II, INFN Napoli, CNR, SPIN, Complesso Universitario di Monte Sant'Angelo, 80126 Naples, Italy
| | - Andrea M Chiariello
- Dipartimento di Fisica, Universitá di Napoli Federico II, INFN Napoli, CNR, SPIN, Complesso Universitario di Monte Sant'Angelo, 80126 Naples, Italy
| | - Simona Bianco
- Dipartimento di Fisica, Universitá di Napoli Federico II, INFN Napoli, CNR, SPIN, Complesso Universitario di Monte Sant'Angelo, 80126 Naples, Italy
| | - Mario Nicodemi
- Dipartimento di Fisica, Universitá di Napoli Federico II, INFN Napoli, CNR, SPIN, Complesso Universitario di Monte Sant'Angelo, 80126 Naples, Italy
| |
Collapse
|
28
|
Dickerson D, Gierliński M, Singh V, Kitamura E, Ball G, Tanaka TU, Owen-Hughes T. High resolution imaging reveals heterogeneity in chromatin states between cells that is not inherited through cell division. BMC Cell Biol 2016; 17:33. [PMID: 27609610 PMCID: PMC5016949 DOI: 10.1186/s12860-016-0111-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 08/25/2016] [Indexed: 01/23/2023] Open
Abstract
Background Genomes of eukaryotes exist as chromatin, and it is known that different chromatin states can influence gene regulation. Chromatin is not a static structure, but is known to be dynamic and vary between cells. In order to monitor the organisation of chromatin in live cells we have engineered fluorescent fusion proteins which recognize specific operator sequences to tag pairs of syntenic gene loci. The separation of these loci was then tracked in three dimensions over time using fluorescence microscopy. Results We established a work flow for measuring the distance between two fluorescently tagged, syntenic gene loci with a mean measurement error of 63 nm. In general, physical separation was observed to increase with increasing genomic separations. However, the extent to which chromatin is compressed varies for different genomic regions. No correlation was observed between compaction and the distribution of chromatin markers from genomic datasets or with contacts identified using capture based approaches. Variation in spatial separation was also observed within cells over time and between cells. Differences in the conformation of individual loci can persist for minutes in individual cells. Separation of reporter loci was found to be similar in related and unrelated daughter cell pairs. Conclusions The directly observed physical separation of reporter loci in live cells is highly dynamic both over time and from cell to cell. However, consistent differences in separation are observed over some chromosomal regions that do not correlate with factors known to influence chromatin states. We conclude that as yet unidentified parameters influence chromatin configuration. We also find that while heterogeneity in chromatin states can be maintained for minutes between cells, it is not inherited through cell division. This may contribute to cell-to-cell transcriptional heterogeneity. Electronic supplementary material The online version of this article (doi:10.1186/s12860-016-0111-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- David Dickerson
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Marek Gierliński
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Vijender Singh
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Etsushi Kitamura
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Graeme Ball
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Tomoyuki U Tanaka
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Tom Owen-Hughes
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK. .,Wellcome Trust Building, University of Dundee, Dow Street, Dundee, DD1 5EH, UK.
| |
Collapse
|
29
|
Relationship between spatial organization and biological function, analyzed using gene ontology and chromosome conformation capture of human and fission yeast genomes. Genes Genomics 2016. [DOI: 10.1007/s13258-016-0413-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
30
|
Bascom GD, Sanbonmatsu KY, Schlick T. Mesoscale Modeling Reveals Hierarchical Looping of Chromatin Fibers Near Gene Regulatory Elements. J Phys Chem B 2016; 120:8642-53. [PMID: 27218881 DOI: 10.1021/acs.jpcb.6b03197] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
While it is well-recognized that chromatin loops play an important role in gene regulation, structural details regarding higher order chromatin loops are only emerging. Here we present a systematic study of restrained chromatin loops ranging from 25 to 427 nucleosomes (fibers of 5-80 Kb DNA in length), mimicking gene elements studied by 3C contact data. We find that hierarchical looping represents a stable configuration that can effectively bring distant regions of the GATA-4 gene together, satisfying connections reported by 3C experiments. Additionally, we find that restrained chromatin fibers larger than 100 nucleosomes (∼20Kb) form closed plectonemes, whereas fibers shorter than 100 nucleosomes form simple hairpin loops. By studying the dependence of loop structures on internal parameters, we show that loop features are sensitive to linker histone concentration, loop length, divalent ions, and DNA linker length. Specifically, increasing loop length, linker histone concentration, and divalent ion concentration are associated with increased persistence length (or decreased bending), while varying DNA linker length in a manner similar to experimentally observed "nucleosome free regions" (found near transcription start sites) disrupts intertwining and leads to loop opening and increased persistence length in linker histone depleted (-LH) fibers. Chromatin fiber structure sensitivity to these parameters, all of which vary throughout the cell cycle, tissue type, and species, suggests that caution is warranted when using uniform polymer models to fit chromatin conformation capture genome-wide data. Furthermore, the folding geometry we observe near the transcription initiation site of the GATA-4 gene suggests that hierarchical looping provides a structural mechanism for gene inhibition, and offers tunable parameters for design of gene regulation elements.
Collapse
Affiliation(s)
- Gavin D Bascom
- Department of Chemistry, New York University , 100 Washington Square East, New York, New York 10003, United States
| | - Karissa Y Sanbonmatsu
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory , Bikini Atoll Road, SM 30, Los Alamos, New Mexico 87545, United States
| | - Tamar Schlick
- Department of Chemistry, New York University , 100 Washington Square East, New York, New York 10003, United States.,Courant Institute of Mathematical Sciences, New York University , 251 Mercer Street, New York, New York 10012, United States
| |
Collapse
|
31
|
Engel KL, Mackiewicz M, Hardigan AA, Myers RM, Savic D. Decoding transcriptional enhancers: Evolving from annotation to functional interpretation. Semin Cell Dev Biol 2016; 57:40-50. [PMID: 27224938 DOI: 10.1016/j.semcdb.2016.05.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 05/06/2016] [Accepted: 05/18/2016] [Indexed: 12/18/2022]
Abstract
Deciphering the intricate molecular processes that orchestrate the spatial and temporal regulation of genes has become an increasingly major focus of biological research. The differential expression of genes by diverse cell types with a common genome is a hallmark of complex cellular functions, as well as the basis for multicellular life. Importantly, a more coherent understanding of gene regulation is critical for defining developmental processes, evolutionary principles and disease etiologies. Here we present our current understanding of gene regulation by focusing on the role of enhancer elements in these complex processes. Although functional genomic methods have provided considerable advances to our understanding of gene regulation, these assays, which are usually performed on a genome-wide scale, typically provide correlative observations that lack functional interpretation. Recent innovations in genome editing technologies have placed gene regulatory studies at an exciting crossroads, as systematic, functional evaluation of enhancers and other transcriptional regulatory elements can now be performed in a coordinated, high-throughput manner across the entire genome. This review provides insights on transcriptional enhancer function, their role in development and disease, and catalogues experimental tools commonly used to study these elements. Additionally, we discuss the crucial role of novel techniques in deciphering the complex gene regulatory landscape and how these studies will shape future research.
Collapse
Affiliation(s)
- Krysta L Engel
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, United States
| | - Mark Mackiewicz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, United States
| | - Andrew A Hardigan
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, United States; Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, United States
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, United States
| | - Daniel Savic
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, United States.
| |
Collapse
|
32
|
Dietschreit JCB, Diestler DJ, Knapp EW. Chemically Realistic Tetrahedral Lattice Models for Polymer Chains: Application to Polyethylene Oxide. J Chem Theory Comput 2016; 12:2388-400. [DOI: 10.1021/acs.jctc.6b00144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Johannes C. B. Dietschreit
- Department
of Biology, Chemistry and Pharmacy, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Fabeckstrasse 36A, D-14195 Berlin, Germany
| | - Dennis J. Diestler
- Department
of Biology, Chemistry and Pharmacy, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Fabeckstrasse 36A, D-14195 Berlin, Germany
- University of Nebraska-Lincoln, Lincoln, Nebraska 68583, United States
| | - Ernst W. Knapp
- Department
of Biology, Chemistry and Pharmacy, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Fabeckstrasse 36A, D-14195 Berlin, Germany
| |
Collapse
|
33
|
Kinney NA, Onufriev AV, Sharakhov IV. Quantified effects of chromosome-nuclear envelope attachments on 3D organization of chromosomes. Nucleus 2016; 6:212-24. [PMID: 26068134 DOI: 10.1080/19491034.2015.1056441] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
We use a combined experimental and computational approach to study the effects of chromosome-nuclear envelope (Chr-NE) attachments on the 3D genome organization of Drosophila melanogaster (fruit fly) salivary gland nuclei. We consider 3 distinct models: a Null model - without specific Chr-NE attachments, a 15-attachment model - with 15 previously known Chr-NE attachments, and a 48-attachment model - with 15 original and 33 recently identified Chr-NE attachments. The radial densities of chromosomes in the models are compared to the densities observed in 100 experimental images of optically sectioned salivary gland nuclei forming "z-stacks." Most of the experimental z-stacks support the Chr-NE 48-attachment model suggesting that as many as 48 chromosome loci with appreciable affinity for the NE are necessary to reproduce the experimentally observed distribution of chromosome density in fruit fly nuclei. Next, we investigate if and how the presence and the number of Chr-NE attachments affect several key characteristics of 3D genome organization: chromosome territories and gene-gene contacts. This analysis leads to novel insight about the possible role of Chr-NE attachments in regulating the genome architecture. Specifically, we find that model nuclei with more numerous Chr-NE attachments form more distinct chromosome territories and their chromosomes intertwine less frequently. Intra-chromosome and intra-arm contacts are more common in model nuclei with Chr-NE attachments compared to the Null model (no specific attachments), while inter-chromosome and inter-arm contacts are less common in nuclei with Chr-NE attachments. We demonstrate that Chr-NE attachments increase the specificity of long-range inter-chromosome and inter-arm contacts. The predicted effects of Chr-NE attachments are rationalized by intuitive volume vs. surface accessibility arguments.
Collapse
Affiliation(s)
- Nicholas Allen Kinney
- a Genomics Bioinformatics and Computational Biology; Virginia Tech ; Blacksburg , VA , USA
| | | | | |
Collapse
|
34
|
Sehgal N, Fritz AJ, Vecerova J, Ding H, Chen Z, Stojkovic B, Bhattacharya S, Xu J, Berezney R. Large-scale probabilistic 3D organization of human chromosome territories. Hum Mol Genet 2016; 25:419-36. [PMID: 26604142 PMCID: PMC4731017 DOI: 10.1093/hmg/ddv479] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Revised: 11/07/2015] [Accepted: 11/16/2015] [Indexed: 01/13/2023] Open
Abstract
There is growing evidence that chromosome territories (CT) have a probabilistic non-random arrangement within the cell nucleus of mammalian cells including radial positioning and preferred patterns of interchromosomal interactions that are cell-type specific. While it is generally assumed that the three-dimensional (3D) arrangement of genes within the CT is linked to genomic regulation, the degree of non-random organization of individual CT remains unclear. As a first step to elucidating the global 3D organization (topology) of individual CT, we performed multi-color fluorescence in situ hybridization using six probes extending across each chromosome in human WI38 lung fibroblasts. Six CT were selected ranging in size and gene density (1, 4, 12, 17, 18 and X). In-house computational geometric algorithms were applied to measure the 3D distances between every combination of probes and to elucidate data-mined structural patterns. Our findings demonstrate a high degree of non-random arrangement of individual CT that vary from chromosome to chromosome and display distinct changes during the cell cycle. Application of a classic, well-defined data mining and pattern recognition approach termed the 'k-means' generated 3D models for the best fit arrangement of each chromosome. These predicted models correlated well with the detailed distance measurements and analysis. We propose that the unique 3D topology of each CT and characteristic changes during the cell cycle provide the structural framework for the global gene expression programs of the individual chromosomes.
Collapse
Affiliation(s)
| | | | | | - Hu Ding
- Department of Computer Science and Engineering, University at Buffalo, State University of New York, Buffalo, NY 14260, USA and
| | - Zihe Chen
- Department of Computer Science and Engineering, University at Buffalo, State University of New York, Buffalo, NY 14260, USA and
| | - Branislav Stojkovic
- Department of Computer Science and Engineering, University at Buffalo, State University of New York, Buffalo, NY 14260, USA and
| | - Sambit Bhattacharya
- Department of Mathematics and Computer Sciences, Fayetteville State University, Fayetteville, NC 28301, USA
| | - Jinhui Xu
- Department of Computer Science and Engineering, University at Buffalo, State University of New York, Buffalo, NY 14260, USA and
| | | |
Collapse
|
35
|
Bianco S, Chiariello AM, Annunziatella C, Esposito A, Nicodemi M. Polymer Physics of the Large-Scale Structure of Chromatin. Methods Mol Biol 2016; 1480:201-206. [PMID: 27659986 DOI: 10.1007/978-1-4939-6380-5_17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We summarize the picture emerging from recently proposed models of polymer physics describing the general features of chromatin large scale spatial architecture, as revealed by microscopy and Hi-C experiments.
Collapse
Affiliation(s)
- Simona Bianco
- Dipartimento di Fisica, Università di Napoli Federico II, INFN, SPIN-CNR, Complesso Universitario di Monte S.Angelo, via Cintia, Naples, 80126, Italy
| | - Andrea Maria Chiariello
- Dipartimento di Fisica, Università di Napoli Federico II, INFN, SPIN-CNR, Complesso Universitario di Monte S.Angelo, via Cintia, Naples, 80126, Italy
| | - Carlo Annunziatella
- Dipartimento di Fisica, Università di Napoli Federico II, INFN, SPIN-CNR, Complesso Universitario di Monte S.Angelo, via Cintia, Naples, 80126, Italy
| | - Andrea Esposito
- Dipartimento di Fisica, Università di Napoli Federico II, INFN, SPIN-CNR, Complesso Universitario di Monte S.Angelo, via Cintia, Naples, 80126, Italy
| | - Mario Nicodemi
- Dipartimento di Fisica, Università di Napoli Federico II, INFN, SPIN-CNR, Complesso Universitario di Monte S.Angelo, via Cintia, Naples, 80126, Italy.
| |
Collapse
|
36
|
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
| |
Collapse
|
37
|
Liang Y, Yang G, Liu F, Wang Y. Monte Carlo simulation of ionizing radiation induced DNA strand breaks utilizing coarse grained high-order chromatin structures. Phys Med Biol 2015; 61:445-60. [DOI: 10.1088/0031-9155/61/1/445] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
38
|
Ortega-Esteban A, Condezo GN, Pérez-Berná AJ, Chillón M, Flint SJ, Reguera D, San Martín C, de Pablo PJ. Mechanics of Viral Chromatin Reveals the Pressurization of Human Adenovirus. ACS NANO 2015; 9:10826-33. [PMID: 26491879 DOI: 10.1021/acsnano.5b03417] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Tight confinement of naked genomes within some viruses results in high internal pressure that facilitates their translocation into the host. Adenovirus, however, encodes histone-like proteins that associate with its genome resulting in a confined DNA-protein condensate (core). Cleavage of these proteins during maturation decreases core condensation and primes the virion for proper uncoating via unidentified mechanisms. Here we open individual, mature and immature adenovirus cages to directly probe the mechanics of their chromatin-like cores. We find that immature cores are more rigid than the mature ones, unveiling a mechanical signature of their condensation level. Conversely, intact mature particles demonstrate more rigidity than immature or empty ones. DNA-condensing polyamines revert the mechanics of mature capsid and cores to near-immature values. The combination of these experiments reveals the pressurization of adenovirus particles induced by maturation. We estimate a pressure of ∼30 atm by continuous elasticity, which is corroborated by modeling the adenovirus mini-chromosome as a confined compact polymer. We propose this pressurization as a mechanism that facilitates initiating the stepwise disassembly of the mature particle, enabling its escape from the endosome and final genome release at the nuclear pore.
Collapse
Affiliation(s)
| | - Gabriela N Condezo
- Department of Macromolecular Structures and NanoBioMedicine Initiative, Centro Nacional de Biotecnología (CNB-CIC) , Darwin 3, 28049 Madrid, Spain
| | - Ana J Pérez-Berná
- Department of Macromolecular Structures and NanoBioMedicine Initiative, Centro Nacional de Biotecnología (CNB-CIC) , Darwin 3, 28049 Madrid, Spain
| | - Miguel Chillón
- Institut Català de Recerca i Estudis Avançats (ICREA), CBATEG-Department of Biochemistry and Molecular Biology, Universitat Autonoma Barcelona , Bellaterra Barcelona, 08010, Spain
| | - S Jane Flint
- Department of Molecular Biology, Princeton University , Princeton, New Jersey 08544, United States
| | - David Reguera
- Departament de Física Fonamental, Facultat de Física, Universitat de Barcelona , Martí i Franqués 1, 08028 Barcelona, Spain
| | - Carmen San Martín
- Department of Macromolecular Structures and NanoBioMedicine Initiative, Centro Nacional de Biotecnología (CNB-CIC) , Darwin 3, 28049 Madrid, Spain
| | | |
Collapse
|
39
|
Pombo A, Nicodemi M. Physical mechanisms behind the large scale features of chromatin organization. Transcription 2015; 5:e28447. [PMID: 25764220 DOI: 10.4161/trns.28447] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
We review the picture emerging from recently published models of classical polymer physics of the general features of chromatin large scale spatial organization, as revealed by microscopy and Hi-C data.
Collapse
Affiliation(s)
- Ana Pombo
- a Berlin Institute for Medical Systems Biology; Max Delbrück Center for Molecular Medicine; Berlin-Buch, Germany
| | | |
Collapse
|
40
|
Caudai C, Salerno E, Zoppè M, Tonazzini A. Inferring 3D chromatin structure using a multiscale approach based on quaternions. BMC Bioinformatics 2015. [PMID: 26220581 PMCID: PMC4518643 DOI: 10.1186/s12859-015-0667-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Background The knowledge of the spatial organisation of the chromatin fibre in cell nuclei helps researchers to understand the nuclear machinery that regulates dna activity. Recent experimental techniques of the type Chromosome Conformation Capture (3c, or similar) provide high-resolution, high-throughput data consisting in the number of times any possible pair of dna fragments is found to be in contact, in a certain population of cells. As these data carry information on the structure of the chromatin fibre, several attempts have been made to use them to obtain high-resolution 3d reconstructions of entire chromosomes, or even an entire genome. The techniques proposed treat the data in different ways, possibly exploiting physical-geometric chromatin models. One popular strategy is to transform contact data into Euclidean distances between pairs of fragments, and then solve a classical distance-to-geometry problem. Results We developed and tested a reconstruction technique that does not require translating contacts into distances, thus avoiding a number of related drawbacks. Also, we introduce a geometrical chromatin chain model that allows us to include sound biochemical and biological constraints in the problem. This model can be scaled at different genomic resolutions, where the structures of the coarser models are influenced by the reconstructions at finer resolutions. The search in the solution space is then performed by a classical simulated annealing, where the model is evolved efficiently through quaternion operators. The presence of appropriate constraints permits the less reliable data to be overlooked, so the result is a set of plausible chromatin configurations compatible with both the data and the prior knowledge. Conclusions To test our method, we obtained a number of 3d chromatin configurations from hi-c data available in the literature for the long arm of human chromosome 1, and validated their features against known properties of gene density and transcriptional activity. Our results are compatible with biological features not introduced a priori in the problem: structurally different regions in our reconstructions highly correlate with functionally different regions as known from literature and genomic repositories. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0667-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Claudia Caudai
- National Research Council of Italy, Institute of Information Science and Technologies, Via Moruzzi, 1, Pisa, 56124, Italy.
| | - Emanuele Salerno
- National Research Council of Italy, Institute of Information Science and Technologies, Via Moruzzi, 1, Pisa, 56124, Italy.
| | - Monica Zoppè
- National Research Council of Italy, Institute of Clinical Physiology, Via Moruzzi, 1, 56124, Pisa, Italy.
| | - Anna Tonazzini
- National Research Council of Italy, Institute of Information Science and Technologies, Via Moruzzi, 1, Pisa, 56124, Italy.
| |
Collapse
|
41
|
Ozer G, Luque A, Schlick T. The chromatin fiber: multiscale problems and approaches. Curr Opin Struct Biol 2015; 31:124-39. [PMID: 26057099 DOI: 10.1016/j.sbi.2015.04.002] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 04/08/2015] [Accepted: 04/09/2015] [Indexed: 12/20/2022]
Abstract
The structure of chromatin, affected by many factors from DNA linker lengths to posttranslational modifications, is crucial to the regulation of eukaryotic cells. Combined experimental and computational methods have led to new insights into its structural and dynamical features, from interactions due to the flexible core histone tails or linker histones to the physical mechanism driving the formation of chromosomal domains. Here we present a perspective of recent advances in chromatin modeling techniques at the atomic, mesoscopic, and chromosomal scales with a view toward developing multiscale computational strategies to integrate such findings. Innovative modeling methods that connect molecular to chromosomal scales are crucial for interpreting experiments and eventually deciphering the complex dynamic organization and function of chromatin in the cell.
Collapse
Affiliation(s)
- Gungor Ozer
- Department of Chemistry, 100 Washington Square East, New York University, New York, NY 10003, USA
| | - Antoni Luque
- Department of Chemistry, 100 Washington Square East, New York University, New York, NY 10003, USA; Current address: Department of Mathematics & Statistics and Viral Information Institute, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182-7720, USA
| | - Tamar Schlick
- Department of Chemistry, 100 Washington Square East, New York University, New York, NY 10003, USA; Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, NY 10012, USA; NYU-ECNU Center for Computational Chemistry at NYU Shanghai, 3663 Zhongshan Road North, Shanghai 200062, China.
| |
Collapse
|
42
|
Hofmann A, Heermann DW. The role of loops on the order of eukaryotes and prokaryotes. FEBS Lett 2015; 589:2958-65. [PMID: 25912650 DOI: 10.1016/j.febslet.2015.04.021] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 04/14/2015] [Accepted: 04/14/2015] [Indexed: 11/29/2022]
Abstract
The study of the three-dimensional organization of chromatin has recently gained much focus in the context of novel techniques for detecting genome-wide contacts using next-generation sequencing. These chromosome conformation capture-based methods give a deep topological insight into the architecture of the genome inside the nucleus. Several recent studies observe a compartmentalization of chromatin interactions into spatially confined domains. This structural feature of interphase chromosomes is not only supported by conventional studies assessing the interaction data of millions of cells, but also by analysis on the level of a single cell. We first present and examine the different models that have been proposed to elucidate these topological domains in eukaryotes. Then we show that a model which relies on the dynamic formation of loops within domains can account for the experimentally observed contact maps. Interestingly, the topological domain structure is not only found in mammalian genomes, but also in bacterial chromosomes.
Collapse
Affiliation(s)
- Andreas Hofmann
- Institute for Theoretical Physics, University of Heidelberg, Philosophenweg 19, 69120 Heidelberg, Germany.
| | - Dieter W Heermann
- Institute for Theoretical Physics, University of Heidelberg, Philosophenweg 19, 69120 Heidelberg, Germany; Institute for Molecular Biophysics, The Jackson Laboratory, Bar Harbor, ME, USA; Shanghai Institute of Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai, PR China; Shanghai Center for Bioinformation Technology (SCBIT), Shanghai, PR China
| |
Collapse
|
43
|
Gavrilov AA, Razin SV. Compartmentalization of the cell nucleus and spatial organization of the genome. Mol Biol 2015. [DOI: 10.1134/s0026893315010033] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
44
|
Helliwell CA, Anderssen RS, Robertson M, Finnegan EJ. How is FLC repression initiated by cold? TRENDS IN PLANT SCIENCE 2015; 20:76-82. [PMID: 25600480 DOI: 10.1016/j.tplants.2014.12.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 11/21/2014] [Accepted: 12/16/2014] [Indexed: 05/07/2023]
Abstract
Vernalization is the promotion of flowering in response to prolonged exposure to low temperatures. In Arabidopsis, FLOWERING LOCUS C (FLC), a suppressor of flowering, is repressed by low temperatures but the mechanism leading to the initial decrease in FLC transcription remains a mystery. No mutants that block the repression of FLC at low temperatures have been identified to date. If the failure to identify such a mutant is assumed to imply that no such mutant exists, then it follows that the first response to the drop in temperature is physical, not genetic. In this Opinion article we propose that the drop in temperature first causes a simple change in the topology of the chromatin polymer, which in turn initiates the repression of FLC transcription.
Collapse
Affiliation(s)
- Chris A Helliwell
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Agriculture, Canberra ACT, Australia
| | | | - Masumi Robertson
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Agriculture, Canberra ACT, Australia
| | - E Jean Finnegan
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Agriculture, Canberra ACT, Australia.
| |
Collapse
|
45
|
Georgieva M, Staneva D, Uzunova K, Efremov T, Balashev K, Harata M, Miloshev G. The linker histone in Saccharomyces cerevisiae interacts with actin-related protein 4 and both regulate chromatin structure and cellular morphology. Int J Biochem Cell Biol 2015; 59:182-92. [DOI: 10.1016/j.biocel.2014.12.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 12/15/2014] [Indexed: 11/28/2022]
|
46
|
Ulianov SV, Gavrilov AA, Razin SV. Nuclear Compartments, Genome Folding, and Enhancer-Promoter Communication. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2015; 315:183-244. [DOI: 10.1016/bs.ircmb.2014.11.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
47
|
Liu Z, Legant WR, Chen BC, Li L, Grimm JB, Lavis LD, Betzig E, Tjian R. 3D imaging of Sox2 enhancer clusters in embryonic stem cells. eLife 2014; 3:e04236. [PMID: 25537195 PMCID: PMC4381973 DOI: 10.7554/elife.04236] [Citation(s) in RCA: 163] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Accepted: 11/26/2014] [Indexed: 12/19/2022] Open
Abstract
Combinatorial cis-regulatory networks encoded in animal genomes represent the foundational gene expression mechanism for directing cell-fate commitment and maintenance of cell identity by transcription factors (TFs). However, the 3D spatial organization of cis-elements and how such sub-nuclear structures influence TF activity remain poorly understood. Here, we combine lattice light-sheet imaging, single-molecule tracking, numerical simulations, and ChIP-exo mapping to localize and functionally probe Sox2 enhancer-organization in living embryonic stem cells. Sox2 enhancers form 3D-clusters that are segregated from heterochromatin but overlap with a subset of Pol II enriched regions. Sox2 searches for specific binding targets via a 3D-diffusion dominant mode when shuttling long-distances between clusters while chromatin-bound states predominate within individual clusters. Thus, enhancer clustering may reduce global search efficiency but enables rapid local fine-tuning of TF search parameters. Our results suggest an integrated model linking cis-element 3D spatial distribution to local-versus-global target search modalities essential for regulating eukaryotic gene transcription.
Collapse
Affiliation(s)
- Zhe Liu
- Junior Fellow Program, Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, United States
| | - Wesley R Legant
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, United States
| | - Bi-Chang Chen
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, United States
| | - Li Li
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, United States
| | - Jonathan B Grimm
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, United States
| | - Luke D Lavis
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, United States
| | - Eric Betzig
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, United States
| | - Robert Tjian
- Transcription Imaging Consortium, Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, United States
| |
Collapse
|
48
|
Maffeo C, Yoo J, Comer J, Wells DB, Luan B, Aksimentiev A. Close encounters with DNA. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2014; 26:413101. [PMID: 25238560 PMCID: PMC4207370 DOI: 10.1088/0953-8984/26/41/413101] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Over the past ten years, the all-atom molecular dynamics method has grown in the scale of both systems and processes amenable to it and in its ability to make quantitative predictions about the behavior of experimental systems. The field of computational DNA research is no exception, witnessing a dramatic increase in the size of systems simulated with atomic resolution, the duration of individual simulations and the realism of the simulation outcomes. In this topical review, we describe the hallmark physical properties of DNA from the perspective of all-atom simulations. We demonstrate the amazing ability of such simulations to reveal the microscopic physical origins of experimentally observed phenomena. We also discuss the frustrating limitations associated with imperfections of present atomic force fields and inadequate sampling. The review is focused on the following four physical properties of DNA: effective electric charge, response to an external mechanical force, interaction with other DNA molecules and behavior in an external electric field.
Collapse
Affiliation(s)
- C Maffeo
- Department of Physics, University of Illinois, Urbana, IL, USA
| | | | | | | | | | | |
Collapse
|
49
|
Tark-Dame M, Jerabek H, Manders EMM, Heermann DW, van Driel R. Depletion of the chromatin looping proteins CTCF and cohesin causes chromatin compaction: insight into chromatin folding by polymer modelling. PLoS Comput Biol 2014; 10:e1003877. [PMID: 25299688 PMCID: PMC4191888 DOI: 10.1371/journal.pcbi.1003877] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 08/18/2014] [Indexed: 11/18/2022] Open
Abstract
Folding of the chromosomal fibre in interphase nuclei is an important element in the regulation of gene expression. For instance, physical contacts between promoters and enhancers are a key element in cell-type-specific transcription. We know remarkably little about the principles that control chromosome folding. Here we explore the view that intrachromosomal interactions, forming a complex pattern of loops, are a key element in chromosome folding. CTCF and cohesin are two abundant looping proteins of interphase chromosomes of higher eukaryotes. To investigate the role of looping in large-scale (supra Mb) folding of human chromosomes, we knocked down the gene that codes for CTCF and the one coding for Rad21, an essential subunit of cohesin. We measured the effect on chromosome folding using systematic 3D fluorescent in situ hybridization (FISH). Results show that chromatin becomes more compact after reducing the concentration of these two looping proteins. The molecular basis for this counter-intuitive behaviour is explored by polymer modelling usingy the Dynamic Loop model (Bohn M, Heermann DW (2010) Diffusion-driven looping provides a consistent framework for chromatin organization. PLoS ONE 5: e12218.). We show that compaction can be explained by selectively decreasing the number of short-range loops, leaving long-range looping unchanged. In support of this model prediction it has recently been shown by others that CTCF and cohesin indeed are responsible primarily for short-range looping. Our results suggest that the local and the overall changes in of chromosome structure are controlled by a delicate balance between short-range and long-range loops, allowing easy switching between, for instance, open and more compact chromatin states.
Collapse
Affiliation(s)
- Mariliis Tark-Dame
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Hansjoerg Jerabek
- Institute for Theoretical Physics, Heidelberg University, Heidelberg, Germany
| | - Erik M. M. Manders
- Van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Amsterdam, The Netherlands
- Department for Molecular Biotechnology, University of Gent, Gent, Belgium
| | - Dieter W. Heermann
- Institute for Theoretical Physics, Heidelberg University, Heidelberg, Germany
| | - Roel van Driel
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| |
Collapse
|
50
|
Abstract
Although it was originally believed that enhancers activate only the nearest promoter, recent global analyses enabled by high-throughput technology suggest that the network of enhancer-promoter interactions is far more complex. The mechanisms that determine the specificity of enhancer-promoter interactions are still poorly understood, but they are thought to include biochemical compatibility, constraints imposed by the three-dimensional architecture of chromosomes, insulator elements, and possibly the effects of local chromatin composition. In this review, we assess the current insights into these determinants, and highlight the functional genomic approaches that will lead the way towards better mechanistic understanding.
Collapse
|