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Abstract
Topologically associating domains (TADs) are megabase-sized building blocks of interphase chromosomes in higher eukaryotes. TADs are chromosomal regions with increased frequency of internal interactions. On average a pair of loci separated by a given genomic distance contact each other 2–3 times more frequently when they are in the same TAD as compared to a pair of loci located in two neighbouring TADs. TADs are also functional blocks of chromosomes as enhancers and their cognate promoters are normally located in the same TAD, even if their genomic distance from each other can be as large as a megabase. The internal structure of TADs, causing their increased frequency of internal interactions, is not established yet. We survey here experimental studies investigating presence of supercoiling in interphase chromosomes. We also review numerical simulation studies testing whether transcription-induced supercoiling of chromatin fibres can explain how TADs are formed and how they can assure very efficient interactions between enhancers and their cognate promoters located in the same TAD.
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Affiliation(s)
- Dusan Racko
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.,Polymer Institute of the Slovak Academy of Sciences, 842 36 Bratislava, Slovakia
| | - Fabrizio Benedetti
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.,Vital-IT, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Julien Dorier
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.,Vital-IT, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Andrzej Stasiak
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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2
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Racko D, Benedetti F, Goundaroulis D, Stasiak A. Chromatin Loop Extrusion and Chromatin Unknotting. Polymers (Basel) 2018; 10:E1126. [PMID: 30961051 PMCID: PMC6403842 DOI: 10.3390/polym10101126] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/03/2018] [Accepted: 10/08/2018] [Indexed: 12/31/2022] Open
Abstract
It has been a puzzle how decondensed interphase chromosomes remain essentially unknotted. The natural expectation is that in the presence of type II DNA topoisomerases that permit passages of double-stranded DNA regions through each other, all chromosomes should reach the state of topological equilibrium. The topological equilibrium in highly crowded interphase chromosomes forming chromosome territories would result in formation of highly knotted chromatin fibres. However, Chromosome Conformation Capture (3C) methods revealed that the decay of contact probabilities with the genomic distance in interphase chromosomes is practically the same as in the crumpled globule state that is formed when long polymers condense without formation of any knots. To remove knots from highly crowded chromatin, one would need an active process that should not only provide the energy to move the system from the state of topological equilibrium but also guide topoisomerase-mediated passages in such a way that knots would be efficiently unknotted instead of making the knots even more complex. We perform coarse-grained molecular dynamics simulations of the process of chromatin loop extrusion involving knotted and catenated chromatin fibres to check whether chromatin loop extrusion may be involved in active unknotting of chromatin fibres. Our simulations show that the process of chromatin loop extrusion is ideally suited to actively unknot, decatenate and demix chromatin fibres in interphase chromosomes.
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Affiliation(s)
- Dusan Racko
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
- Polymer Institute of the Slovak Academy of Sciences, 842 36 Bratislava, Slovakia.
| | - Fabrizio Benedetti
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
| | - Dimos Goundaroulis
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
| | - Andrzej Stasiak
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
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Racko D, Benedetti F, Dorier J, Stasiak A. Transcription-induced supercoiling as the driving force of chromatin loop extrusion during formation of TADs in interphase chromosomes. Nucleic Acids Res 2018; 46:1648-1660. [PMID: 29140466 PMCID: PMC5829651 DOI: 10.1093/nar/gkx1123] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 10/03/2017] [Accepted: 10/30/2017] [Indexed: 12/16/2022] Open
Abstract
Using molecular dynamics simulations, we show here that growing plectonemes resulting from transcription-induced supercoiling have the ability to actively push cohesin rings along chromatin fibres. The pushing direction is such that within each topologically associating domain (TAD) cohesin rings forming handcuffs move from the source of supercoiling, constituted by RNA polymerase with associated DNA topoisomerase TOP1, towards borders of TADs, where supercoiling is released by topoisomerase TOPIIB. Cohesin handcuffs are pushed by continuous flux of supercoiling that is generated by transcription and is then progressively released by action of TOPIIB located at TADs borders. Our model explains what can be the driving force of chromatin loop extrusion and how it can be ensured that loops grow quickly and in a good direction. In addition, the supercoiling-driven loop extrusion mechanism is consistent with earlier explanations proposing why TADs flanked by convergent CTCF binding sites form more stable chromatin loops than TADs flanked by divergent CTCF binding sites. We discuss the role of supercoiling in stimulating enhancer promoter contacts and propose that transcription of eRNA sends the first wave of supercoiling that can activate mRNA transcription in a given TAD.
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Affiliation(s)
- Dusan Racko
- Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, 1015-Lausanne, Switzerland
- Polymer Institute of the Slovak Academy of Sciences, 842 36 Bratislava, Slovakia
| | - Fabrizio Benedetti
- Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland
- Vital-IT, SIB Swiss Institute of Bioinformatics, 1015-Lausanne, Switzerland
| | - Julien Dorier
- Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland
- Vital-IT, SIB Swiss Institute of Bioinformatics, 1015-Lausanne, Switzerland
| | - Andrzej Stasiak
- Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, 1015-Lausanne, Switzerland
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Benedetti F, Racko D, Dorier J, Burnier Y, Stasiak A. Transcription-induced supercoiling explains formation of self-interacting chromatin domains in S. pombe. Nucleic Acids Res 2017; 45:9850-9859. [PMID: 28973473 PMCID: PMC5622301 DOI: 10.1093/nar/gkx716] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 08/04/2017] [Indexed: 12/12/2022] Open
Abstract
The question of how self-interacting chromatin domains in interphase chromosomes are structured and generated dominates current discussions on eukaryotic chromosomes. Numerical simulations using standard polymer models have been helpful in testing the validity of various models of chromosome organization. Experimental contact maps can be compared with simulated contact maps and thus verify how good is the model. With increasing resolution of experimental contact maps, it became apparent though that active processes need to be introduced into models to recapitulate the experimental data. Since transcribing RNA polymerases are very strong molecular motors that induce axial rotation of transcribed DNA, we present here models that include such rotational motors. We also include into our models swivels and sites for intersegmental passages that account for action of DNA topoisomerases releasing torsional stress. Using these elements in our models, we show that transcription-induced supercoiling generated in the regions with divergent-transcription and supercoiling relaxation occurring between these regions are sufficient to explain formation of self-interacting chromatin domains in chromosomes of fission yeast (S. pombe).
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Affiliation(s)
- Fabrizio Benedetti
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.,Vital-IT, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Dusan Racko
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.,Polymer Institute of the Slovak Academy of Sciences, 842 36 Bratislava, Slovakia
| | - Julien Dorier
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.,Vital-IT, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Yannis Burnier
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.,Institute of Theoretical Physics, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Andrzej Stasiak
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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Racko D, Benedetti F, Dorier J, Burnier Y, Stasiak A. Molecular Dynamics Simulation of Supercoiled, Knotted, and Catenated DNA Molecules, Including Modeling of Action of DNA Gyrase. Methods Mol Biol 2017; 1624:339-372. [PMID: 28842894 DOI: 10.1007/978-1-4939-7098-8_24] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A detailed protocol of molecular dynamics simulations of supercoiled DNA molecules that can be in addition knotted or catenated is described. We also describe how to model ongoing action of DNA gyrase that introduces negative supercoing into DNA molecules. The protocols provide detailed instructions about model parameters, equations of used potentials, simulation, and visualization. Implementation of the model into a frequently used molecular dynamics simulation environment, ESPResSo, is shown step by step.
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Affiliation(s)
- Dusan Racko
- Center for Integrative Genomics, University of Lausanne, 1015, Lausanne, Switzerland.
- SIB Swiss Institute for Bioinformatics, 1015, Lausanne, Switzerland.
- Polymer Institute of the Slovak Academy of Sciences, 842 36, Bratislava, Slovak Republic.
| | - Fabrizio Benedetti
- Center for Integrative Genomics, University of Lausanne, 1015, Lausanne, Switzerland
- Vital-IT, SIB Swiss Institute for Bioinformatics, 1015, Lausanne, Switzerland
| | - Julien Dorier
- Center for Integrative Genomics, University of Lausanne, 1015, Lausanne, Switzerland
- Vital-IT, SIB Swiss Institute for Bioinformatics, 1015, Lausanne, Switzerland
| | - Yannis Burnier
- Center for Integrative Genomics, University of Lausanne, 1015, Lausanne, Switzerland
- Institute of Theoretical Physics, Ecole Polytechnique Federal de Lausanne, 1015, Lausanne, Switzerland
| | - Andrzej Stasiak
- Center for Integrative Genomics, University of Lausanne, 1015, Lausanne, Switzerland
- SIB Swiss Institute for Bioinformatics, 1015, Lausanne, Switzerland
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Rawdon EJ, Dorier J, Racko D, Millett KC, Stasiak A. How topoisomerase IV can efficiently unknot and decatenate negatively supercoiled DNA molecules without causing their torsional relaxation. Nucleic Acids Res 2016; 44:4528-38. [PMID: 27106058 PMCID: PMC4889953 DOI: 10.1093/nar/gkw311] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 04/12/2016] [Indexed: 12/13/2022] Open
Abstract
Freshly replicated DNA molecules initially form multiply interlinked right-handed catenanes. In bacteria, these catenated molecules become supercoiled by DNA gyrase before they undergo a complete decatenation by topoisomerase IV (Topo IV). Topo IV is also involved in the unknotting of supercoiled DNA molecules. Using Metropolis Monte Carlo simulations, we investigate the shapes of supercoiled DNA molecules that are either knotted or catenated. We are especially interested in understanding how Topo IV can unknot right-handed knots and decatenate right-handed catenanes without acting on right-handed plectonemes in negatively supercoiled DNA molecules. To this end, we investigate how the topological consequences of intersegmental passages depend on the geometry of the DNA-DNA juxtapositions at which these passages occur. We observe that there are interesting differences between the geometries of DNA-DNA juxtapositions in the interwound portions and in the knotted or catenated portions of the studied molecules. In particular, in negatively supercoiled, multiply interlinked, right-handed catenanes, we detect specific regions where DNA segments belonging to two freshly replicated sister DNA molecules form left-handed crossings. We propose that, due to its geometrical preference to act on left-handed crossings, Topo IV can specifically unknot supercoiled DNA, as well as decatenate postreplicative catenanes, without causing their torsional relaxation.
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Affiliation(s)
- Eric J Rawdon
- Department of Mathematics, University of St. Thomas, Saint Paul, MN 55105, USA
| | - Julien Dorier
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland Vital-IT, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Dusan Racko
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland Polymer Institute of the Slovak Academy of Sciences, 842 36 Bratislava, Slovakia
| | - Kenneth C Millett
- Department of Mathematics, University of California, Santa Barbara, CA 93106, USA
| | - Andrzej Stasiak
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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Racko D, Benedetti F, Dorier J, Burnier Y, Stasiak A. Generation of supercoils in nicked and gapped DNA drives DNA unknotting and postreplicative decatenation. Nucleic Acids Res 2015; 43:7229-36. [PMID: 26150424 PMCID: PMC4551925 DOI: 10.1093/nar/gkv683] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 06/23/2015] [Indexed: 01/01/2023] Open
Abstract
Due to the helical structure of DNA the process of DNA replication is topologically complex. Freshly replicated DNA molecules are catenated with each other and are frequently knotted. For proper functioning of DNA it is necessary to remove all of these entanglements. This is done by DNA topoisomerases that pass DNA segments through each other. However, it has been a riddle how DNA topoisomerases select the sites of their action. In highly crowded DNA in living cells random passages between contacting segments would only increase the extent of entanglement. Using molecular dynamics simulations we observed that in actively supercoiled DNA molecules the entanglements resulting from DNA knotting or catenation spontaneously approach sites of nicks and gaps in the DNA. Type I topoisomerases, that preferentially act at sites of nick and gaps, are thus naturally provided with DNA–DNA juxtapositions where a passage results in an error-free DNA unknotting or DNA decatenation.
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Affiliation(s)
- Dusan Racko
- Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland SIB Swiss Institute of Bioinformatics, 1015-Lausanne, Switzerland Polymer Institute of the Slovak Academy of Sciences, 842 36 Bratislava, Slovakia
| | - Fabrizio Benedetti
- Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland SIB Swiss Institute of Bioinformatics, 1015-Lausanne, Switzerland
| | - Julien Dorier
- Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland Vital-IT, SIB Swiss Institute of Bioinformatics, 1015-Lausanne, Switzerland
| | - Yannis Burnier
- Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland Institute of Theoretical Physics, École Polytechnique Fédérale de Lausanne (EPFL), 1015-Lausanne, Switzerland
| | - Andrzej Stasiak
- Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland SIB Swiss Institute of Bioinformatics, 1015-Lausanne, Switzerland
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Benedetti F, Japaridze A, Dorier J, Racko D, Kwapich R, Burnier Y, Dietler G, Stasiak A. Effects of physiological self-crowding of DNA on shape and biological properties of DNA molecules with various levels of supercoiling. Nucleic Acids Res 2015; 43:2390-9. [PMID: 25653164 PMCID: PMC4344501 DOI: 10.1093/nar/gkv055] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
DNA in bacterial chromosomes and bacterial plasmids is supercoiled. DNA supercoiling is essential for DNA replication and gene regulation. However, the density of supercoiling in vivo is circa twice smaller than in deproteinized DNA molecules isolated from bacteria. What are then the specific advantages of reduced supercoiling density that is maintained in vivo? Using Brownian dynamics simulations and atomic force microscopy we show here that thanks to physiological DNA–DNA crowding DNA molecules with reduced supercoiling density are still sufficiently supercoiled to stimulate interaction between cis-regulatory elements. On the other hand, weak supercoiling permits DNA molecules to modulate their overall shape in response to physiological changes in DNA crowding. This plasticity of DNA shapes may have regulatory role and be important for the postreplicative spontaneous segregation of bacterial chromosomes.
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Affiliation(s)
- Fabrizio Benedetti
- Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland SIB Swiss Institute of Bioinformatics, 1015-Lausanne, Switzerland
| | - Aleksandre Japaridze
- Institute of Physics of Biological Systems, École Polytechnique Fédérale de Lausanne (EPFL), 1015-Lausanne, Switzerland
| | - Julien Dorier
- Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland Vital-IT, SIB Swiss Institute of Bioinformatics, 1015-Lausanne, Switzerland
| | - Dusan Racko
- Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland SIB Swiss Institute of Bioinformatics, 1015-Lausanne, Switzerland Polymer Institute of the Slovak Academy of Sciences, 845 41 Bratislava, Slovakia
| | - Robert Kwapich
- Institute of Physics of Biological Systems, École Polytechnique Fédérale de Lausanne (EPFL), 1015-Lausanne, Switzerland Department of Medical Physics, University of Silesia in Katowice, 40-007 Katowice, Poland
| | - Yannis Burnier
- Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland Institute of Theoretical Physics, École Polytechnique Fédérale de Lausanne (EPFL), 1015-Lausanne, Switzerland
| | - Giovanni Dietler
- Institute of Physics of Biological Systems, École Polytechnique Fédérale de Lausanne (EPFL), 1015-Lausanne, Switzerland
| | - Andrzej Stasiak
- Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland SIB Swiss Institute of Bioinformatics, 1015-Lausanne, Switzerland
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Danko M, Libiszowski J, Wolszczak M, Racko D, Duda A. Fluorescence study of the dynamics of a star-shaped poly(ɛ-caprolactone)s in THF: A comparison with a star-shaped poly(l-lactide)s. POLYMER 2009. [DOI: 10.1016/j.polymer.2009.03.027] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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