1
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Salari H, Fourel G, Jost D. Transcription regulates the spatio-temporal dynamics of genes through micro-compartmentalization. Nat Commun 2024; 15:5393. [PMID: 38918438 PMCID: PMC11199603 DOI: 10.1038/s41467-024-49727-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 06/17/2024] [Indexed: 06/27/2024] Open
Abstract
Although our understanding of the involvement of heterochromatin architectural factors in shaping nuclear organization is improving, there is still ongoing debate regarding the role of active genes in this process. In this study, we utilize publicly-available Micro-C data from mouse embryonic stem cells to investigate the relationship between gene transcription and 3D gene folding. Our analysis uncovers a nonmonotonic - globally positive - correlation between intragenic contact density and Pol II occupancy, independent of cohesin-based loop extrusion. Through the development of a biophysical model integrating the role of transcription dynamics within a polymer model of chromosome organization, we demonstrate that Pol II-mediated attractive interactions with limited valency between transcribed regions yield quantitative predictions consistent with chromosome-conformation-capture and live-imaging experiments. Our work provides compelling evidence that transcriptional activity shapes the 4D genome through Pol II-mediated micro-compartmentalization.
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Affiliation(s)
- Hossein Salari
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS, UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, 46 Allée d'Italie, 69007, Lyon, France.
- École Normale Supérieure de Lyon, CNRS, Laboratoire de Physique, 46 Allée d'Italie, 69007, Lyon, France.
| | - Geneviève Fourel
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS, UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, 46 Allée d'Italie, 69007, Lyon, France
| | - Daniel Jost
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS, UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, 46 Allée d'Italie, 69007, Lyon, France.
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2
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DeHaro-Arbona FJ, Roussos C, Baloul S, Townson J, Gómez Lamarca MJ, Bray S. Dynamic modes of Notch transcription hubs conferring memory and stochastic activation revealed by live imaging the co-activator Mastermind. eLife 2024; 12:RP92083. [PMID: 38727722 PMCID: PMC11087053 DOI: 10.7554/elife.92083] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2024] Open
Abstract
Developmental programming involves the accurate conversion of signalling levels and dynamics to transcriptional outputs. The transcriptional relay in the Notch pathway relies on nuclear complexes containing the co-activator Mastermind (Mam). By tracking these complexes in real time, we reveal that they promote the formation of a dynamic transcription hub in Notch ON nuclei which concentrates key factors including the Mediator CDK module. The composition of the hub is labile and persists after Notch withdrawal conferring a memory that enables rapid reformation. Surprisingly, only a third of Notch ON hubs progress to a state with nascent transcription, which correlates with polymerase II and core Mediator recruitment. This probability is increased by a second signal. The discovery that target-gene transcription is probabilistic has far-reaching implications because it implies that stochastic differences in Notch pathway output can arise downstream of receptor activation.
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Affiliation(s)
- F Javier DeHaro-Arbona
- Department of Physiology Development and Neuroscience, University of CambridgeCambridgeUnited Kingdom
| | - Charalambos Roussos
- Department of Physiology Development and Neuroscience, University of CambridgeCambridgeUnited Kingdom
| | - Sarah Baloul
- Department of Physiology Development and Neuroscience, University of CambridgeCambridgeUnited Kingdom
| | - Jonathan Townson
- Department of Physiology Development and Neuroscience, University of CambridgeCambridgeUnited Kingdom
| | - María J Gómez Lamarca
- Department of Physiology Development and Neuroscience, University of CambridgeCambridgeUnited Kingdom
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocıo/CSIC/Universidad de Sevilla, Departamento de Biologıa CelularSevilleSpain
| | - Sarah Bray
- Department of Physiology Development and Neuroscience, University of CambridgeCambridgeUnited Kingdom
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3
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Ulferts S, Lopes M, Miyamoto K, Grosse R. Nuclear actin dynamics and functions at a glance. J Cell Sci 2024; 137:jcs261630. [PMID: 38563209 DOI: 10.1242/jcs.261630] [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: 04/04/2024] Open
Abstract
Actin is well known for its cytoskeletal functions, where it helps to control and maintain cell shape and architecture, as well as regulating cell migration and intracellular cargo transport, among others. However, actin is also prevalent in the nucleus, where genome-regulating roles have been described, including it being part of chromatin-remodeling complexes. More recently, with the help of advances in microscopy techniques and specialized imaging probes, direct visualization of nuclear actin filament dynamics has helped elucidate new roles for nuclear actin, such as in cell cycle regulation, DNA replication and repair, chromatin organization and transcriptional condensate formation. In this Cell Science at a Glance article, we summarize the known signaling events driving the dynamic assembly of actin into filaments of various structures within the nuclear compartment for essential genome functions. Additionally, we highlight the physiological role of nuclear F-actin in meiosis and early embryonic development.
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Affiliation(s)
- Svenja Ulferts
- Institute for Clinical and Experimental Pharmacology and Toxicology I, Medical Faculty, University of Freiburg, 79104 Freiburg, Germany
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, 8057 Zurich, Switzerland
| | - Kei Miyamoto
- Faculty of Biology-Oriented Science and Technology, Kindai University, Wakayama 649-6493, Japan
| | - Robert Grosse
- Institute for Clinical and Experimental Pharmacology and Toxicology I, Medical Faculty, University of Freiburg, 79104 Freiburg, Germany
- Centre for Integrative Biological Signalling Studies (CIBSS), 79104 Freiburg, Germany
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4
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Shivashankar GV. Mechanical forces and the 3D genome. Curr Opin Struct Biol 2023; 83:102728. [PMID: 37948897 DOI: 10.1016/j.sbi.2023.102728] [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: 07/10/2023] [Revised: 10/09/2023] [Accepted: 10/16/2023] [Indexed: 11/12/2023]
Abstract
Traditionally, the field of genomics has been studied from a biochemical perspective. Besides chemical influences, cells are subject to a variety of mechanical signals from their surrounding tissue microenvironment. These mechanical signals can not only cause changes to a cell's physical structure but can also lead to alterations in their genomes and gene expression programs. Understanding the mechanical control of genome organization and expression may provide a new perspective on gene regulation.
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5
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Mark KG, Kolla S, Aguirre JD, Garshott DM, Schmitt S, Haakonsen DL, Xu C, Kater L, Kempf G, Martínez-González B, Akopian D, See SK, Thomä NH, Rapé M. Orphan quality control shapes network dynamics and gene expression. Cell 2023; 186:3460-3475.e23. [PMID: 37478862 DOI: 10.1016/j.cell.2023.06.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 04/13/2023] [Accepted: 06/21/2023] [Indexed: 07/23/2023]
Abstract
All eukaryotes require intricate protein networks to translate developmental signals into accurate cell fate decisions. Mutations that disturb interactions between network components often result in disease, but how the composition and dynamics of complex networks are established remains poorly understood. Here, we identify the E3 ligase UBR5 as a signaling hub that helps degrade unpaired subunits of multiple transcriptional regulators that act within a network centered on the c-Myc oncoprotein. Biochemical and structural analyses show that UBR5 binds motifs that only become available upon complex dissociation. By rapidly turning over unpaired transcription factor subunits, UBR5 establishes dynamic interactions between transcriptional regulators that allow cells to effectively execute gene expression while remaining receptive to environmental signals. We conclude that orphan quality control plays an essential role in establishing dynamic protein networks, which may explain the conserved need for protein degradation during transcription and offers opportunities to modulate gene expression in disease.
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Affiliation(s)
- Kevin G Mark
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - SriDurgaDevi Kolla
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Jacob D Aguirre
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Danielle M Garshott
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Stefan Schmitt
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Diane L Haakonsen
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA, USA
| | - Christina Xu
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Lukas Kater
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Georg Kempf
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Brenda Martínez-González
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - David Akopian
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Stephanie K See
- Center for Emerging and Neglected Diseases, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Nicolas H Thomä
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
| | - Michael Rapé
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA, USA; California Institute for Quantitative Biosciences (QB3), University of California at Berkeley, Berkeley, CA 94720, USA.
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6
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Ochiai H, Ohishi H, Sato Y, Kimura H. Organization of transcription and 3D genome as revealed by live-cell imaging. Curr Opin Struct Biol 2023; 81:102615. [PMID: 37257205 DOI: 10.1016/j.sbi.2023.102615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 04/03/2023] [Accepted: 05/01/2023] [Indexed: 06/02/2023]
Abstract
Higher-order genomic structures play a critical role in regulating gene expression by influencing the spatial proximity of promoters and enhancers. Live-cell imaging studies have demonstrated that three-dimensional genome structures undergo dynamic changes over time. Transcription is also dynamic, with genes frequently switching between active and inactive states. Recent observations suggest that the formation of condensates, composed of transcription-related factors, RNA, and RNA-binding proteins, around genes can regulate transcription. Advancements in technology have facilitated the visualization of the intricate spatiotemporal relationship between higher-order genomic structures, condensate formation, and transcriptional activity in living cells.
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Affiliation(s)
- Hiroshi Ochiai
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-0054, Japan.
| | - Hiroaki Ohishi
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-0054, Japan
| | - Yuko Sato
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan; Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8503, Japan
| | - Hiroshi Kimura
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan; Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8503, Japan.
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7
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Goel VY, Huseyin MK, Hansen AS. Region Capture Micro-C reveals coalescence of enhancers and promoters into nested microcompartments. Nat Genet 2023; 55:1048-1056. [PMID: 37157000 PMCID: PMC10424778 DOI: 10.1038/s41588-023-01391-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 04/05/2023] [Indexed: 05/10/2023]
Abstract
Although enhancers are central regulators of mammalian gene expression, the mechanisms underlying enhancer-promoter (E-P) interactions remain unclear. Chromosome conformation capture (3C) methods effectively capture large-scale three-dimensional (3D) genome structure but struggle to achieve the depth necessary to resolve fine-scale E-P interactions. Here, we develop Region Capture Micro-C (RCMC) by combining micrococcal nuclease (MNase)-based 3C with a tiling region-capture approach and generate the deepest 3D genome maps reported with only modest sequencing. By applying RCMC in mouse embryonic stem cells and reaching the genome-wide equivalent of ~317 billion unique contacts, RCMC reveals previously unresolvable patterns of highly nested and focal 3D interactions, which we term microcompartments. Microcompartments frequently connect enhancers and promoters, and although loss of loop extrusion and inhibition of transcription disrupts some microcompartments, most are largely unaffected. We therefore propose that many E-P interactions form through a compartmentalization mechanism, which may partially explain why acute cohesin depletion only modestly affects global gene expression.
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Affiliation(s)
- Viraat Y Goel
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Miles K Huseyin
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Anders S Hansen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA.
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8
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Rawat P, Sawarkar R. SPTing across condensates: SEC-mediated translocation of SPT complex from pausing condensates to elongation condensates. EMBO Rep 2023; 24:e56810. [PMID: 36762438 PMCID: PMC9986807 DOI: 10.15252/embr.202356810] [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: 01/11/2023] [Accepted: 01/31/2023] [Indexed: 02/11/2023] Open
Abstract
Several independent studies in the last few years have suggested that phase separation and biomolecular condensation play a critical role in regulating different transcription steps from initiation to pausing and elongation. However, how components of the transcription machinery translocate among different types of condensates during transcription remains poorly understood. Guo et al have now identified a potential mechanism underlying translocation of the DSIF complex from pausing to elongation condensates during promoter pause release, as reported in this issue of EMBO reports.
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Affiliation(s)
- Prashant Rawat
- Institute of BiochemistrySwiss Federal Institute of Technology (ETH)ZurichSwitzerland
| | - Ritwick Sawarkar
- Medical Research Council (MRC), Department of GeneticsUniversity of CambridgeCambridgeUK
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9
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SOX2 Modulates the Nuclear Organization and Transcriptional Activity of the Glucocorticoid Receptor. J Mol Biol 2022; 434:167869. [PMID: 36309135 DOI: 10.1016/j.jmb.2022.167869] [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: 07/11/2022] [Revised: 10/07/2022] [Accepted: 10/19/2022] [Indexed: 11/07/2022]
Abstract
Steroid receptors (SRs) are ligand-dependent transcription factors (TFs) relevant to key cellular processes in both physiology and pathology, including some types of cancer. SOX2 is a master TF of pluripotency and self-renewal of embryonic stem cells, and its dysregulation is also associated with various types of human cancers. A potential crosstalk between these TFs could be relevant in malignant cells yet, to the best of our knowledge, no formal study has been performed thus far. Here we show, by quantitative live-cell imaging microscopy, that ectopic expression of SOX2 disrupts the formation of hormone-dependent intranuclear condensates of many steroid receptors (SRs), including those formed by the glucocorticoid receptor (GR). SOX2 also reduces GR's binding to specific DNA targets and modulates its transcriptional activity. SOX2-driven effects on GR condensates do not require the intrinsically disordered N-terminal domain of the receptor and, surprisingly, neither relies on GR/SOX2 interactions. SOX2 also alters the intranuclear dynamics and compartmentalization of the SR coactivator NCoA-2 and impairs GR/NCoA-2 interactions. These results suggest an indirect mechanism underlying SOX2-driven effects on SRs involving this coactivator. Together, these results highlight that the transcriptional program elicited by GR relies on its nuclear organization and is intimately linked to the distribution of other GR partners, such as the NCoA-2 coactivator. Abnormal expression of SOX2, commonly observed in many tumors, may alter the biological action of GR and, probably, other SRs as well. Understanding this crosstalk may help to improve steroid hormone-based therapies in cancers with elevated SOX2 expression.
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10
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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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11
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Hurst Z, Liu W, Shi Q, Herman PK. A distinct P-body-like granule is induced in response to the disruption of microtubule integrity in Saccharomyces cerevisiae. Genetics 2022; 222:6649695. [PMID: 35876801 PMCID: PMC9434292 DOI: 10.1093/genetics/iyac105] [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: 06/09/2022] [Accepted: 07/08/2022] [Indexed: 11/12/2022] Open
Abstract
The Processing-body (P-body) is a conserved membraneless organelle that has been implicated in the storage and/or decay of mRNAs. Although P-bodies have been shown to be induced by a variety of conditions, the mechanisms controlling their assembly and their precise physiological roles in eukaryotic cells are still being worked out. In this study, we find that a distinct subtype of P-body is induced in response to conditions that disrupt microtubule integrity in the budding yeast, Saccharomyces cerevisiae. For example, treatment with the microtubule-destabilizing agent, benomyl, led to the induction of these novel ribonucleoprotein (RNP) granules. A link to microtubules had been noted previously and the observations here extend our understanding by demonstrating that the induced foci differ from traditional P-bodies in a number of significant ways. These include differences in overall granule morphology, protein composition and the manner in which their induction is regulated. Of particular note, several key P-body constituents are absent from these Benomyl-Induced Granules (BIGs), including the Pat1 protein that is normally required for efficient P-body assembly. However, these novel RNP structures still contain many known P-body proteins and exhibit similar hallmarks of a liquid-like compartment. In all, the data suggest that the disruption of microtubule integrity leads to the formation of a novel type of P-body granule that may have distinct biological activities in the cell. Future work will aim to identify the biological activities of these BIGs and to determine, in turn, whether these P-body-like granules have any role in the regulation of microtubule dynamics.
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Affiliation(s)
- Zachary Hurst
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210 USA
| | - Wenfang Liu
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210 USA
| | - Qian Shi
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210 USA
| | - Paul K Herman
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210 USA
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12
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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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13
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Krischuns T, Isel C, Drncova P, Lukarska M, Pflug A, Paisant S, Navratil V, Cusack S, Naffakh N. Type B and type A influenza polymerases have evolved distinct binding interfaces to recruit the RNA polymerase II CTD. PLoS Pathog 2022; 18:e1010328. [PMID: 35605026 PMCID: PMC9242477 DOI: 10.1371/journal.ppat.1010328] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 06/29/2022] [Accepted: 04/09/2022] [Indexed: 01/05/2023] Open
Abstract
During annual influenza epidemics, influenza B viruses (IBVs) co-circulate with influenza A viruses (IAVs), can become predominant and cause severe morbidity and mortality. Phylogenetic analyses suggest that IAVs (primarily avian viruses) and IBVs (primarily human viruses) have diverged over long time scales. Identifying their common and distinctive features is an effective approach to increase knowledge about the molecular details of influenza infection. The virus-encoded RNA-dependent RNA polymerases (FluPolB and FluPolA) are PB1-PB2-PA heterotrimers that perform transcription and replication of the viral genome in the nucleus of infected cells. Initiation of viral mRNA synthesis requires a direct association of FluPol with the host RNA polymerase II (RNAP II), in particular the repetitive C-terminal domain (CTD) of the major RNAP II subunit, to enable "cap-snatching" whereby 5'-capped oligomers derived from nascent RNAP II transcripts are pirated to prime viral transcription. Here, we present the first high-resolution co-crystal structure of FluPolB bound to a CTD mimicking peptide at a binding site crossing from PA to PB2. By performing structure-based mutagenesis of FluPolB and FluPolA followed by a systematic investigation of FluPol-CTD binding, FluPol activity and viral phenotype, we demonstrate that IBVs and IAVs have evolved distinct binding interfaces to recruit the RNAP II CTD, despite the CTD sequence being highly conserved across host species. We find that the PB2 627 subdomain, a major determinant of FluPol-host cell interactions and IAV host-range, is involved in CTD-binding for IBVs but not for IAVs, and we show that FluPolB and FluPolA bind to the host RNAP II independently of the CTD. Altogether, our results suggest that the CTD-binding modes of IAV and IBV may represent avian- and human-optimized binding modes, respectively, and that their divergent evolution was shaped by the broader interaction network between the FluPol and the host transcriptional machinery.
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Affiliation(s)
- Tim Krischuns
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité Biologie des ARN et Virus Influenza, Paris, France
| | - Catherine Isel
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité Biologie des ARN et Virus Influenza, Paris, France
| | - Petra Drncova
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, Grenoble, France
| | - Maria Lukarska
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, Grenoble, France
| | - Alexander Pflug
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, Grenoble, France
| | - Sylvain Paisant
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité Biologie des ARN et Virus Influenza, Paris, France
| | - Vincent Navratil
- PRABI, Rhône Alpes Bioinformatics Center, UCBL, Lyon1, Université de Lyon, Lyon, France
| | - Stephen Cusack
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, Grenoble, France
- * E-mail: (SC); (NN)
| | - Nadia Naffakh
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité Biologie des ARN et Virus Influenza, Paris, France
- * E-mail: (SC); (NN)
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Transcription activation is enhanced by multivalent interactions independent of phase separation. Mol Cell 2022; 82:1878-1893.e10. [DOI: 10.1016/j.molcel.2022.04.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 02/28/2022] [Accepted: 04/11/2022] [Indexed: 12/23/2022]
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