1
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Attar AG, Paturej J, Banigan EJ, Erbaş A. Chromatin phase separation and nuclear shape fluctuations are correlated in a polymer model of the nucleus. Nucleus 2024; 15:2351957. [PMID: 38753956 DOI: 10.1080/19491034.2024.2351957] [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: 01/30/2024] [Accepted: 04/28/2024] [Indexed: 05/18/2024] Open
Abstract
Abnormal cell nuclear shapes are hallmarks of diseases, including progeria, muscular dystrophy, and many cancers. Experiments have shown that disruption of heterochromatin and increases in euchromatin lead to nuclear deformations, such as blebs and ruptures. However, the physical mechanisms through which chromatin governs nuclear shape are poorly understood. To investigate how heterochromatin and euchromatin might govern nuclear morphology, we studied chromatin microphase separation in a composite coarse-grained polymer and elastic shell simulation model. By varying chromatin density, heterochromatin composition, and heterochromatin-lamina interactions, we show how the chromatin phase organization may perturb nuclear shape. Increasing chromatin density stabilizes the lamina against large fluctuations. However, increasing heterochromatin levels or heterochromatin-lamina interactions enhances nuclear shape fluctuations by a "wetting"-like interaction. In contrast, fluctuations are insensitive to heterochromatin's internal structure. Our simulations suggest that peripheral heterochromatin accumulation could perturb nuclear morphology, while nuclear shape stabilization likely occurs through mechanisms other than chromatin microphase organization.
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Affiliation(s)
- Ali Goktug Attar
- UNAM-National Nanotechnology Research Center and Institute of Materials Science & Nanotechnology, Bilkent University, Ankara, Turkey
| | | | - Edward J Banigan
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Aykut Erbaş
- UNAM-National Nanotechnology Research Center and Institute of Materials Science & Nanotechnology, Bilkent University, Ankara, Turkey
- Institute of Physics, University of Silesia, Chorzów, Poland
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2
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Solovei I, Mirny L. Spandrels of the cell nucleus. Curr Opin Cell Biol 2024; 90:102421. [PMID: 39180905 DOI: 10.1016/j.ceb.2024.102421] [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: 06/08/2024] [Revised: 07/18/2024] [Accepted: 08/02/2024] [Indexed: 08/27/2024]
Abstract
S.J. Gould and R. Lewontin in their famous "Spandrels paper" (1979) argued that many anatomical elements arise in evolution not due to their "current utility" but rather due to other "reasons for origin", such as other developmental processes, physical constraints and mechanical forces. Here, in the same spirit, we argue that a variety of molecular processes, physical constraints, and mechanical forces, alone or together, generate structures that are detectable in the cell nucleus, yet these structures themselves may not carry any specific function, being a mere reflection of processes that produced them.
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Affiliation(s)
- Irina Solovei
- Biocenter, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany.
| | - Leonid Mirny
- Institute for Medical Engineering and Science, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA.
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3
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Li H, Playter C, Das P, McCord RP. Chromosome compartmentalization: causes, changes, consequences, and conundrums. Trends Cell Biol 2024; 34:707-727. [PMID: 38395734 PMCID: PMC11339242 DOI: 10.1016/j.tcb.2024.01.009] [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: 10/31/2023] [Revised: 01/12/2024] [Accepted: 01/22/2024] [Indexed: 02/25/2024]
Abstract
The spatial segregation of the genome into compartments is a major feature of 3D genome organization. New data on mammalian chromosome organization across different conditions reveal important information about how and why these compartments form and change. A combination of epigenetic state, nuclear body tethering, physical forces, gene expression, and replication timing (RT) can all influence the establishment and alteration of chromosome compartments. We review the causes and implications of genomic regions undergoing a 'compartment switch' that changes their physical associations and spatial location in the nucleus. About 20-30% of genomic regions change compartment during cell differentiation or cancer progression, whereas alterations in response to a stimulus within a cell type are usually much more limited. However, even a change in 1-2% of genomic bins may have biologically relevant implications. Finally, we review the effects of compartment changes on gene regulation, DNA damage repair, replication, and the physical state of the cell.
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Affiliation(s)
- Heng Li
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA
| | - Christopher Playter
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA
| | - Priyojit Das
- University of Tennessee-Oak Ridge National Laboratory (UT-ORNL) Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, USA
| | - Rachel Patton McCord
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA.
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4
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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.
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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
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5
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Nie Y, Wang M. Dynamic Changes in Histone Modifications Are Associated with Differential Chromatin Interactions. Genes (Basel) 2024; 15:988. [PMID: 39202349 PMCID: PMC11353334 DOI: 10.3390/genes15080988] [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: 06/13/2024] [Revised: 07/19/2024] [Accepted: 07/24/2024] [Indexed: 09/03/2024] Open
Abstract
Eukaryotic genomes are organized into chromatin domains through long-range chromatin interactions which are mediated by the binding of architectural proteins, such as CTCF and cohesin, and histone modifications. Based on the published Hi-C and ChIP-seq datasets in human monocyte-derived macrophages, we identified 206 and 127 differential chromatin interactions (DCIs) that were not located within transcription readthrough regions in influenza A virus- and interferon β-treated cells, respectively, and found that the binding positions of CTCF and RAD21 within more than half of the DCI sites did not change. However, five histone modifications, H3K4me3, H3K27ac, H3K36me3, H3K9me3, and H3K27me3, showed significantly more dramatic changes than CTCF and RAD21 within the DCI sites. For H3K4me3, H3K27ac, H3K36me3, and H3K27me3, significantly more dramatic changes were observed outside than within the DCI sites. We further applied a motif scanning approach to discover proteins that might correlate with changes in histone modifications and chromatin interactions and found that PRDM9, ZNF384, and STAT2 frequently bound to DNA sequences corresponding to 1 kb genomic intervals with gains or losses of a histone modification within the DCI sites. This study explores the dynamic regulation of chromatin interactions and extends the current knowledge of the relationship between histone modifications and chromatin interactions.
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Affiliation(s)
- Yumin Nie
- Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing 211166, China
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6
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Gil J, Rosin LF, Navarrete E, Chowdhury N, Abraham S, Cornilleau G, Lei EP, Mozziconacci J, Mirny LA, Muller H, Drinnenberg IA. Unique territorial and compartmental organization of chromosomes in the holocentric silkmoth. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.14.557757. [PMID: 37745315 PMCID: PMC10515926 DOI: 10.1101/2023.09.14.557757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
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 silkworm, 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.
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7
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Wang B, Bian Q. Regulation of 3D genome organization during T cell activation. FEBS J 2024. [PMID: 38944686 DOI: 10.1111/febs.17211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 04/23/2024] [Accepted: 06/14/2024] [Indexed: 07/01/2024]
Abstract
Within the three-dimensional (3D) nuclear space, the genome organizes into a series of orderly structures that impose important influences on gene regulation. T lymphocytes, crucial players in adaptive immune responses, undergo intricate transcriptional remodeling upon activation, leading to differentiation into specific effector and memory T cell subsets. Recent evidence suggests that T cell activation is accompanied by dynamic changes in genome architecture at multiple levels, providing a unique biological context to explore the functional relevance and molecular mechanisms of 3D genome organization. Here, we summarize recent advances that link the reorganization of genome architecture to the remodeling of transcriptional programs and conversion of cell fates during T cell activation and differentiation. We further discuss how various chromatin architecture regulators, including CCCTC-binding factor and several transcription factors, collectively modulate the genome architecture during this process.
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Affiliation(s)
- Bao Wang
- Shanghai lnstitute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, China
- Shanghai Key Laboratory of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, China
| | - Qian Bian
- Shanghai lnstitute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, China
- Shanghai Key Laboratory of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, China
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8
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Salari H, Fourel G, Jost D. Transcription regulates the spatio-temporal dynamics of genes through micro-compartmentalization. Nat Commun 2024; 15:5393. [PMID: 38918438 PMCID: PMC11199603 DOI: 10.1038/s41467-024-49727-7] [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: 07/24/2023] [Accepted: 06/17/2024] [Indexed: 06/27/2024] Open
Abstract
Although our understanding of the involvement of heterochromatin architectural factors in shaping nuclear organization is improving, there is still ongoing debate regarding the role of active genes in this process. In this study, we utilize publicly-available Micro-C data from mouse embryonic stem cells to investigate the relationship between gene transcription and 3D gene folding. Our analysis uncovers a nonmonotonic - globally positive - correlation between intragenic contact density and Pol II occupancy, independent of cohesin-based loop extrusion. Through the development of a biophysical model integrating the role of transcription dynamics within a polymer model of chromosome organization, we demonstrate that Pol II-mediated attractive interactions with limited valency between transcribed regions yield quantitative predictions consistent with chromosome-conformation-capture and live-imaging experiments. Our work provides compelling evidence that transcriptional activity shapes the 4D genome through Pol II-mediated micro-compartmentalization.
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Affiliation(s)
- Hossein Salari
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS, UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, 46 Allée d'Italie, 69007, Lyon, France.
- École Normale Supérieure de Lyon, CNRS, Laboratoire de Physique, 46 Allée d'Italie, 69007, Lyon, France.
| | - Geneviève Fourel
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS, UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, 46 Allée d'Italie, 69007, Lyon, France
| | - Daniel Jost
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS, UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, 46 Allée d'Italie, 69007, Lyon, France.
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9
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Huber J, Tanasie NL, Zernia S, Stigler J. Single-molecule imaging reveals a direct role of CTCF's zinc fingers in SA interaction and cluster-dependent RNA recruitment. Nucleic Acids Res 2024; 52:6490-6506. [PMID: 38742641 PMCID: PMC11194110 DOI: 10.1093/nar/gkae391] [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: 01/03/2024] [Revised: 03/21/2024] [Accepted: 05/01/2024] [Indexed: 05/16/2024] Open
Abstract
CTCF is a zinc finger protein associated with transcription regulation that also acts as a barrier factor for topologically associated domains (TADs) generated by cohesin via loop extrusion. These processes require different properties of CTCF-DNA interaction, and it is still unclear how CTCF's structural features may modulate its diverse roles. Here, we employ single-molecule imaging to study both full-length CTCF and truncation mutants. We show that CTCF enriches at CTCF binding sites (CBSs), displaying a longer lifetime than observed previously. We demonstrate that the zinc finger domains mediate CTCF clustering and that clustering enables RNA recruitment, possibly creating a scaffold for interaction with RNA-binding proteins like cohesin's subunit SA. We further reveal a direct recruitment and an increase of SA residence time by CTCF bound at CBSs, suggesting that CTCF-SA interactions are crucial for cohesin stability on chromatin at TAD borders. Furthermore, we establish a single-molecule T7 transcription assay and show that although a transcribing polymerase can remove CTCF from CBSs, transcription is impaired. Our study shows that context-dependent nucleic acid binding determines the multifaceted CTCF roles in genome organization and transcription regulation.
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Affiliation(s)
- Jonas Huber
- Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany
| | | | - Sarah Zernia
- Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Johannes Stigler
- Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany
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10
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Žumer K, Ochmann M, Aljahani A, Zheenbekova A, Devadas A, Maier KC, Rus P, Neef U, Oudelaar AM, Cramer P. FACT maintains chromatin architecture and thereby stimulates RNA polymerase II pausing during transcription in vivo. Mol Cell 2024; 84:2053-2069.e9. [PMID: 38810649 DOI: 10.1016/j.molcel.2024.05.003] [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: 10/30/2023] [Revised: 03/06/2024] [Accepted: 05/02/2024] [Indexed: 05/31/2024]
Abstract
Facilitates chromatin transcription (FACT) is a histone chaperone that supports transcription through chromatin in vitro, but its functional roles in vivo remain unclear. Here, we analyze the in vivo functions of FACT with the use of multi-omics analysis after rapid FACT depletion from human cells. We show that FACT depletion destabilizes chromatin and leads to transcriptional defects, including defective promoter-proximal pausing and elongation, and increased premature termination of RNA polymerase II. Unexpectedly, our analysis revealed that promoter-proximal pausing depends not only on the negative elongation factor (NELF) but also on the +1 nucleosome, which is maintained by FACT.
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Affiliation(s)
- Kristina Žumer
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany.
| | - Moritz Ochmann
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Abrar Aljahani
- Max Planck Institute for Multidisciplinary Sciences, Genome Organization and Regulation, Am Fassberg 11, 37077 Göttingen, Germany
| | - Aiturgan Zheenbekova
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Arjun Devadas
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Kerstin Caroline Maier
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Petra Rus
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Ute Neef
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - A Marieke Oudelaar
- Max Planck Institute for Multidisciplinary Sciences, Genome Organization and Regulation, Am Fassberg 11, 37077 Göttingen, Germany.
| | - Patrick Cramer
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany.
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11
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Abdennur N, Abraham S, Fudenberg G, Flyamer IM, Galitsyna AA, Goloborodko A, Imakaev M, Oksuz BA, Venev SV, Xiao Y. Cooltools: Enabling high-resolution Hi-C analysis in Python. PLoS Comput Biol 2024; 20:e1012067. [PMID: 38709825 PMCID: PMC11098495 DOI: 10.1371/journal.pcbi.1012067] [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: 10/11/2023] [Revised: 05/16/2024] [Accepted: 04/10/2024] [Indexed: 05/08/2024] Open
Abstract
Chromosome conformation capture (3C) technologies reveal the incredible complexity of genome organization. Maps of increasing size, depth, and resolution are now used to probe genome architecture across cell states, types, and organisms. Larger datasets add challenges at each step of computational analysis, from storage and memory constraints to researchers' time; however, analysis tools that meet these increased resource demands have not kept pace. Furthermore, existing tools offer limited support for customizing analysis for specific use cases or new biology. Here we introduce cooltools (https://github.com/open2c/cooltools), a suite of computational tools that enables flexible, scalable, and reproducible analysis of high-resolution contact frequency data. Cooltools leverages the widely-adopted cooler format which handles storage and access for high-resolution datasets. Cooltools provides a paired command line interface (CLI) and Python application programming interface (API), which respectively facilitate workflows on high-performance computing clusters and in interactive analysis environments. In short, cooltools enables the effective use of the latest and largest genome folding datasets.
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Affiliation(s)
- Open2C
- https://open2c.github.io/
| | - Nezar Abdennur
- Department of Genomics and Computational Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America
| | - Sameer Abraham
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
| | - Geoffrey Fudenberg
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California, United States of America
| | - Ilya M. Flyamer
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Aleksandra A. Galitsyna
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
| | - Anton Goloborodko
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Maxim Imakaev
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
| | - Betul A. Oksuz
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America
| | - Sergey V. Venev
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America
| | - Yao Xiao
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California, United States of America
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12
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Sarıyer OS, Erbaş A. Polymer physics view of peripheral chromatin: de Gennes' self-similar carpet. Phys Rev E 2024; 109:054403. [PMID: 38907468 DOI: 10.1103/physreve.109.054403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 04/09/2024] [Indexed: 06/24/2024]
Abstract
Using scaling arguments to model peripheral chromatin localized near the inner surface of the nuclear envelope (NE) as a flexible polymer chain, we discuss the structural properties of the peripheral chromatin composed of alternating lamin-associated domains (LADs) and inter-LADs. Modeling the attraction of LADs to NE by de Gennes' self-similar carpet, which treats the chromatin layer as a polymer fractal, explains two major experimental observations. (i) The high density of chromatin close to the nuclear periphery decays to a constant density as the distance to the periphery increases. (ii) Due to the decreasing mesh size towards the nuclear periphery, the chromatin carpet inside NE excludes molecules (via nonspecific interactions) above a threshold size that depends on the distance from the nuclear periphery.
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Affiliation(s)
- Ozan S Sarıyer
- Pîrî Reis University, School of Arts and Sciences, Tuzla 34940, Istanbul, Turkey
| | - Aykut Erbaş
- UNAM National Nanotechnology Research Center and Institute of Materials Science & Nanotechnology, Bilkent University, Ankara 06800, Turkey and University of Silesia, Institute of Physics, 41-500 Katowice, Poland
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13
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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.
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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
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14
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Segev A, Heady L, Crewe M, Madabhushi R. Mapping catalytically engaged TOP2B in neurons reveals the principles of topoisomerase action within the genome. Cell Rep 2024; 43:113809. [PMID: 38377005 PMCID: PMC11064056 DOI: 10.1016/j.celrep.2024.113809] [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: 03/20/2023] [Revised: 12/22/2023] [Accepted: 01/31/2024] [Indexed: 02/22/2024] Open
Abstract
We trapped catalytically engaged topoisomerase IIβ (TOP2B) in covalent DNA cleavage complexes (TOP2Bccs) and mapped their positions genome-wide in cultured mouse cortical neurons. We report that TOP2Bcc distribution varies with both nucleosome and compartmental chromosome organization. While TOP2Bccs in gene bodies correlate with their level of transcription, highly expressed genes that lack the usually associated chromatin marks, such as H3K36me3, show reduced TOP2Bccs, suggesting that histone posttranslational modifications regulate TOP2B activity. Promoters with high RNA polymerase II occupancy show elevated TOP2B chromatin immunoprecipitation sequencing signals but low TOP2Bccs, indicating that TOP2B catalytic engagement is curtailed at active promoters. Surprisingly, either poisoning or inhibiting TOP2B increases nascent transcription at most genes and enhancers but reduces transcription within long genes. These effects are independent of transcript length and instead correlate with the presence of intragenic enhancers. Together, these results clarify how cells modulate the catalytic engagement of topoisomerases to affect transcription.
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Affiliation(s)
- Amir Segev
- Departments of Psychiatry, Neuroscience, and Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Peter O' Donnell Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Lance Heady
- Departments of Psychiatry, Neuroscience, and Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Peter O' Donnell Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Morgan Crewe
- Departments of Psychiatry, Neuroscience, and Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Peter O' Donnell Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ram Madabhushi
- Departments of Psychiatry, Neuroscience, and Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Peter O' Donnell Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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15
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Stortz M, Presman DM, Levi V. Transcriptional condensates: a blessing or a curse for gene regulation? Commun Biol 2024; 7:187. [PMID: 38365945 PMCID: PMC10873363 DOI: 10.1038/s42003-024-05892-5] [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: 10/26/2023] [Accepted: 02/06/2024] [Indexed: 02/18/2024] Open
Abstract
Whether phase-separation is involved in the organization of the transcriptional machinery and if it aids or inhibits the transcriptional process is a matter of intense debate. In this Mini Review, we will cover the current knowledge regarding the role of transcriptional condensates on gene expression regulation. We will summarize the latest discoveries on the relationship between condensate formation, genome organization, and transcriptional activity, focusing on the strengths and weaknesses of the experimental approaches used to interrogate these aspects of transcription in living cells. Finally, we will discuss the challenges for future research.
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Grants
- PICT 2020-00818 Ministry of Science, Technology and Productive Innovation, Argentina | Agencia Nacional de Promoción Científica y Tecnológica (National Agency for Science and Technology, Argentina)
- PICT-2018-1921 Ministry of Science, Technology and Productive Innovation, Argentina | Agencia Nacional de Promoción Científica y Tecnológica (National Agency for Science and Technology, Argentina)
- PICT 2019-0397 Ministry of Science, Technology and Productive Innovation, Argentina | Agencia Nacional de Promoción Científica y Tecnológica (National Agency for Science and Technology, Argentina)
- 20020190100101BA University of Buenos Aires | Secretaría de Ciencia y Técnica, Universidad de Buenos Aires (Secretaría de Ciencia y Técnica de la Universidad de Buenos Aires)
- 2022-11220210100212CO Consejo Nacional de Investigaciones Científicas y Técnicas (National Scientific and Technical Research Council)
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Affiliation(s)
- Martin Stortz
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET-Universidad de Buenos Aires, Buenos Aires, C1428EGA, Argentina
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Diego M Presman
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires, C1428EGA, Argentina.
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, C1428EGA, Argentina.
| | - Valeria Levi
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET-Universidad de Buenos Aires, Buenos Aires, C1428EGA, Argentina.
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, C1428EGA, Argentina.
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16
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Allyn BM, Hayer KE, Oyeniran C, Nganga V, Lee K, Mishra B, Sacan A, Oltz EM, Bassing CH. Locus folding mechanisms determine modes of antigen receptor gene assembly. J Exp Med 2024; 221:e20230985. [PMID: 38189780 PMCID: PMC10772921 DOI: 10.1084/jem.20230985] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 10/12/2023] [Accepted: 12/15/2023] [Indexed: 01/09/2024] Open
Abstract
The dynamic folding of genomes regulates numerous biological processes, including antigen receptor (AgR) gene assembly. We show that, unlike other AgR loci, homotypic chromatin interactions and bidirectional chromosome looping both contribute to structuring Tcrb for efficient long-range V(D)J recombination. Inactivation of the CTCF binding element (CBE) or promoter at the most 5'Vβ segment (Trbv1) impaired loop extrusion originating locally and extending to DβJβ CBEs at the opposite end of Tcrb. Promoter or CBE mutation nearly eliminated Trbv1 contacts and decreased RAG endonuclease-mediated Trbv1 recombination. Importantly, Trbv1 rearrangement can proceed independent of substrate orientation, ruling out scanning by DβJβ-bound RAG as the sole mechanism of Vβ recombination, distinguishing it from Igh. Our data indicate that CBE-dependent generation of loops cooperates with promoter-mediated activation of chromatin to juxtapose Vβ and DβJβ segments for recombination through diffusion-based synapsis. Thus, the mechanisms that fold a genomic region can influence molecular processes occurring in that space, which may include recombination, repair, and transcriptional programming.
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Affiliation(s)
- Brittney M. Allyn
- Immunology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Katharina E. Hayer
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Biomedical Engineering Doctoral Degree Program, School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Perelman School of Medicine, Philadelphia, PA, USA
| | - Clement Oyeniran
- Department of Microbial Infection and Immunity, Ohio State College of Medicine, Ohio State University, Columbus, OH, USA
| | - Vincent Nganga
- Department of Microbial Infection and Immunity, Ohio State College of Medicine, Ohio State University, Columbus, OH, USA
| | - Kyutae Lee
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Bikash Mishra
- Department of Microbial Infection and Immunity, Ohio State College of Medicine, Ohio State University, Columbus, OH, USA
| | - Ahmet Sacan
- Biomedical Engineering Doctoral Degree Program, School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Eugene M. Oltz
- Department of Microbial Infection and Immunity, Ohio State College of Medicine, Ohio State University, Columbus, OH, USA
| | - Craig H. Bassing
- Immunology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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17
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Hung TC, Kingsley DM, Boettiger AN. Boundary stacking interactions enable cross-TAD enhancer-promoter communication during limb development. Nat Genet 2024; 56:306-314. [PMID: 38238628 DOI: 10.1038/s41588-023-01641-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 12/06/2023] [Indexed: 02/15/2024]
Abstract
Although promoters and their enhancers are frequently contained within a topologically associating domain (TAD), some developmentally important genes have their promoter and enhancers within different TADs. Hypotheses about molecular mechanisms enabling cross-TAD interactions remain to be assessed. To test these hypotheses, we used optical reconstruction of chromatin architecture to characterize the conformations of the Pitx1 locus on single chromosomes in developing mouse limbs. Our data support a model in which neighboring boundaries are stacked as a result of loop extrusion, bringing boundary-proximal cis-elements into contact. This stacking interaction also contributes to the appearance of architectural stripes in the population average maps. Through molecular dynamics simulations, we found that increasing boundary strengths facilitates the formation of the stacked boundary conformation, counter-intuitively facilitating border bypass. This work provides a revised view of the TAD borders' function, both facilitating and preventing cis-regulatory interactions, and introduces a framework to distinguish border-crossing from border-respecting enhancer-promoter pairs.
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Affiliation(s)
- Tzu-Chiao Hung
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - David M Kingsley
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Alistair N Boettiger
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA.
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18
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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.
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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.
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19
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Attar AG, Paturej J, Banigan EJ, Erbas A. Chromatin phase separation and nuclear shape fluctuations are correlated in a polymer model of the nucleus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.16.571697. [PMID: 38168411 PMCID: PMC10760070 DOI: 10.1101/2023.12.16.571697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Abnormalities in the shapes of mammalian cell nuclei are hallmarks of a variety of diseases, including progeria, muscular dystrophy, and various cancers. Experiments have shown that there is a causal relationship between chromatin organization and nuclear morphology. Decreases in heterochromatin levels, perturbations to heterochromatin organization, and increases in euchromatin levels all lead to misshapen nuclei, which exhibit deformations, such as nuclear blebs and nuclear ruptures. However, the polymer physical mechanisms of how chromatin governs nuclear shape and integrity are poorly understood. To investigate how heterochromatin and euchromatin, which are thought to microphase separate in vivo , govern nuclear morphology, we implemented a composite coarse-grained polymer and elastic shell model. By varying chromatin volume fraction (density), heterochromatin levels and structure, and heterochromatin-lamina interactions, we show how the spatial organization of chromatin polymer phases within the nucleus could perturb nuclear shape in some scenarios. Increasing the volume fraction of chromatin in the cell nucleus stabilizes the nuclear lamina against large fluctuations. However, surprisingly, we find that increasing heterochromatin levels or heterochromatin-lamina interactions enhances nuclear shape fluctuations in our simulations by a "wetting"-like interaction. In contrast, shape fluctuations are largely insensitive to the internal structure of the heterochromatin, such as the presence or absence of chromatin-chromatin crosslinks. Therefore, our simulations suggest that heterochromatin accumulation at the nuclear periphery could perturb nuclear morphology in a nucleus or nuclear region that is sufficiently soft, while stabilization of the nucleus via heterochromatin likely occurs through mechanisms other than chromatin microphase organization.
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20
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Fiche JB, Schaeffer M, Houbron C, Elkhoury Youhanna C, Messina O, Barho F, Nollmann M. Hi-M: A Multiplex Oligopaint FISH Method to Capture Chromatin Conformations In Situ and Accompanying Open-Source Acquisition Software. Methods Mol Biol 2024; 2784:227-257. [PMID: 38502490 DOI: 10.1007/978-1-0716-3766-1_16] [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] [Indexed: 03/21/2024]
Abstract
The simultaneous observation of three-dimensional (3D) chromatin structure and transcription in single cells is critical to understand how DNA is organized inside cells and how this organization influences or is affected by other processes, such as transcription. We have recently introduced an innovative technology known as Hi-M, which enables the sequential tagging, 3D visualization, and precise localization of multiple genomic DNA regions alongside RNA expression within individual cells. In this chapter, we present a comprehensive guide outlining the creation of probes, as well as sample preparation and labeling. Finally, we provide a step-by-step guide to conduct a complete Hi-M acquisition using our open-source software package, Qudi-HiM, which controls the robotic microscope handling the entire acquisition procedure.
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Affiliation(s)
- Jean-Bernard Fiche
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR5048, INSERM U1054, Montpellier, France
| | - Marie Schaeffer
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR5048, INSERM U1054, Montpellier, France
| | - Christophe Houbron
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR5048, INSERM U1054, Montpellier, France
| | | | - Olivier Messina
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR5048, INSERM U1054, Montpellier, France
| | - Franziska Barho
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR5048, INSERM U1054, Montpellier, France
| | - Marcelo Nollmann
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR5048, INSERM U1054, Montpellier, France.
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21
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Kolbin D, Walker BL, Hult C, Stanton JD, Adalsteinsson D, Forest MG, Bloom K. Polymer Modeling Reveals Interplay between Physical Properties of Chromosomal DNA and the Size and Distribution of Condensin-Based Chromatin Loops. Genes (Basel) 2023; 14:2193. [PMID: 38137015 PMCID: PMC10742461 DOI: 10.3390/genes14122193] [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: 10/23/2023] [Revised: 11/28/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
Transient DNA loops occur throughout the genome due to thermal fluctuations of DNA and the function of SMC complex proteins such as condensin and cohesin. Transient crosslinking within and between chromosomes and loop extrusion by SMCs have profound effects on high-order chromatin organization and exhibit specificity in cell type, cell cycle stage, and cellular environment. SMC complexes anchor one end to DNA with the other extending some distance and retracting to form a loop. How cells regulate loop sizes and how loops distribute along chromatin are emerging questions. To understand loop size regulation, we employed bead-spring polymer chain models of chromatin and the activity of an SMC complex on chromatin. Our study shows that (1) the stiffness of the chromatin polymer chain, (2) the tensile stiffness of chromatin crosslinking complexes such as condensin, and (3) the strength of the internal or external tethering of chromatin chains cooperatively dictate the loop size distribution and compaction volume of induced chromatin domains. When strong DNA tethers are invoked, loop size distributions are tuned by condensin stiffness. When DNA tethers are released, loop size distributions are tuned by chromatin stiffness. In this three-way interaction, the presence and strength of tethering unexpectedly dictates chromatin conformation within a topological domain.
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Affiliation(s)
- Daniel Kolbin
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (D.K.); (J.D.S.)
| | - Benjamin L. Walker
- Department of Mathematics, University of California-Irvine, Irvine, CA 92697, USA;
| | - Caitlin Hult
- Department of Mathematics, Gettysburg College, Gettysburg, PA 17325, USA
| | - John Donoghue Stanton
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (D.K.); (J.D.S.)
| | - David Adalsteinsson
- Department of Mathematics and Carolina Center for Interdisciplinary Applied Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (D.A.); (M.G.F.)
| | - M. Gregory Forest
- Department of Mathematics and Carolina Center for Interdisciplinary Applied Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (D.A.); (M.G.F.)
- Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kerry Bloom
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (D.K.); (J.D.S.)
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22
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Cai L, Wang GG. Through the lens of phase separation: intrinsically unstructured protein and chromatin looping. Nucleus 2023; 14:2179766. [PMID: 36821650 PMCID: PMC9980480 DOI: 10.1080/19491034.2023.2179766] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
The establishment, maintenance and dynamic regulation of three-dimensional (3D) chromatin structures provide an important means for partitioning of genome into functionally distinctive domains, which helps to define specialized gene expression programs associated with developmental stages and cell types. Increasing evidence supports critical roles for intrinsically disordered regions (IDRs) harbored within transcription factors (TFs) and chromatin-modulatory proteins in inducing phase separation, a phenomenon of forming membrane-less condensates through partitioning of biomolecules. Such a process is also critically involved in the establishment of high-order chromatin structures and looping. IDR- and phase separation-driven 3D genome (re)organization often goes wrong in disease such as cancer. This review discusses about recent advances in understanding how phase separation of intrinsically disordered proteins (IDPs) modulates chromatin looping and gene expression.
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Affiliation(s)
- Ling Cai
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA,Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA,Ling Cai Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC27599, USA
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA,Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA,CONTACT Gang Greg Wang Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC27599, USA
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23
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Barajas-Mora EM, Feeney AJ. Enhancers within the Ig V Gene Region Orchestrate Chromatin Topology and Regulate V Gene Rearrangement Frequency to Shape the B Cell Receptor Repertoire Specificities. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:1613-1622. [PMID: 37983521 PMCID: PMC10662671 DOI: 10.4049/jimmunol.2300261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/01/2023] [Indexed: 11/22/2023]
Abstract
Effective Ab-mediated responses depend on a highly diverse Ab repertoire with the ability to bind a wide range of epitopes in disease-causing agents. The generation of this repertoire depends on the somatic recombination of the variable (V), diversity (D), and joining (J) genes in the Ig loci of developing B cells. It has been known for some time that individual V, D, and J gene segments rearrange at different frequencies, but the mechanisms behind this unequal V gene usage have not been well understood. However, recent work has revealed that newly described enhancers scattered throughout the V gene-containing portion of the Ig loci regulate the V gene recombination frequency in a regional manner. Deletion of three of these enhancers revealed that these elements exert many layers of control during V(D)J recombination, including long-range chromatin interactions, epigenetic milieu, chromatin accessibility, and compartmentalization.
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Affiliation(s)
- E. Mauricio Barajas-Mora
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA, USA, Current address: Poseida Therapeutics, Inc. San Diego, CA
| | - Ann J. Feeney
- Scripps Research, Department of Immunology and Microbiology, La Jolla, CA 92014
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24
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Soroczynski J, Risca VI. Technological advances in probing 4D genome organization. Curr Opin Cell Biol 2023; 84:102211. [PMID: 37556867 PMCID: PMC10588670 DOI: 10.1016/j.ceb.2023.102211] [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: 04/01/2023] [Revised: 05/13/2023] [Accepted: 06/29/2023] [Indexed: 08/11/2023]
Abstract
The last two decades of work on chromosome conformation in eukaryotic nuclei have revealed a complex and highly regulated hierarchy of architectural features, from self-associating domains and compartmental interactions to locus-specific loops. Recent findings have shown that these structures are dynamic and heterogeneous, with emerging insights into the factors that shape them and implications for the control of transcription and other nuclear processes. Here, we review the latest advances in the DNA sequencing- and microscopy-based technologies for probing these features in space and time (4D) and discuss how they have been combined with complementary approaches such as genetic perturbations, protein and RNA measurements, and modeling to gain mechanistic insights about genome regulation across space and time.
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Affiliation(s)
- Jan Soroczynski
- Laboratory of Genome Architecture and Dynamics, The Rockefeller University, 1230 York Ave., Box 176, New York, NY 10065, USA; David Rockefeller Graduate Program in Bioscience, The Rockefeller University, 1230 York Ave., New York, NY 10065, USA
| | - Viviana I Risca
- Laboratory of Genome Architecture and Dynamics, The Rockefeller University, 1230 York Ave., Box 176, New York, NY 10065, USA.
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25
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Al-Jibury E, King JWD, Guo Y, Lenhard B, Fisher AG, Merkenschlager M, Rueckert D. A deep learning method for replicate-based analysis of chromosome conformation contacts using Siamese neural networks. Nat Commun 2023; 14:5007. [PMID: 37591842 PMCID: PMC10435498 DOI: 10.1038/s41467-023-40547-9] [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: 12/11/2022] [Accepted: 07/31/2023] [Indexed: 08/19/2023] Open
Abstract
The organisation of the genome in nuclear space is an important frontier of biology. Chromosome conformation capture methods such as Hi-C and Micro-C produce genome-wide chromatin contact maps that provide rich data containing quantitative and qualitative information about genome architecture. Most conventional approaches to genome-wide chromosome conformation capture data are limited to the analysis of pre-defined features, and may therefore miss important biological information. One constraint is that biologically important features can be masked by high levels of technical noise in the data. Here we introduce a replicate-based method for deep learning from chromatin conformation contact maps. Using a Siamese network configuration our approach learns to distinguish technical noise from biological variation and outperforms image similarity metrics across a range of biological systems. The features extracted from Hi-C maps after perturbation of cohesin and CTCF reflect the distinct biological functions of cohesin and CTCF in the formation of domains and boundaries, respectively. The learnt distance metrics are biologically meaningful, as they mirror the density of cohesin and CTCF binding. These properties make our method a powerful tool for the exploration of chromosome conformation capture data, such as Hi-C capture Hi-C, and Micro-C.
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Affiliation(s)
- Ediem Al-Jibury
- MRC LMS, Imperial College London, London, W12 0NN, UK.
- Department of Computing, Imperial College London, London, SW7 2RH, UK.
| | | | - Ya Guo
- MRC LMS, Imperial College London, London, W12 0NN, UK
- Sheng Yushou Center of Cell Biology and Immunology, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- WLA Laboratories, Shanghai, 201203, China
| | - Boris Lenhard
- MRC LMS, Imperial College London, London, W12 0NN, UK
- Sars International Centre for Marine Molecular Biology, University of Bergen, 5008, Bergen, Norway
| | | | | | - Daniel Rueckert
- Department of Computing, Imperial College London, London, SW7 2RH, UK.
- Klinikum rechts der Isar, Technical University of Munich, 81675, Munich, Germany.
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26
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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.
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Affiliation(s)
- Leonid A Mirny
- Institute for Medical Engineering and Science, and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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27
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Yildirim A, Hua N, Boninsegna L, Zhan Y, Polles G, Gong K, Hao S, Li W, Zhou XJ, Alber F. Evaluating the role of the nuclear microenvironment in gene function by population-based modeling. Nat Struct Mol Biol 2023; 30:1193-1206. [PMID: 37580627 PMCID: PMC10442234 DOI: 10.1038/s41594-023-01036-1] [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: 11/03/2021] [Accepted: 06/16/2023] [Indexed: 08/16/2023]
Abstract
The nuclear folding of chromosomes relative to nuclear bodies is an integral part of gene function. Here, we demonstrate that population-based modeling-from ensemble Hi-C data-provides a detailed description of the nuclear microenvironment of genes and its role in gene function. We define the microenvironment by the subnuclear positions of genomic regions with respect to nuclear bodies, local chromatin compaction, and preferences in chromatin compartmentalization. These structural descriptors are determined in single-cell models, thereby revealing the structural variability between cells. We demonstrate that the microenvironment of a genomic region is linked to its functional potential in gene transcription, replication, and chromatin compartmentalization. Some chromatin regions feature a strong preference for a single microenvironment, due to association with specific nuclear bodies in most cells. Other chromatin shows high structural variability, which is a strong indicator of functional heterogeneity. Moreover, we identify specialized nuclear microenvironments, which distinguish chromatin in different functional states and reveal a key role of nuclear speckles in chromosome organization. We demonstrate that our method produces highly predictive three-dimensional genome structures, which accurately reproduce data from a variety of orthogonal experiments, thus considerably expanding the range of Hi-C data analysis.
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Affiliation(s)
- Asli Yildirim
- Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA, USA
| | - Nan Hua
- Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA, USA
| | - Lorenzo Boninsegna
- Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA, USA
| | - Yuxiang Zhan
- Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA, USA
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Guido Polles
- Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA, USA
| | - Ke Gong
- Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA, USA
| | - Shengli Hao
- Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA, USA
| | - Wenyuan Li
- Department of Pathology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Xianghong Jasmine Zhou
- Department of Pathology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Frank Alber
- Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, USA.
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA, USA.
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA.
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28
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Liu H, Tsai H, Yang M, Li G, Bian Q, Ding G, Wu D, Dai J. Three-dimensional genome structure and function. MedComm (Beijing) 2023; 4:e326. [PMID: 37426677 PMCID: PMC10329473 DOI: 10.1002/mco2.326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 05/31/2023] [Accepted: 06/09/2023] [Indexed: 07/11/2023] Open
Abstract
Linear DNA undergoes a series of compression and folding events, forming various three-dimensional (3D) structural units in mammalian cells, including chromosomal territory, compartment, topologically associating domain, and chromatin loop. These structures play crucial roles in regulating gene expression, cell differentiation, and disease progression. Deciphering the principles underlying 3D genome folding and the molecular mechanisms governing cell fate determination remains a challenge. With advancements in high-throughput sequencing and imaging techniques, the hierarchical organization and functional roles of higher-order chromatin structures have been gradually illuminated. This review systematically discussed the structural hierarchy of the 3D genome, the effects and mechanisms of cis-regulatory elements interaction in the 3D genome for regulating spatiotemporally specific gene expression, the roles and mechanisms of dynamic changes in 3D chromatin conformation during embryonic development, and the pathological mechanisms of diseases such as congenital developmental abnormalities and cancer, which are attributed to alterations in 3D genome organization and aberrations in key structural proteins. Finally, prospects were made for the research about 3D genome structure, function, and genetic intervention, and the roles in disease development, prevention, and treatment, which may offer some clues for precise diagnosis and treatment of related diseases.
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Affiliation(s)
- Hao Liu
- Department of Oral and Cranio‐Maxillofacial SurgeryShanghai Ninth People's Hospital, Shanghai Jiao Tong University School of MedicineCollege of Stomatology, Shanghai Jiao Tong UniversityNational Center for StomatologyNational Clinical Research Center for Oral DiseasesShanghai Key Laboratory of StomatologyShanghaiChina
- School of StomatologyWeifang Medical UniversityWeifangChina
| | - Hsiangyu Tsai
- Department of Oral and Cranio‐Maxillofacial SurgeryShanghai Ninth People's Hospital, Shanghai Jiao Tong University School of MedicineCollege of Stomatology, Shanghai Jiao Tong UniversityNational Center for StomatologyNational Clinical Research Center for Oral DiseasesShanghai Key Laboratory of StomatologyShanghaiChina
| | - Maoquan Yang
- School of Clinical MedicineWeifang Medical UniversityWeifangChina
| | - Guozhi Li
- Department of Oral and Cranio‐Maxillofacial SurgeryShanghai Ninth People's Hospital, Shanghai Jiao Tong University School of MedicineCollege of Stomatology, Shanghai Jiao Tong UniversityNational Center for StomatologyNational Clinical Research Center for Oral DiseasesShanghai Key Laboratory of StomatologyShanghaiChina
| | - Qian Bian
- Shanghai Institute of Precision MedicineShanghaiChina
| | - Gang Ding
- School of StomatologyWeifang Medical UniversityWeifangChina
| | - Dandan Wu
- Department of Oral and Cranio‐Maxillofacial SurgeryShanghai Ninth People's Hospital, Shanghai Jiao Tong University School of MedicineCollege of Stomatology, Shanghai Jiao Tong UniversityNational Center for StomatologyNational Clinical Research Center for Oral DiseasesShanghai Key Laboratory of StomatologyShanghaiChina
| | - Jiewen Dai
- Department of Oral and Cranio‐Maxillofacial SurgeryShanghai Ninth People's Hospital, Shanghai Jiao Tong University School of MedicineCollege of Stomatology, Shanghai Jiao Tong UniversityNational Center for StomatologyNational Clinical Research Center for Oral DiseasesShanghai Key Laboratory of StomatologyShanghaiChina
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29
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Hertzog M, Erdel F. The Material Properties of the Cell Nucleus: A Matter of Scale. Cells 2023; 12:1958. [PMID: 37566037 PMCID: PMC10416959 DOI: 10.3390/cells12151958] [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: 06/30/2023] [Revised: 07/26/2023] [Accepted: 07/26/2023] [Indexed: 08/12/2023] Open
Abstract
Chromatin regulatory processes physically take place in the environment of the cell nucleus, which is filled with the chromosomes and a plethora of smaller biomolecules. The nucleus contains macromolecular assemblies of different sizes, from nanometer-sized protein complexes to micrometer-sized biomolecular condensates, chromosome territories, and nuclear bodies. This multiscale organization impacts the transport processes within the nuclear interior, the global mechanical properties of the nucleus, and the way the nucleus senses and reacts to mechanical stimuli. Here, we discuss recent work on these aspects, including microrheology and micromanipulation experiments assessing the material properties of the nucleus and its subcomponents. We summarize how the properties of multiscale media depend on the time and length scales probed in the experiment, and we reconcile seemingly contradictory observations made on different scales. We also revisit the concept of liquid-like and solid-like material properties for complex media such as the nucleus. We propose that the nucleus can be considered a multiscale viscoelastic medium composed of three major components with distinct properties: the lamina, the chromatin network, and the nucleoplasmic fluid. This multicomponent organization enables the nucleus to serve its different functions as a reaction medium on the nanoscale and as a mechanosensor and structural scaffold on the microscale.
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Affiliation(s)
| | - Fabian Erdel
- MCD, Center for Integrative Biology (CBI), University of Toulouse, CNRS, 169 Avenue Marianne Grunberg-Manago, 31062 Toulouse, France
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30
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Wang R, Xu Q, Wang C, Tian K, Wang H, Ji X. Multiomic analysis of cohesin reveals that ZBTB transcription factors contribute to chromatin interactions. Nucleic Acids Res 2023; 51:6784-6805. [PMID: 37264934 PMCID: PMC10359638 DOI: 10.1093/nar/gkad401] [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: 12/15/2022] [Accepted: 05/23/2023] [Indexed: 06/03/2023] Open
Abstract
One bottleneck in understanding the principles of 3D chromatin structures is caused by the paucity of known regulators. Cohesin is essential for 3D chromatin organization, and its interacting partners are candidate regulators. Here, we performed proteomic profiling of the cohesin in chromatin and identified transcription factors, RNA-binding proteins and chromatin regulators associated with cohesin. Acute protein degradation followed by time-series genomic binding quantitation and BAT Hi-C analysis were conducted, and the results showed that the transcription factor ZBTB21 contributes to cohesin chromatin binding, 3D chromatin interactions and transcriptional repression. Strikingly, multiomic analyses revealed that the other four ZBTB factors interacted with cohesin, and double degradation of ZBTB21 and ZBTB7B led to a further decrease in cohesin chromatin occupancy. We propose that multiple ZBTB transcription factors orchestrate the chromatin binding of cohesin to regulate chromatin interactions, and we provide a catalog of many additional proteins associated with cohesin that warrant further investigation.
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Affiliation(s)
- Rui Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Qiqin Xu
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Chenlu Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Kai Tian
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Hui Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Xiong Ji
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
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31
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Powell SK, Liao W, O’Shea C, Kammourh S, Ghorbani S, Rigat R, Elahi R, Deans PJM, Le DJ, Agarwal P, Seow WQ, Wang KC, Akbarian S, Brennand KJ. Schizophrenia Risk Mapping and Functional Engineering of the 3D Genome in Three Neuronal Subtypes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.17.549339. [PMID: 37502907 PMCID: PMC10370055 DOI: 10.1101/2023.07.17.549339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Common variants associated with schizophrenia are concentrated in non-coding regulatory sequences, but their precise target genes are context-dependent and impacted by cell-type-specific three-dimensional spatial chromatin organization. Here, we map long-range chromosomal conformations in isogenic human dopaminergic, GABAergic, and glutamatergic neurons to track developmentally programmed shifts in the regulatory activity of schizophrenia risk loci. Massive repressive compartmentalization, concomitant with the emergence of hundreds of neuron-specific multi-valent chromatin architectural stripes, occurs during neuronal differentiation, with genes interconnected to genetic risk loci through these long-range chromatin structures differing in their biological roles from genes more proximal to sequences conferring heritable risk. Chemically induced CRISPR-guided chromosomal loop-engineering for the proximal risk gene SNAP91 and distal risk gene BHLHE22 profoundly alters synaptic development and functional activity. Our findings highlight the large-scale cell-type-specific reorganization of chromosomal conformations at schizophrenia risk loci during neurodevelopment and establish a causal link between risk-associated gene-regulatory loop structures and neuronal function.
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Affiliation(s)
- Samuel K. Powell
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Division of Molecular Psychiatry, Department of Psychiatry, Yale University, New Haven CT, 06511
| | - Will Liao
- New York Genome Center, New York, NY, 10029
| | - Callan O’Shea
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Division of Molecular Psychiatry, Department of Psychiatry, Yale University, New Haven CT, 06511
| | - Sarah Kammourh
- Division of Molecular Psychiatry, Department of Psychiatry, Yale University, New Haven CT, 06511
| | - Sadaf Ghorbani
- Division of Molecular Psychiatry, Department of Psychiatry, Yale University, New Haven CT, 06511
| | - Raymond Rigat
- Division of Molecular Psychiatry, Department of Psychiatry, Yale University, New Haven CT, 06511
| | - Rahat Elahi
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - PJ Michael Deans
- Division of Molecular Psychiatry, Department of Psychiatry, Yale University, New Haven CT, 06511
| | - Derek J. Le
- Department of Dermatology, Program in Epithelial Biology, Stanford University School of Medicine, Stanford, 94305, California, USA
- Cancer Biology Program, Stanford University School of Medicine, Stanford, California, 94305, USA
| | - Poonam Agarwal
- Department of Dermatology, Program in Epithelial Biology, Stanford University School of Medicine, Stanford, 94305, California, USA
| | - Wei Qiang Seow
- Department of Dermatology, Program in Epithelial Biology, Stanford University School of Medicine, Stanford, 94305, California, USA
| | - Kevin C. Wang
- Department of Dermatology, Program in Epithelial Biology, Stanford University School of Medicine, Stanford, 94305, California, USA
- Cancer Biology Program, Stanford University School of Medicine, Stanford, California, 94305, USA
- Veterans Affairs Palo Alto Healthcare System, Palo Alto, California, 94304, USA
| | - Schahram Akbarian
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Kristen J. Brennand
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Division of Molecular Psychiatry, Department of Psychiatry, Yale University, New Haven CT, 06511
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32
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Langer CCH, Mitter M, Stocsits RR, Gerlich DW. HiCognition: a visual exploration and hypothesis testing tool for 3D genomics. Genome Biol 2023; 24:158. [PMID: 37408019 DOI: 10.1186/s13059-023-02996-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 06/25/2023] [Indexed: 07/07/2023] Open
Abstract
Genome browsers facilitate integrated analysis of multiple genomics datasets yet visualize only a few regions at a time and lack statistical functions for extracting meaningful information. We present HiCognition, a visual exploration and machine-learning tool based on a new genomic region set concept, enabling detection of patterns and associations between 3D chromosome conformation and collections of 1D genomics profiles of any type. By revealing how transcription and cohesion subunit isoforms contribute to chromosome conformation, we showcase how the flexible user interface and machine learning tools of HiCognition help to understand the relationship between the structure and function of the genome.
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Affiliation(s)
- Christoph C H Langer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Michael Mitter
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Roman R Stocsits
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Daniel W Gerlich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria.
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33
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Rappoport N, Chomsky E, Nagano T, Seibert C, Lubling Y, Baran Y, Lifshitz A, Leung W, Mukamel Z, Shamir R, Fraser P, Tanay A. Single cell Hi-C identifies plastic chromosome conformations underlying the gastrulation enhancer landscape. Nat Commun 2023; 14:3844. [PMID: 37386027 PMCID: PMC10310791 DOI: 10.1038/s41467-023-39549-4] [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: 11/27/2022] [Accepted: 06/19/2023] [Indexed: 07/01/2023] Open
Abstract
Embryonic development involves massive proliferation and differentiation of cell lineages. This must be supported by chromosome replication and epigenetic reprogramming, but how proliferation and cell fate acquisition are balanced in this process is not well understood. Here we use single cell Hi-C to map chromosomal conformations in post-gastrulation mouse embryo cells and study their distributions and correlations with matching embryonic transcriptional atlases. We find that embryonic chromosomes show a remarkably strong cell cycle signature. Despite that, replication timing, chromosome compartment structure, topological associated domains (TADs) and promoter-enhancer contacts are shown to be variable between distinct epigenetic states. About 10% of the nuclei are identified as primitive erythrocytes, showing exceptionally compact and organized compartment structure. The remaining cells are broadly associated with ectoderm and mesoderm identities, showing only mild differentiation of TADs and compartment structures, but more specific localized contacts in hundreds of ectoderm and mesoderm promoter-enhancer pairs. The data suggest that while fully committed embryonic lineages can rapidly acquire specific chromosomal conformations, most embryonic cells are showing plastic signatures driven by complex and intermixed enhancer landscapes.
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Affiliation(s)
- Nimrod Rappoport
- Department of Computer Science and Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
- The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Elad Chomsky
- Department of Computer Science and Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Takashi Nagano
- Laboratory for Nuclear Dynamics, Institute for Protein Research, Osaka University, Osaka, Japan
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, UK
| | - Charlie Seibert
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Yaniv Lubling
- Department of Computer Science and Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Yael Baran
- Department of Computer Science and Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Aviezer Lifshitz
- Department of Computer Science and Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Wing Leung
- Laboratory for Nuclear Dynamics, Institute for Protein Research, Osaka University, Osaka, Japan
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, UK
| | - Zohar Mukamel
- Department of Computer Science and Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Ron Shamir
- The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Peter Fraser
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, UK.
- Department of Biological Science, Florida State University, Tallahassee, FL, USA.
| | - Amos Tanay
- Department of Computer Science and Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel.
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34
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Chen LF, Long HK, Park M, Swigut T, Boettiger AN, Wysocka J. Structural elements promote architectural stripe formation and facilitate ultra-long-range gene regulation at a human disease locus. Mol Cell 2023; 83:1446-1461.e6. [PMID: 36996812 DOI: 10.1016/j.molcel.2023.03.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 02/15/2023] [Accepted: 03/07/2023] [Indexed: 03/31/2023]
Abstract
Enhancer clusters overlapping disease-associated mutations in Pierre Robin sequence (PRS) patients regulate SOX9 expression at genomic distances over 1.25 Mb. We applied optical reconstruction of chromatin architecture (ORCA) imaging to trace 3D locus topology during PRS-enhancer activation. We observed pronounced changes in locus topology between cell types. Subsequent analysis of single-chromatin fiber traces revealed that these ensemble-average differences arise through changes in the frequency of commonly sampled topologies. We further identified two CTCF-bound elements, internal to the SOX9 topologically associating domain, which promote stripe formation, are positioned near the domain's 3D geometric center, and bridge enhancer-promoter contacts in a series of chromatin loops. Ablation of these elements results in diminished SOX9 expression and altered domain-wide contacts. Polymer models with uniform loading across the domain and frequent cohesin collisions recapitulate this multi-loop, centrally clustered geometry. Together, we provide mechanistic insights into architectural stripe formation and gene regulation over ultra-long genomic ranges.
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Affiliation(s)
- Liang-Fu Chen
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Hannah Katherine Long
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Minhee Park
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Tomek Swigut
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alistair Nicol Boettiger
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
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35
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Amin A, Kadam S, Mieczkowski J, Ahmed I, Bhat YA, Shah F, Tolstorukov MY, Kingston RE, Padinhateeri R, Wani AH. Disruption of polyhomeotic polymerization decreases nucleosome occupancy and alters genome accessibility. Life Sci Alliance 2023; 6:e202201768. [PMID: 36849253 PMCID: PMC9973501 DOI: 10.26508/lsa.202201768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 02/16/2023] [Accepted: 02/16/2023] [Indexed: 03/01/2023] Open
Abstract
Chromatin attains its three-dimensional (3D) conformation by establishing contacts between different noncontiguous regions. Sterile Alpha Motif (SAM)-mediated polymerization of the polyhomeotic (PH) protein regulates subnuclear clustering of Polycomb Repressive Complex 1 (PRC1) and chromatin topology. The mutations that perturb the ability of the PH to polymerize, disrupt long-range chromatin contacts, alter Hox gene expression, and lead to developmental defects. To understand the underlying mechanism, we combined the experiments and theory to investigate the effect of this SAM domain mutation on nucleosome occupancy and accessibility on a genome wide scale. Our data show that disruption of PH polymerization because of SAM domain mutation decreases nucleosome occupancy and alters accessibility. Polymer simulations investigating the interplay between distant chromatin contacts and nucleosome occupancy, both of which are regulated by PH polymerization, suggest that nucleosome density increases when contacts between different regions of chromatin are established. Taken together, it appears that SAM domain-mediated PH polymerization biomechanically regulates the organization of chromatin at multiple scales from nucleosomes to chromosomes and we suggest that higher order organization can have a top-down causation effect on nucleosome occupancy.
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Affiliation(s)
- Adfar Amin
- Department of Biotechnology, School of Biological Sciences, University of Kashmir, Srinagar, India
| | - Sangram Kadam
- Department of Biosciences and Bioengineering, IIT, Bombay, India
| | - Jakub Mieczkowski
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Ikhlak Ahmed
- CIRI, School of Biological Sciences, University of Kashmir, Srinagar, India
| | - Younus A Bhat
- Department of Biotechnology, School of Biological Sciences, University of Kashmir, Srinagar, India
| | - Fouziya Shah
- Department of Biotechnology, School of Biological Sciences, University of Kashmir, Srinagar, India
| | | | - Robert E Kingston
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | | | - Ajazul H Wani
- Department of Biotechnology, School of Biological Sciences, University of Kashmir, Srinagar, India
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36
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Keough KC, Whalen S, Inoue F, Przytycki PF, Fair T, Deng C, Steyert M, Ryu H, Lindblad-Toh K, Karlsson E, Nowakowski T, Ahituv N, Pollen A, Pollard KS. Three-dimensional genome rewiring in loci with human accelerated regions. Science 2023; 380:eabm1696. [PMID: 37104607 PMCID: PMC10999243 DOI: 10.1126/science.abm1696] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 03/01/2023] [Indexed: 04/29/2023]
Abstract
Human accelerated regions (HARs) are conserved genomic loci that evolved at an accelerated rate in the human lineage and may underlie human-specific traits. We generated HARs and chimpanzee accelerated regions with an automated pipeline and an alignment of 241 mammalian genomes. Combining deep learning with chromatin capture experiments in human and chimpanzee neural progenitor cells, we discovered a significant enrichment of HARs in topologically associating domains containing human-specific genomic variants that change three-dimensional (3D) genome organization. Differential gene expression between humans and chimpanzees at these loci suggests rewiring of regulatory interactions between HARs and neurodevelopmental genes. Thus, comparative genomics together with models of 3D genome folding revealed enhancer hijacking as an explanation for the rapid evolution of HARs.
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Affiliation(s)
- Kathleen C Keough
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Sean Whalen
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
| | - Fumitaka Inoue
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Pawel F Przytycki
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
| | - Tyler Fair
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Chengyu Deng
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Marilyn Steyert
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
- Department of Psychiatry and Behavioral Sciences, University of California San Francisco, San Francisco, CA, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
| | - Hane Ryu
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Kerstin Lindblad-Toh
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Elinor Karlsson
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA, USA
- Program in Molecular Medicine, UMass Chan Medical School, Worcester, MA, USA
| | - Tomasz Nowakowski
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
- Department of Psychiatry and Behavioral Sciences, University of California San Francisco, San Francisco, CA, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Alex Pollen
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Katherine S Pollard
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Department of Epidemiology & Biostatistics and Bakar Institute for Computational Health Sciences, University of California San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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37
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Wang R, Lee JH, Kim J, Xiong F, Hasani LA, Shi Y, Simpson EN, Zhu X, Chen YT, Shivshankar P, Krakowiak J, Wang Y, Gilbert DM, Yuan X, Eltzschig HK, Li W. SARS-CoV-2 restructures host chromatin architecture. Nat Microbiol 2023; 8:679-694. [PMID: 36959507 PMCID: PMC10116496 DOI: 10.1038/s41564-023-01344-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 02/14/2023] [Indexed: 03/25/2023]
Abstract
Some viruses restructure host chromatin, influencing gene expression, with implications for disease outcome. Whether this occurs for SARS-CoV-2, the virus causing COVID-19, is largely unknown. Here we characterized the 3D genome and epigenome of human cells after SARS-CoV-2 infection, finding widespread host chromatin restructuring that features widespread compartment A weakening, A-B mixing, reduced intra-TAD contacts and decreased H3K27ac euchromatin modification levels. Such changes were not found following common-cold-virus HCoV-OC43 infection. Intriguingly, the cohesin complex was notably depleted from intra-TAD regions, indicating that SARS-CoV-2 disrupts cohesin loop extrusion. These altered 3D genome/epigenome structures correlated with transcriptional suppression of interferon response genes by the virus, while increased H3K4me3 was found in the promoters of pro-inflammatory genes highly induced during severe COVID-19. These findings show that SARS-CoV-2 acutely rewires host chromatin, facilitating future studies of the long-term epigenomic impacts of its infection.
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Affiliation(s)
- Ruoyu Wang
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Joo-Hyung Lee
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Jieun Kim
- Department of Anesthesiology, Critical Care and Pain Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Center for Perioperative Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Feng Xiong
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Lana Al Hasani
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Yuqiang Shi
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Erin N Simpson
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Xiaoyu Zhu
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Yi-Ting Chen
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Pooja Shivshankar
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Department of Anesthesiology, Critical Care and Pain Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Center for Perioperative Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Joanna Krakowiak
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Yanyu Wang
- Department of Anesthesiology, Critical Care and Pain Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Center for Perioperative Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - David M Gilbert
- Laboratory of Chromosome Replication and Epigenome Regulation, San Diego Biomedical Research Institute, San Diego, CA, USA
| | - Xiaoyi Yuan
- Department of Anesthesiology, Critical Care and Pain Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Center for Perioperative Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Holger K Eltzschig
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Department of Anesthesiology, Critical Care and Pain Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Center for Perioperative Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Wenbo Li
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA.
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, The University of Texas Health Science Center at Houston, Houston, TX, USA.
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Kabirova E, Nurislamov A, Shadskiy A, Smirnov A, Popov A, Salnikov P, Battulin N, Fishman V. Function and Evolution of the Loop Extrusion Machinery in Animals. Int J Mol Sci 2023; 24:5017. [PMID: 36902449 PMCID: PMC10003631 DOI: 10.3390/ijms24055017] [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: 02/07/2023] [Revised: 02/25/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Structural maintenance of chromosomes (SMC) complexes are essential proteins found in genomes of all cellular organisms. Essential functions of these proteins, such as mitotic chromosome formation and sister chromatid cohesion, were discovered a long time ago. Recent advances in chromatin biology showed that SMC proteins are involved in many other genomic processes, acting as active motors extruding DNA, which leads to the formation of chromatin loops. Some loops formed by SMC proteins are highly cell type and developmental stage specific, such as SMC-mediated DNA loops required for VDJ recombination in B-cell progenitors, or dosage compensation in Caenorhabditis elegans and X-chromosome inactivation in mice. In this review, we focus on the extrusion-based mechanisms that are common for multiple cell types and species. We will first describe an anatomy of SMC complexes and their accessory proteins. Next, we provide biochemical details of the extrusion process. We follow this by the sections describing the role of SMC complexes in gene regulation, DNA repair, and chromatin topology.
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Affiliation(s)
- Evelyn Kabirova
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Artem Nurislamov
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Artem Shadskiy
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Alexander Smirnov
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Andrey Popov
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Pavel Salnikov
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Nariman Battulin
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Veniamin Fishman
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
- Artificial Intelligence Research Institute (AIRI), 121108 Moscow, Russia
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39
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Maslova A, Plotnikov V, Nuriddinov M, Gridina M, Fishman V, Krasikova A. Hi-C analysis of genomic contacts revealed karyotype abnormalities in chicken HD3 cell line. BMC Genomics 2023; 24:66. [PMID: 36750787 PMCID: PMC9906895 DOI: 10.1186/s12864-023-09158-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/31/2023] [Indexed: 02/09/2023] Open
Abstract
BACKGROUND Karyotype abnormalities are frequent in immortalized continuous cell lines either transformed or derived from primary tumors. Chromosomal rearrangements can cause dramatic changes in gene expression and affect cellular phenotype and behavior during in vitro culture. Structural variations of chromosomes in many continuous mammalian cell lines are well documented, but chromosome aberrations in cell lines from other vertebrate models often remain understudied. The chicken LSCC-HD3 cell line (HD3), generated from erythroid precursors, was used as an avian model for erythroid differentiation and lineage-specific gene expression. However, karyotype abnormalities in the HD3 cell line were not assessed. In the present study, we applied high-throughput chromosome conformation capture to analyze 3D genome organization and to detect chromosome rearrangements in the HD3 cell line. RESULTS We obtained Hi-C maps of genomic interactions for the HD3 cell line and compared A/B compartments and topologically associating domains between HD3 and several other cell types. By analysis of contact patterns in the Hi-C maps of HD3 cells, we identified more than 25 interchromosomal translocations of regions ≥ 200 kb on both micro- and macrochromosomes. We classified most of the observed translocations as unbalanced, leading to the formation of heteromorphic chromosomes. In many cases of microchromosome rearrangements, an entire microchromosome together with other macro- and microchromosomes participated in the emergence of a derivative chromosome, resembling "chromosomal fusions'' between acrocentric microchromosomes. Intrachromosomal inversions, deletions and duplications were also detected in HD3 cells. Several of the identified simple and complex chromosomal rearrangements, such as between GGA2 and GGA1qter; GGA5, GGA4p and GGA7p; GGA4q, GGA6 and GGA19; and duplication of the sex chromosome GGAW, were confirmed by FISH. CONCLUSIONS In the erythroid progenitor HD3 cell line, in contrast to mature and immature erythrocytes, the genome is organized into distinct topologically associating domains. The HD3 cell line has a severely rearranged karyotype with most of the chromosomes engaged in translocations and can be used in studies of genome structure-function relationships. Hi-C proved to be a reliable tool for simultaneous assessment of the spatial genome organization and chromosomal aberrations in karyotypes of birds with a large number of microchromosomes.
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Affiliation(s)
- A. Maslova
- grid.15447.330000 0001 2289 6897Saint Petersburg State University, Saint Petersburg, Russia
| | - V. Plotnikov
- grid.15447.330000 0001 2289 6897Saint Petersburg State University, Saint Petersburg, Russia
| | - M. Nuriddinov
- grid.418953.2Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - M. Gridina
- grid.418953.2Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - V. Fishman
- grid.418953.2Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - A. Krasikova
- grid.15447.330000 0001 2289 6897Saint Petersburg State University, Saint Petersburg, Russia
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40
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Kahn TG, Savitsky M, Kuong C, Jacquier C, Cavalli G, Chang JM, Schwartz YB. Topological screen identifies hundreds of Cp190- and CTCF-dependent Drosophila chromatin insulator elements. SCIENCE ADVANCES 2023; 9:eade0090. [PMID: 36735780 PMCID: PMC9897668 DOI: 10.1126/sciadv.ade0090] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 01/03/2023] [Indexed: 06/18/2023]
Abstract
Drosophila insulators were the first DNA elements found to regulate gene expression by delimiting chromatin contacts. We still do not know how many of them exist and what impact they have on the Drosophila genome folding. Contrary to vertebrates, there is no evidence that fly insulators block cohesin-mediated chromatin loop extrusion. Therefore, their mechanism of action remains uncertain. To bridge these gaps, we mapped chromatin contacts in Drosophila cells lacking the key insulator proteins CTCF and Cp190. With this approach, we found hundreds of insulator elements. Their study indicates that Drosophila insulators play a minor role in the overall genome folding but affect chromatin contacts locally at many loci. Our observations argue that Cp190 promotes cobinding of other insulator proteins and that the model, where Drosophila insulators block chromatin contacts by forming loops, needs revision. Our insulator catalog provides an important resource to study mechanisms of genome folding.
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Affiliation(s)
- Tatyana G. Kahn
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | | | - Chikuan Kuong
- Department of Computer Science, National Chengchi University, Taipei City, Taiwan
| | | | - Giacomo Cavalli
- Institute of Human Genetics, UMR9002 CNRS, Montpellier, France
| | - Jia-Ming Chang
- Department of Computer Science, National Chengchi University, Taipei City, Taiwan
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41
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de Wit E, Nora EP. New insights into genome folding by loop extrusion from inducible degron technologies. Nat Rev Genet 2023; 24:73-85. [PMID: 36180596 DOI: 10.1038/s41576-022-00530-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2022] [Indexed: 01/24/2023]
Abstract
Chromatin folds into dynamic loops that often span hundreds of kilobases and physically wire distant loci together for gene regulation. These loops are continuously created, extended and positioned by structural maintenance of chromosomes (SMC) protein complexes, such as condensin and cohesin, and their regulators, including CTCF, in a highly dynamic process known as loop extrusion. Genetic loss of extrusion factors is lethal, complicating their study. Inducible protein degradation technologies enable the depletion of loop extrusion factors within hours, leading to the rapid reconfiguration of chromatin folding. Here, we review how these technologies have changed our understanding of genome organization, upsetting long-held beliefs on its role in transcription. Finally, we examine recent models that attempt to reconcile observations after chronic versus acute perturbations, and discuss future developments in this rapidly developing field of research.
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Affiliation(s)
- Elzo de Wit
- Division of Gene Regulation, Oncode Institute, Amsterdam, the Netherlands.
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands.
| | - Elphège P Nora
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA.
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
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42
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Alavattam KG, Mitzelfelt KA, Bonora G, Fields PA, Yang X, Chiu HS, Pabon L, Bertero A, Palpant NJ, Noble WS, Murry CE. Dynamic chromatin organization and regulatory interactions in human endothelial cell differentiation. Stem Cell Reports 2023; 18:159-174. [PMID: 36493778 PMCID: PMC9860068 DOI: 10.1016/j.stemcr.2022.11.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 11/07/2022] [Accepted: 11/07/2022] [Indexed: 12/10/2022] Open
Abstract
Vascular endothelial cells are a mesoderm-derived lineage with many essential functions, including angiogenesis and coagulation. The gene-regulatory mechanisms underpinning endothelial specialization are largely unknown, as are the roles of chromatin organization in regulating endothelial cell transcription. To investigate the relationships between chromatin organization and gene expression, we induced endothelial cell differentiation from human pluripotent stem cells and performed Hi-C and RNA-sequencing assays at specific time points. Long-range intrachromosomal contacts increase over the course of differentiation, accompanied by widespread heteroeuchromatic compartment transitions that are tightly associated with transcription. Dynamic topologically associating domain boundaries strengthen and converge on an endothelial cell state, and function to regulate gene expression. Chromatin pairwise point interactions (DNA loops) increase in frequency during differentiation and are linked to the expression of genes essential to vascular biology. Chromatin dynamics guide transcription in endothelial cell development and promote the divergence of endothelial cells from cardiomyocytes.
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Affiliation(s)
- Kris G Alavattam
- Department of Laboratory Medicine and Pathology, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA; Center for Cardiovascular Biology, University of Washington, 850 Republican Street, Brotman Building, Seattle, WA 98109, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, William H. Foege Hall, 3720 15th Avenue NE, Seattle, WA 98195, USA
| | - Katie A Mitzelfelt
- Department of Laboratory Medicine and Pathology, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA; Center for Cardiovascular Biology, University of Washington, 850 Republican Street, Brotman Building, Seattle, WA 98109, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, WA 98109, USA
| | - Giancarlo Bonora
- Department of Genome Sciences, University of Washington, William H. Foege Hall, 3720 15th Avenue NE, Seattle, WA 98195, USA
| | - Paul A Fields
- Department of Laboratory Medicine and Pathology, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA; Center for Cardiovascular Biology, University of Washington, 850 Republican Street, Brotman Building, Seattle, WA 98109, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, WA 98109, USA
| | - Xiulan Yang
- Department of Laboratory Medicine and Pathology, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA; Center for Cardiovascular Biology, University of Washington, 850 Republican Street, Brotman Building, Seattle, WA 98109, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, WA 98109, USA
| | - Han Sheng Chiu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; Centre for Cardiac and Vascular Biology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Lil Pabon
- Department of Laboratory Medicine and Pathology, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA; Center for Cardiovascular Biology, University of Washington, 850 Republican Street, Brotman Building, Seattle, WA 98109, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, WA 98109, USA; Sana Biotechnology, Seattle, WA 98102, USA
| | - Alessandro Bertero
- Department of Laboratory Medicine and Pathology, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA; Center for Cardiovascular Biology, University of Washington, 850 Republican Street, Brotman Building, Seattle, WA 98109, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, WA 98109, USA
| | - Nathan J Palpant
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; Centre for Cardiac and Vascular Biology, The University of Queensland, Brisbane, QLD 4072, Australia; School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - William S Noble
- Department of Genome Sciences, University of Washington, William H. Foege Hall, 3720 15th Avenue NE, Seattle, WA 98195, USA; Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA 98195, USA.
| | - Charles E Murry
- Department of Laboratory Medicine and Pathology, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA; Center for Cardiovascular Biology, University of Washington, 850 Republican Street, Brotman Building, Seattle, WA 98109, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, WA 98109, USA; Sana Biotechnology, Seattle, WA 98102, USA; Department of Medicine/Cardiology, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA; Department of Bioengineering, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA.
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43
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Suwara J, Radzikowska-Cieciura E, Chworos A, Pawlowska R. The ATP-dependent Pathways and Human Diseases. Curr Med Chem 2023; 30:1232-1255. [PMID: 35319356 DOI: 10.2174/0929867329666220322104552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 12/31/2021] [Accepted: 01/04/2022] [Indexed: 11/22/2022]
Abstract
Adenosine triphosphate (ATP) is one of the most important molecules of life, present both inside the cells and extracellularly. It is an essential building block for nucleic acids biosynthesis and crucial intracellular energy storage. However, one of the most interesting functions of ATP is the role of a signaling molecule. Numerous studies indicate the involvement of ATP-dependent pathways in maintaining the proper functioning of individual tissues and organs. Herein, the latest data indicating the ATP function in the network of intra- and extracellular signaling pathways including purinergic signaling, MAP kinase pathway, mTOR and calcium signaling are collected. The main ATP-dependent processes maintaining the proper functioning of the nervous, cardiovascular and immune systems, as well as skin and bones, are summarized. The disturbances in the ATP amount, its cellular localization, or interaction with target elements may induce pathological changes in signaling pathways leading to the development of serious diseases. The impact of an ATP imbalance on the development of dangerous health dysfunctions such as neurodegeneration diseases, cardiovascular diseases (CVDs), diabetes mellitus, obesity, cancers and immune pathogenesis are discussed here.
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Affiliation(s)
- Justyna Suwara
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Lodz, Poland
| | - Ewa Radzikowska-Cieciura
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Lodz, Poland
| | - Arkadiusz Chworos
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Lodz, Poland
| | - Roza Pawlowska
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Lodz, Poland
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Abstract
In animals, the sequences for controlling gene expression do not concentrate just at the transcription start site of genes, but are frequently thousands to millions of base pairs distal to it. The interaction of these sequences with one another and their transcription start sites is regulated by factors that shape the three-dimensional (3D) organization of the genome within the nucleus. Over the past decade, indirect tools exploiting high-throughput DNA sequencing have helped to map this 3D organization, have identified multiple key regulators of its structure and, in the process, have substantially reshaped our view of how 3D genome architecture regulates transcription. Now, new tools for high-throughput super-resolution imaging of chromatin have directly visualized the 3D chromatin organization, settling some debates left unresolved by earlier indirect methods, challenging some earlier models of regulatory specificity and creating hypotheses about the role of chromatin structure in transcriptional regulation.
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45
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Spracklin G, Abdennur N, Imakaev M, Chowdhury N, Pradhan S, Mirny LA, Dekker J. Diverse silent chromatin states modulate genome compartmentalization and loop extrusion barriers. Nat Struct Mol Biol 2023; 30:38-51. [PMID: 36550219 PMCID: PMC9851908 DOI: 10.1038/s41594-022-00892-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 11/01/2022] [Indexed: 12/24/2022]
Abstract
The relationships between chromosomal compartmentalization, chromatin state and function are poorly understood. Here by profiling long-range contact frequencies in HCT116 colon cancer cells, we distinguish three silent chromatin states, comprising two types of heterochromatin and a state enriched for H3K9me2 and H2A.Z that exhibits neutral three-dimensional interaction preferences and which, to our knowledge, has not previously been characterized. We find that heterochromatin marked by H3K9me3, HP1α and HP1β correlates with strong compartmentalization. We demonstrate that disruption of DNA methyltransferase activity greatly remodels genome compartmentalization whereby domains lose H3K9me3-HP1α/β binding and acquire the neutrally interacting state while retaining late replication timing. Furthermore, we show that H3K9me3-HP1α/β heterochromatin is permissive to loop extrusion by cohesin but refractory to CTCF binding. Together, our work reveals a dynamic structural and organizational diversity of the silent portion of the genome and establishes connections between the regulation of chromatin state and chromosome organization, including an interplay between DNA methylation, compartmentalization and loop extrusion.
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Affiliation(s)
- George Spracklin
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA.
- Department of Systems Biology, University of Massachusetts Medical School, Worcester, MA, USA.
| | - Nezar Abdennur
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Maxim Imakaev
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Neil Chowdhury
- Program for Research in Mathematics, Engineering and Science for High School Students (PRIMES), MIT, Cambridge, MA, USA
| | - Sriharsa Pradhan
- Genome Biology Division, New England Biolabs, Inc., Ipswich, MA, USA
| | - Leonid A Mirny
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Department of Physics, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Job Dekker
- Department of Systems Biology, University of Massachusetts Medical School, Worcester, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, USA.
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Guo Y, Al-Jibury E, Garcia-Millan R, Ntagiantas K, King JWD, Nash AJ, Galjart N, Lenhard B, Rueckert D, Fisher AG, Pruessner G, Merkenschlager M. Chromatin jets define the properties of cohesin-driven in vivo loop extrusion. Mol Cell 2022; 82:3769-3780.e5. [PMID: 36182691 DOI: 10.1016/j.molcel.2022.09.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 07/26/2022] [Accepted: 09/01/2022] [Indexed: 01/01/2023]
Abstract
Complex genomes show intricate organization in three-dimensional (3D) nuclear space. Current models posit that cohesin extrudes loops to form self-interacting domains delimited by the DNA binding protein CTCF. Here, we describe and quantitatively characterize cohesin-propelled, jet-like chromatin contacts as landmarks of loop extrusion in quiescent mammalian lymphocytes. Experimental observations and polymer simulations indicate that narrow origins of loop extrusion favor jet formation. Unless constrained by CTCF, jets propagate symmetrically for 1-2 Mb, providing an estimate for the range of in vivo loop extrusion. Asymmetric CTCF binding deflects the angle of jet propagation as experimental evidence that cohesin-mediated loop extrusion can switch from bi- to unidirectional and is controlled independently in both directions. These data offer new insights into the physiological behavior of in vivo cohesin-mediated loop extrusion and further our understanding of the principles that underlie genome organization.
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Affiliation(s)
- Ya Guo
- MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, UK; Sheng Yushou Center of Cell Biology and Immunology, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; WLA Laboratories, Shanghai 201203, China
| | - Ediem Al-Jibury
- MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, UK; Department of Computing, Imperial College London, London SW7 2RH, UK
| | - Rosalba Garcia-Millan
- Department of Mathematics, Imperial College London, London SW7 2RH, UK; Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge CB3 0WA, UK; St John's College, University of Cambridge, Cambridge CB2 1TP, UK
| | | | - James W D King
- MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, UK
| | - Alex J Nash
- MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, UK
| | - Niels Galjart
- Department of Cell Biology, Erasmus University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Boris Lenhard
- MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, UK; Sars International Centre for Marine Molecular Biology, University of Bergen, 5008 Bergen, Norway
| | - Daniel Rueckert
- Department of Computing, Imperial College London, London SW7 2RH, UK; Chair for AI in Healthcare and Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Amanda G Fisher
- MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, UK
| | - Gunnar Pruessner
- Department of Mathematics, Imperial College London, London SW7 2RH, UK.
| | - Matthias Merkenschlager
- MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, UK.
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47
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Golloshi R, Playter C, Freeman TF, Das P, Raines TI, Garretson JH, Thurston D, McCord RP. Constricted migration is associated with stable 3D genome structure differences in cancer cells. EMBO Rep 2022; 23:e52149. [PMID: 35969179 PMCID: PMC9535800 DOI: 10.15252/embr.202052149] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 07/01/2022] [Accepted: 07/12/2022] [Indexed: 01/14/2023] Open
Abstract
To spread from a localized tumor, metastatic cancer cells must squeeze through constrictions that cause major nuclear deformations. Since chromosome structure affects nucleus stiffness, gene regulation, and DNA repair, here, we investigate the relationship between 3D genome structure and constricted migration in cancer cells. Using melanoma (A375) cells, we identify phenotypic differences in cells that have undergone multiple rounds of constricted migration. These cells display a stably higher migration efficiency, elongated morphology, and differences in the distribution of Lamin A/C and heterochromatin. Hi-C experiments reveal differences in chromosome spatial compartmentalization specific to cells that have passed through constrictions and related alterations in expression of genes associated with migration and metastasis. Certain features of the 3D genome structure changes, such as a loss of B compartment interaction strength, are consistently observed after constricted migration in clonal populations of A375 cells and in MDA-MB-231 breast cancer cells. Our observations suggest that consistent types of chromosome structure changes are induced or selected by passage through constrictions and that these may epigenetically encode stable differences in gene expression and cellular migration phenotype.
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Affiliation(s)
- Rosela Golloshi
- Biochemistry & Cellular and Molecular Biology DepartmentUniversity of TennesseeKnoxvilleTNUSA
| | - Christopher Playter
- Biochemistry & Cellular and Molecular Biology DepartmentUniversity of TennesseeKnoxvilleTNUSA
| | - Trevor F Freeman
- Biochemistry & Cellular and Molecular Biology DepartmentUniversity of TennesseeKnoxvilleTNUSA
| | - Priyojit Das
- UT‐ORNL Graduate School of Genome Science and TechnologyUniversity of TennesseeKnoxvilleTNUSA
| | - Thomas Isaac Raines
- Biochemistry & Cellular and Molecular Biology DepartmentUniversity of TennesseeKnoxvilleTNUSA
| | - Joshua H Garretson
- Biochemistry & Cellular and Molecular Biology DepartmentUniversity of TennesseeKnoxvilleTNUSA
| | - Delaney Thurston
- Biochemistry & Cellular and Molecular Biology DepartmentUniversity of TennesseeKnoxvilleTNUSA
| | - Rachel Patton McCord
- Biochemistry & Cellular and Molecular Biology DepartmentUniversity of TennesseeKnoxvilleTNUSA
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48
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Keizer VIP, Grosse-Holz S, Woringer M, Zambon L, Aizel K, Bongaerts M, Delille F, Kolar-Znika L, Scolari VF, Hoffmann S, Banigan EJ, Mirny LA, Dahan M, Fachinetti D, Coulon A. Live-cell micromanipulation of a genomic locus reveals interphase chromatin mechanics. Science 2022; 377:489-495. [PMID: 35901134 DOI: 10.1126/science.abi9810] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Our understanding of the physical principles organizing the genome in the nucleus is limited by the lack of tools to directly exert and measure forces on interphase chromosomes in vivo and probe their material nature. Here, we introduce an approach to actively manipulate a genomic locus using controlled magnetic forces inside the nucleus of a living human cell. We observed viscoelastic displacements over micrometers within minutes in response to near-piconewton forces, which are consistent with a Rouse polymer model. Our results highlight the fluidity of chromatin, with a moderate contribution of the surrounding material, revealing minor roles for cross-links and topological effects and challenging the view that interphase chromatin is a gel-like material. Our technology opens avenues for future research in areas from chromosome mechanics to genome functions.
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Affiliation(s)
- Veer I P Keizer
- Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR3664, Laboratoire Dynamique du Noyau, 75005 Paris, France.,Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005 Paris, France.,Institut Curie, PSL Research University, CNRS UMR144, Laboratoire Biologie Cellulaire et Cancer, 75005 Paris, France
| | - Simon Grosse-Holz
- Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR3664, Laboratoire Dynamique du Noyau, 75005 Paris, France.,Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005 Paris, France.,Department of Physics and Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Maxime Woringer
- Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR3664, Laboratoire Dynamique du Noyau, 75005 Paris, France.,Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005 Paris, France
| | - Laura Zambon
- Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR3664, Laboratoire Dynamique du Noyau, 75005 Paris, France.,Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005 Paris, France.,Institut Curie, PSL Research University, CNRS UMR144, Laboratoire Biologie Cellulaire et Cancer, 75005 Paris, France
| | - Koceila Aizel
- Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005 Paris, France
| | - Maud Bongaerts
- Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005 Paris, France
| | - Fanny Delille
- ESPCI Paris, PSL Research University, Sorbonne Université, CNRS UMR8213, Laboratoire de Physique et d'Étude des Matériaux, 75005 Paris, France
| | - Lorena Kolar-Znika
- Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR3664, Laboratoire Dynamique du Noyau, 75005 Paris, France.,Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005 Paris, France
| | - Vittore F Scolari
- Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR3664, Laboratoire Dynamique du Noyau, 75005 Paris, France.,Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005 Paris, France
| | - Sebastian Hoffmann
- Institut Curie, PSL Research University, CNRS UMR144, Laboratoire Biologie Cellulaire et Cancer, 75005 Paris, France
| | - Edward J Banigan
- Department of Physics and Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Leonid A Mirny
- Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR3664, Laboratoire Dynamique du Noyau, 75005 Paris, France.,Department of Physics and Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Maxime Dahan
- Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005 Paris, France
| | - Daniele Fachinetti
- Institut Curie, PSL Research University, CNRS UMR144, Laboratoire Biologie Cellulaire et Cancer, 75005 Paris, France
| | - Antoine Coulon
- Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR3664, Laboratoire Dynamique du Noyau, 75005 Paris, France.,Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005 Paris, France
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49
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Integrative genome modeling platform reveals essentiality of rare contact events in 3D genome organizations. Nat Methods 2022; 19:938-949. [PMID: 35817938 PMCID: PMC9349046 DOI: 10.1038/s41592-022-01527-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 05/18/2022] [Indexed: 02/07/2023]
Abstract
A multitude of sequencing-based and microscopy technologies provide the means to unravel the relationship between the three-dimensional organization of genomes and key regulatory processes of genome function. Here, we develop a multimodal data integration approach to produce populations of single-cell genome structures that are highly predictive for nuclear locations of genes and nuclear bodies, local chromatin compaction and spatial segregation of functionally related chromatin. We demonstrate that multimodal data integration can compensate for systematic errors in some of the data and can greatly increase accuracy and coverage of genome structure models. We also show that alternative combinations of different orthogonal data sources can converge to models with similar predictive power. Moreover, our study reveals the key contributions of low-frequency (‘rare’) interchromosomal contacts to accurately predicting the global nuclear architecture, including the positioning of genes and chromosomes. Overall, our results highlight the benefits of multimodal data integration for genome structure analysis, available through the Integrative Genome Modeling software package. The Integrative Genome Modeling platform is a tool for population-based three-dimensional genome structure modeling and analysis by integrating various experimental data sources.
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50
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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.
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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
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