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Natesan R, Gowrishankar K, Kuttippurathu L, Kumar PBS, Rao M. Active Remodeling of Chromatin and Implications for In Vivo Folding. J Phys Chem B 2021; 126:100-109. [DOI: 10.1021/acs.jpcb.1c08655] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ramakrishnan Natesan
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department of Physics, Indian Institute of Technology Madras, Chennai 600036, India
| | | | - Lakshmi Kuttippurathu
- Department of Physics, Indian Institute of Technology Madras, Chennai 600036, India
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, United States
| | - P. B. Sunil Kumar
- Department of Physics, Indian Institute of Technology Madras, Chennai 600036, India
- Department of Physics, Indian Institute of Technology Palakkad, Palakkad 668557, Kerala, India
| | - Madan Rao
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences (TIFR), Bengaluru 560065, India
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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.
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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
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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.
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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.
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Christian WV, Oliver LD, Paustenbach DJ, Kreider ML, Finley BL. Toxicology-based cancer causation analysis of CoCr-containing hip implants: a quantitative assessment of genotoxicity and tumorigenicity studies. J Appl Toxicol 2014; 34:939-67. [DOI: 10.1002/jat.3039] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 05/23/2014] [Accepted: 05/24/2014] [Indexed: 12/12/2022]
Affiliation(s)
| | - Lindsay D. Oliver
- Cardno ChemRisk; LLC, 4840 Pearl East Circle, Suite 300 West Boulder CO 80301 USA
| | | | - Marisa L. Kreider
- Cardno ChemRisk, LLC; 20 Stanwix St., Suite 505 Pittsburgh PA 15222 USA
| | - Brent L. Finley
- Cardno ChemRisk; LLC, 231 Front St., Suite 201 Brooklyn NY 11201 USA
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Yanao T, Yoshikawa K. Chiral symmetry breaking of a double-stranded helical chain through bend-writhe coupling. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 89:062713. [PMID: 25019820 DOI: 10.1103/physreve.89.062713] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Indexed: 06/03/2023]
Abstract
This paper explores asymmetric elasticity of a double-stranded helical chain, which serves as a minimal model of biopolymers. The model consists of two elastic chains that mutually intertwine in a right-handed manner, forming a double-stranded helix. A simple numerical experiment for structural relaxation, which reduces the total elastic energy of the model monotonically without thermal fluctuations, reveals possible asymmetric elasticity inherent in the helical chain. It is first shown that a short segment of the double-stranded helical chain has a tendency to unwind when it is bent. It is also shown that a short segment of the helical chain has a tendency to writhe in the left direction upon bending. This tendency gives rise to a propensity for a longer segment of the chain to form a left-handed superhelix spontaneously upon bending. Finally, this propensity of the helical chain to form a left-handed superhelix is proposed to be a possible origin of the uniform left-handed wrapping of DNA around nucleosome core particles in nature. The results presented here could provide deeper insights into the roles and significance of helical chirality of biopolymers.
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Affiliation(s)
- Tomohiro Yanao
- Department of Applied Mechanics and Aerospace Engineering, Waseda University, Tokyo 169-8555, Japan
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto 610-0394, Japan
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Bach C, Sherman W, Pallis J, Patra P, Bajwa H. Evaluation of novel design strategies for developing zinc finger nucleases tools for treating human diseases. BIOTECHNOLOGY RESEARCH INTERNATIONAL 2014; 2014:970595. [PMID: 24808958 PMCID: PMC3997970 DOI: 10.1155/2014/970595] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 01/02/2014] [Accepted: 01/02/2014] [Indexed: 11/24/2022]
Abstract
Zinc finger nucleases (ZFNs) are associated with cell death and apoptosis by binding at countless undesired locations. This cytotoxicity is associated with the binding ability of engineered zinc finger domains to bind dissimilar DNA sequences with high affinity. In general, binding preferences of transcription factors are associated with significant degenerated diversity and complexity which convolutes the design and engineering of precise DNA binding domains. Evolutionary success of natural zinc finger proteins, however, evinces that nature created specific evolutionary traits and strategies, such as modularity and rank-specific recognition to cope with binding complexity that are critical for creating clinical viable tools to precisely modify the human genome. Our findings indicate preservation of general modularity and significant alteration of the rank-specific binding preferences of the three-finger binding domain of transcription factor SP1 when exchanging amino acids in the 2nd finger.
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Affiliation(s)
- Christian Bach
- University of Bridgeport, Biomedical Engineering, 221 University Avenue, Bridgeport, CT 06604, USA
| | - William Sherman
- Physics Faculty, BHSEC Queens, 30-20 Thomson Avenue, Long Island City, NY 11101, USA
| | - Jani Pallis
- University of Bridgeport, Mechanical Engineering, 221 University Avenue, Bridgeport, CT 06604, USA
| | - Prabir Patra
- University of Bridgeport, Biomedical Engineering, 221 University Avenue, Bridgeport, CT 06604, USA
| | - Hassan Bajwa
- University of Bridgeport, Electrical Engineering, 221 University Avenue, Bridgeport, CT 06604, USA
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Lemieux JE, Kyes SA, Otto TD, Feller AI, Eastman RT, Pinches RA, Berriman M, Su XZ, Newbold CI. Genome-wide profiling of chromosome interactions in Plasmodium falciparum characterizes nuclear architecture and reconfigurations associated with antigenic variation. Mol Microbiol 2013; 90:519-37. [PMID: 23980881 PMCID: PMC3894959 DOI: 10.1111/mmi.12381] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/25/2013] [Indexed: 12/31/2022]
Abstract
Spatial relationships within the eukaryotic nucleus are essential for proper nuclear function. In Plasmodium falciparum, the repositioning of chromosomes has been implicated in the regulation of the expression of genes responsible for antigenic variation, and the formation of a single, peri-nuclear nucleolus results in the clustering of rDNA. Nevertheless, the precise spatial relationships between chromosomes remain poorly understood, because, until recently, techniques with sufficient resolution have been lacking. Here we have used chromosome conformation capture and second-generation sequencing to study changes in chromosome folding and spatial positioning that occur during switches in var gene expression. We have generated maps of chromosomal spatial affinities within the P. falciparum nucleus at 25 Kb resolution, revealing a structured nucleolus, an absence of chromosome territories, and confirming previously identified clustering of heterochromatin foci. We show that switches in var gene expression do not appear to involve interaction with a distant enhancer, but do result in local changes at the active locus. These maps reveal the folding properties of malaria chromosomes, validate known physical associations, and characterize the global landscape of spatial interactions. Collectively, our data provide critical information for a better understanding of gene expression regulation and antigenic variation in malaria parasites.
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Affiliation(s)
- Jacob E Lemieux
- Weatherall Institute of Molecular Medicine, Headington, Oxford, OX3 9DS, UK; National Institute of Allergy and Infectious Disease, NIH, Rockville, MD, 20892, USA
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Meluzzi D, Arya G. Recovering ensembles of chromatin conformations from contact probabilities. Nucleic Acids Res 2012; 41:63-75. [PMID: 23143266 PMCID: PMC3592477 DOI: 10.1093/nar/gks1029] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The 3D higher order organization of chromatin within the nucleus of eukaryotic cells has so far remained elusive. A wealth of relevant information, however, is increasingly becoming available from chromosome conformation capture (3C) and related experimental techniques, which measure the probabilities of contact between large numbers of genomic sites in fixed cells. Such contact probabilities (CPs) can in principle be used to deduce the 3D spatial organization of chromatin. Here, we propose a computational method to recover an ensemble of chromatin conformations consistent with a set of given CPs. Compared with existing alternatives, this method does not require conversion of CPs to mean spatial distances. Instead, we estimate CPs by simulating a physically realistic, bead-chain polymer model of the 30-nm chromatin fiber. We then use an approach from adaptive filter theory to iteratively adjust the parameters of this polymer model until the estimated CPs match the given CPs. We have validated this method against reference data sets obtained from simulations of test systems with up to 45 beads and 4 loops. With additional testing against experiments and with further algorithmic refinements, our approach could become a valuable tool for researchers examining the higher order organization of chromatin.
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Affiliation(s)
- Dario Meluzzi
- Department of NanoEngineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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Iyer BVS, Arya G. Lattice animal model of chromosome organization. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 86:011911. [PMID: 23005456 DOI: 10.1103/physreve.86.011911] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Indexed: 06/01/2023]
Abstract
Polymer models tied together by constraints of looping and confinement have been used to explain many of the observed organizational characteristics of interphase chromosomes. Here we introduce a simple lattice animal representation of interphase chromosomes that combines the features of looping and confinement constraints into a single framework. We show through Monte Carlo simulations that this model qualitatively captures both the leveling off in the spatial distance between genomic markers observed in fluorescent in situ hybridization experiments and the inverse decay in the looping probability as a function of genomic separation observed in chromosome conformation capture experiments. The model also suggests that the collapsed state of chromosomes and their segregation into territories with distinct looping activities might be a natural consequence of confinement.
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Affiliation(s)
- Balaji V S Iyer
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0448, USA
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Albert B, Léger-Silvestre I, Normand C, Gadal O. Nuclear organization and chromatin dynamics in yeast: biophysical models or biologically driven interactions? BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1819:468-81. [PMID: 22245105 DOI: 10.1016/j.bbagrm.2011.12.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Revised: 12/21/2011] [Accepted: 12/22/2011] [Indexed: 12/26/2022]
Abstract
Over the past decade, tremendous progress has been made in understanding the spatial organization of genes and chromosomes. Nuclear organization can be thought of as information that is not encoded in DNA, but which nevertheless impacts gene expression. Nuclear organizational influences can be cell-specific and are potentially heritable. Thus, nuclear organization fulfills all the criteria necessary for it to be considered an authentic level of epigenetic information. Chromosomal nuclear organization is primarily dictated by the biophysical properties of chromatin. Diffusion models of polymers confined in the crowded nuclear space accurately recapitulate experimental observation. Diffusion is a Brownian process, which implies that the positions of chromosomes and genes are not defined deterministically but are likely to be dictated by the laws of probability. Despite the small size of their nuclei, budding yeast have been instrumental in discovering how epigenetic information is encoded in the spatial organization of the genome. The relatively simple organization of the yeast nucleus and the very high number of genetically identical cells that can be observed under fluorescent microscopy allow statistically robust definitions of the gene and chromosome positions in the nuclear space to be constructed. In this review, we will focus on how the spatial organization of the chromatin in the yeast nucleus might impact transcription. This article is part of a Special Issue entitled: Nuclear Transport and RNA Processing.
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Bossen C, Mansson R, Murre C. Chromatin topology and the regulation of antigen receptor assembly. Annu Rev Immunol 2012; 30:337-56. [PMID: 22224771 DOI: 10.1146/annurev-immunol-020711-075003] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
During an organism's ontogeny and in the adult, each B and T lymphocyte generates a unique antigen receptor, thereby creating the organism's ability to respond to a vast number of different antigens. The antigen receptor loci are organized into distinct regions that contain multiple variable (V), diversity (D), and/or joining (J) and constant (C) coding elements that are scattered across large genomic regions. In this review, we discuss the epigenetic modifications that take place in the different antigen receptor loci, the chromatin structure adopted by the antigen receptor loci to allow recombination of elements separated by large genomic distances, and the relationship between epigenetics and chromatin structure and how they relate to the generation of antigen receptor diversity.
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Affiliation(s)
- Claudia Bossen
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, California 92093-0377, USA
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