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Pei G, Lyons H, Li P, Sabari BR. Transcription regulation by biomolecular condensates. Nat Rev Mol Cell Biol 2025; 26:213-236. [PMID: 39516712 DOI: 10.1038/s41580-024-00789-x] [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: 09/30/2024] [Indexed: 11/16/2024]
Abstract
Biomolecular condensates regulate transcription by dynamically compartmentalizing the transcription machinery. Classic models of transcription regulation focus on the recruitment and regulation of RNA polymerase II by the formation of complexes at the 1-10 nm length scale, which are driven by structured and stoichiometric interactions. These complexes are further organized into condensates at the 100-1,000 nm length scale, which are driven by dynamic multivalent interactions often involving domain-ligand pairs or intrinsically disordered regions. Regulation through condensate-mediated organization does not supersede the processes occurring at the 1-10 nm scale, but it provides regulatory mechanisms for promoting or preventing these processes in the crowded nuclear environment. Regulation of transcription by transcriptional condensates is involved in cell state transitions during animal and plant development, cell signalling and cellular responses to the environment. These condensate-mediated processes are dysregulated in developmental disorders, cancer and neurodegeneration. In this Review, we discuss the principles underlying the regulation of transcriptional condensates, their roles in physiology and their dysregulation in human diseases.
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Affiliation(s)
- Gaofeng Pei
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Heankel Lyons
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Pilong Li
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing, China.
- Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, China.
| | - Benjamin R Sabari
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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2
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Selivanovskiy AV, Molodova MN, Khrameeva EE, Ulianov SV, Razin SV. Liquid condensates: a new barrier to loop extrusion? Cell Mol Life Sci 2025; 82:80. [PMID: 39976773 PMCID: PMC11842697 DOI: 10.1007/s00018-024-05559-8] [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: 07/10/2024] [Revised: 12/04/2024] [Accepted: 12/20/2024] [Indexed: 02/23/2025]
Abstract
Liquid-liquid phase separation (LLPS), driven by dynamic, low-affinity multivalent interactions of proteins and RNA, results in the formation of macromolecular condensates on chromatin. These structures are likely to provide high local concentrations of effector factors responsible for various processes including transcriptional regulation and DNA repair. In particular, enhancers, super-enhancers, and promoters serve as platforms for condensate assembly. In the current paradigm, enhancer-promoter (EP) interaction could be interpreted as a result of enhancer- and promoter-based condensate contact/fusion. There is increasing evidence that the spatial juxtaposition of enhancers and promoters could be provided by loop extrusion (LE) by SMC complexes. Here, we propose that condensates may act as barriers to LE, thereby contributing to various nuclear processes including spatial contacts between regulatory genomic elements.
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Affiliation(s)
- Arseniy V Selivanovskiy
- Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119234, Moscow, Russia
| | - Maria N Molodova
- Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia
- Skolkovo Institute of Science and Technology, 121205, Moscow, Russia
| | | | - Sergey V Ulianov
- Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119234, Moscow, Russia
| | - Sergey V Razin
- Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia.
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119234, Moscow, Russia.
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3
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Miao J, Chong S. Roles of intrinsically disordered protein regions in transcriptional regulation and genome organization. Curr Opin Genet Dev 2025; 90:102285. [PMID: 39631290 DOI: 10.1016/j.gde.2024.102285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2024] [Revised: 10/31/2024] [Accepted: 11/12/2024] [Indexed: 12/07/2024]
Abstract
Eukaryotic transcription is a complex process regulated by transcription factors (TFs), coactivators, and RNA polymerase machineries, many of which contain sizable intrinsically disordered regions (IDRs). Many TFs activate transcription through multivalent IDR-IDR interactions. Optimal levels of such multivalent interactions associated with appropriate IDR concentrations, interaction strengths, or interaction valencies are required for effective transcriptional activation. The interaction selectivity of IDRs is crucial for the precise regulation of transcription, and this selectivity is dependent on the IDR sequences. Furthermore, IDRs modulate gene expression by bringing chromatin sites together to form transcriptionally active chromatin hubs. Mutations in IDRs may cause dysregulation of their multivalent interactions, contributing to diseases, including cancers and neurodegenerative disorders. Understanding the effects of IDR-related mutations on transcription control and genome organization opens new opportunities for developing targeted therapeutic strategies. In this review, we discuss recent reports documenting important functions of IDRs in transcriptional regulation and their implications for human health and disease.
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Affiliation(s)
- Jiapei Miao
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Shasha Chong
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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4
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Zhang M, Hu T, Ma T, Huang W, Wang Y. Epigenetics and environmental health. Front Med 2024; 18:571-596. [PMID: 38806988 DOI: 10.1007/s11684-023-1038-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 10/15/2023] [Indexed: 05/30/2024]
Abstract
Epigenetic modifications including DNA methylation, histone modifications, chromatin remodeling, and RNA modifications complicate gene regulation and heredity and profoundly impact various physiological and pathological processes. In recent years, accumulating evidence indicates that epigenetics is vulnerable to environmental changes and regulates the growth, development, and diseases of individuals by affecting chromatin activity and regulating gene expression. Environmental exposure or induced epigenetic changes can regulate the state of development and lead to developmental disorders, aging, cardiovascular disease, Alzheimer's disease, cancers, and so on. However, epigenetic modifications are reversible. The use of specific epigenetic inhibitors targeting epigenetic changes in response to environmental exposure is useful in disease therapy. Here, we provide an overview of the role of epigenetics in various diseases. Furthermore, we summarize the mechanism of epigenetic alterations induced by different environmental exposures, the influence of different environmental exposures, and the crosstalk between environmental variation epigenetics, and genes that are implicated in the body's health. However, the interaction of multiple factors and epigenetics in regulating the initiation and progression of various diseases complicates clinical treatments. We discuss some commonly used epigenetic drugs targeting epigenetic modifications and methods to prevent or relieve various diseases regulated by environmental exposure and epigenetics through diet.
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Affiliation(s)
- Min Zhang
- Key Laboratory of Cancer and Microbiome, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Ting Hu
- Key Laboratory of Cancer and Microbiome, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Tianyu Ma
- Key Laboratory of Cancer and Microbiome, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
| | - Wei Huang
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China.
| | - Yan Wang
- Key Laboratory of Cancer and Microbiome, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China.
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5
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Hayward-Lara G, Fischer MD, Mir M. Dynamic microenvironments shape nuclear organization and gene expression. Curr Opin Genet Dev 2024; 86:102177. [PMID: 38461773 PMCID: PMC11162947 DOI: 10.1016/j.gde.2024.102177] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 02/11/2024] [Accepted: 02/14/2024] [Indexed: 03/12/2024]
Abstract
Live imaging has revealed that the regulation of gene expression is largely driven by transient interactions. For example, many regulatory proteins bind chromatin for just seconds, and loop-like genomic contacts are rare and last only minutes. These discoveries have been difficult to reconcile with our canonical models that are predicated on stable and hierarchical interactions. Proteomic microenvironments that concentrate nuclear factors may explain how brief interactions can still mediate gene regulation by creating conditions where reactions occur more frequently. Here, we summarize new imaging technologies and recent discoveries implicating microenvironments as a potential driver of nuclear function. Finally, we propose that key properties of proteomic microenvironments, such as their size, enrichment, and lifetimes, are directly linked to regulatory function.
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Affiliation(s)
- Gabriela Hayward-Lara
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania. Philadelphia, PA 19104
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia. Philadelphia, PA 19104
- Developmental, Stem Cell, and Regenerative Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania. Philadelphia, PA 19104
| | - Matthew D. Fischer
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania. Philadelphia, PA 19104
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia. Philadelphia, PA 19104
| | - Mustafa Mir
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania. Philadelphia, PA 19104
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia. Philadelphia, PA 19104
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania. Philadelphia, PA 19104
- Howard Hughes Medical Institute, Children’s Hospital of Philadelphia. Philadelphia, PA 19104
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6
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Lavaud M, Tesfaye R, Lassous L, Brounais B, Baud'huin M, Verrecchia F, Lamoureux F, Georges S, Ory B. Super-enhancers: drivers of cells' identities and cells' debacles. Epigenomics 2024; 16:681-700. [PMID: 38587919 PMCID: PMC11160454 DOI: 10.2217/epi-2023-0409] [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: 11/21/2023] [Accepted: 03/18/2024] [Indexed: 04/10/2024] Open
Abstract
Precise spatiotemporal regulations of gene expression are essential for determining cells' fates and functions. Enhancers are cis-acting DNA elements that act as periodic transcriptional thrusters and their activities are cell type specific. Clusters of enhancers, called super-enhancers, are more densely occupied by transcriptional activators than enhancers, driving stronger expression of their target genes, which have prominent roles in establishing and maintaining cellular identities. Here we review the current knowledge on the composition and structure of super-enhancers to understand how they robustly stimulate the expression of cellular identity genes. We also review their involvement in the development of various cell types and both noncancerous and cancerous disorders, implying the therapeutic interest of targeting them to fight against various diseases.
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Affiliation(s)
- Mélanie Lavaud
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
| | - Robel Tesfaye
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
- Cancéropôle Grand-Ouest, Réseau Épigénétique, Medical School, Nantes, 44035, France
- EpiSAVMEN, Epigenetic consortium Pays de la Loire, France
| | - Léa Lassous
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
| | - Bénédicte Brounais
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
| | - Marc Baud'huin
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
| | - Franck Verrecchia
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
| | - François Lamoureux
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
| | - Steven Georges
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
| | - Benjamin Ory
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
- Cancéropôle Grand-Ouest, Réseau Épigénétique, Medical School, Nantes, 44035, France
- EpiSAVMEN, Epigenetic consortium Pays de la Loire, France
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7
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Karakatsanis NM, Hamey JJ, Wilkins MR. Taking Me away: the function of phosphorylation on histone lysine demethylases. Trends Biochem Sci 2024; 49:257-276. [PMID: 38233282 DOI: 10.1016/j.tibs.2023.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 12/06/2023] [Accepted: 12/08/2023] [Indexed: 01/19/2024]
Abstract
Histone lysine demethylases (KDMs) regulate eukaryotic gene transcription by catalysing the removal of methyl groups from histone proteins. These enzymes are intricately regulated by the kinase signalling system in response to internal and external stimuli. Here, we review the mechanisms by which kinase-mediated phosphorylation influence human histone KDM function. These include the changing of histone KDM subcellular localisation or chromatin binding, the altering of protein half-life, changes to histone KDM complex formation that result in histone demethylation, non-histone demethylation or demethylase-independent effects, and effects on histone KDM complex dissociation. We also explore the structural context of phospho-sites on histone KDMs and evaluate how this relates to function.
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Affiliation(s)
- Nicola M Karakatsanis
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, Australia
| | - Joshua J Hamey
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, Australia
| | - Marc R Wilkins
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, Australia.
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8
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Vicioso-Mantis M, Aguirre S, Martínez-Balbás MA. JmjC Family of Histone Demethylases Form Nuclear Condensates. Int J Mol Sci 2022; 23:ijms23147664. [PMID: 35887017 PMCID: PMC9319511 DOI: 10.3390/ijms23147664] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 07/08/2022] [Accepted: 07/08/2022] [Indexed: 12/16/2022] Open
Abstract
The Jumonji-C (JmjC) family of lysine demethylases (KDMs) (JMJC-KDMs) plays an essential role in controlling gene expression and chromatin structure. In most cases, their function has been attributed to the demethylase activity. However, accumulating evidence demonstrates that these proteins play roles distinct from histone demethylation. This raises the possibility that they might share domains that contribute to their functional outcome. Here, we show that the JMJC-KDMs contain low-complexity domains and intrinsically disordered regions (IDR), which in some cases reached 70% of the protein. Our data revealed that plant homeodomain finger protein (PHF2), KDM2A, and KDM4B cluster by phase separation. Moreover, our molecular analysis implies that PHF2 IDR contributes to transcription regulation. These data suggest that clustering via phase separation is a common feature that JMJC-KDMs utilize to facilitate their functional responses. Our study uncovers a novel potential function for the JMJC-KDM family that sheds light on the mechanisms to achieve the competent concentration of molecules in time and space within the cell nucleus.
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