1
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Liang T, Dong Y, Cheng I, Wen P, Li F, Liu F, Wu Q, Ren E, Liu P, Li H, Gu Z. In situ formation of biomolecular condensates as intracellular drug reservoirs for augmenting chemotherapy. Nat Biomed Eng 2024:10.1038/s41551-024-01254-y. [PMID: 39271933 DOI: 10.1038/s41551-024-01254-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 08/10/2024] [Indexed: 09/15/2024]
Abstract
Biomolecular condensates, which arise from liquid-liquid phase separation within cells, may provide a means of enriching and prolonging the retention of small-molecule drugs within cells. Here we report a method for the controlled in situ formation of biomolecular condensates as reservoirs for the enrichment and retention of chemotherapeutics in cancer cells, and show that the approach can be leveraged to enhance antitumour efficacies in mice with drug-resistant tumours. The method involves histones as positively charged proteins and doxorubicin-intercalated DNA strands bioorthogonally linked via a click-to-release reaction between trans-cyclooctene and tetrazine groups. The reaction temporarily impaired the phase separation of histones in vitro, favoured the initiation of liquid-liquid phase separation within cells and led to the formation of biomolecular condensates that were sufficiently large to be retained within tumour cells. The controlled formation of biomolecular condensates as drug reservoirs within cells may offer new options for boosting the efficacies of cancer therapies.
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Affiliation(s)
- Tingxizi Liang
- State Key Laboratory of Advanced Drug Delivery and Release Systems, and Liangzhu Laboratory, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Yuxiang Dong
- School of Materials Science and Engineering, Suzhou University of Science and Technology, Suzhou, China
| | - Irina Cheng
- State Key Laboratory of Advanced Drug Delivery and Release Systems, and Liangzhu Laboratory, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Ping Wen
- State Key Laboratory of Advanced Drug Delivery and Release Systems, and Liangzhu Laboratory, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Fengqin Li
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Feng Liu
- State Key Laboratory of Advanced Drug Delivery and Release Systems, and Liangzhu Laboratory, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Qing Wu
- State Key Laboratory of Advanced Drug Delivery and Release Systems, and Liangzhu Laboratory, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - En Ren
- State Key Laboratory of Advanced Drug Delivery and Release Systems, and Liangzhu Laboratory, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Peifeng Liu
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Hongjun Li
- State Key Laboratory of Advanced Drug Delivery and Release Systems, and Liangzhu Laboratory, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.
- Department of Hepatobiliary and Pancreatic Surgery, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.
| | - Zhen Gu
- State Key Laboratory of Advanced Drug Delivery and Release Systems, and Liangzhu Laboratory, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China.
- Jinhua Institute of Zhejiang University, Jinhua, China.
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, China.
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2
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Chen Y, Xiang H, Li X, Chen Y, Zhang J. Near-Infrared Laser-Switching DNA Phase Separation Nanoinducer for Glioma Therapy. ACS NANO 2024; 18:24426-24440. [PMID: 39171897 DOI: 10.1021/acsnano.4c07514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
DNA phase separation participates in chromatin packing for the modulation of gene transcription, but the induction of DNA phase separation in living cells for disease treatment faces huge challenges. Herein, we construct a Ru(II)-polypyridyl-loaded upconversion nanoplatform (denoted as UCSNs-R) to achieve the manipulation of DNA phase separation and production of abundant singlet oxygen (1O2) for efficient treatment of gliomas. The utilization of the UCSN not only facilitates high loading of Ru(II)-polypyridyl complexes (RuC) but also promotes the conversion of near-infrared (NIR) laser to ultraviolet light for efficient 1O2 generation. The released RuC exhibit DNA "light-switch" behavior and high DNA binding affinity that induce phase separation of DNA in living cells, thus resulting in DNA damage and suppressing tumor-cell growth. In vivo investigation demonstrates the high capability of UCSNs-R in inhibiting tumor proliferation under NIR laser illumination. This work represents a paradigm for designing a DNA phase separation nanoinducer through integration of the UCSN with Ru(II)-polypyridyl-based complexes for efficient therapy of gliomas.
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Affiliation(s)
- Yixin Chen
- Department of Radiology, Huashan Hospital, State Key Laboratory of Medical Neurobiology, Fudan University, Shanghai 200040, P. R. China
| | - Huijing Xiang
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Xiaodan Li
- Department of Radiology, Huashan Hospital, State Key Laboratory of Medical Neurobiology, Fudan University, Shanghai 200040, P. R. China
| | - Yu Chen
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
- Shanghai Institute of Materdicine, Shanghai 200051, P. R. China
| | - Jun Zhang
- Department of Radiology, Huashan Hospital, State Key Laboratory of Medical Neurobiology, Fudan University, Shanghai 200040, P. R. China
- National Center for Neurological Disorders, Shanghai 200040, P. R. China
- Institute of Functional and Molecular Medical Imaging, Fudan University, Shanghai 200040, P. R. China
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3
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Lao Z, Kamat KD, Jiang Z, Zhang B. OpenNucleome for high-resolution nuclear structural and dynamical modeling. eLife 2024; 13:RP93223. [PMID: 39146200 PMCID: PMC11326778 DOI: 10.7554/elife.93223] [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] [Indexed: 08/17/2024] Open
Abstract
The intricate structural organization of the human nucleus is fundamental to cellular function and gene regulation. Recent advancements in experimental techniques, including high-throughput sequencing and microscopy, have provided valuable insights into nuclear organization. Computational modeling has played significant roles in interpreting experimental observations by reconstructing high-resolution structural ensembles and uncovering organization principles. However, the absence of standardized modeling tools poses challenges for furthering nuclear investigations. We present OpenNucleome-an open-source software designed for conducting GPU-accelerated molecular dynamics simulations of the human nucleus. OpenNucleome offers particle-based representations of chromosomes at a resolution of 100 KB, encompassing nuclear lamina, nucleoli, and speckles. This software furnishes highly accurate structural models of nuclear architecture, affording the means for dynamic simulations of condensate formation, fusion, and exploration of non-equilibrium effects. We applied OpenNucleome to uncover the mechanisms driving the emergence of 'fixed points' within the nucleus-signifying genomic loci robustly anchored in proximity to specific nuclear bodies for functional purposes. This anchoring remains resilient even amidst significant fluctuations in chromosome radial positions and nuclear shapes within individual cells. Our findings lend support to a nuclear zoning model that elucidates genome functionality. We anticipate OpenNucleome to serve as a valuable tool for nuclear investigations, streamlining mechanistic explorations and enhancing the interpretation of experimental observations.
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Affiliation(s)
- Zhuohan Lao
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
| | - Kartik D Kamat
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
| | - Zhongling Jiang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
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4
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An Y, Gao T, Wang T, Zhang D, Bharti B. Effects of charge asymmetry on the liquid-liquid phase separation of polyampholytes and their condensate properties. SOFT MATTER 2024; 20:6150-6159. [PMID: 39044475 DOI: 10.1039/d4sm00532e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
Liquid-liquid phase separation (LLPS) is the mechanism underlying the formation of bio-molecular condensates which are important compartments regulating intra- and extra-cellular functions. Electrostatic interactions are some of the important driving forces of the LLPS behaviors of biomolecules. However, the understanding of the electrostatic interactions is still limited, especially in the mixtures of biomolecules with different charge patterns. Here, we focus on the electrostatic interactions in mixtures of charge-asymmetric and charge-symmetric polyampholytes and their roles in the phase separation behaviors. We build charge-asymmetric and charge-symmetric model proteins consisting of both glutamic acid (E, negatively charged) and lysine (K, positively charged), i.e. polyampholytes of E35K15 (charge asymmetric) and E25K25 (charge symmetric). Pure E25K25 can undergo LLPS. To investigate the effects of charge-asymmetric polyampholytes on the mixtures of E25K25/E35K15, we perform coarse-grained simulations to determine their phase separation. The charge-asymmetric polyampholyte E35K15 is resistant to the LLPS of the mixtures of E25K25/E35K15. The condensate density decreases with the molar fraction of E35K15 increasing to 0.4, and no LLPS occurs at the molar fraction of 0.5 and above. This can be attributed to the electrostatic repulsion between the negatively charged E35K15 polymers. We further investigate the effects of charge asymmetry on the conformations and properties of the condensates. The E35K15 polymers in the condensates exhibit a more collapsed state as the molar fraction of E35K15 increases. However, the conformation of E25K25 polymers changes slightly across different condensates. The surface tensions of condensates decline with the increase of the molar fraction of E35K15 polymers, while the diffusivity of polymers in the condensed phases is enhanced. This work elucidates the role of charge-asymmetric polyampholytes in determining the LLPS behaviours of binary mixtures of charge-symmetric and charge-asymmetric proteins as well as the properties of condensed phases.
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Affiliation(s)
- Yaxin An
- Department of Chemical Engineering, Louisiana State University, USA.
| | - Tong Gao
- Department of Chemical Engineering, Louisiana State University, USA.
| | - Tianyi Wang
- Department of Chemical Engineering, Louisiana State University, USA.
| | - Donghui Zhang
- Department of Chemistry, Louisiana State University, USA
| | - Bhuvnesh Bharti
- Department of Chemical Engineering, Louisiana State University, USA.
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Benchorin G, Cho RJ, Li MJ, Molotkova N, Kohwi M. Dan forms condensates in neuroblasts and regulates nuclear architecture and progenitor competence in vivo. Nat Commun 2024; 15:5097. [PMID: 38877037 PMCID: PMC11178893 DOI: 10.1038/s41467-024-49326-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 05/30/2024] [Indexed: 06/16/2024] Open
Abstract
Genome organization is thought to underlie cell type specific gene expression, yet how it is regulated in progenitors to produce cellular diversity is unknown. In Drosophila, a developmentally-timed genome reorganization in neural progenitors terminates competence to produce early-born neurons. These events require downregulation of Distal antenna (Dan), part of the conserved pipsqueak DNA-binding superfamily. Here we find that Dan forms liquid-like condensates with high protein mobility, and whose size and subnuclear distribution are balanced with its DNA-binding. Further, we identify a LARKS domain, a structural motif associated with condensate-forming proteins. Deleting just 13 amino acids from LARKS abrogates Dan's ability to retain the early-born neural fate gene, hunchback, in the neuroblast nuclear interior and maintain competence in vivo. Conversely, domain-swapping with LARKS from known phase-separating proteins rescues Dan's effects on competence. Together, we provide in vivo evidence for condensate formation and the regulation of progenitor nuclear architecture underlying neuronal diversification.
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Affiliation(s)
- Gillie Benchorin
- Department of Biological Sciences, Columbia University, New York, NY, USA
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Richard Jangwon Cho
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- Department of Neuroscience, Columbia University, New York, NY, USA
| | - Maggie Jiaqi Li
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- Department of Neuroscience, Columbia University, New York, NY, USA
| | - Natalia Molotkova
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- Department of Neuroscience, Columbia University, New York, NY, USA
| | - Minoree Kohwi
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA.
- Department of Neuroscience, Columbia University, New York, NY, USA.
- Kavli Institute for Brain Science, Columbia University, New York, NY, USA.
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6
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Arsenadze G, Caragine CM, Coakley T, Eshghi I, Yang Y, Wofford A, Zidovska A. Anomalous coarsening of coalescing nucleoli in human cells. Biophys J 2024; 123:1467-1480. [PMID: 38192101 PMCID: PMC11163295 DOI: 10.1016/j.bpj.2024.01.005] [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: 05/31/2023] [Revised: 09/20/2023] [Accepted: 01/03/2024] [Indexed: 01/10/2024] Open
Abstract
Coarsening is a ubiquitous phenomenon in droplet systems near thermodynamic equilibrium-as an increase in droplet size lowers the system's free energy-however, coarsening of droplets in nonequilibrium systems, such as the cell nucleus, is far from understood. Liquid condensates in the cell nucleus, like nucleoli, form by liquid-liquid phase separation and play a key role in the nuclear organization. In human cells, nucleolar droplets are nucleated at the beginning of the cell cycle and coarsen with time by coalescing with each other. Upon coarsening, human nucleoli exhibit an anomalous volume distribution P(V)∼V-1, which cannot be explained by any existing theory. In this work, we investigate physical mechanisms behind the anomalous coarsening of human nucleoli. Using spinning disk confocal microscopy, we simultaneously record dynamic behavior of nucleoli and their surrounding chromatin before their coalescence in live human cells. We find that nucleolar anomalous coarsening persists during the entire cell cycle. We measure chromatin flows and density between and around nucleoli, as well as relative motion of two nucleoli before they coalesce. We find that, before nucleolar coalescence, chromatin concentration decreases in the space between nucleoli and the nucleoli move faster toward each other, resembling an effective depletion attraction between the coalescing nucleoli. Indeed, our computational simulations of nucleolar dynamics show that short-ranged attraction is sufficient to explain the observed anomalous volume distribution of human nucleoli. Overall, our results reveal a potential physical mechanism contributing to coarsening of human nucleoli. Such knowledge expands our picture of the physical behavior of liquid condensates inside the cell nucleus and our understanding of the dynamic nuclear organization.
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Affiliation(s)
- Giorgi Arsenadze
- Center for Soft Matter Research, Department of Physics, New York University, New York, New York
| | - Christina M Caragine
- Center for Soft Matter Research, Department of Physics, New York University, New York, New York
| | - Taylor Coakley
- Center for Soft Matter Research, Department of Physics, New York University, New York, New York
| | - Iraj Eshghi
- Center for Soft Matter Research, Department of Physics, New York University, New York, New York
| | - Yuwei Yang
- Center for Soft Matter Research, Department of Physics, New York University, New York, New York
| | - Alex Wofford
- Center for Soft Matter Research, Department of Physics, New York University, New York, New York
| | - Alexandra Zidovska
- Center for Soft Matter Research, Department of Physics, New York University, New York, New York.
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7
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Wu ZP, Bloom KS, Forest MG, Cao XZ. Transient crosslinking controls the condensate formation pathway within chromatin networks. Phys Rev E 2024; 109:L042401. [PMID: 38755828 PMCID: PMC11137846 DOI: 10.1103/physreve.109.l042401] [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: 09/10/2023] [Accepted: 02/26/2024] [Indexed: 05/18/2024]
Abstract
The network structure of densely packed chromatin within the nucleus of eukaryotic cells acts in concert with nonequilibrium processes. Using statistical physics simulations, we explore the control provided by transient crosslinking of the chromatin network by structural-maintenance-of-chromosome (SMC) proteins over (i) the physical properties of the chromatin network and (ii) condensate formation of embedded molecular species. We find that the density and lifetime of transient SMC crosslinks regulate structural relaxation modes and tune the sol-vs-gel state of the chromatin network, which imparts control over the kinetic pathway to condensate formation. Specifically, lower density, shorter-lived crosslinks induce sollike networks and a droplet-fusion pathway, whereas higher density, longer-lived crosslinks induce gellike networks and an Ostwald-ripening pathway.
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Affiliation(s)
- Zong-Pei Wu
- Department of Physics at Xiamen University, Xiamen 361005, P.R. China
| | - Kerry S. Bloom
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - M. Gregory Forest
- Departments of Mathematics, Applied Physical Sciences and Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Xue-Zheng Cao
- Department of Physics at Xiamen University, Xiamen 361005, P.R. China
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8
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Lao Z, Kamat K, Jiang Z, Zhang B. OpenNucleome for high resolution nuclear structural and dynamical modeling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.16.562451. [PMID: 37905090 PMCID: PMC10614770 DOI: 10.1101/2023.10.16.562451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
The intricate structural organization of the human nucleus is fundamental to cellular function and gene regulation. Recent advancements in experimental techniques, including high-throughput sequencing and microscopy, have provided valuable insights into nuclear organization. Computational modeling has played significant roles in interpreting experimental observations by reconstructing high-resolution structural ensembles and uncovering organization principles. However, the absence of standardized modeling tools poses challenges for furthering nuclear investigations. We present OpenNucleome-an open-source software designed for conducting GPU-accelerated molecular dynamics simulations of the human nucleus. OpenNucleome offers particle-based representations of chromosomes at a resolution of 100 KB, encompassing nuclear lamina, nucleoli, and speckles. This software furnishes highly accurate structural models of nuclear architecture, affording the means for dynamic simulations of condensate formation, fusion, and exploration of non-equilibrium effects. We applied OpenNucleome to uncover the mechanisms driving the emergence of "fixed points" within the nucleus-signifying genomic loci robustly anchored in proximity to specific nuclear bodies for functional purposes. This anchoring remains resilient even amidst significant fluctuations in chromosome radial positions and nuclear shapes within individual cells. Our findings lend support to a nuclear zoning model that elucidates genome functionality. We anticipate OpenNucleome to serve as a valuable tool for nuclear investigations, streamlining mechanistic explorations and enhancing the interpretation of experimental observations.
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Affiliation(s)
- Zhuohan Lao
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kartik Kamat
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Zhongling Jiang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
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9
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Shu J, Jiang J, Wang X, Yang X, Zhao G, Cai T. MDM2 provides TOP2 poison resistance by promoting proteolysis of TOP2βcc in a p53-independent manner. Cell Death Dis 2024; 15:83. [PMID: 38263255 PMCID: PMC10806188 DOI: 10.1038/s41419-024-06474-3] [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: 09/15/2023] [Revised: 01/14/2024] [Accepted: 01/15/2024] [Indexed: 01/25/2024]
Abstract
DNA topoisomerase II (TOP2) is an enzyme that performs a critical function in manipulating DNA topology during replication, transcription, and chromosomal compaction by forming a vital intermediate known as the TOP2-DNA cleavage complex (TOP2cc). Although the TOP2cc is often transient, stabilization can be achieved by TOP2 poisons, a family of anti-cancer chemotherapeutic agents targeting TOP2, such as etoposide (VP-16), and then induce double-strand breaks (DSBs) in cellular DNA. TOP2cc first needs to be proteolyzed before it can be processed by TDP2 for the removal of these protein adducts and to produce clean DNA ends necessary for proper repair. However, the mechanism by which TOP2βcc is proteolyzed has not been thoroughly studied. In this study, we report that after exposure to VP-16, MDM2, a RING-type E3 ubiquitin ligase, attaches to TOP2β and initiates polyubiquitination and proteasomal degradation. Mechanistically, during exposure to VP-16, TOP2β binds to DNA to form TOP2βcc, which promotes MDM2 binding and subsequent TOP2β ubiquitination and degradation, and results in a decrease in TOP2βcc levels. Biologically, MDM2 inactivation abrogates TOP2β degradation, stabilizes TOP2βcc, and subsequently increases the number of TOP2β-concealed DSBs, resulting in the rapid death of cancer cells via the apoptotic process. Furthermore, we demonstrate the combination activity of VP-16 and RG7112, an MDM2 inhibitor, in the xenograft tumor model and in situ lung cancer mouse model. Taken together, the results of our research reveal an underlying mechanism by which MDM2 promotes cancer cell survival in the presence of TOP2 poisons by activating proteolysis of TOP2βcc in a p53-independent manner, and provides a rationale for the combination of MDM2 inhibitors with TOP2 poisons for cancer therapy.
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Affiliation(s)
- Jianfeng Shu
- Department of Thoracic Surgery, Ningbo No.2 Hospital, Ningbo, 315010, Zhejiang, China
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, 315000, Zhejiang, China
| | - Jinni Jiang
- Department of Thoracic Surgery, Ningbo No.2 Hospital, Ningbo, 315010, Zhejiang, China
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, 315000, Zhejiang, China
| | - Xiaofang Wang
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, 315000, Zhejiang, China
| | - Xuejie Yang
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, 315000, Zhejiang, China
| | - Guofang Zhao
- Department of Thoracic Surgery, Ningbo No.2 Hospital, Ningbo, 315010, Zhejiang, China.
| | - Ting Cai
- Department of Thoracic Surgery, Ningbo No.2 Hospital, Ningbo, 315010, Zhejiang, China.
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, 315000, Zhejiang, China.
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10
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Lin AZ, Ruff KM, Dar F, Jalihal A, King MR, Lalmansingh JM, Posey AE, Erkamp NA, Seim I, Gladfelter AS, Pappu RV. Dynamical control enables the formation of demixed biomolecular condensates. Nat Commun 2023; 14:7678. [PMID: 37996438 PMCID: PMC10667521 DOI: 10.1038/s41467-023-43489-4] [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: 08/02/2023] [Accepted: 11/10/2023] [Indexed: 11/25/2023] Open
Abstract
Cellular matter can be organized into compositionally distinct biomolecular condensates. For example, in Ashbya gossypii, the RNA-binding protein Whi3 forms distinct condensates with different RNA molecules. Using criteria derived from a physical framework for explaining how compositionally distinct condensates can form spontaneously via thermodynamic considerations, we find that condensates in vitro form mainly via heterotypic interactions in binary mixtures of Whi3 and RNA. However, within these condensates, RNA molecules become dynamically arrested. As a result, in ternary systems, simultaneous additions of Whi3 and pairs of distinct RNA molecules lead to well-mixed condensates, whereas delayed addition of an RNA component results in compositional distinctness. Therefore, compositional identities of condensates can be achieved via dynamical control, being driven, at least partially, by the dynamical arrest of RNA molecules. Finally, we show that synchronizing the production of different RNAs leads to more well-mixed, as opposed to compositionally distinct condensates in vivo.
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Affiliation(s)
- Andrew Z Lin
- Division of Biology and Biomedical Sciences, Plant and Microbial Biosciences, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Kiersten M Ruff
- Department of Biomedical Engineering and Center for Biomolecular Condensates, James F. McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Furqan Dar
- Department of Biomedical Engineering and Center for Biomolecular Condensates, James F. McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Ameya Jalihal
- Department of Cell Biology, Duke University, Durham, NC, 27708, USA
| | - Matthew R King
- Department of Biomedical Engineering and Center for Biomolecular Condensates, James F. McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Jared M Lalmansingh
- Department of Biomedical Engineering and Center for Biomolecular Condensates, James F. McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Ammon E Posey
- Department of Biomedical Engineering and Center for Biomolecular Condensates, James F. McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Nadia A Erkamp
- Department of Biomedical Engineering and Center for Biomolecular Condensates, James F. McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Ian Seim
- Department of Cell Biology, Duke University, Durham, NC, 27708, USA
| | - Amy S Gladfelter
- Department of Cell Biology, Duke University, Durham, NC, 27708, USA.
| | - Rohit V Pappu
- Division of Biology and Biomedical Sciences, Plant and Microbial Biosciences, Washington University in St. Louis, St. Louis, MO, 63130, USA.
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11
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Liu JX, Haataja MP, Košmrlj A, Datta SS, Arnold CB, Priestley RD. Liquid-liquid phase separation within fibrillar networks. Nat Commun 2023; 14:6085. [PMID: 37770446 PMCID: PMC10539382 DOI: 10.1038/s41467-023-41528-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 09/06/2023] [Indexed: 09/30/2023] Open
Abstract
Complex fibrillar networks mediate liquid-liquid phase separation of biomolecular condensates within the cell. Mechanical interactions between these condensates and the surrounding networks are increasingly implicated in the physiology of the condensates and yet, the physical principles underlying phase separation within intracellular media remain poorly understood. Here, we elucidate the dynamics and mechanics of liquid-liquid phase separation within fibrillar networks by condensing oil droplets within biopolymer gels. We find that condensates constrained within the network pore space grow in abrupt temporal bursts. The subsequent restructuring of condensates and concomitant network deformation is contingent on the fracture of network fibrils, which is determined by a competition between condensate capillarity and network strength. As a synthetic analog to intracellular phase separation, these results further our understanding of the mechanical interactions between biomolecular condensates and fibrillar networks in the cell.
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Affiliation(s)
- Jason X Liu
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ, 08544, USA
- Princeton Materials Institute, Princeton University, Princeton, NJ, 08544, USA
| | - Mikko P Haataja
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ, 08544, USA
- Princeton Materials Institute, Princeton University, Princeton, NJ, 08544, USA
| | - Andrej Košmrlj
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ, 08544, USA
- Princeton Materials Institute, Princeton University, Princeton, NJ, 08544, USA
| | - Sujit S Datta
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, 08544, USA
| | - Craig B Arnold
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ, 08544, USA
- Princeton Materials Institute, Princeton University, Princeton, NJ, 08544, USA
| | - Rodney D Priestley
- Princeton Materials Institute, Princeton University, Princeton, NJ, 08544, USA.
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, 08544, USA.
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12
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Schuette G, Ding X, Zhang B. Efficient Hi-C inversion facilitates chromatin folding mechanism discovery and structure prediction. Biophys J 2023; 122:3425-3438. [PMID: 37496267 PMCID: PMC10502442 DOI: 10.1016/j.bpj.2023.07.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 07/10/2023] [Accepted: 07/24/2023] [Indexed: 07/28/2023] Open
Abstract
Genome-wide chromosome conformation capture (Hi-C) experiments have revealed many structural features of chromatin across multiple length scales. Further understanding genome organization requires relating these discoveries to the mechanisms that establish chromatin structures and reconstructing these structures in three dimensions, but both objectives are difficult to achieve with existing algorithms that are often computationally expensive. To alleviate this challenge, we present an algorithm that efficiently converts Hi-C data into contact energies, which measure the interaction strength between genomic loci brought into proximity. Contact energies are local quantities unaffected by the topological constraints that correlate Hi-C contact probabilities. Thus, extracting contact energies from Hi-C contact probabilities distills the biologically unique information contained in the data. We show that contact energies reveal the location of chromatin loop anchors, support a phase separation mechanism for genome compartmentalization, and parameterize polymer simulations that predict three-dimensional chromatin structures. Therefore, we anticipate that contact energy extraction will unleash the full potential of Hi-C data and that our inversion algorithm will facilitate the widespread adoption of contact energy analysis.
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Affiliation(s)
- Greg Schuette
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Xinqiang Ding
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts.
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13
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Liu S, Wang C, Latham AP, Ding X, Zhang B. OpenABC enables flexible, simplified, and efficient GPU accelerated simulations of biomolecular condensates. PLoS Comput Biol 2023; 19:e1011442. [PMID: 37695778 PMCID: PMC10513381 DOI: 10.1371/journal.pcbi.1011442] [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: 04/21/2023] [Revised: 09/21/2023] [Accepted: 08/19/2023] [Indexed: 09/13/2023] Open
Abstract
Biomolecular condensates are important structures in various cellular processes but are challenging to study using traditional experimental techniques. In silico simulations with residue-level coarse-grained models strike a balance between computational efficiency and chemical accuracy. They could offer valuable insights by connecting the emergent properties of these complex systems with molecular sequences. However, existing coarse-grained models often lack easy-to-follow tutorials and are implemented in software that is not optimal for condensate simulations. To address these issues, we introduce OpenABC, a software package that greatly simplifies the setup and execution of coarse-grained condensate simulations with multiple force fields using Python scripting. OpenABC seamlessly integrates with the OpenMM molecular dynamics engine, enabling efficient simulations with performance on a single GPU that rivals the speed achieved by hundreds of CPUs. We also provide tools that convert coarse-grained configurations to all-atom structures for atomistic simulations. We anticipate that OpenABC will significantly facilitate the adoption of in silico simulations by a broader community to investigate the structural and dynamical properties of condensates.
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Affiliation(s)
- Shuming Liu
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Cong Wang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Andrew P. Latham
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, California, United States of America
| | - Xinqiang Ding
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
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14
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Tortora MMC, Brennan LD, Karpen G, Jost D. HP1-driven phase separation recapitulates the thermodynamics and kinetics of heterochromatin condensate formation. Proc Natl Acad Sci U S A 2023; 120:e2211855120. [PMID: 37549295 PMCID: PMC10438847 DOI: 10.1073/pnas.2211855120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 06/28/2023] [Indexed: 08/09/2023] Open
Abstract
The spatial segregation of pericentromeric heterochromatin (PCH) into distinct, membrane-less nuclear compartments involves the binding of Heterochromatin Protein 1 (HP1) to H3K9me2/3-rich genomic regions. While HP1 exhibits liquid-liquid phase separation properties in vitro, its mechanistic impact on the structure and dynamics of PCH condensate formation in vivo remains largely unresolved. Here, using a minimal theoretical framework, we systematically investigate the mutual coupling between self-interacting HP1-like molecules and the chromatin polymer. We reveal that the specific affinity of HP1 for H3K9me2/3 loci facilitates coacervation in nucleo and promotes the formation of stable PCH condensates at HP1 levels far below the concentration required to observe phase separation in purified protein assays in vitro. These heterotypic HP1-chromatin interactions give rise to a strong dependence of the nucleoplasmic HP1 density on HP1-H3K9me2/3 stoichiometry, consistent with the thermodynamics of multicomponent phase separation. The dynamical cross talk between HP1 and the viscoelastic chromatin scaffold also leads to anomalously slow equilibration kinetics, which strongly depend on the genomic distribution of H3K9me2/3 domains and result in the coexistence of multiple long-lived, microphase-separated PCH compartments. The morphology of these complex coacervates is further found to be governed by the dynamic establishment of the underlying H3K9me2/3 landscape, which may drive their increasingly abnormal, aspherical shapes during cell development. These findings compare favorably to 4D microscopy measurements of HP1 condensate formation in live Drosophila embryos and suggest a general quantitative model of PCH formation based on the interplay between HP1-based phase separation and chromatin polymer mechanics.
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Affiliation(s)
- Maxime M. C. Tortora
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS, UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, 69007Lyon, France
| | - Lucy D. Brennan
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Gary Karpen
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
- Department of BioEngineering and BioMedical Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Daniel Jost
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS, UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, 69007Lyon, France
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15
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Sanchez-Burgos I, Herriott L, Collepardo-Guevara R, Espinosa JR. Surfactants or scaffolds? RNAs of varying lengths control the thermodynamic stability of condensates differently. Biophys J 2023; 122:2973-2987. [PMID: 36883003 PMCID: PMC10398262 DOI: 10.1016/j.bpj.2023.03.006] [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: 11/09/2022] [Revised: 02/23/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Biomolecular condensates, thought to form via liquid-liquid phase separation of intracellular mixtures, are multicomponent systems that can include diverse types of proteins and RNAs. RNA is a critical modulator of RNA-protein condensate stability, as it induces an RNA concentration-dependent reentrant phase transition-increasing stability at low RNA concentrations and decreasing it at high concentrations. Beyond concentration, RNAs inside condensates can be heterogeneous in length, sequence, and structure. Here, we use multiscale simulations to understand how different RNA parameters interact with one another to modulate the properties of RNA-protein condensates. To do so, we perform residue/nucleotide resolution coarse-grained molecular dynamics simulations of multicomponent RNA-protein condensates containing RNAs of different lengths and concentrations, and either FUS or PR25 proteins. Our simulations reveal that RNA length regulates the reentrant phase behavior of RNA-protein condensates: increasing RNA length sensitively rises the maximum value that the critical temperature of the mixture reaches, and the maximum concentration of RNA that the condensate can incorporate before beginning to become unstable. Strikingly, RNAs of different lengths are organized heterogeneously inside condensates, which allows them to enhance condensate stability via two distinct mechanisms: shorter RNA chains accumulate at the condensate's surface acting as natural biomolecular surfactants, while longer RNA chains concentrate inside the core to saturate their bonds and enhance the density of molecular connections in the condensate. Using a patchy particle model, we additionally demonstrate that the combined impact of RNA length and concentration on condensate properties is dictated by the valency, binding affinity, and polymer length of the various biomolecules involved. Our results postulate that diversity on RNA parameters within condensates allows RNAs to increase condensate stability by fulfilling two different criteria: maximizing enthalpic gain and minimizing interfacial free energy; hence, RNA diversity should be considered when assessing the impact of RNA on biomolecular condensates regulation.
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Affiliation(s)
- Ignacio Sanchez-Burgos
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, United Kingdom
| | - Lara Herriott
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, United Kingdom
| | - Rosana Collepardo-Guevara
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom; Department of Genetics, University of Cambridge, Cambridge, United Kingdom.
| | - Jorge R Espinosa
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, United Kingdom; Departament of Chemical Physics, Faculty of Chemical Sciences, Universidad Complutense de Madrid, Madrid, Spain.
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16
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Schuette G, Ding X, Zhang B. Efficient Hi-C inversion facilitates chromatin folding mechanism discovery and structure prediction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.17.533194. [PMID: 36993500 PMCID: PMC10055272 DOI: 10.1101/2023.03.17.533194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Genome-wide chromosome conformation capture (Hi-C) experiments have revealed many structural features of chromatin across multiple length scales. Further understanding genome organization requires relating these discoveries to the mechanisms that establish chromatin structures and reconstructing these structures in three dimensions, but both objectives are difficult to achieve with existing algorithms that are often computationally expensive. To alleviate this challenge, we present an algorithm that efficiently converts Hi-C data into contact energies, which measure the interaction strength between genomic loci brought into proximity. Contact energies are local quantities unaffected by the topological constraints that correlate Hi-C contact probabilities. Thus, extracting contact energies from Hi-C contact probabilities distills the biologically unique information contained in the data. We show that contact energies reveal the location of chromatin loop anchors, support a phase separation mechanism for genome compartmentalization, and parameterize polymer simulations that predict three-dimensional chromatin structures. Therefore, we anticipate that contact energy extraction will unleash the full potential of Hi-C data and that our inversion algorithm will facilitate the widespread adoption of contact energy analysis.
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Affiliation(s)
- Greg Schuette
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Xinqiang Ding
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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17
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Ziethen N, Kirschbaum J, Zwicker D. Nucleation of Chemically Active Droplets. PHYSICAL REVIEW LETTERS 2023; 130:248201. [PMID: 37390433 DOI: 10.1103/physrevlett.130.248201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 05/10/2023] [Indexed: 07/02/2023]
Abstract
Driven chemical reactions can control the macroscopic properties of droplets, like their size. Such active droplets are critical in structuring the interior of biological cells. Cells also need to control where and when droplets appear, so they need to control droplet nucleation. Our numerical simulations demonstrate that reactions generally suppress nucleation if they stabilize the homogeneous state. An equilibrium surrogate model reveals that reactions increase the effective energy barrier of nucleation, enabling quantitative predictions of the increased nucleation times. Moreover, the surrogate model allows us to construct a phase diagram, which summarizes how reactions affect the stability of the homogeneous phase and the droplet state. This simple picture provides accurate predictions of how driven reactions delay nucleation, which is relevant for understanding droplets in biological cells and chemical engineering.
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Affiliation(s)
- Noah Ziethen
- Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17 37077, Göttingen, Germany
| | - Jan Kirschbaum
- Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17 37077, Göttingen, Germany
| | - David Zwicker
- Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17 37077, Göttingen, Germany
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18
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Liu S, Wang C, Latham A, Ding X, Zhang B. OpenABC Enables Flexible, Simplified, and Efficient GPU Accelerated Simulations of Biomolecular Condensates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.19.537533. [PMID: 37131742 PMCID: PMC10153273 DOI: 10.1101/2023.04.19.537533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Biomolecular condensates are important structures in various cellular processes but are challenging to study using traditional experimental techniques. In silico simulations with residue-level coarse-grained models strike a balance between computational efficiency and chemical accuracy. They could offer valuable insights by connecting the emergent properties of these complex systems with molecular sequences. However, existing coarse-grained models often lack easy-to-follow tutorials and are implemented in software that is not optimal for condensate simulations. To address these issues, we introduce OpenABC, a software package that greatly simplifies the setup and execution of coarse-grained condensate simulations with multiple force fields using Python scripting. OpenABC seamlessly integrates with the OpenMM molecular dynamics engine, enabling efficient simulations with performances on a single GPU that rival the speed achieved by hundreds of CPUs. We also provide tools that convert coarse-grained configurations to all-atom structures for atomistic simulations. We anticipate that Open-ABC will significantly facilitate the adoption of in silico simulations by a broader community to investigate the structural and dynamical properties of condensates. Open-ABC is available at https://github.com/ZhangGroup-MITChemistry/OpenABC.
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Affiliation(s)
- Shuming Liu
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Cong Wang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Andrew Latham
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Xinqiang Ding
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
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19
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Radhakrishnan S, Martin CA, Rammohan A, Vij M, Chandrasekar M, Rela M. Significance of nucleologenesis, ribogenesis, and nucleolar proteome in the pathogenesis and recurrence of hepatocellular carcinoma. Expert Rev Gastroenterol Hepatol 2023; 17:363-378. [PMID: 36919496 DOI: 10.1080/17474124.2023.2191189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
INTRODUCTION Emerging evidence suggests that enhanced ribosome biogenesis, increased size, and quantitative distribution of nucleoli are associated with dysregulated transcription, which in turn drives a cell into aberrant cellular proliferation and malignancy. Nucleolar alterations have been considered a prognostic histological marker for aggressive tumors. More recently, advancements in the understanding of chromatin network (nucleoplasm viscosity) regulated liquid-liquid phase separation mechanism of nucleolus formation and their multifunctional role shed light on other regulatory processes, apart from ribosomal biogenesis of the nucleolus. AREAS COVERED Using hepatocellular carcinoma as a model to study the role of nucleoli in tumor progression, we review the potential of nucleolus coalescence in the onset and development of tumors through non-ribosomal biogenesis pathways, thereby providing new avenues for early diagnosis and cancer therapy. EXPERT OPINION Molecular-based classifications have failed to identify the nucleolar-based molecular targets that facilitate cell-cycle progression. However, the algorithm-based tumor risk identification with high-resolution medical images suggests prominent nucleoli, karyotheca, and increased nucleus/cytoplasm ratio as largely associated with tumor recurrence. Nonetheless, the role of the non-ribosomal functions of nucleoli in tumorigenesis remains elusive. This clearly indicates the lacunae in the study of the nucleolar proteins pertaining to cancer. [Figure: see text].
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Affiliation(s)
| | | | - Ashwin Rammohan
- The Institute of Liver Disease & Transplantation, Dr. Rela Institute & Medical Centre, Chennai, India
| | - Mukul Vij
- Department of Pathology, Dr. Rela Institute & Medical Centre, Chennai, India
| | - Mani Chandrasekar
- Department of Oncology, Dr. Rela Institute & Medical Centre, Chennai, India
| | - Mohamed Rela
- Cell Laboratory, National Foundation for Liver Research, Chennai, India
- The Institute of Liver Disease & Transplantation, Dr. Rela Institute & Medical Centre, Chennai, India
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20
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Lin TY, Ma YW, Tsai MY. Early-Stage Oligomerization of Prion-like Polypeptides Reveals the Molecular Mechanism of Amyloid-Disrupting Capacity by Proline Residues. J Phys Chem B 2023; 127:1074-1088. [PMID: 36705662 PMCID: PMC9924260 DOI: 10.1021/acs.jpcb.2c05463] [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: 08/01/2022] [Revised: 12/09/2022] [Indexed: 01/28/2023]
Abstract
Proline cis/trans isomerization governs protein local conformational changes via its local mechanical rigidity. The amyloid-disrupting capacity of proline is widely acknowledged; however, the molecular mechanism is still not clear. To understand how proline residues in polypeptide chains influence amyloid propensity, we study several truncated sequences of the TDP-43 C-terminal region (287-322) and their triple proline variants (308PPP310). We use coarse-grained molecular simulation to study the time evolution of the process of aggregation in the early stages in an effective high-concentration condition (∼25 mM). This ensures the long time scales for protein association at laboratory concentrations. We use several experimentally determined structure templates as initial structures of monomer conformations. We carry out oligomer size analysis and cluster analysis, along with several structural measures, to characterize the size distributions of oligomers and their morphological/structural properties. We show that average oligomer size is not a good indicator of amyloid propensity. Structural order and/or morphological properties are better alternatives. We show that proline variants can efficiently maintain the formation of large "ordered" oligomers of shorter truncated sequences, i.e., 307-322. This "order" maintenance is weakened when using longer truncated sequences (i.e., 287-322), leading to the formation of "disordered" oligomers. From an energy trade-off perspective, if the entropic effect is weak (short sequence length), the shape-complementarity of proline variants effectively guides the oligomerization process to form "ordered" oligomer intermediates. This leads to a distinct aggregation pathway that promotes amyloid formation (on-pathway). Strong entropic effects (long sequence length), however, would cause the formation of "disordered" oligomers. This in turn will suppress amyloid formation (off-pathway). The proline shape-complementary effects provide a guided morphological restraint to facilitate the pathways of amyloid formation. Our study supports the importance of structure-based kinetic heterogeneity of prion-like sequence fragments in driving different aggregation pathways. This work sheds light on the role of morphological and structural order of early-stage oligomeric species in regulating amyloid-disrupting capacity by prolines.
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Affiliation(s)
- Tong-You Lin
- Department of Chemistry, Tamkang
University, New Taipei
City, Taiwan251301
| | - Yuan-Wei Ma
- Department of Chemistry, Tamkang
University, New Taipei
City, Taiwan251301
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21
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Consistencies and contradictions in different polymer models of chromatin architecture. Comput Struct Biotechnol J 2023; 21:1084-1091. [PMID: 36789261 PMCID: PMC9900451 DOI: 10.1016/j.csbj.2023.01.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/23/2023] [Accepted: 01/23/2023] [Indexed: 01/26/2023] Open
Abstract
Genetic information is stored in very long DNA molecules, which are folded to form chromatin, a similarly long polymer fibre that is ultimately organised into chromosomes. The organisation of chromatin is fundamental to many cellular functions, from the expression of the genetic information to cell division. As a long polymer, chromatin is very flexible and may adopt a myriad of shapes. Globally, the polymer physics governing chromatin dynamics is very well understood. But chromatin is not uniform and regions of it, with chemical modifications and bound effectors, form domains and compartments through mechanisms not yet clear. Polymer models have been successfully used to investigate these mechanisms to explain cytological observations and build hypothesis for experimental validation. Many different approaches to conceptualise chromatin in polymer models can be envisioned and each reflects different aspects. Here, we compare recent approaches that aim at reproducing prominent features of interphase chromatin organisation: the compartmentalisation into eu- and heterochromatin compartments, the formation of a nucleolus, chromatin loops and the rosette and Rabl conformations of interphase chromosomes. We highlight commonalities and contradictions that point to a modulation of the mechanisms involved to fine degree. Consolidating models will require the inclusion of yet hidden or neglected parameters.
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22
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Lin AZ, Ruff KM, Jalihal A, Dar F, King MR, Lalmansingh JM, Posey AE, Seim I, Gladfelter AS, Pappu RV. Dynamical control enables the formation of demixed biomolecular condensates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.04.522702. [PMID: 36711465 PMCID: PMC9881950 DOI: 10.1101/2023.01.04.522702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Macromolecular phase separation underlies the regulated formation and dissolution of biomolecular condensates. What is unclear is how condensates of distinct and shared macromolecular compositions form and coexist within cellular milieus. Here, we use theory and computation to establish thermodynamic criteria that must be satisfied to achieve compositionally distinct condensates. We applied these criteria to an archetypal ribonucleoprotein condensate and discovered that demixing into distinct protein-RNA condensates cannot be the result of purely thermodynamic considerations. Instead, demixed, compositionally distinct condensates arise due to asynchronies in timescales that emerge from differences in long-lived protein-RNA and RNA-RNA crosslinks. This type of dynamical control is also found to be active in live cells whereby asynchronous production of molecules is required for realizing demixed protein-RNA condensates. We find that interactions that exert dynamical control provide a versatile and generalizable way to influence the compositions of coexisting condensates in live cells.
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23
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Peng Q, Huang Z, Sun K, Liu Y, Yoon CW, Harrison RES, Schmitt DL, Zhu L, Wu Y, Tasan I, Zhao H, Zhang J, Zhong S, Chien S, Wang Y. Engineering inducible biomolecular assemblies for genome imaging and manipulation in living cells. Nat Commun 2022; 13:7933. [PMID: 36566209 PMCID: PMC9789998 DOI: 10.1038/s41467-022-35504-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 12/06/2022] [Indexed: 12/25/2022] Open
Abstract
Genome architecture and organization play critical roles in cell life. However, it remains largely unknown how genomic loci are dynamically coordinated to regulate gene expression and determine cell fate at the single cell level. We have developed an inducible system which allows Simultaneous Imaging and Manipulation of genomic loci by Biomolecular Assemblies (SIMBA) in living cells. In SIMBA, the human heterochromatin protein 1α (HP1α) is fused to mCherry and FRB, which can be induced to form biomolecular assemblies (BAs) with FKBP-scFv, guided to specific genomic loci by a nuclease-defective Cas9 (dCas9) or a transcriptional factor (TF) carrying tandem repeats of SunTag. The induced BAs can not only enhance the imaging signals at target genomic loci using a single sgRNA, either at repetitive or non-repetitive sequences, but also recruit epigenetic modulators such as histone methyltransferase SUV39H1 to locally repress transcription. As such, SIMBA can be applied to simultaneously visualize and manipulate, in principle, any genomic locus with controllable timing in living cells.
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Affiliation(s)
- Qin Peng
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, La Jolla, CA, 92093-0435, USA.
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, 518132, P. R. China.
| | - Ziliang Huang
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, La Jolla, CA, 92093-0435, USA
| | - Kun Sun
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, 518132, P. R. China
| | - Yahan Liu
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, La Jolla, CA, 92093-0435, USA
| | - Chi Woo Yoon
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, La Jolla, CA, 92093-0435, USA
| | - Reed E S Harrison
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, La Jolla, CA, 92093-0435, USA
| | - Danielle L Schmitt
- Department of Pharmacology, University of California, La Jolla, CA, 92093-0435, USA
| | - Linshan Zhu
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, La Jolla, CA, 92093-0435, USA
| | - Yiqian Wu
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, La Jolla, CA, 92093-0435, USA
| | - Ipek Tasan
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Huimin Zhao
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Chemical and Biomolecular Engineering, University of Illinois, Urbana-Champaign, Urbana, IL, 61801, USA
| | - Jin Zhang
- Department of Pharmacology, University of California, La Jolla, CA, 92093-0435, USA
| | - Sheng Zhong
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, La Jolla, CA, 92093-0435, USA
| | - Shu Chien
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, La Jolla, CA, 92093-0435, USA
- Department of Medicine, University of California, La Jolla, CA, 92093-0435, USA
| | - Yingxiao Wang
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, La Jolla, CA, 92093-0435, USA.
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24
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Latham AP, Zhang B. Molecular Determinants for the Layering and Coarsening of Biological Condensates. AGGREGATE (HOBOKEN, N.J.) 2022; 3:e306. [PMID: 37065433 PMCID: PMC10101022 DOI: 10.1002/agt2.306] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Many membraneless organelles, or biological condensates, form through phase separation, and play key roles in signal sensing and transcriptional regulation. While the functional importance of these condensates has inspired many studies to characterize their stability and spatial organization, the underlying principles that dictate these emergent properties are still being uncovered. In this review, we examine recent work on biological condensates, especially multicomponent systems. We focus on connecting molecular factors such as binding energy, valency, and stoichiometry with the interfacial tension, explaining the nontrivial interior organization in many condensates. We further discuss mechanisms that arrest condensate coalescence by lowering the surface tension or introducing kinetic barriers to stabilize the multidroplet state.
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Affiliation(s)
- Andrew P Latham
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139
- Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco, San Francisco, CA 94143
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139
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25
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Regulation of Polyhomeotic Condensates by Intrinsically Disordered Sequences That Affect Chromatin Binding. EPIGENOMES 2022; 6:epigenomes6040040. [PMID: 36412795 PMCID: PMC9680516 DOI: 10.3390/epigenomes6040040] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/30/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022] Open
Abstract
The Polycomb group (PcG) complex PRC1 localizes in the nucleus in condensed structures called Polycomb bodies. The PRC1 subunit Polyhomeotic (Ph) contains an oligomerizing sterile alpha motif (SAM) that is implicated in both PcG body formation and chromatin organization in Drosophila and mammalian cells. A truncated version of Ph containing the SAM (mini-Ph) forms phase-separated condensates with DNA or chromatin in vitro, suggesting that PcG bodies may form through SAM-driven phase separation. In cells, Ph forms multiple small condensates, while mini-Ph typically forms a single large nuclear condensate. We therefore hypothesized that sequences outside of mini-Ph, which are predicted to be intrinsically disordered, are required for proper condensate formation. We identified three distinct low-complexity regions in Ph based on sequence composition. We systematically tested the role of each of these sequences in Ph condensates using live imaging of transfected Drosophila S2 cells. Each sequence uniquely affected Ph SAM-dependent condensate size, number, and morphology, but the most dramatic effects occurred when the central, glutamine-rich intrinsically disordered region (IDR) was removed, which resulted in large Ph condensates. Like mini-Ph condensates, condensates lacking the glutamine-rich IDR excluded chromatin. Chromatin fractionation experiments indicated that the removal of the glutamine-rich IDR reduced chromatin binding and that the removal of either of the other IDRs increased chromatin binding. Our data suggest that all three IDRs, and functional interactions among them, regulate Ph condensate size and number. Our results can be explained by a model in which tight chromatin binding by Ph IDRs antagonizes Ph SAM-driven phase separation. Our observations highlight the complexity of regulation of biological condensates housed in single proteins.
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Kim CG, Hwang DE, Kumar R, Chung M, Eom YG, Kim H, Koo DH, Choi JM. Recent trends in studies of biomolecular phase separation. BMB Rep 2022. [PMID: 35880435 PMCID: PMC9442351 DOI: 10.5483/bmbrep.2022.55.8.101] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Biomolecular phase separation has recently attracted broad in-terest, due to its role in the spatiotemporal compartmentalization of living cells. It governs the formation, regulation, and dissociation of biomolecular condensates, which play multiple roles in vivo, from activating specific biochemical reactions to organizing chromatin. Interestingly, biomolecular phase separation seems to be a mainly passive process, which can be ex-plained by relatively simple physical principles and reproduced in vitro with a minimal set of components. This Mini review focuses on our current understanding of the fundamental principles of biomolecular phase separation and the recent progress in the research on this topic.
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Affiliation(s)
- Chan-Geun Kim
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Da-Eun Hwang
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Rajeev Kumar
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Min Chung
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Yu-Gon Eom
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Hyunji Kim
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Da-Hyun Koo
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Jeong-Mo Choi
- Department of Chemistry, Pusan National University, Busan 46241, Korea
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Liu S, Lin X, Zhang B. Chromatin fiber breaks into clutches under tension and crowding. Nucleic Acids Res 2022; 50:9738-9747. [PMID: 36029149 PMCID: PMC9508854 DOI: 10.1093/nar/gkac725] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 07/08/2022] [Accepted: 08/12/2022] [Indexed: 11/18/2022] Open
Abstract
The arrangement of nucleosomes inside chromatin is of extensive interest. While in vitro experiments have revealed the formation of 30 nm fibers, most in vivo studies have failed to confirm their presence in cell nuclei. To reconcile the diverging experimental findings, we characterized chromatin organization using a residue-level coarse-grained model. The computed force–extension curve matches well with measurements from single-molecule experiments. Notably, we found that a dodeca-nucleosome in the two-helix zigzag conformation breaks into structures with nucleosome clutches and a mix of trimers and tetramers under tension. Such unfolded configurations can also be stabilized through trans interactions with other chromatin chains. Our study suggests that unfolding from chromatin fibers could contribute to the irregularity of in vivo chromatin configurations. We further revealed that chromatin segments with fibril or clutch structures engaged in distinct binding modes and discussed the implications of these inter-chain interactions for a potential sol–gel phase transition.
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Affiliation(s)
- Shuming Liu
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Xingcheng Lin
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
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Abstract
The human genome is arranged in the cell nucleus nonrandomly, and phase separation has been proposed as an important driving force for genome organization. However, the cell nucleus is an active system, and the contribution of nonequilibrium activities to phase separation and genome structure and dynamics remains to be explored. We simulated the genome using an energy function parametrized with chromosome conformation capture (Hi-C) data with the presence of active, nondirectional forces that break the detailed balance. We found that active forces that may arise from transcription and chromatin remodeling can dramatically impact the spatial localization of heterochromatin. When applied to euchromatin, active forces can drive heterochromatin to the nuclear envelope and compete with passive interactions among heterochromatin that tend to pull them in opposite directions. Furthermore, active forces induce long-range spatial correlations among genomic loci beyond single chromosome territories. We further showed that the impact of active forces could be understood from the effective temperature defined as the fluctuation-dissipation ratio. Our study suggests that nonequilibrium activities can significantly impact genome structure and dynamics, producing unexpected collective phenomena.
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Affiliation(s)
- Zhongling Jiang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, United States
| | - Yifeng Qi
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, United States
| | - Kartik Kamat
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, United States
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, United States
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Kim CG, Hwang DE, Kumar R, Chung M, Eom YG, Kim H, Koo DH, Choi JM. Recent trends in studies of biomolecular phase separation. BMB Rep 2022; 55:363-369. [PMID: 35880435 PMCID: PMC9442351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/07/2022] [Accepted: 07/20/2022] [Indexed: 03/08/2024] Open
Abstract
Biomolecular phase separation has recently attracted broad interest, due to its role in the spatiotemporal compartmentalization of living cells. It governs the formation, regulation, and dissociation of biomolecular condensates, which play multiple roles in vivo, from activating specific biochemical reactions to organizing chromatin. Interestingly, biomolecular phase separation seems to be a mainly passive process, which can be explained by relatively simple physical principles and reproduced in vitro with a minimal set of components. This Mini review focuses on our current understanding of the fundamental principles of biomolecular phase separation and the recent progress in the research on this topic. [BMB Reports 2022; 55(8): 363-369].
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Affiliation(s)
- Chan-Geun Kim
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Da-Eun Hwang
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Rajeev Kumar
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Min Chung
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Yu-Gon Eom
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Hyunji Kim
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Da-Hyun Koo
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Jeong-Mo Choi
- Department of Chemistry, Pusan National University, Busan 46241, Korea
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30
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Mora A, Huang X, Jauhari S, Jiang Q, Li X. Chromatin Hubs: A biological and computational outlook. Comput Struct Biotechnol J 2022; 20:3796-3813. [PMID: 35891791 PMCID: PMC9304431 DOI: 10.1016/j.csbj.2022.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/02/2022] [Accepted: 07/02/2022] [Indexed: 11/20/2022] Open
Abstract
This review discusses our current understanding of chromatin biology and bioinformatics under the unifying concept of “chromatin hubs.” The first part reviews the biology of chromatin hubs, including chromatin–chromatin interaction hubs, chromatin hubs at the nuclear periphery, hubs around macromolecules such as RNA polymerase or lncRNAs, and hubs around nuclear bodies such as the nucleolus or nuclear speckles. The second part reviews existing computational methods, including enhancer–promoter interaction prediction, network analysis, chromatin domain callers, transcription factory predictors, and multi-way interaction analysis. We introduce an integrated model that makes sense of the existing evidence. Understanding chromatin hubs may allow us (i) to explain long-unsolved biological questions such as interaction specificity and redundancy of mechanisms, (ii) to develop more realistic kinetic and functional predictions, and (iii) to explain the etiology of genomic disease.
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Affiliation(s)
- Antonio Mora
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health (Chinese Academy of Sciences), Guangzhou 511436, PR China
- Corresponding authors.
| | - Xiaowei Huang
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health (Chinese Academy of Sciences), Guangzhou 511436, PR China
| | - Shaurya Jauhari
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health (Chinese Academy of Sciences), Guangzhou 511436, PR China
| | - Qin Jiang
- Affiliated Eye Hospital of Nanjing Medical University, Nanjing 210000, PR China
| | - Xuri Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, and Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, PR China
- Corresponding authors.
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31
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Latham AP, Zhang B. On the stability and layered organization of protein-DNA condensates. Biophys J 2022; 121:1727-1737. [PMID: 35364104 PMCID: PMC9117872 DOI: 10.1016/j.bpj.2022.03.028] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/02/2021] [Accepted: 03/24/2022] [Indexed: 11/17/2022] Open
Abstract
Multi-component phase separation is emerging as a key mechanism for the formation of biological condensates that play essential roles in signal sensing and transcriptional regulation. The molecular factors that dictate these condensates' stability and spatial organization are not fully understood, and it remains challenging to predict their microstructures. Using a near-atomistic, chemically accurate force field, we studied the phase behavior of chromatin regulators that are crucial for heterochromatin organization and their interactions with DNA. Our computed phase diagrams recapitulated previous experimental findings on different proteins. They revealed a strong dependence of condensate stability on the protein-DNA mixing ratio as a result of balancing protein-protein interactions and charge neutralization. Notably, a layered organization was observed in condensates formed by mixing HP1, histone H1, and DNA. This layered organization may be of biological relevance, as it enables cooperative DNA packaging between the two chromatin regulators: histone H1 softens the DNA to facilitate the compaction induced by HP1 droplets. Our study supports near-atomistic models as a valuable tool for characterizing the structure and stability of biological condensates.
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Affiliation(s)
- Andrew P Latham
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts.
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32
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Huertas J, Woods EJ, Collepardo-Guevara R. Multiscale modelling of chromatin organisation: Resolving nucleosomes at near-atomistic resolution inside genes. Curr Opin Cell Biol 2022; 75:102067. [DOI: 10.1016/j.ceb.2022.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/24/2022] [Accepted: 02/04/2022] [Indexed: 12/15/2022]
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Laghmach R, Di Pierro M, Potoyan D. A Liquid State Perspective on Dynamics of Chromatin Compartments. Front Mol Biosci 2022; 8:781981. [PMID: 35096966 PMCID: PMC8793688 DOI: 10.3389/fmolb.2021.781981] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 12/22/2021] [Indexed: 12/11/2022] Open
Abstract
The interior of the eukaryotic cell nucleus has a crowded and heterogeneous environment packed with chromatin polymers, regulatory proteins, and RNA molecules. Chromatin polymer, assisted by epigenetic modifications, protein and RNA binders, forms multi-scale compartments which help regulate genes in response to cellular signals. Furthermore, chromatin compartments are dynamic and tend to evolve in size and composition in ways that are not fully understood. The latest super-resolution imaging experiments have revealed a much more dynamic and stochastic nature of chromatin compartments than was appreciated before. An emerging mechanism explaining chromatin compartmentalization dynamics is the phase separation of protein and nucleic acids into membraneless liquid condensates. Consequently, concepts and ideas from soft matter and polymer systems have been rapidly entering the lexicon of cell biology. In this respect, the role of computational models is crucial for establishing a rigorous and quantitative foundation for the new concepts and disentangling the complex interplay of forces that contribute to the emergent patterns of chromatin dynamics and organization. Several multi-scale models have emerged to address various aspects of chromatin dynamics, ranging from equilibrium polymer simulations, hybrid non-equilibrium simulations coupling protein binding and chromatin folding, and mesoscopic field-theoretic models. Here, we review these emerging theoretical paradigms and computational models with a particular focus on chromatin’s phase separation and liquid-like properties as a basis for nuclear organization and dynamics.
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Affiliation(s)
- Rabia Laghmach
- Department of Chemistry, Iowa State University, Ames, IA, United States
| | - Michele Di Pierro
- Department of Physics, Northeastern University, Boston, MA, United States
| | - Davit Potoyan
- Department of Chemistry, Iowa State University, Ames, IA, United States
- *Correspondence: Davit Potoyan,
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34
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Bridger JM, Pereira RT, Pina C, Tosi S, Lewis A. Alterations to Genome Organisation in Stem Cells, Their Differentiation and Associated Diseases. Results Probl Cell Differ 2022; 70:71-102. [PMID: 36348105 DOI: 10.1007/978-3-031-06573-6_3] [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: 06/16/2023]
Abstract
The organisation of the genome in its home, the cell nucleus, is reliant on a number of different aspects to establish, maintain and alter its functional non-random positioning. The genome is dispersed throughout a cell nucleus in specific chromosome territories which are further divided into topologically associated domains (TADs), where regions of the genome from different and the same chromosomes come together. This organisation is both controlled by DNA and chromatin epigenetic modification and the association of the genome with nuclear structures such as the nuclear lamina, the nucleolus and nuclear bodies and speckles. Indeed, sequences that are associated with the first two structures mentioned are termed lamina-associated domains (LADs) and nucleolar-associated domains (NADs), respectively. The modifications and nuclear structures that regulate genome function are altered through a cell's life from stem cell to differentiated cell through to reversible quiescence and irreversible senescence, and hence impacting on genome organisation, altering it to silence specific genes and permit others to be expressed in a controlled way in different cell types and cell cycle statuses. The structures and enzymes and thus the organisation of the genome can also be deleteriously affected, leading to disease and/or premature ageing.
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Affiliation(s)
- Joanna M Bridger
- Division of Biosciences, Department of Life Sciences, Centre for Genome Engineering and Maintenance (cenGEM), College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UK.
| | - Rita Torres Pereira
- Division of Biosciences, Department of Life Sciences, Centre for Genome Engineering and Maintenance (cenGEM), College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UK
| | - Cristina Pina
- Division of Biosciences, Department of Life Sciences, Centre for Genome Engineering and Maintenance (cenGEM), College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UK
| | - Sabrina Tosi
- Division of Biosciences, Department of Life Sciences, Centre for Genome Engineering and Maintenance (cenGEM), College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UK
| | - Annabelle Lewis
- Division of Biosciences, Department of Life Sciences, Centre for Genome Engineering and Maintenance (cenGEM), College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UK
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