1
|
Starkov D, Belan S. Effect of active loop extrusion on the two-contact correlations in the interphase chromosome. J Chem Phys 2024; 161:074903. [PMID: 39149990 DOI: 10.1063/5.0221933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Accepted: 08/01/2024] [Indexed: 08/17/2024] Open
Abstract
The population-averaged contact maps generated by the chromosome conformation capture technique provide important information about the average frequency of contact between pairs of chromatin loci as a function of the genetic distance between them. However, these datasets do not tell us anything about the joint statistics of simultaneous contacts between genomic loci in individual cells. This kind of statistical information can be extracted using the single-cell Hi-C method, which is capable of detecting a large fraction of simultaneous contacts within a single cell, as well as through modern methods of fluorescent labeling and super-resolution imaging. Motivated by the prospect of the imminent availability of relevant experimental data, in this work, we theoretically model the joint statistics of pairs of contacts located along a line perpendicular to the main diagonal of the single-cell contact map. The analysis is performed within the framework of an ideal polymer model with quenched disorder of random loops, which, as previous studies have shown, allows us to take into account the influence of the loop extrusion process on the conformational properties of interphase chromatin.
Collapse
Affiliation(s)
- Dmitry Starkov
- Landau Institute for Theoretical Physics, Russian Academy of Sciences, 1-A Akademika Semenova Ave., 142432 Chernogolovka, Russia
- Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
| | - Sergey Belan
- Landau Institute for Theoretical Physics, Russian Academy of Sciences, 1-A Akademika Semenova Ave., 142432 Chernogolovka, Russia
- Faculty of Physics, National Research University Higher School of Economics, Myasnitskaya 20, 101000 Moscow, Russia
| |
Collapse
|
2
|
Hibino K, Sakai Y, Tamura S, Takagi M, Minami K, Natsume T, Shimazoe MA, Kanemaki MT, Imamoto N, Maeshima K. Single-nucleosome imaging unveils that condensins and nucleosome-nucleosome interactions differentially constrain chromatin to organize mitotic chromosomes. Nat Commun 2024; 15:7152. [PMID: 39169041 PMCID: PMC11339268 DOI: 10.1038/s41467-024-51454-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 08/08/2024] [Indexed: 08/23/2024] Open
Abstract
For accurate mitotic cell division, replicated chromatin must be assembled into chromosomes and faithfully segregated into daughter cells. While protein factors like condensin play key roles in this process, it is unclear how chromosome assembly proceeds as molecular events of nucleosomes in living cells and how condensins act on nucleosomes to organize chromosomes. To approach these questions, we investigate nucleosome behavior during mitosis of living human cells using single-nucleosome tracking, combined with rapid-protein depletion technology and computational modeling. Our results show that local nucleosome motion becomes increasingly constrained during mitotic chromosome assembly, which is functionally distinct from condensed apoptotic chromatin. Condensins act as molecular crosslinkers, locally constraining nucleosomes to organize chromosomes. Additionally, nucleosome-nucleosome interactions via histone tails constrain and compact whole chromosomes. Our findings elucidate the physical nature of the chromosome assembly process during mitosis.
Collapse
Affiliation(s)
- Kayo Hibino
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, Japan
| | - Yuji Sakai
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Kanagawa, Japan
- Department of Biosystems Science, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Sachiko Tamura
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Masatoshi Takagi
- Cellular Dynamics Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
- Laboratory for Cell Function Dynamics, RIKEN Center for Brain Science, Wako, Saitama, Japan
| | - Katsuhiko Minami
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, Japan
| | - Toyoaki Natsume
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, Japan
- Molecular Cell Engineering Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
- Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Masa A Shimazoe
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, Japan
| | - Masato T Kanemaki
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, Japan
- Molecular Cell Engineering Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
- Department of Biological Science, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Naoko Imamoto
- Cellular Dynamics Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
- Graduate School of Medical Safety Management, Jikei University of Health Care Sciences, Osaka, Japan
| | - Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan.
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, Japan.
| |
Collapse
|
3
|
Titus KR, Simandi Z, Chandrashekar H, Paquet D, Phillips-Cremins JE. Cell-type-specific loops linked to RNA polymerase II elongation in human neural differentiation. CELL GENOMICS 2024; 4:100606. [PMID: 38991604 PMCID: PMC11406193 DOI: 10.1016/j.xgen.2024.100606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 05/11/2024] [Accepted: 06/17/2024] [Indexed: 07/13/2024]
Abstract
DNA is folded into higher-order structures that shape and are shaped by genome function. The role of long-range loops in the establishment of new gene expression patterns during cell fate transitions remains poorly understood. Here, we investigate the link between cell-specific loops and RNA polymerase II (RNA Pol II) during neural lineage commitment. We find thousands of loops decommissioned or gained de novo upon differentiation of human induced pluripotent stem cells (hiPSCs) to neural progenitor cells (NPCs) and post-mitotic neurons. During hiPSC-to-NPC and NPC-to-neuron transitions, genes changing from RNA Pol II initiation to elongation are >4-fold more likely to anchor cell-specific loops than repressed genes. Elongated genes exhibit significant mRNA upregulation when connected in cell-specific promoter-enhancer loops but not invariant promoter-enhancer loops or promoter-promoter loops or when unlooped. Genes transitioning from repression to RNA Pol II initiation exhibit a slight mRNA increase independent of loop status. Our data link cell-specific loops and robust RNA Pol II-mediated elongation during neural cell fate transitions.
Collapse
Affiliation(s)
- Katelyn R Titus
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Zoltan Simandi
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Harshini Chandrashekar
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Dominik Paquet
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Jennifer E Phillips-Cremins
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
4
|
Kumar S, Padinhateeri R, Thakur S. Shear flow as a tool to distinguish microscopic activities of molecular machines in a chromatin loop. SOFT MATTER 2024; 20:6500-6506. [PMID: 39099470 DOI: 10.1039/d4sm00636d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/06/2024]
Abstract
Several types of molecular machines move along biopolymers like chromatin. However, the details about the microscopic activity of these machines and how to distinguish their modes of action are not well understood. We propose that the activity of such machines can be classified by studying looped chromatin under shear flow. Our simulations show that a chromatin-like polymer with two types of activities-constant (type-I) or local curvature-dependent tangential forces (type-II)-exhibits very different behavior under shear flow. We show that one can distinguish both activities by measuring the nature of a globule-to-extended coil transition, tank treading, and tumbling dynamics.
Collapse
Affiliation(s)
- Sandeep Kumar
- Department of Physics, Indian Institute of Science Education and Research Bhopal, Bhopal 462066, India.
| | - Ranjith Padinhateeri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India.
| | - Snigdha Thakur
- Department of Physics, Indian Institute of Science Education and Research Bhopal, Bhopal 462066, India.
| |
Collapse
|
5
|
Gil J, Navarrete E, Rosin L, Chowdhury N, Abraham S, Cornilleau G, Lei E, Mozziconacci J, Mirny L, Muller H, Drinnenberg I. Unique territorial and compartmental organization of chromosomes in the holocentric silkmoth. RESEARCH SQUARE 2024:rs.3.rs-4732646. [PMID: 39149482 PMCID: PMC11326380 DOI: 10.21203/rs.3.rs-4732646/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
The hallmarks of chromosome organization in multicellular eukaryotes are chromosome territories (CT), chromatin compartments, and insulated domains, including topologically associated domains (TADs). Yet, most of these elements of chromosome organization are derived from analyses of a limited set of model organisms, while large eukaryotic groups, including insects, remain mostly unexplored. Here we combine Hi-C, biophysical modeling, and microscopy to characterize the 3D genome architecture of the silkmoth, Bombyx mori. In contrast to other eukaryotes, B. mori chromosomes form highly separated territories. Similar to other eukaryotes, B. mori chromosomes segregate into active A and inactive B compartments, yet unlike in vertebrate systems, contacts between euchromatic A regions appear to be a strong driver of compartmentalization. Remarkably, we also identify a third compartment, called secluded "S," with a unique contact pattern. Each S region shows prominent short-range self-contacts and is remarkably devoid of contacts with the rest of the chromosome, including other S regions. Compartment S hosts a unique combination of genetic and epigenetic features, localizes towards the periphery of CTs, and shows developmental plasticity. Biophysical modeling reveals that the formation of such secluded domains requires highly localized loop extrusion within them, along with a low level of extrusion in A and B. Our Hi-C data supports predicted genome-wide and localized extrusion. Such a broad, non-uniform distribution of extruders has not been seen in other organisms. Overall, our analyses support loop extrusion in insects and highlight the evolutionary plasticity of 3D genome organization, driven by a new combination of known processes.
Collapse
Affiliation(s)
- J. Gil
- Institut Curie, PSL University, Sorbonne Université, CNRS, Nuclear Dynamics, 75005 Paris, France
| | - E. Navarrete
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Institute for Medical Engineering and Science, and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - L.F. Rosin
- Nuclear Organization and Gene Expression Section; Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| | - N. Chowdhury
- Institute for Medical Engineering and Science, and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - S. Abraham
- Institute for Medical Engineering and Science, and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - G. Cornilleau
- Institut Curie, PSL University, Sorbonne Université, CNRS, Nuclear Dynamics, 75005 Paris, France
| | - E.P. Lei
- Nuclear Organization and Gene Expression Section; Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| | - J. Mozziconacci
- StrInG Lab, Museum National d’Histoire Naturelle, Paris, France
| | - L.A. Mirny
- Institut Curie, PSL University, Sorbonne Université, CNRS, Nuclear Dynamics, 75005 Paris, France
- Institute for Medical Engineering and Science, and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - H. Muller
- Institut Curie, PSL University, Sorbonne Université, CNRS, Nuclear Dynamics, 75005 Paris, France
| | - I.A. Drinnenberg
- Institut Curie, PSL University, Sorbonne Université, CNRS, Nuclear Dynamics, 75005 Paris, France
| |
Collapse
|
6
|
Munshi R. How Transcription Factor Clusters Shape the Transcriptional Landscape. Biomolecules 2024; 14:875. [PMID: 39062589 PMCID: PMC11274464 DOI: 10.3390/biom14070875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 07/14/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024] Open
Abstract
In eukaryotic cells, gene transcription typically occurs in discrete periods of promoter activity, interspersed with intervals of inactivity. This pattern deviates from simple stochastic events and warrants a closer examination of the molecular interactions that activate the promoter. Recent studies have identified transcription factor (TF) clusters as key precursors to transcriptional bursting. Often, these TF clusters form at chromatin segments that are physically distant from the promoter, making changes in chromatin conformation crucial for promoter-TF cluster interactions. In this review, I explore the formation and constituents of TF clusters, examining how the dynamic interplay between chromatin architecture and TF clustering influences transcriptional bursting. Additionally, I discuss techniques for visualizing TF clusters and provide an outlook on understanding the remaining gaps in this field.
Collapse
Affiliation(s)
- Rahul Munshi
- Joseph Henry Laboratories of Physics and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| |
Collapse
|
7
|
Cao Z, Wolynes PG. Motorized chain models of the ideal chromosome. Proc Natl Acad Sci U S A 2024; 121:e2407077121. [PMID: 38954553 PMCID: PMC11252987 DOI: 10.1073/pnas.2407077121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 06/06/2024] [Indexed: 07/04/2024] Open
Abstract
An array of motor proteins consumes chemical energy in setting up the architectures of chromosomes. Here, we explore how the structure of ideal polymer chains is influenced by two classes of motors. The first class which we call "swimming motors" acts to propel the chromatin fiber through three-dimensional space. They represent a caricature of motors such as RNA polymerases. Previously, they have often been described by adding a persistent flow onto Brownian diffusion of the chain. The second class of motors, which we call "grappling motors" caricatures the loop extrusion processes in which segments of chromatin fibers some distance apart are brought together. We analyze these models using a self-consistent variational phonon approximation to a many-body Master equation incorporating motor activities. We show that whether the swimming motors lead to contraction or expansion depends on the susceptibility of the motors, that is, how their activity depends on the forces they must exert. Grappling motors in contrast to swimming motors lead to long-ranged correlations that resemble those first suggested for fractal globules and that are consistent with the effective interactions inferred by energy landscape analyses of Hi-C data on the interphase chromosome.
Collapse
Affiliation(s)
- Zhiyu Cao
- Center for Theoretical Biological Physics, Rice University, Houston, TX77005
- Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui230026, China
| | - Peter G. Wolynes
- Center for Theoretical Biological Physics, Rice University, Houston, TX77005
- Department of Chemistry, Rice University, Houston, TX77005
- Department of Physics, Rice University, Houston, TX77005
| |
Collapse
|
8
|
Li J, Zhang B, Wang ZY. Activity-induced stiffness, entanglement network and dynamic slowdown in unentangled semidilute polymer solutions. SOFT MATTER 2024; 20:5174-5182. [PMID: 38895794 DOI: 10.1039/d4sm00341a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Active polymers possess numerous unique properties that are quite different from those observed in the system of small active molecules due to the intricate interplay between their activity and topological constraints. This study focuses on the conformational changes induced by activity, impacting effective stiffness and crucially influencing entanglement and dynamics. When the two terminals of a linear chain undergo active modification through coupling to a high-temperature thermal bath, there is a substantial increase in chain size, indicating a notable enhancement in effective stiffness. Unlike in passive semiflexible chains where stiffness predominantly affects local bond angles, activity-induced stiffness manifests at the scale of tens of monomers. While activity raises the ambient temperature, it significantly decreases diffusion by over an order of magnitude. The slowdown of the dynamics observed can be attributed to increased entanglement due to chain elongation.
Collapse
Affiliation(s)
- Jing Li
- School of Physical Science and Technology, Southwest University, Chongqing 400715, China.
- Chongqing Key Laboratory of Micro-Nano Structure Optoelectronics, Chongqing 400715, China
| | - Bokai Zhang
- School of Physical Science and Technology, Southwest University, Chongqing 400715, China.
- Chongqing Key Laboratory of Micro-Nano Structure Optoelectronics, Chongqing 400715, China
| | - Zhi-Yong Wang
- School of Physical Science and Technology, Southwest University, Chongqing 400715, China.
- Chongqing Key Laboratory of Micro-Nano Structure Optoelectronics, Chongqing 400715, China
| |
Collapse
|
9
|
Prevo B, Earnshaw WC. DNA packaging by molecular motors: from bacteriophage to human chromosomes. Nat Rev Genet 2024:10.1038/s41576-024-00740-y. [PMID: 38886215 DOI: 10.1038/s41576-024-00740-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/29/2024] [Indexed: 06/20/2024]
Abstract
Dense packaging of genomic DNA is crucial for organismal survival, as DNA length always far exceeds the dimensions of the cells that contain it. Organisms, therefore, use sophisticated machineries to package their genomes. These systems range across kingdoms from a single ultra-powerful rotary motor that spools the DNA into a bacteriophage head, to hundreds of thousands of relatively weak molecular motors that coordinate the compaction of mitotic chromosomes in eukaryotic cells. Recent technological advances, such as DNA proximity-based sequencing approaches, polymer modelling and in vitro reconstitution of DNA loop extrusion, have shed light on the biological mechanisms driving DNA organization in different systems. Here, we discuss DNA packaging in bacteriophage, bacteria and eukaryotic cells, which, despite their extreme variation in size, structure and genomic content, all rely on the action of molecular motors to package their genomes.
Collapse
Affiliation(s)
- Bram Prevo
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK.
| | - William C Earnshaw
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK.
| |
Collapse
|
10
|
Borando F, Tiana G. Effective model of protein-mediated interactions in chromatin. Phys Rev E 2024; 109:064406. [PMID: 39021027 DOI: 10.1103/physreve.109.064406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 05/30/2024] [Indexed: 07/20/2024]
Abstract
Protein-mediated interactions are ubiquitous in the cellular environment, and particularly in the nucleus, where they are responsible for the structuring of chromatin. We show through molecular-dynamics simulations of a polymer surrounded by binders that the strength of the binder-polymer interaction separates an equilibrium from a nonequilibrium regime. In the equilibrium regime, the system can be efficiently described by an effective model in which the binders are traced out. Even in this case, the polymers display features that are different from those of a standard homopolymer interacting with two-body interactions. We then extend the effective model to deal with the case where binders cannot be regarded as in equilibrium and a new phenomenology appears, including local blobs in the polymer. An effective description of this system can be useful in elucidating the fundamental mechanisms that govern chromatin structuring in particular and indirect interactions in general.
Collapse
|
11
|
Aharonoff A, Kim J, Washington A, Ercan S. SMC-mediated dosage compensation in C. elegans evolved in the presence of an ancestral nematode mechanism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.21.595224. [PMID: 38826443 PMCID: PMC11142195 DOI: 10.1101/2024.05.21.595224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Mechanisms of X chromosome dosage compensation have been studied extensively in a few model species representing clades of shared sex chromosome ancestry. However, the diversity within each clade as a function of sex chromosome evolution is largely unknown. Here, we anchor ourselves to the nematode Caenorhabditis elegans, for which a well-studied mechanism of dosage compensation occurs through a specialized structural maintenance of chromosomes (SMC) complex, and explore the diversity of dosage compensation in the surrounding phylogeny of nematodes. Through phylogenetic analysis of the C. elegans dosage compensation complex and a survey of its epigenetic signatures, including X-specific topologically associating domains (TADs) and X-enrichment of H4K20me1, we found that the condensin-mediated mechanism evolved recently in the lineage leading to Caenorhabditis through an SMC-4 duplication. Intriguingly, an independent duplication of SMC-4 and the presence of X-specific TADs in Pristionchus pacificus suggest that condensin-mediated dosage compensation arose more than once. mRNA-seq analyses of gene expression in several nematode species indicate that dosage compensation itself is ancestral, as expected from the ancient XO sex determination system. Indicative of the ancestral mechanism, H4K20me1 is enriched on the X chromosomes in Oscheius tipulae, which does not contain X-specific TADs or SMC-4 paralogs. Together, our results indicate that the dosage compensation system in C. elegans is surprisingly new, and condensin may have been co-opted repeatedly in nematodes, suggesting that the process of evolving a chromosome-wide gene regulatory mechanism for dosage compensation is constrained. Significance statement X chromosome dosage compensation mechanisms evolved in response to Y chromosome degeneration during sex chromosome evolution. However, establishment of dosage compensation is not an endpoint. As sex chromosomes change, dosage compensation strategies may have also changed. In this study, we performed phylogenetic and epigenomic analyses surrounding Caenorhabditis elegans and found that the condensin-mediated dosage compensation mechanism in C. elegans is surprisingly new, and has evolved in the presence of an ancestral mechanism. Intriguingly, condensin-based dosage compensation may have evolved more than once in the nematode lineage, the other time in Pristionchus. Together, our work highlights a previously unappreciated diversity of dosage compensation mechanisms within a clade, and suggests constraints in evolving new mechanisms in the presence of an existing one.
Collapse
Affiliation(s)
- Avrami Aharonoff
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003
| | - Jun Kim
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003
| | - Aaliyah Washington
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003
| | - Sevinç Ercan
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003
| |
Collapse
|
12
|
Lizana L, Schwartz YB. The scales, mechanisms, and dynamics of the genome architecture. SCIENCE ADVANCES 2024; 10:eadm8167. [PMID: 38598632 PMCID: PMC11006219 DOI: 10.1126/sciadv.adm8167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 03/06/2024] [Indexed: 04/12/2024]
Abstract
Even when split into several chromosomes, DNA molecules that make up our genome are too long to fit into the cell nuclei unless massively folded. Such folding must accommodate the need for timely access to selected parts of the genome by transcription factors, RNA polymerases, and DNA replication machinery. Here, we review our current understanding of the genome folding inside the interphase nuclei. We consider the resulting genome architecture at three scales with a particular focus on the intermediate (meso) scale and summarize the insights gained from recent experimental observations and diverse computational models.
Collapse
Affiliation(s)
- Ludvig Lizana
- Integrated Science Lab, Department of Physics, Umeå University, Umeå, Sweden
| | | |
Collapse
|
13
|
Yuan T, Yan H, Bailey MLP, Williams JF, Surovtsev I, King MC, Mochrie SGJ. Effect of loops on the mean-square displacement of Rouse-model chromatin. Phys Rev E 2024; 109:044502. [PMID: 38755928 DOI: 10.1103/physreve.109.044502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 02/16/2024] [Indexed: 05/18/2024]
Abstract
Chromatin polymer dynamics are commonly described using the classical Rouse model. The subsequent discovery, however, of intermediate-scale chromatin organization known as topologically associating domains (TADs) in experimental Hi-C contact maps for chromosomes across the tree of life, together with the success of loop extrusion factor (LEF) model in explaining TAD formation, motivates efforts to understand the effect of loops and loop extrusion on chromatin dynamics. This paper seeks to fulfill this need by combining LEF-model simulations with extended Rouse-model polymer simulations to investigate the dynamics of chromatin with loops and dynamic loop extrusion. We show that loops significantly suppress the averaged mean-square displacement (MSD) of a gene locus, consistent with recent experiments that track fluorescently labeled chromatin loci. We also find that loops reduce the MSD's stretching exponent from the classical Rouse-model value of 1/2 to a loop-density-dependent value in the 0.45-0.40 range. Remarkably, stretching exponent values in this range have also been observed in recent experiments [Weber et al., Phys. Rev. Lett. 104, 238102 (2010)0031-900710.1103/PhysRevLett.104.238102; Bailey et al., Mol. Biol. Cell 34, ar78 (2023)1059-152410.1091/mbc.E23-04-0119]. We also show that the dynamics of loop extrusion itself negligibly affects chromatin mobility. By studying static "rosette" loop configurations, we also demonstrate that chromatin MSDs and stretching exponents depend on the location of the locus in question relative to the position of the loops and on the local friction environment.
Collapse
Affiliation(s)
- Tianyu Yuan
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520, USA
- Department of Physics, Yale University, New Haven, Connecticut 06520, USA
| | - Hao Yan
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520, USA
- Department of Physics, Yale University, New Haven, Connecticut 06520, USA
| | - Mary Lou P Bailey
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520, USA
- Department of Applied Physics, Yale University, New Haven, Connecticut 06520, USA
| | - Jessica F Williams
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Ivan Surovtsev
- Department of Physics, Yale University, New Haven, Connecticut 06520, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Megan C King
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Department of Molecular, Cell and Developmental Biology, Yale University, New Haven, Connecticut 06511, USA
| | - Simon G J Mochrie
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520, USA
- Department of Physics, Yale University, New Haven, Connecticut 06520, USA
- Department of Applied Physics, Yale University, New Haven, Connecticut 06520, USA
| |
Collapse
|
14
|
Belan S, Parfenyev V. Footprints of loop extrusion in statistics of intra-chromosomal distances: An analytically solvable model. J Chem Phys 2024; 160:124901. [PMID: 38516975 DOI: 10.1063/5.0199573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 03/06/2024] [Indexed: 03/23/2024] Open
Abstract
Active loop extrusion-the process of formation of dynamically growing chromatin loops due to the motor activity of DNA-binding protein complexes-is a firmly established mechanism responsible for chromatin spatial organization at different stages of a cell cycle in eukaryotes and bacteria. The theoretical insight into the effect of loop extrusion on the experimentally measured statistics of chromatin conformation can be gained with an appropriately chosen polymer model. Here, we consider the simplest analytically solvable model of an interphase chromosome, which is treated as an ideal chain with disorder of sufficiently sparse random loops whose conformations are sampled from the equilibrium ensemble. This framework allows us to arrive at the closed-form analytical expression for the mean-squared distance between pairs of genomic loci, which is valid beyond the one-loop approximation in diagrammatic representation. In addition, we analyze the loop-induced deviation of chain conformations from the Gaussian statistics by calculating kurtosis of probability density of the pairwise separation vector. The presented results suggest the possible ways of estimating the characteristics of the loop extrusion process based on the experimental data on the scale-dependent statistics of intra-chromosomal pair-wise distances.
Collapse
Affiliation(s)
- Sergey Belan
- Landau Institute for Theoretical Physics, Russian Academy of Sciences, 1-A Akademika Semenova Av., 142432 Chernogolovka, Russia
- National Research University Higher School of Economics, Faculty of Physics, Myasnitskaya 20, 101000 Moscow, Russia
| | - Vladimir Parfenyev
- Landau Institute for Theoretical Physics, Russian Academy of Sciences, 1-A Akademika Semenova Av., 142432 Chernogolovka, Russia
- National Research University Higher School of Economics, Faculty of Physics, Myasnitskaya 20, 101000 Moscow, Russia
| |
Collapse
|
15
|
Bastié N, Chapard C, Cournac A, Nejmi S, Mboumba H, Gadal O, Thierry A, Beckouët F, Koszul R. Sister chromatid cohesion halts DNA loop expansion. Mol Cell 2024; 84:1139-1148.e5. [PMID: 38452765 DOI: 10.1016/j.molcel.2024.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 12/02/2023] [Accepted: 02/06/2024] [Indexed: 03/09/2024]
Abstract
Eukaryotic genomes are folded into DNA loops mediated by structural maintenance of chromosomes (SMC) complexes such as cohesin, condensin, and Smc5/6. This organization regulates different DNA-related processes along the cell cycle, such as transcription, recombination, segregation, and DNA repair. During the G2 stage, SMC-mediated DNA loops coexist with cohesin complexes involved in sister chromatid cohesion (SCC). However, the articulation between the establishment of SCC and the formation of SMC-mediated DNA loops along the chromatin remains unknown. Here, we show that SCC is indeed a barrier to cohesin-mediated DNA loop expansion along G2/M Saccharomyces cerevisiae chromosomes.
Collapse
Affiliation(s)
- Nathalie Bastié
- Molecular, Cellular, and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Christophe Chapard
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, 75015 Paris, France
| | - Axel Cournac
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, 75015 Paris, France
| | - Sanae Nejmi
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France
| | - Henri Mboumba
- Molecular, Cellular, and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Olivier Gadal
- Molecular, Cellular, and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Agnès Thierry
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, 75015 Paris, France
| | - Frederic Beckouët
- Molecular, Cellular, and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France.
| | - Romain Koszul
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, 75015 Paris, France.
| |
Collapse
|
16
|
Zhang Y, Boninsegna L, Yang M, Misteli T, Alber F, Ma J. Computational methods for analysing multiscale 3D genome organization. Nat Rev Genet 2024; 25:123-141. [PMID: 37673975 PMCID: PMC11127719 DOI: 10.1038/s41576-023-00638-1] [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] [Accepted: 07/12/2023] [Indexed: 09/08/2023]
Abstract
Recent progress in whole-genome mapping and imaging technologies has enabled the characterization of the spatial organization and folding of the genome in the nucleus. In parallel, advanced computational methods have been developed to leverage these mapping data to reveal multiscale three-dimensional (3D) genome features and to provide a more complete view of genome structure and its connections to genome functions such as transcription. Here, we discuss how recently developed computational tools, including machine-learning-based methods and integrative structure-modelling frameworks, have led to a systematic, multiscale delineation of the connections among different scales of 3D genome organization, genomic and epigenomic features, functional nuclear components and genome function. However, approaches that more comprehensively integrate a wide variety of genomic and imaging datasets are still needed to uncover the functional role of 3D genome structure in defining cellular phenotypes in health and disease.
Collapse
Affiliation(s)
- Yang Zhang
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Lorenzo Boninsegna
- Department of Microbiology, Immunology and Molecular Genetics and Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, USA
| | - Muyu Yang
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Tom Misteli
- Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
| | - Frank Alber
- Department of Microbiology, Immunology and Molecular Genetics and Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, USA.
| | - Jian Ma
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA.
| |
Collapse
|
17
|
Remini L, Segers M, Palmeri J, Walter JC, Parmeggiani A, Carlon E. Chromatin structure from high resolution microscopy: Scaling laws and microphase separation. Phys Rev E 2024; 109:024408. [PMID: 38491617 DOI: 10.1103/physreve.109.024408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 01/11/2024] [Indexed: 03/18/2024]
Abstract
Recent advances in experimental fluorescence microscopy allow high accuracy determination (resolution of 50 nm) of the three-dimensional physical location of multiple (up to ∼10^{2}) tagged regions of the chromosome. We investigate publicly available microscopy data for two loci of the human Chr21 obtained from multiplexed fluorescence in situ hybridization (FISH) methods for different cell lines and treatments. Inspired by polymer physics models, our analysis centers around distance distributions between different tags with the aim being to unravel the chromatin conformational arrangements. We show that for any specific genomic site, there are (at least) two different conformational arrangements of chromatin, implying coexisting distinct topologies which we refer to as phase α and phase β. These two phases show different scaling behaviors: the former is consistent with a crumpled globule, while the latter indicates a confined, but more extended conformation, such as a looped domain. The identification of these distinct phases sheds light on the coexistence of multiple chromatin topologies and provides insights into the effects of cellular context and/or treatments on chromatin structure.
Collapse
Affiliation(s)
- Loucif Remini
- Laboratoire Charles Coulomb (L2C), Université de Montpellier, CNRS UMR5221, Montpellier, France
| | - Midas Segers
- Soft Matter and Biophysics, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - John Palmeri
- Laboratoire Charles Coulomb (L2C), Université de Montpellier, CNRS UMR5221, Montpellier, France
| | - Jean-Charles Walter
- Laboratoire Charles Coulomb (L2C), Université de Montpellier, CNRS UMR5221, Montpellier, France
| | - Andrea Parmeggiani
- Laboratoire Charles Coulomb (L2C), Université de Montpellier, CNRS UMR5221, Montpellier, France
| | - Enrico Carlon
- Soft Matter and Biophysics, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| |
Collapse
|
18
|
Titus KR, Simandi Z, Chandrashekar H, Paquet D, Phillips-Cremins JE. Cell type-specific loops linked to RNA polymerase II elongation in human neural differentiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.04.569731. [PMID: 38106199 PMCID: PMC10723365 DOI: 10.1101/2023.12.04.569731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
DNA is folded into higher-order structures that shape and are shaped by genome function. The role for long-range loops in the establishment of new gene expression patterns during cell fate transitions remains poorly understood. Here, we investigate the link between cell-specific loops and RNA polymerase II (RNAPolII) during neural lineage commitment. We find thousands of loops decommissioned or gained de novo upon differentiation of human induced pluripotent stem cells (hiPSCs) to neural progenitors (NPCs) and post-mitotic neurons. During hiPSC-to-NPC and NPC-to-neuron transitions, genes changing from RNAPolII initiation to elongation are >4-fold more likely to anchor cell-specific loops than repressed genes. Elongated genes exhibit significant mRNA upregulation when connected in cell-specific promoter-enhancer loops but not invariant promoter-enhancer loops, promoter-promoter loops, or unlooped. Genes transitioning from repression to RNAPolII initiation exhibit slight mRNA increase independent of loop status. Our data link cell-specific loops and robust RNAPolII-mediated elongation during neural cell fate transitions.
Collapse
Affiliation(s)
- Katelyn R Titus
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania
| | - Zoltan Simandi
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania
| | - Harshini Chandrashekar
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania
| | - Dominik Paquet
- Institute for Stroke and Dementia Research, Ludwig Maximilians Universitat, Munich, Germany
| | - Jennifer E Phillips-Cremins
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania
| |
Collapse
|
19
|
Yamamoto T, Kinoshita K, Hirano T. Elasticity control of entangled chromosomes: Crosstalk between condensin complexes and nucleosomes. Biophys J 2023; 122:3869-3881. [PMID: 37571823 PMCID: PMC10560673 DOI: 10.1016/j.bpj.2023.08.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 07/18/2023] [Accepted: 08/08/2023] [Indexed: 08/13/2023] Open
Abstract
Condensin-mediated loop extrusion is now considered as the main driving force of mitotic chromosome assembly. Recent experiments have shown, however, that a class of mutant condensin complexes deficient in loop extrusion can assemble chromosome-like structures in Xenopus egg extracts, although these structures are somewhat different from those assembled by wild-type condensin complexes. In the absence of topoisomerase II (topo II), the mutant condensin complexes produce an unusual round-shaped structure termed a bean, which consists of a DNA-dense central core surrounded by a DNA-sparse halo. The mutant condensin complexes accumulate in the core, whereas histones are more concentrated in the halo than in the core. We consider that this peculiar structure serves as a model system to study how DNA entanglements, nucleosomes, and condensin functionally crosstalk with each other. To gain insight into how the bean structure is formed, here we construct a theoretical model. Our theory predicts that the core is formed by attractive interactions between mutant condensin complexes, whereas the halo is stabilized by the energy reduction through the selective accumulation of nucleosomes. The formation of the halo increases the elastic free energy due to the DNA entanglement in the core, but the latter free energy is compensated by condensin complexes that suppress the assembly of nucleosomes.
Collapse
Affiliation(s)
- Tetsuya Yamamoto
- Institute for Chemical Reaction Design and Discovery (ICReDD), Hokkaido University, Sapporo, Hokkaido, Japan.
| | | | - Tatsuya Hirano
- Chromosome Dynamics Laboratory, RIKEN, Wako, Saitama, Japan
| |
Collapse
|
20
|
Agarwal A, Korsak S, Choudhury A, Plewczynski D. The dynamic role of cohesin in maintaining human genome architecture. Bioessays 2023; 45:e2200240. [PMID: 37603403 DOI: 10.1002/bies.202200240] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 08/03/2023] [Accepted: 08/07/2023] [Indexed: 08/22/2023]
Abstract
Recent advances in genomic and imaging techniques have revealed the complex manner of organizing billions of base pairs of DNA necessary for maintaining their functionality and ensuring the proper expression of genetic information. The SMC proteins and cohesin complex primarily contribute to forming higher-order chromatin structures, such as chromosomal territories, compartments, topologically associating domains (TADs) and chromatin loops anchored by CCCTC-binding factor (CTCF) protein or other genome organizers. Cohesin plays a fundamental role in chromatin organization, gene expression and regulation. This review aims to describe the current understanding of the dynamic nature of the cohesin-DNA complex and its dependence on cohesin for genome maintenance. We discuss the current 3C technique and numerous bioinformatics pipelines used to comprehend structural genomics and epigenetics focusing on the analysis of Cohesin-centred interactions. We also incorporate our present comprehension of Loop Extrusion (LE) and insights from stochastic modelling.
Collapse
Affiliation(s)
- Abhishek Agarwal
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Sevastianos Korsak
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | | | - Dariusz Plewczynski
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| |
Collapse
|
21
|
Polovnikov KE, Slavov B, Belan S, Imakaev M, Brandão HB, Mirny LA. Crumpled polymer with loops recapitulates key features of chromosome organization. PHYSICAL REVIEW. X 2023; 13:041029. [PMID: 38774252 PMCID: PMC11108028 DOI: 10.1103/physrevx.13.041029] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/24/2024]
Abstract
Chromosomes are exceedingly long topologically-constrained polymers compacted in a cell nucleus. We recently suggested that chromosomes are organized into loops by an active process of loop extrusion. Yet loops remain elusive to direct observations in living cells; detection and characterization of myriads of such loops is a major challenge. The lack of a tractable physical model of a polymer folded into loops limits our ability to interpret experimental data and detect loops. Here, we introduce a new physical model - a polymer folded into a sequence of loops, and solve it analytically. Our model and a simple geometrical argument show how loops affect statistics of contacts in a polymer across different scales, explaining universally observed shapes of the contact probability. Moreover, we reveal that folding into loops reduces the density of topological entanglements, a novel phenomenon we refer as "the dilution of entanglements". Supported by simulations this finding suggests that up to ~ 1 - 2Mb chromosomes with loops are not topologically constrained, yet become crumpled at larger scales. Our theoretical framework allows inference of loop characteristics, draws a new picture of chromosome organization, and shows how folding into loops affects topological properties of crumpled polymers.
Collapse
Affiliation(s)
- Kirill E. Polovnikov
- Current address: Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR3664, Paris, France
- Institute of Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139
| | | | - Sergey Belan
- Landau Institute for Theoretical Physics, Russian Academy of Sciences, Chernogolovka, Russia
- National Research University Higher School of Economics, Faculty of Physics, Moscow, Russia
| | - Maxim Imakaev
- Institute of Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Hugo B. Brandão
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142
| | - Leonid A. Mirny
- Institute of Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139
| |
Collapse
|
22
|
Forte G, Buckle A, Boyle S, Marenduzzo D, Gilbert N, Brackley CA. Transcription modulates chromatin dynamics and locus configuration sampling. Nat Struct Mol Biol 2023; 30:1275-1285. [PMID: 37537334 PMCID: PMC10497412 DOI: 10.1038/s41594-023-01059-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 07/07/2023] [Indexed: 08/05/2023]
Abstract
In living cells, the 3D structure of gene loci is dynamic, but this is not revealed by 3C and FISH experiments in fixed samples, leaving a notable gap in our understanding. To overcome these limitations, we applied the highly predictive heteromorphic polymer (HiP-HoP) model to determine chromatin fiber mobility at the Pax6 locus in three mouse cell lines with different transcription states. While transcriptional activity minimally affects movement of 40-kbp regions, we observed that motion of smaller 1-kbp regions depends strongly on local disruption to chromatin fiber structure marked by H3K27 acetylation. This also substantially influenced locus configuration dynamics by modulating protein-mediated promoter-enhancer loops. Importantly, these simulations indicate that chromatin dynamics are sufficiently fast to sample all possible locus conformations within minutes, generating wide dynamic variability within single cells. This combination of simulation and experimental validation provides insight into how transcriptional activity influences chromatin structure and gene dynamics.
Collapse
Affiliation(s)
- Giada Forte
- SUPA, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Adam Buckle
- MRC Human Genetics Unit, Institute of Genetics & Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Shelagh Boyle
- MRC Human Genetics Unit, Institute of Genetics & Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Davide Marenduzzo
- SUPA, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Nick Gilbert
- MRC Human Genetics Unit, Institute of Genetics & Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK.
| | - Chris A Brackley
- SUPA, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK.
| |
Collapse
|
23
|
Batty P, Langer CCH, Takács Z, Tang W, Blaukopf C, Peters J, Gerlich DW. Cohesin-mediated DNA loop extrusion resolves sister chromatids in G2 phase. EMBO J 2023; 42:e113475. [PMID: 37357575 PMCID: PMC10425840 DOI: 10.15252/embj.2023113475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 05/26/2023] [Accepted: 06/14/2023] [Indexed: 06/27/2023] Open
Abstract
Genetic information is stored in linear DNA molecules, which are highly folded inside cells. DNA replication along the folded template path yields two sister chromatids that initially occupy the same nuclear region in an intertwined arrangement. Dividing cells must disentangle and condense the sister chromatids into separate bodies such that a microtubule-based spindle can move them to opposite poles. While the spindle-mediated transport of sister chromatids has been studied in detail, the chromosome-intrinsic mechanics presegregating sister chromatids have remained elusive. Here, we show that human sister chromatids resolve extensively already during interphase, in a process dependent on the loop-extruding activity of cohesin, but not that of condensins. Increasing cohesin's looping capability increases sister DNA resolution in interphase nuclei to an extent normally seen only during mitosis, despite the presence of abundant arm cohesion. That cohesin can resolve sister chromatids so extensively in the absence of mitosis-specific activities indicates that DNA loop extrusion is a generic mechanism for segregating replicated genomes, shared across different Structural Maintenance of Chromosomes (SMC) protein complexes in all kingdoms of life.
Collapse
Affiliation(s)
- Paul Batty
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)Vienna BioCenter (VBC)ViennaAustria
- Vienna BioCenter PhD ProgramDoctoral School of the University of Vienna and Medical University of ViennaViennaAustria
| | - Christoph CH Langer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)Vienna BioCenter (VBC)ViennaAustria
| | - Zsuzsanna Takács
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)Vienna BioCenter (VBC)ViennaAustria
| | - Wen Tang
- Research Institute of Molecular Pathology (IMP)Vienna BioCenter (VBC)ViennaAustria
| | - Claudia Blaukopf
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)Vienna BioCenter (VBC)ViennaAustria
| | - Jan‐Michael Peters
- Research Institute of Molecular Pathology (IMP)Vienna BioCenter (VBC)ViennaAustria
| | - Daniel W Gerlich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)Vienna BioCenter (VBC)ViennaAustria
| |
Collapse
|
24
|
Gilbert BR, Thornburg ZR, Brier TA, Stevens JA, Grünewald F, Stone JE, Marrink SJ, Luthey-Schulten Z. Dynamics of chromosome organization in a minimal bacterial cell. Front Cell Dev Biol 2023; 11:1214962. [PMID: 37621774 PMCID: PMC10445541 DOI: 10.3389/fcell.2023.1214962] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 07/10/2023] [Indexed: 08/26/2023] Open
Abstract
Computational models of cells cannot be considered complete unless they include the most fundamental process of life, the replication and inheritance of genetic material. By creating a computational framework to model systems of replicating bacterial chromosomes as polymers at 10 bp resolution with Brownian dynamics, we investigate changes in chromosome organization during replication and extend the applicability of an existing whole-cell model (WCM) for a genetically minimal bacterium, JCVI-syn3A, to the entire cell-cycle. To achieve cell-scale chromosome structures that are realistic, we model the chromosome as a self-avoiding homopolymer with bending and torsional stiffnesses that capture the essential mechanical properties of dsDNA in Syn3A. In addition, the conformations of the circular DNA must avoid overlapping with ribosomes identitied in cryo-electron tomograms. While Syn3A lacks the complex regulatory systems known to orchestrate chromosome segregation in other bacteria, its minimized genome retains essential loop-extruding structural maintenance of chromosomes (SMC) protein complexes (SMC-scpAB) and topoisomerases. Through implementing the effects of these proteins in our simulations of replicating chromosomes, we find that they alone are sufficient for simultaneous chromosome segregation across all generations within nested theta structures. This supports previous studies suggesting loop-extrusion serves as a near-universal mechanism for chromosome organization within bacterial and eukaryotic cells. Furthermore, we analyze ribosome diffusion under the influence of the chromosome and calculate in silico chromosome contact maps that capture inter-daughter interactions. Finally, we present a methodology to map the polymer model of the chromosome to a Martini coarse-grained representation to prepare molecular dynamics models of entire Syn3A cells, which serves as an ultimate means of validation for cell states predicted by the WCM.
Collapse
Affiliation(s)
- Benjamin R. Gilbert
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Zane R. Thornburg
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Troy A. Brier
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Jan A. Stevens
- Molecular Dynamics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Fabian Grünewald
- Molecular Dynamics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - John E. Stone
- NVIDIA Corporation, Santa Clara, CA, United States
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Siewert J. Marrink
- Molecular Dynamics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Zaida Luthey-Schulten
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- NSF Center for the Physics of Living Cells, Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| |
Collapse
|
25
|
Spicer MFD, Gerlich DW. The material properties of mitotic chromosomes. Curr Opin Struct Biol 2023; 81:102617. [PMID: 37279615 PMCID: PMC10448380 DOI: 10.1016/j.sbi.2023.102617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/28/2023] [Accepted: 05/04/2023] [Indexed: 06/08/2023]
Abstract
Chromosomes transform during the cell cycle, allowing transcription and replication during interphase and chromosome segregation during mitosis. Morphological changes are thought to be driven by the combined effects of DNA loop extrusion and a chromatin solubility phase transition. By extruding the chromatin fibre into loops, condensins enrich at an axial core and provide resistance to spindle pulling forces. Mitotic chromosomes are further compacted by deacetylation of histone tails, rendering chromatin insoluble and resistant to penetration by microtubules. Regulation of surface properties by Ki-67 allows independent chromosome movement in early mitosis and clustering during mitotic exit. Recent progress has provided insight into how the extraordinary material properties of chromatin emerge from these activities, and how these properties facilitate faithful chromosome segregation.
Collapse
Affiliation(s)
- Maximilian F D Spicer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030, Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, A-1030, Vienna, Austria. https://twitter.com/Spicer__Max
| | - Daniel W Gerlich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030, Vienna, Austria.
| |
Collapse
|
26
|
Mirny LA. Chromosome and protein folding: In search for unified principles. Curr Opin Struct Biol 2023; 81:102610. [PMID: 37327690 DOI: 10.1016/j.sbi.2023.102610] [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: 03/18/2023] [Revised: 04/24/2023] [Accepted: 04/24/2023] [Indexed: 06/18/2023]
Abstract
Structural biology has traditionally focused on the structures of proteins, short nucleic acids, small molecules, and their complexes. However, it is now widely recognized that the 3D organization of chromosomes should also be included in this list, despite significant differences in scale and complexity of organization. Here we highlight some notable similarities between the folding processes that shape proteins and chromosomes. Both biomolecules are folded by two types of processes: the affinity-mediated interactions, and by active (ATP-dependent) processes. Both chromosome and proteins in vivo can have partially unstructured and non-equilibrium ensembles with yet to be understood functional roles. By analyzing these biological systems in parallel, we can uncover universal principles of biomolecular organization that transcend specific biopolymers.
Collapse
Affiliation(s)
- Leonid A Mirny
- Institute for Medical Engineering and Science, and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| |
Collapse
|
27
|
Corsi F, Rusch E, Goloborodko A. Loop extrusion rules: the next generation. Curr Opin Genet Dev 2023; 81:102061. [PMID: 37354885 DOI: 10.1016/j.gde.2023.102061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 05/12/2023] [Accepted: 05/18/2023] [Indexed: 06/26/2023]
Abstract
The interphase genome of vertebrates contains roughly 100 000 dynamic loops formed by cohesins. These loops are thought to play important roles in many functions, but their exact contribution in each case remains hotly disputed. The key challenge in studying these loops is the lack of a single experimental technique that could reliably and comprehensively visualize their locations and dynamics. Yet, we can infer them using theoretical models that integrate complementary experimental observations. Modeling proved instrumental in showing that cohesins form loops via extrusion. The loop extrusion model made numerous successful qualitative and quantitative predictions and inspired many experiments. However, it also demonstrated limited accuracy in predicting contact maps. Recent research suggests that the original model did not fully account for the intricate details of the mechanism of loop extrusion and its complex regulation. Here, we review the progress in visualizing extrusion and characterizing the cohesin cofactors. These discoveries can be summarized as 'rules' of cohesin movement along chromosomes and incorporated into the next generation of models. Such improved models will enable more accurate inferences of positions and dynamics of cohesin loops and generate better predictions for designing experiments.
Collapse
Affiliation(s)
- Flavia Corsi
- Institute of Molecular Biotechnology, Dr. Bohr-Gasse 3, 1030 Vienna, Austria. https://twitter.com/@flavia_corsi
| | - Emma Rusch
- Institute of Molecular Biotechnology, Dr. Bohr-Gasse 3, 1030 Vienna, Austria. https://twitter.com/@emma__rush
| | - Anton Goloborodko
- Institute of Molecular Biotechnology, Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
| |
Collapse
|
28
|
Galitsyna A, Ulianov SV, Bykov NS, Veil M, Gao M, Perevoschikova K, Gelfand M, Razin SV, Mirny L, Onichtchouk D. Extrusion fountains are hallmarks of chromosome organization emerging upon zygotic genome activation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.15.549120. [PMID: 37503128 PMCID: PMC10370019 DOI: 10.1101/2023.07.15.549120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The first activation of gene expression during development (zygotic genome activation, ZGA) is accompanied by massive changes in chromosome organization. The connection between these two processes remains unknown. Using Hi-C for zebrafish embryos, we found that chromosome folding starts by establishing "fountains", novel elements of chromosome organization, emerging selectively at enhancers upon ZGA. Using polymer simulations, we demonstrate that fountains can emerge as sites of targeted cohesin loading and require two-sided, yet desynchronized, loop extrusion. Specific loss of fountains upon loss of pioneer transcription factors that drive ZGA reveals a causal connection between enhancer activity and fountain formation. Finally, we show that fountains emerge in early Medaka and Xenopus embryos; moreover, we found cohesin-dependent fountain pattern on enhancers of mouse embryonic stem cells. Taken together, fountains are the first enhancer-specific elements of chromosome organization; they constitute starting points of chromosome folding during early development, likely serving as sites of targeted cohesin loading.
Collapse
Affiliation(s)
- Aleksandra Galitsyna
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sergey V. Ulianov
- Institute of Gene Biology, Russian Academy of Sciences, 119334, Russia
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Nikolai S. Bykov
- Institute for Information Transmission Problems (the Kharkevich Institute), Russian Academy of Sciences, Moscow, 127051, Russia
- Centro Nacional de Análisis Genómico (CNAG), Baldiri Reixac 4, Barcelona, 08028 Spain
| | - Marina Veil
- Department of Developmental Biology, University of Freiburg, Freiburg, 79104, Germany
| | - Meijiang Gao
- Department of Developmental Biology, University of Freiburg, Freiburg, 79104, Germany
- Signalling Research Centres BIOSS and CIBSS, Freiburg, 79104, Germany
| | - Kristina Perevoschikova
- Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Mikhail Gelfand
- Institute for Information Transmission Problems (the Kharkevich Institute), Russian Academy of Sciences, Moscow, 127051, Russia
| | - Sergey V. Razin
- Institute of Gene Biology, Russian Academy of Sciences, 119334, Russia
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Leonid Mirny
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Daria Onichtchouk
- Department of Developmental Biology, University of Freiburg, Freiburg, 79104, Germany
- Signalling Research Centres BIOSS and CIBSS, Freiburg, 79104, Germany
- Koltzov Institute of Developmental Biology RAS, Moscow, 119991, Russia
| |
Collapse
|
29
|
Kadam S, Kumari K, Manivannan V, Dutta S, Mitra MK, Padinhateeri R. Predicting scale-dependent chromatin polymer properties from systematic coarse-graining. Nat Commun 2023; 14:4108. [PMID: 37433821 PMCID: PMC10336007 DOI: 10.1038/s41467-023-39907-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 06/30/2023] [Indexed: 07/13/2023] Open
Abstract
Simulating chromatin is crucial for predicting genome organization and dynamics. Although coarse-grained bead-spring polymer models are commonly used to describe chromatin, the relevant bead dimensions, elastic properties, and the nature of inter-bead potentials are unknown. Using nucleosome-resolution contact probability (Micro-C) data, we systematically coarse-grain chromatin and predict quantities essential for polymer representation of chromatin. We compute size distributions of chromatin beads for different coarse-graining scales, quantify fluctuations and distributions of bond lengths between neighboring regions, and derive effective spring constant values. Unlike the prevalent notion, our findings argue that coarse-grained chromatin beads must be considered as soft particles that can overlap, and we derive an effective inter-bead soft potential and quantify an overlap parameter. We also compute angle distributions giving insights into intrinsic folding and local bendability of chromatin. While the nucleosome-linker DNA bond angle naturally emerges from our work, we show two populations of local structural states. The bead sizes, bond lengths, and bond angles show different mean behavior at Topologically Associating Domain (TAD) boundaries and TAD interiors. We integrate our findings into a coarse-grained polymer model and provide quantitative estimates of all model parameters, which can serve as a foundational basis for all future coarse-grained chromatin simulations.
Collapse
Affiliation(s)
- Sangram Kadam
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076, India.
| | - Kiran Kumari
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Vinoth Manivannan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Shuvadip Dutta
- Department of Physics, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Mithun K Mitra
- Department of Physics, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Ranjith Padinhateeri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076, India.
- Sunita Sanghi Centre of Aging and Neurodegenerative Diseases, Indian Institute of Technology Bombay, Mumbai, 400076, India.
| |
Collapse
|
30
|
Jia BB, Jussila A, Kern C, Zhu Q, Ren B. A spatial genome aligner for resolving chromatin architectures from multiplexed DNA FISH. Nat Biotechnol 2023; 41:1004-1017. [PMID: 36593410 PMCID: PMC10344783 DOI: 10.1038/s41587-022-01568-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 10/13/2022] [Indexed: 01/03/2023]
Abstract
Multiplexed fluorescence in situ hybridization (FISH) is a widely used approach for analyzing three-dimensional genome organization, but it is challenging to derive chromosomal conformations from noisy fluorescence signals, and tracing chromatin is not straightforward. Here we report a spatial genome aligner that parses true chromatin signal from noise by aligning signals to a DNA polymer model. Using genomic distances separating imaged loci, our aligner estimates spatial distances expected to separate loci on a polymer in three-dimensional space. Our aligner then evaluates the physical probability observed signals belonging to these loci are connected, thereby tracing chromatin structures. We demonstrate that this spatial genome aligner can efficiently model chromosome architectures from DNA FISH data across multiple scales and be used to predict chromosome ploidies de novo in interphase cells. Reprocessing of previous whole-genome chromosome tracing data with this method indicates the spatial aggregation of sister chromatids in S/G2 phase cells in asynchronous mouse embryonic stem cells and provides evidence for extranumerary chromosomes that remain tightly paired in postmitotic neurons of the adult mouse cortex.
Collapse
Affiliation(s)
- Bojing Blair Jia
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
- Medical Scientist Training Program, University of California San Diego, La Jolla, CA, USA
| | - Adam Jussila
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Colin Kern
- Department of Cellular and Molecular Medicine, Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
| | - Quan Zhu
- Department of Cellular and Molecular Medicine, Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
| | - Bing Ren
- Department of Cellular and Molecular Medicine, Center for Epigenomics, University of California San Diego, La Jolla, CA, USA.
- Ludwig Institute for Cancer Research, La Jolla, CA, USA.
- Institute of Genomic Medicine, Moores Cancer Center, School of Medicine, University of California San Diego, La Jolla, CA, USA.
| |
Collapse
|
31
|
Bajpai G, Safran S. Mesoscale, long-time mixing of chromosomes and its connection to polymer dynamics. PLoS Comput Biol 2023; 19:e1011142. [PMID: 37228178 DOI: 10.1371/journal.pcbi.1011142] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 05/01/2023] [Indexed: 05/27/2023] Open
Abstract
Chromosomes are arranged in distinct territories within the nucleus of animal cells. Recent experiments have shown that these territories overlap at their edges, suggesting partial mixing during interphase. Experiments that knock-down of condensin II proteins during interphase indicate increased chromosome mixing, which demonstrates control of the mixing. In this study, we use a generic polymer simulation to quantify the dynamics of chromosome mixing over time. We introduce the chromosome mixing index, which quantifies the mixing of distinct chromosomes in the nucleus. We find that the chromosome mixing index in a small confinement volume (as a model of the nucleus), increases as a power-law of the time, with the scaling exponent varying non-monotonically with self-interaction and volume fraction. By comparing the chromosome mixing index with both monomer subdiffusion due to (non-topological) intermingling of chromosomes as well as even slower reptation, we show that for relatively large volume fractions, the scaling exponent of the chromosome mixing index is related to Rouse dynamics for relatively weak chromosome attractions and to reptation for strong attractions. In addition, we extend our model to more realistically account for the situation of the Drosophila chromosome by including the heterogeneity of the polymers and their lengths to account for microphase separation of euchromatin and heterochromatin and their interactions with the nuclear lamina. We find that the interaction with the lamina further impedes chromosome mixing.
Collapse
Affiliation(s)
- Gaurav Bajpai
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Samuel Safran
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| |
Collapse
|
32
|
Yang JH, Brandão HB, Hansen AS. DNA double-strand break end synapsis by DNA loop extrusion. Nat Commun 2023; 14:1913. [PMID: 37024496 PMCID: PMC10079674 DOI: 10.1038/s41467-023-37583-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 03/23/2023] [Indexed: 04/08/2023] Open
Abstract
DNA double-strand breaks (DSBs) occur every cell cycle and must be efficiently repaired. Non-homologous end joining (NHEJ) is the dominant pathway for DSB repair in G1-phase. The first step of NHEJ is to bring the two DSB ends back into proximity (synapsis). Although synapsis is generally assumed to occur through passive diffusion, we show that passive diffusion is unlikely to produce the synapsis speed observed in cells. Instead, we hypothesize that DNA loop extrusion facilitates synapsis. By combining experimentally constrained simulations and theory, we show that a simple loop extrusion model constrained by previous live-cell imaging data only modestly accelerates synapsis. Instead, an expanded loop extrusion model with targeted loading of loop extruding factors (LEFs), a small portion of long-lived LEFs, and LEF stabilization by boundary elements and DSB ends achieves fast synapsis with near 100% efficiency. We propose that loop extrusion contributes to DSB repair by mediating fast synapsis.
Collapse
Affiliation(s)
- Jin H Yang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Koch Institute for Integrative Cancer Research, Cambridge, MA, 02142, USA
| | - Hugo B Brandão
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Koch Institute for Integrative Cancer Research, Cambridge, MA, 02142, USA.
- Illumina Inc., San Diego, CA, 92122, USA.
| | - Anders S Hansen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Koch Institute for Integrative Cancer Research, Cambridge, MA, 02142, USA.
| |
Collapse
|
33
|
Banigan EJ, Tang W, van den Berg AA, Stocsits RR, Wutz G, Brandão HB, Busslinger GA, Peters JM, Mirny LA. Transcription shapes 3D chromatin organization by interacting with loop extrusion. Proc Natl Acad Sci U S A 2023; 120:e2210480120. [PMID: 36897969 PMCID: PMC10089175 DOI: 10.1073/pnas.2210480120] [Citation(s) in RCA: 52] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 12/03/2022] [Indexed: 03/12/2023] Open
Abstract
Cohesin folds mammalian interphase chromosomes by extruding the chromatin fiber into numerous loops. "Loop extrusion" can be impeded by chromatin-bound factors, such as CTCF, which generates characteristic and functional chromatin organization patterns. It has been proposed that transcription relocalizes or interferes with cohesin and that active promoters are cohesin loading sites. However, the effects of transcription on cohesin have not been reconciled with observations of active extrusion by cohesin. To determine how transcription modulates extrusion, we studied mouse cells in which we could alter cohesin abundance, dynamics, and localization by genetic "knockouts" of the cohesin regulators CTCF and Wapl. Through Hi-C experiments, we discovered intricate, cohesin-dependent contact patterns near active genes. Chromatin organization around active genes exhibited hallmarks of interactions between transcribing RNA polymerases (RNAPs) and extruding cohesins. These observations could be reproduced by polymer simulations in which RNAPs were moving barriers to extrusion that obstructed, slowed, and pushed cohesins. The simulations predicted that preferential loading of cohesin at promoters is inconsistent with our experimental data. Additional ChIP-seq experiments showed that the putative cohesin loader Nipbl is not predominantly enriched at promoters. Therefore, we propose that cohesin is not preferentially loaded at promoters and that the barrier function of RNAP accounts for cohesin accumulation at active promoters. Altogether, we find that RNAP is an extrusion barrier that is not stationary, but rather, translocates and relocalizes cohesin. Loop extrusion and transcription might interact to dynamically generate and maintain gene interactions with regulatory elements and shape functional genomic organization.
Collapse
Affiliation(s)
- Edward J. Banigan
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA02139
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Wen Tang
- Research Institute of Molecular Pathology, Vienna BioCenter1030Vienna, Austria
| | - Aafke A. van den Berg
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA02139
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Roman R. Stocsits
- Research Institute of Molecular Pathology, Vienna BioCenter1030Vienna, Austria
| | - Gordana Wutz
- Research Institute of Molecular Pathology, Vienna BioCenter1030Vienna, Austria
| | - Hugo B. Brandão
- Graduate Program in Biophysics, Harvard University, Cambridge, MA02138
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
- The Broad Institute of MIT and Harvard, Cambridge, MA02142
| | - Georg A. Busslinger
- Research Institute of Molecular Pathology, Vienna BioCenter1030Vienna, Austria
- Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna1090, Austria
- Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, Vienna1090, Austria
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology, Vienna BioCenter1030Vienna, Austria
| | - Leonid A. Mirny
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA02139
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA02139
| |
Collapse
|
34
|
Li YC, Wu ZP, Zong ZH, Cao XZ. Rheological Role of Stiff Nanorings on Concurrently Strengthening and Toughening Polymer Nanocomposites. ACS Macro Lett 2023; 12:183-188. [PMID: 36692488 DOI: 10.1021/acsmacrolett.2c00610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Nanorings, which are increasingly uncovered in natural systems and synthesized in man-made materials, exhibit dynamics distinct from those known for linear chains. We show in this study that, when immersed in a polymer melt matrix, segments of a stiff nanoring (SNR) have more facilitated subdiffusion, i.e., with a larger scaling exponent in the mean squared displacement, than those belonging to one flexible counterpart, while the whole SNR is more suppressed by its surroundings. It is revealed that adding SNRs contributes to achieving the long-anticipated rheological objective of sol- and gel-like characteristics at high and low shearing frequencies, respectively. This study suggests the promising prospect of exploiting SNRs to concurrently strengthen and toughen target polymer nanocomposites.
Collapse
Affiliation(s)
- Yu-Chao Li
- Department of Physics and Fujian Provincial Key Laboratory for Soft Functional Materials Research, College of Physical Science and Technology, Xiamen University, Xiamen 361005, P.R. China
| | - Zong-Pei Wu
- Department of Physics and Fujian Provincial Key Laboratory for Soft Functional Materials Research, College of Physical Science and Technology, Xiamen University, Xiamen 361005, P.R. China
| | - Ze-Hao Zong
- Department of Physics and Fujian Provincial Key Laboratory for Soft Functional Materials Research, College of Physical Science and Technology, Xiamen University, Xiamen 361005, P.R. China
| | - Xue-Zheng Cao
- Department of Physics and Fujian Provincial Key Laboratory for Soft Functional Materials Research, College of Physical Science and Technology, Xiamen University, Xiamen 361005, P.R. China
| |
Collapse
|
35
|
Unveiling the Machinery behind Chromosome Folding by Polymer Physics Modeling. Int J Mol Sci 2023; 24:ijms24043660. [PMID: 36835064 PMCID: PMC9967178 DOI: 10.3390/ijms24043660] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/06/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
Understanding the mechanisms underlying the complex 3D architecture of mammalian genomes poses, at a more fundamental level, the problem of how two or multiple genomic sites can establish physical contacts in the nucleus of the cells. Beyond stochastic and fleeting encounters related to the polymeric nature of chromatin, experiments have revealed specific, privileged patterns of interactions that suggest the existence of basic organizing principles of folding. In this review, we focus on two major and recently proposed physical processes of chromatin organization: loop-extrusion and polymer phase-separation, both supported by increasing experimental evidence. We discuss their implementation into polymer physics models, which we test against available single-cell super-resolution imaging data, showing that both mechanisms can cooperate to shape chromatin structure at the single-molecule level. Next, by exploiting the comprehension of the underlying molecular mechanisms, we illustrate how such polymer models can be used as powerful tools to make predictions in silico that can complement experiments in understanding genome folding. To this aim, we focus on recent key applications, such as the prediction of chromatin structure rearrangements upon disease-associated mutations and the identification of the putative chromatin organizing factors that orchestrate the specificity of DNA regulatory contacts genome-wide.
Collapse
|
36
|
Consistencies and contradictions in different polymer models of chromatin architecture. Comput Struct Biotechnol J 2023; 21:1084-1091. [PMID: 36789261 PMCID: PMC9900451 DOI: 10.1016/j.csbj.2023.01.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/23/2023] [Accepted: 01/23/2023] [Indexed: 01/26/2023] Open
Abstract
Genetic information is stored in very long DNA molecules, which are folded to form chromatin, a similarly long polymer fibre that is ultimately organised into chromosomes. The organisation of chromatin is fundamental to many cellular functions, from the expression of the genetic information to cell division. As a long polymer, chromatin is very flexible and may adopt a myriad of shapes. Globally, the polymer physics governing chromatin dynamics is very well understood. But chromatin is not uniform and regions of it, with chemical modifications and bound effectors, form domains and compartments through mechanisms not yet clear. Polymer models have been successfully used to investigate these mechanisms to explain cytological observations and build hypothesis for experimental validation. Many different approaches to conceptualise chromatin in polymer models can be envisioned and each reflects different aspects. Here, we compare recent approaches that aim at reproducing prominent features of interphase chromatin organisation: the compartmentalisation into eu- and heterochromatin compartments, the formation of a nucleolus, chromatin loops and the rosette and Rabl conformations of interphase chromosomes. We highlight commonalities and contradictions that point to a modulation of the mechanisms involved to fine degree. Consolidating models will require the inclusion of yet hidden or neglected parameters.
Collapse
|
37
|
Guha S, Mitra MK. Multivalent binding proteins can drive collapse and reswelling of chromatin in confinement. SOFT MATTER 2022; 19:153-163. [PMID: 36484149 DOI: 10.1039/d2sm00612j] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Collapsed conformations of chromatin have been long suspected of being mediated by interactions with multivalent binding proteins, which can bring together distant sections of the chromatin fiber. In this study, we use Langevin dynamics simulation of a coarse grained chromatin polymer to show that the role of binding proteins can be more nuanced than previously suspected. In particular, for chromatin polymer in confinement, entropic forces can drive reswelling of collapsed chromatin with increasing binder concentrations, and this reswelling transition happens at physiologically relevant binder concentrations. Both the extent of collapse, and also of reswelling depends on the strength of confinement. We also study the kinetics of collapse and reswelling and show that both processes occur in similar timescales. We characterise this reswelling of chromatin in biologically relevant regimes and discuss the non-trivial role of multivalent binding proteins in mediating the spatial organisation of the genome.
Collapse
Affiliation(s)
- Sougata Guha
- Department of Physics, Indian Institute of Technology Bombay, Mumbai 400076, India.
| | - Mithun K Mitra
- Department of Physics, Indian Institute of Technology Bombay, Mumbai 400076, India.
| |
Collapse
|
38
|
Sitmukhambetov S, Dinh B, Lai Y, Banigan EJ, Pan Z, Jia X, Chi Y. Development and implementation of a metaphase DNA model for ionizing radiation induced DNA damage calculation. Phys Med Biol 2022; 68:10.1088/1361-6560/aca5ea. [PMID: 36533598 PMCID: PMC9969557 DOI: 10.1088/1361-6560/aca5ea] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 11/24/2022] [Indexed: 11/25/2022]
Abstract
Objective. To develop a metaphase chromosome model representing the complete genome of a human lymphocyte cell to support microscopic Monte Carlo (MMC) simulation-based radiation-induced DNA damage studies.Approach. We first employed coarse-grained polymer physics simulation to obtain a rod-shaped chromatid segment of 730 nm in diameter and 460 nm in height to match Hi-C data. We then voxelized the segment with a voxel size of 11 nm per side and connected the chromatid with 30 types of pre-constructed nucleosomes and 6 types of linker DNAs in base pair (bp) resolutions. Afterward, we piled different numbers of voxelized chromatid segments to create 23 pairs of chromosomes of 1-5μm long. Finally, we arranged the chromosomes at the cell metaphase plate of 5.5μm in radius to create the complete set of metaphase chromosomes. We implemented the model in gMicroMC simulation by denoting the DNA structure in a four-level hierarchical tree: nucleotide pairs, nucleosomes and linker DNAs, chromatid segments, and chromosomes. We applied the model to compute DNA damage under different radiation conditions and compared the results to those obtained with G0/G1 model and experimental measurements. We also performed uncertainty analysis for relevant simulation parameters.Main results. The chromatid segment was successfully voxelized and connected in bps resolution, containing 26.8 mega bps (Mbps) of DNA. With 466 segments, we obtained the metaphase chromosome containing 12.5 Gbps of DNA. Applying it to compute the radiation-induced DNA damage, the obtained results were self-consistent and agreed with experimental measurements. Through the parameter uncertainty study, we found that the DNA damage ratio between metaphase and G0/G1 phase models was not sensitive to the chemical simulation time. The damage was also not sensitive to the specific parameter settings in the polymer physics simulation, as long as the produced metaphase model followed a similar contact map distribution.Significance. Experimental data reveal that ionizing radiation induced DNA damage is cell cycle dependent. Yet, DNA chromosome models, except for the G0/G1 phase, are not available in the state-of-the-art MMC simulation. For the first time, we successfully built a metaphase chromosome model and implemented it into MMC simulation for radiation-induced DNA damage computation.
Collapse
Affiliation(s)
| | - Bryan Dinh
- Department of Physics, the University of Texas at Arlington, Arlington, TX 76019, USA
| | - Youfang Lai
- Department of Physics, the University of Texas at Arlington, Arlington, TX 76019, USA
| | - Edward J. Banigan
- Institute for Medical Engineering & Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Zui Pan
- Graduate Nursing, the University of Texas at Arlington, Arlington, TX 76019, USA
| | - Xun Jia
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University, MD 21231, USA
| | - Yujie Chi
- Department of Physics, the University of Texas at Arlington, Arlington, TX 76019, USA
| |
Collapse
|
39
|
Rossini R, Kumar V, Mathelier A, Rognes T, Paulsen J. MoDLE: high-performance stochastic modeling of DNA loop extrusion interactions. Genome Biol 2022; 23:247. [PMID: 36451166 PMCID: PMC9710047 DOI: 10.1186/s13059-022-02815-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 11/17/2022] [Indexed: 12/03/2022] Open
Abstract
DNA loop extrusion emerges as a key process establishing genome structure and function. We introduce MoDLE, a computational tool for fast, stochastic modeling of molecular contacts from DNA loop extrusion capable of simulating realistic contact patterns genome wide in a few minutes. MoDLE accurately simulates contact maps in concordance with existing molecular dynamics approaches and with Micro-C data and does so orders of magnitude faster than existing approaches. MoDLE runs efficiently on machines ranging from laptops to high performance computing clusters and opens up for exploratory and predictive modeling of 3D genome structure in a wide range of settings.
Collapse
Affiliation(s)
- Roberto Rossini
- Department of Biosciences, University of Oslo, 0316, Oslo, Norway
| | - Vipin Kumar
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318, Oslo, Norway
| | - Anthony Mathelier
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318, Oslo, Norway
| | - Torbjørn Rognes
- Centre for Bioinformatics, Department of Informatics, University of Oslo, 0316, Oslo, Norway
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, 0424, Oslo, Norway
| | - Jonas Paulsen
- Department of Biosciences, University of Oslo, 0316, Oslo, Norway.
- Centre for Bioinformatics, Department of Informatics, University of Oslo, 0316, Oslo, Norway.
| |
Collapse
|
40
|
Kim J, Jimenez DS, Ragipani B, Zhang B, Street LA, Kramer M, Albritton SE, Winterkorn LH, Morao AK, Ercan S. Condensin DC loads and spreads from recruitment sites to create loop-anchored TADs in C. elegans. eLife 2022; 11:e68745. [PMID: 36331876 PMCID: PMC9635877 DOI: 10.7554/elife.68745] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 10/23/2022] [Indexed: 11/06/2022] Open
Abstract
Condensins are molecular motors that compact DNA via linear translocation. In Caenorhabditis elegans, the X-chromosome harbors a specialized condensin that participates in dosage compensation (DC). Condensin DC is recruited to and spreads from a small number of recruitment elements on the X-chromosome (rex) and is required for the formation of topologically associating domains (TADs). We take advantage of autosomes that are largely devoid of condensin DC and TADs to address how rex sites and condensin DC give rise to the formation of TADs. When an autosome and X-chromosome are physically fused, despite the spreading of condensin DC into the autosome, no TAD was created. Insertion of a strong rex on the X-chromosome results in the TAD boundary formation regardless of sequence orientation. When the same rex is inserted on an autosome, despite condensin DC recruitment, there was no spreading or features of a TAD. On the other hand, when a 'super rex' composed of six rex sites or three separate rex sites are inserted on an autosome, recruitment and spreading of condensin DC led to the formation of TADs. Therefore, recruitment to and spreading from rex sites are necessary and sufficient for recapitulating loop-anchored TADs observed on the X-chromosome. Together our data suggest a model in which rex sites are both loading sites and bidirectional barriers for condensin DC, a one-sided loop-extruder with movable inactive anchor.
Collapse
Affiliation(s)
- Jun Kim
- Department of Biology and Center for Genomics and Systems Biology, New York UniversityNew YorkUnited States
| | - David S Jimenez
- Department of Biology and Center for Genomics and Systems Biology, New York UniversityNew YorkUnited States
| | - Bhavana Ragipani
- Department of Biology and Center for Genomics and Systems Biology, New York UniversityNew YorkUnited States
| | - Bo Zhang
- UCSF HSWSan FranciscoUnited States
| | - Lena A Street
- Department of Biology and Center for Genomics and Systems Biology, New York UniversityNew YorkUnited States
| | - Maxwell Kramer
- Department of Biology and Center for Genomics and Systems Biology, New York UniversityNew YorkUnited States
| | - Sarah E Albritton
- Department of Biology and Center for Genomics and Systems Biology, New York UniversityNew YorkUnited States
| | - Lara H Winterkorn
- Department of Biology and Center for Genomics and Systems Biology, New York UniversityNew YorkUnited States
| | - Ana K Morao
- Department of Biology and Center for Genomics and Systems Biology, New York UniversityNew YorkUnited States
| | - Sevinc Ercan
- Department of Biology and Center for Genomics and Systems Biology, New York UniversityNew YorkUnited States
| |
Collapse
|
41
|
Luppino JM, Field A, Nguyen SC, Park DS, Shah PP, Abdill RJ, Lan Y, Yunker R, Jain R, Adelman K, Joyce EF. Co-depletion of NIPBL and WAPL balance cohesin activity to correct gene misexpression. PLoS Genet 2022. [PMID: 36449519 DOI: 10.1101/2022.04.19.488785] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
The relationship between cohesin-mediated chromatin looping and gene expression remains unclear. NIPBL and WAPL are two opposing regulators of cohesin activity; depletion of either is associated with changes in both chromatin folding and transcription across a wide range of cell types. However, a direct comparison of their individual and combined effects on gene expression in the same cell type is lacking. We find that NIPBL or WAPL depletion in human HCT116 cells each alter the expression of ~2,000 genes, with only ~30% of the genes shared between the conditions. We find that clusters of differentially expressed genes within the same topologically associated domain (TAD) show coordinated misexpression, suggesting some genomic domains are especially sensitive to both more or less cohesin. Finally, co-depletion of NIPBL and WAPL restores the majority of gene misexpression as compared to either knockdown alone. A similar set of NIPBL-sensitive genes are rescued following CTCF co-depletion. Together, this indicates that altered transcription due to reduced cohesin activity can be functionally offset by removal of either its negative regulator (WAPL) or the physical barriers (CTCF) that restrict loop-extrusion events.
Collapse
Affiliation(s)
- Jennifer M Luppino
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Andrew Field
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Ludwig Center at Harvard, Boston, Massachusetts, United States of America
| | - Son C Nguyen
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Daniel S Park
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Parisha P Shah
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Cell and Developmental Biology, Department of Medicine, Institute of Regenerative Medicine, Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Richard J Abdill
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Cell and Developmental Biology, Department of Medicine, Institute of Regenerative Medicine, Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Yemin Lan
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Rebecca Yunker
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Rajan Jain
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Cell and Developmental Biology, Department of Medicine, Institute of Regenerative Medicine, Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Karen Adelman
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Ludwig Center at Harvard, Boston, Massachusetts, United States of America
- The Eli and Edythe L. Broad Institute, Cambridge, Massachusetts, United States of America
| | - Eric F Joyce
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| |
Collapse
|
42
|
Kumari K, Ravi Prakash J, Padinhateeri R. Heterogeneous interactions and polymer entropy decide organization and dynamics of chromatin domains. Biophys J 2022; 121:2794-2812. [PMID: 35672951 PMCID: PMC9382282 DOI: 10.1016/j.bpj.2022.06.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 04/28/2022] [Accepted: 06/01/2022] [Indexed: 11/02/2022] Open
Abstract
Chromatin is known to be organized into multiple domains of varying sizes and compaction. While these domains are often imagined as static structures, they are highly dynamic and show cell-to-cell variability. Since processes such as gene regulation and DNA replication occur in the context of these domains, it is important to understand their organization, fluctuation, and dynamics. To simulate chromatin domains, one requires knowledge of interaction strengths among chromatin segments. Here, we derive interaction-strength parameters from experimentally known contact maps and use them to predict chromatin organization and dynamics. Taking two domains on the human chromosome as examples, we investigate its three-dimensional organization, size/shape fluctuations, and dynamics of different segments within a domain, accounting for hydrodynamic effects. Considering different cell types, we quantify changes in interaction strengths and chromatin shape fluctuations in different epigenetic states. Perturbing the interaction strengths systematically, we further investigate how epigenetic-like changes can alter the spatio-temporal nature of the domains. Our results show that heterogeneous weak interactions are crucial in determining the organization of the domains. Computing effective stiffness and relaxation times, we investigate how perturbations in interactions affect the solid- and liquid-like nature of chromatin domains. Quantifying dynamics of chromatin segments within a domain, we show how the competition between polymer entropy and interaction energy influence the timescales of loop formation and maintenance of stable loops.
Collapse
Affiliation(s)
- Kiran Kumari
- IITB-Monash Research Academy, Indian Institute of Technology Bombay, Mumbai, Maharashtra, 400076, India; Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra 400076, India; Department of Chemical Engineering, Monash University, Melbourne, VIC 3800, Australia.
| | - J Ravi Prakash
- Department of Chemical Engineering, Monash University, Melbourne, VIC 3800, Australia.
| | - Ranjith Padinhateeri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra 400076, India.
| |
Collapse
|
43
|
Conte M, Irani E, Chiariello AM, Abraham A, Bianco S, Esposito A, Nicodemi M. Loop-extrusion and polymer phase-separation can co-exist at the single-molecule level to shape chromatin folding. Nat Commun 2022; 13:4070. [PMID: 35831310 PMCID: PMC9279381 DOI: 10.1038/s41467-022-31856-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 07/06/2022] [Indexed: 11/09/2022] Open
Abstract
Loop-extrusion and phase-separation have been proposed as mechanisms that shape chromosome spatial organization. It is unclear, however, how they perform relative to each other in explaining chromatin architecture data and whether they compete or co-exist at the single-molecule level. Here, we compare models of polymer physics based on loop-extrusion and phase-separation, as well as models where both mechanisms act simultaneously in a single molecule, against multiplexed FISH data available in human loci in IMR90 and HCT116 cells. We find that the different models recapitulate bulk Hi-C and average multiplexed microscopy data. Single-molecule chromatin conformations are also well captured, especially by phase-separation based models that better reflect the experimentally reported segregation in globules of the considered genomic loci and their cell-to-cell structural variability. Such a variability is consistent with two main concurrent causes: single-cell epigenetic heterogeneity and an intrinsic thermodynamic conformational degeneracy of folding. Overall, the model combining loop-extrusion and polymer phase-separation provides a very good description of the data, particularly higher-order contacts, showing that the two mechanisms can co-exist in shaping chromatin architecture in single cells.
Collapse
Affiliation(s)
- Mattia Conte
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, 80126, Naples, Italy
| | - Ehsan Irani
- Berlin Institute for Medical Systems Biology, Max-Delbrück Centre (MDC) for Molecular Medicine, Berlin, Germany
- Berlin Institute of Health (BIH), MDC-Berlin, Berlin, Germany
| | - Andrea M Chiariello
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, 80126, Naples, Italy
| | - Alex Abraham
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, 80126, Naples, Italy
| | - Simona Bianco
- Berlin Institute for Medical Systems Biology, Max-Delbrück Centre (MDC) for Molecular Medicine, Berlin, Germany
| | - Andrea Esposito
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, 80126, Naples, Italy
| | - Mario Nicodemi
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, 80126, Naples, Italy.
- Berlin Institute for Medical Systems Biology, Max-Delbrück Centre (MDC) for Molecular Medicine, Berlin, Germany.
- Berlin Institute of Health (BIH), MDC-Berlin, Berlin, Germany.
| |
Collapse
|
44
|
Mirny L, Dekker J. Mechanisms of Chromosome Folding and Nuclear Organization: Their Interplay and Open Questions. Cold Spring Harb Perspect Biol 2022; 14:a040147. [PMID: 34518339 PMCID: PMC9248823 DOI: 10.1101/cshperspect.a040147] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Microscopy and genomic approaches provide detailed descriptions of the three-dimensional folding of chromosomes and nuclear organization. The fundamental question is how activity of molecules at the nanometer scale can lead to complex and orchestrated spatial organization at the scale of chromosomes and the whole nucleus. At least three key mechanisms can bridge across scales: (1) tethering of specific loci to nuclear landmarks leads to massive reorganization of the nucleus; (2) spatial compartmentalization of chromatin, which is driven by molecular affinities, results in spatial isolation of active and inactive chromatin; and (3) loop extrusion activity of SMC (structural maintenance of chromosome) complexes can explain many features of interphase chromatin folding and underlies key phenomena during mitosis. Interestingly, many features of chromosome organization ultimately result from collective action and the interplay between these mechanisms, and are further modulated by transcription and topological constraints. Finally, we highlight some outstanding questions that are critical for our understanding of nuclear organization and function. We believe many of these questions can be answered in the coming years.
Collapse
Affiliation(s)
- Leonid Mirny
- Institute for Medical Engineering and Science, and Department of Physics, MIT, Cambridge, Massachusetts 02139, USA
| | - Job Dekker
- Howard Hughes Medical Institute, and Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| |
Collapse
|
45
|
Yamamoto T, Schiessel H. Loop extrusion driven volume phase transition of entangled chromosomes. Biophys J 2022; 121:2742-2750. [PMID: 35706364 DOI: 10.1016/j.bpj.2022.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/26/2022] [Accepted: 06/09/2022] [Indexed: 11/24/2022] Open
Abstract
Experiments on reconstituted chromosomes have revealed that mitotic chromosomes are assembled even without nucleosomes. When topoisomerase II (topo II) is depleted from such reconstituted chromosomes, these chromosomes are not disentangled and form "sparklers," where DNA and linker histone are condensed in the core and condensin is localized at the periphery. To understand the mechanism of the assembly of sparklers, we here take into account the loop extrusion by condensin in an extension of the theory of entangled polymer gels. The loop extrusion stiffens an entangled DNA network because DNA segments in the elastically effective chains are translocated to loops, which are elastically ineffective. Our theory predicts that the loop extrusion by condensin drives the volume phase transition that collapses a swollen entangled DNA gel because the stiffening of the network destabilizes the swollen phase. This may be an important piece to understand the mechanism of the assembly of mitotic chromosomes.
Collapse
Affiliation(s)
- Tetsuya Yamamoto
- Institute for Chemical Reaction Design and Discovery, Hokkaido University, Sapporo, Japan.
| | - Helmut Schiessel
- Cluster of Excellence Physics of Life, TU Dresden, Dresden, Germany
| |
Collapse
|
46
|
Yildirim A, Boninsegna L, Zhan Y, Alber F. Uncovering the Principles of Genome Folding by 3D Chromatin Modeling. Cold Spring Harb Perspect Biol 2022; 14:a039693. [PMID: 34400556 PMCID: PMC9248826 DOI: 10.1101/cshperspect.a039693] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Our understanding of how genomic DNA is tightly packed inside the nucleus, yet is still accessible for vital cellular processes, has grown dramatically over recent years with advances in microscopy and genomics technologies. Computational methods have played a pivotal role in the structural interpretation of experimental data, which helped unravel some organizational principles of genome folding. Here, we give an overview of current computational efforts in mechanistic and data-driven 3D chromatin structure modeling. We discuss strengths and limitations of different methods and evaluate the added value and benefits of computational approaches to infer the 3D structural and dynamic properties of the genome and its underlying mechanisms at different scales and resolution, ranging from the dynamic formation of chromatin loops and topological associated domains to nuclear compartmentalization of chromatin and nuclear bodies.
Collapse
Affiliation(s)
- Asli Yildirim
- Institute for Quantitative and Computational Biosciences, Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Lorenzo Boninsegna
- Institute for Quantitative and Computational Biosciences, Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Yuxiang Zhan
- Institute for Quantitative and Computational Biosciences, Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, California 90095, USA
- Quantitative and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
| | - Frank Alber
- Institute for Quantitative and Computational Biosciences, Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, California 90095, USA
- Quantitative and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
| |
Collapse
|
47
|
Nomidis SK, Carlon E, Gruber S, Marko JF. DNA tension-modulated translocation and loop extrusion by SMC complexes revealed by molecular dynamics simulations. Nucleic Acids Res 2022; 50:4974-4987. [PMID: 35474142 PMCID: PMC9122525 DOI: 10.1093/nar/gkac268] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 03/21/2022] [Accepted: 04/04/2022] [Indexed: 12/19/2022] Open
Abstract
Structural Maintenance of Chromosomes (SMC) complexes play essential roles in genome organization across all domains of life. To determine how the activities of these large (≈50 nm) complexes are controlled by ATP binding and hydrolysis, we developed a molecular dynamics model that accounts for conformational motions of the SMC and DNA. The model combines DNA loop capture with an ATP-induced 'power stroke' to translocate the SMC complex along DNA. This process is sensitive to DNA tension: at low tension (0.1 pN), the model makes loop-capture steps of average 60 nm and up to 200 nm along DNA (larger than the complex itself), while at higher tension, a distinct inchworm-like translocation mode appears. By tethering DNA to an experimentally-observed additional binding site ('safety belt'), the model SMC complex can perform loop extrusion (LE). The dependence of LE on DNA tension is distinct for fixed DNA tension vs. fixed DNA end points: LE reversal occurs above 0.5 pN for fixed tension, while LE stalling without reversal occurs at about 2 pN for fixed end points. Our model matches recent experimental results for condensin and cohesin, and makes testable predictions for how specific structural variations affect SMC function.
Collapse
Affiliation(s)
- Stefanos K Nomidis
- Laboratory for Soft Matter and Biophysics, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
- Flemish Institute for Technological Research (VITO), Boeretang 200, B-2400 Mol, Belgium
| | - Enrico Carlon
- Laboratory for Soft Matter and Biophysics, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Stephan Gruber
- Départment de Microbiologie Fondamentale, Université de Lausanne, 1015 Lausanne, Switzerland
| | - John F Marko
- Department of Physics and Astronomy, and Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA
| |
Collapse
|
48
|
Brahmachari S, Contessoto V, Di Pierro M, Onuchic J. Shaping the genome via lengthwise compaction, phase separation, and lamina adhesion. Nucleic Acids Res 2022; 50:4258-4271. [PMID: 35420130 PMCID: PMC9071446 DOI: 10.1093/nar/gkac231] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/02/2022] [Accepted: 04/11/2022] [Indexed: 01/13/2023] Open
Abstract
The link between genomic structure and biological function is yet to be consolidated, it is, however, clear that physical manipulation of the genome, driven by the activity of a variety of proteins, is a crucial step. To understand the consequences of the physical forces underlying genome organization, we build a coarse-grained polymer model of the genome, featuring three fundamentally distinct classes of interactions: lengthwise compaction, i.e., compaction of chromosomes along its contour, self-adhesion among epigenetically similar genomic segments, and adhesion of chromosome segments to the nuclear envelope or lamina. We postulate that these three types of interactions sufficiently represent the concerted action of the different proteins organizing the genome architecture and show that an interplay among these interactions can recapitulate the architectural variants observed across the tree of life. The model elucidates how an interplay of forces arising from the three classes of genomic interactions can drive drastic, yet predictable, changes in the global genome architecture, and makes testable predictions. We posit that precise control over these interactions in vivo is key to the regulation of genome architecture.
Collapse
Affiliation(s)
| | | | - Michele Di Pierro
- Department of Physics, and Center for Theoretical Biological Physics, Northeastern University, Boston, MA 02115, USA
| | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
- Department of Physics and Astronomy, Department of Chemistry, Department of BioSciences, Rice University, Houston TX 77005, USA
| |
Collapse
|
49
|
Galupa R, Picard C, Servant N, Nora EP, Zhan Y, van Bemmel JG, El Marjou F, Johanneau C, Borensztein M, Ancelin K, Giorgetti L, Heard E. Inversion of a topological domain leads to restricted changes in its gene expression and affects interdomain communication. Development 2022; 149:275259. [PMID: 35502750 PMCID: PMC9148567 DOI: 10.1242/dev.200568] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 02/28/2022] [Indexed: 01/02/2023]
Abstract
The interplay between the topological organization of the genome and the regulation of gene expression remains unclear. Depletion of molecular factors (e.g. CTCF) underlying topologically associating domains (TADs) leads to modest alterations in gene expression, whereas genomic rearrangements involving TAD boundaries disrupt normal gene expression and can lead to pathological phenotypes. Here, we targeted the TAD neighboring that of the noncoding transcript Xist, which controls X-chromosome inactivation. Inverting 245 kb within the TAD led to expected rearrangement of CTCF-based contacts but revealed heterogeneity in the 'contact' potential of different CTCF sites. Expression of most genes therein remained unaffected in mouse embryonic stem cells and during differentiation. Interestingly, expression of Xist was ectopically upregulated. The same inversion in mouse embryos led to biased Xist expression. Smaller inversions and deletions of CTCF clusters led to similar results: rearrangement of contacts and limited changes in local gene expression, but significant changes in Xist expression in embryos. Our study suggests that the wiring of regulatory interactions within a TAD can influence the expression of genes in neighboring TADs, highlighting the existence of mechanisms of inter-TAD communication.
Collapse
Affiliation(s)
- Rafael Galupa
- Mammalian Developmental Epigenetics Group, Genetics and Developmental Biology Unit, Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris 75005, France
| | - Christel Picard
- Mammalian Developmental Epigenetics Group, Genetics and Developmental Biology Unit, Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris 75005, France
| | - Nicolas Servant
- Bioinformatics, Biostatistics, Epidemiology and Computational Systems Unit, Institut Curie, PSL Research University, INSERM U900, Paris 75005, France.,MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris 75006, France
| | - Elphège P Nora
- Mammalian Developmental Epigenetics Group, Genetics and Developmental Biology Unit, Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris 75005, France
| | - Yinxiu Zhan
- Friedrich Miescher Institute for Biomedical Research, Basel 4058, Switzerland.,University of Basel, Basel 4001, Switzerland
| | - Joke G van Bemmel
- Mammalian Developmental Epigenetics Group, Genetics and Developmental Biology Unit, Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris 75005, France
| | | | | | - Maud Borensztein
- Mammalian Developmental Epigenetics Group, Genetics and Developmental Biology Unit, Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris 75005, France
| | - Katia Ancelin
- Mammalian Developmental Epigenetics Group, Genetics and Developmental Biology Unit, Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris 75005, France
| | - Luca Giorgetti
- Friedrich Miescher Institute for Biomedical Research, Basel 4058, Switzerland
| | - Edith Heard
- Mammalian Developmental Epigenetics Group, Genetics and Developmental Biology Unit, Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris 75005, France.,Collège de France, Paris 75231, France
| |
Collapse
|
50
|
Gabriele M, Brandão HB, Grosse-Holz S, Jha A, Dailey GM, Cattoglio C, Hsieh THS, Mirny L, Zechner C, Hansen AS. Dynamics of CTCF- and cohesin-mediated chromatin looping revealed by live-cell imaging. Science 2022; 376:496-501. [PMID: 35420890 PMCID: PMC9069445 DOI: 10.1126/science.abn6583] [Citation(s) in RCA: 185] [Impact Index Per Article: 92.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Animal genomes are folded into loops and topologically associating domains (TADs) by CTCF and loop-extruding cohesins, but the live dynamics of loop formation and stability remain unknown. Here, we directly visualized chromatin looping at the Fbn2 TAD in mouse embryonic stem cells using super-resolution live-cell imaging and quantified looping dynamics by Bayesian inference. Unexpectedly, the Fbn2 loop was both rare and dynamic, with a looped fraction of approximately 3 to 6.5% and a median loop lifetime of approximately 10 to 30 minutes. Our results establish that the Fbn2 TAD is highly dynamic, and about 92% of the time, cohesin-extruded loops exist within the TAD without bridging both CTCF boundaries. This suggests that single CTCF boundaries, rather than the fully CTCF-CTCF looped state, may be the primary regulators of functional interactions.
Collapse
Affiliation(s)
- Michele Gabriele
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- The Broad Institute of MIT and Harvard; Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research; Cambridge, MA, 02139, USA
| | - Hugo B. Brandão
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- The Broad Institute of MIT and Harvard; Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research; Cambridge, MA, 02139, USA
| | - Simon Grosse-Holz
- Department of Physics, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Institut Curie; Paris 75005, France
| | - Asmita Jha
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- The Broad Institute of MIT and Harvard; Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research; Cambridge, MA, 02139, USA
| | - Gina M. Dailey
- Department of Molecular and Cell Biology, University of California, Berkeley; Berkeley, CA 94720, USA
| | - Claudia Cattoglio
- Department of Molecular and Cell Biology, University of California, Berkeley; Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley; Berkeley, CA 94720, USA
| | - Tsung-Han S. Hsieh
- Department of Molecular and Cell Biology, University of California, Berkeley; Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley; Berkeley, CA 94720, USA
| | - Leonid Mirny
- Department of Physics, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Institut Curie; Paris 75005, France
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Christoph Zechner
- Max Planck Institute of Molecular Cell Biology & Genetics; Dresden, Germany
- Center for Systems Biology Dresden; Dresden, Germany
- Cluster of Excellence Physics of Life and Faculty of Computer Science, TU Dresden; Dresden, Germany
| | - Anders S. Hansen
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- The Broad Institute of MIT and Harvard; Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research; Cambridge, MA, 02139, USA
| |
Collapse
|