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Hoboth P, Sztacho M, Hozák P. Nuclear patterns of phosphatidylinositol 4,5- and 3,4-bisphosphate revealed by super-resolution microscopy differ between the consecutive stages of RNA polymerase II transcription. FEBS J 2024. [PMID: 38734927 DOI: 10.1111/febs.17136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 12/12/2023] [Accepted: 04/05/2024] [Indexed: 05/13/2024]
Abstract
Phosphatidylinositol phosphates are powerful signaling molecules that orchestrate signaling and direct membrane trafficking in the cytosol. Interestingly, phosphatidylinositol phosphates also localize within the membrane-less compartments of the cell nucleus, where they participate in the regulation of gene expression. Nevertheless, current models of gene expression, which include condensates of proteins and nucleic acids, do not include nuclear phosphatidylinositol phosphates. This gap is partly a result of the missing detailed analysis of the subnuclear distribution of phosphatidylinositol phosphates and their relationships with gene expression. Here, we used quantitative dual-color direct stochastic optical reconstruction microscopy to analyze the nanoscale co-patterning between RNA polymerase II transcription initiation and elongation markers with respect to phosphatidylinositol 4,5- or 3,4-bisphosphate in the nucleoplasm and nuclear speckles and compared it with randomized data and cells with inhibited transcription. We found specific co-patterning of the transcription initiation marker P-S5 with phosphatidylinositol 4,5-bisphosphate in the nucleoplasm and with phosphatidylinositol 3,4-bisphosphate at the periphery of nuclear speckles. We showed the specific accumulation of the transcription elongation marker PS-2 and of nascent RNA in the proximity of phosphatidylinositol 3,4-bisphosphate associated with nuclear speckles. Taken together, this shows that the distinct spatial associations between the consecutive stages of RNA polymerase II transcription and nuclear phosphatidylinositol phosphates exhibit specificity within the gene expression compartments. Thus, in analogy to the cellular membranes, where phospholipid composition orchestrates signaling pathways and directs membrane trafficking, we propose a model in which the phospholipid identity of gene expression compartments orchestrates RNA polymerase II transcription.
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Affiliation(s)
- Peter Hoboth
- Laboratory of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
- Viničná Microscopy Core Facility, Faculty of Science, Charles University, Prague, Czech Republic
| | - Martin Sztacho
- Laboratory of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
- Laboratory of Cancer Cell Architecture, Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Pavel Hozák
- Laboratory of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
- Microscopy Centre, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
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2
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Tullius TW, Isaac RS, Ranchalis J, Dubocanin D, Churchman LS, Stergachis AB. RNA polymerases reshape chromatin and coordinate transcription on individual fibers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.22.573133. [PMID: 38187631 PMCID: PMC10769320 DOI: 10.1101/2023.12.22.573133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
During eukaryotic transcription, RNA polymerases must initiate and pause within a crowded, complex environment, surrounded by nucleosomes and other transcriptional activity. This environment creates a spatial arrangement along individual chromatin fibers ripe for both competition and coordination, yet these relationships remain largely unknown owing to the inherent limitations of traditional structural and sequencing methodologies. To address these limitations, we employed long-read chromatin fiber sequencing (Fiber-seq) to visualize RNA polymerases within their native chromatin context at single-molecule and near single-nucleotide resolution along up to 30 kb fibers. We demonstrate that Fiber-seq enables the identification of single-molecule RNA Polymerase (Pol) II and III transcription associated footprints, which, in aggregate, mirror bulk short-read sequencing-based measurements of transcription. We show that Pol II pausing destabilizes downstream nucleosomes, with frequently paused genes maintaining a short-term memory of these destabilized nucleosomes. Furthermore, we demonstrate pervasive direct coordination and anti-coordination between nearby Pol II genes, Pol III genes, transcribed enhancers, and insulator elements. This coordination is largely limited to spatially organized elements within 5 kb of each other, implicating short-range chromatin environments as a predominant determinant of coordinated polymerase initiation. Overall, transcription initiation reshapes surrounding nucleosome architecture and coordinates nearby transcriptional machinery along individual chromatin fibers.
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Affiliation(s)
- Thomas W Tullius
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - R Stefan Isaac
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jane Ranchalis
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA
| | - Danilo Dubocanin
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA
| | - L Stirling Churchman
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Andrew B Stergachis
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA
- Department of Genome Sciences, University of Washington, Seattle, WA
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Sylvers J, Wang Y, Yuan F. Nuclear Entry of DNA and Transgene Expression in Dividing and Non-dividing Cells. Cell Mol Bioeng 2023; 16:459-474. [PMID: 38099212 PMCID: PMC10716082 DOI: 10.1007/s12195-023-00784-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 09/03/2023] [Indexed: 12/17/2023] Open
Abstract
Introduction Plasmid DNA (pDNA) must be delivered into the nucleus for transgene expression in mammalian cells. The entry may happen passively during the nuclear envelope breakdown and reformation in dividing cells or actively through the nuclear pore complexes. The goal of this study was to investigate the relative importance of these two pathways for pDNA nuclear entry and subsequent gene expression. Methods To measure nuclear entry of pDNA encoding enhanced green florescence protein (EGFP) in electrotransfected cells, we developed a sensitive technique for quantitative analysis of pDNA in the nuclei, based on a hybridization probe for pDNA detection at the single molecule level and automatic image analysis. In matched experiments, we used an mRNA targeted hybridization probe to quantify reporter mRNA expression per cell, and flow cytometry to quantify expression of EGFP. Results We discovered two distinct patterns of pDNA distribution in the nuclei: punctate and diffuse, which were dominant in arrested and unarrested cells, respectively. The cell cycle arrest decreased diffuse pDNA and increased punctate pDNA. Its net effect was a decrease in the total intranuclear pDNA. Additionally, the cell cycle arrest increased the reporter mRNA synthesis but had no substantial impact on reporter protein expression. Conclusion Results from the study demonstrated that the efficient nuclear entry of pDNA during cell division did not necessarily lead to a high level of transgene expression. They also suggested that the punctate pDNA was more transcriptionally active than diffuse pDNA in the nuclei. These data will be useful in future studies for understanding mechanisms of nonviral gene delivery.
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Affiliation(s)
- Justin Sylvers
- Department of Biomedical Engineering, Duke University, Durham, NC 27708 USA
| | - Yifei Wang
- Department of Biomedical Engineering, Duke University, Durham, NC 27708 USA
| | - Fan Yuan
- Department of Biomedical Engineering, Duke University, Durham, NC 27708 USA
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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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Richter WF, Nayak S, Iwasa J, Taatjes DJ. The Mediator complex as a master regulator of transcription by RNA polymerase II. Nat Rev Mol Cell Biol 2022; 23:732-749. [PMID: 35725906 PMCID: PMC9207880 DOI: 10.1038/s41580-022-00498-3] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/17/2022] [Indexed: 02/08/2023]
Abstract
The Mediator complex, which in humans is 1.4 MDa in size and includes 26 subunits, controls many aspects of RNA polymerase II (Pol II) function. Apart from its size, a defining feature of Mediator is its intrinsic disorder and conformational flexibility, which contributes to its ability to undergo phase separation and to interact with a myriad of regulatory factors. In this Review, we discuss Mediator structure and function, with emphasis on recent cryogenic electron microscopy data of the 4.0-MDa transcription preinitiation complex. We further discuss how Mediator and sequence-specific DNA-binding transcription factors enable enhancer-dependent regulation of Pol II function at distal gene promoters, through the formation of molecular condensates (or transcription hubs) and chromatin loops. Mediator regulation of Pol II reinitiation is also discussed, in the context of transcription bursting. We propose a working model for Mediator function that combines experimental results and theoretical considerations related to enhancer-promoter interactions, which reconciles contradictory data regarding whether enhancer-promoter communication is direct or indirect. We conclude with a discussion of Mediator's potential as a therapeutic target and of future research directions.
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Affiliation(s)
- William F Richter
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Shraddha Nayak
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Janet Iwasa
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Dylan J Taatjes
- Department of Biochemistry, University of Colorado, Boulder, CO, USA.
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Nair SJ, Suter T, Wang S, Yang L, Yang F, Rosenfeld MG. Transcriptional enhancers at 40: evolution of a viral DNA element to nuclear architectural structures. Trends Genet 2022; 38:1019-1047. [PMID: 35811173 PMCID: PMC9474616 DOI: 10.1016/j.tig.2022.05.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/05/2022] [Accepted: 05/31/2022] [Indexed: 02/08/2023]
Abstract
Gene regulation by transcriptional enhancers is the dominant mechanism driving cell type- and signal-specific transcriptional diversity in metazoans. However, over four decades since the original discovery, how enhancers operate in the nuclear space remains largely enigmatic. Recent multidisciplinary efforts combining real-time imaging, genome sequencing, and biophysical strategies provide insightful but conflicting models of enhancer-mediated gene control. Here, we review the discovery and progress in enhancer biology, emphasizing the recent findings that acutely activated enhancers assemble regulatory machinery as mesoscale architectural structures with distinct physical properties. These findings help formulate novel models that explain several mysterious features of the assembly of transcriptional enhancers and the mechanisms of spatial control of gene expression.
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Affiliation(s)
- Sreejith J Nair
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA.
| | - Tom Suter
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Susan Wang
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Cellular and Molecular Medicine Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Lu Yang
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Feng Yang
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Michael G Rosenfeld
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
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7
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de Jonge WJ, Patel HP, Meeussen JVW, Lenstra TL. Following the tracks: how transcription factor binding dynamics control transcription. Biophys J 2022; 121:1583-1592. [PMID: 35337845 PMCID: PMC9117886 DOI: 10.1016/j.bpj.2022.03.026] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/28/2022] [Accepted: 03/21/2022] [Indexed: 11/29/2022] Open
Abstract
Transcription, the process of copying genetic information from DNA to messenger RNA, is regulated by sequence-specific DNA binding proteins known as transcription factors (TFs). Recent advances in single-molecule tracking (SMT) technologies have enabled visualization of individual TF molecules as they diffuse and interact with the DNA in the context of living cells. These SMT studies have uncovered multiple populations of DNA binding events characterized by their distinctive DNA residence times. In this perspective, we review recent insights into how these residence times relate to specific and non-specific DNA binding, as well as the contribution of TF domains on the DNA binding dynamics. We discuss different models that aim to link transient DNA binding by TFs to bursts of transcription and present an outlook for how future advances in microscopy development may broaden our understanding of the dynamics of the molecular steps that underlie transcription activation.
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Affiliation(s)
- Wim J de Jonge
- Division of Gene Regulation, The Netherlands Cancer Institute, Oncode Institute, 1066CX Amsterdam, the Netherlands
| | - Heta P Patel
- Division of Gene Regulation, The Netherlands Cancer Institute, Oncode Institute, 1066CX Amsterdam, the Netherlands
| | - Joseph V W Meeussen
- Division of Gene Regulation, The Netherlands Cancer Institute, Oncode Institute, 1066CX Amsterdam, the Netherlands
| | - Tineke L Lenstra
- Division of Gene Regulation, The Netherlands Cancer Institute, Oncode Institute, 1066CX Amsterdam, the Netherlands.
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8
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Rippe K, Papantonis A. Functional organization of RNA polymerase II in nuclear subcompartments. Curr Opin Cell Biol 2022; 74:88-96. [PMID: 35217398 DOI: 10.1016/j.ceb.2022.01.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/08/2022] [Accepted: 01/14/2022] [Indexed: 12/22/2022]
Abstract
Distinct clusters of RNA polymerase II are responsible for gene transcription inside eukaryotic cell nuclei. Despite the functional implications of such subnuclear organization, the attributes of these clusters and the mechanisms underlying their formation remain only partially understood. Recently, the concept of proteins and RNA phase-separating into liquid-like droplets was proposed to drive the formation of transcriptionally-active subcompartments. Here, we attempt to reconcile previous with more recent findings, and discuss how the different ways of assembling the active RNA polymerase II transcriptional machinery relate to nuclear compartmentalization.
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Affiliation(s)
- Karsten Rippe
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany.
| | - Argyris Papantonis
- Translational Epigenetics Group, Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany.
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9
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The Mediator kinase module: an interface between cell signaling and transcription. Trends Biochem Sci 2022; 47:314-327. [DOI: 10.1016/j.tibs.2022.01.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 01/11/2022] [Accepted: 01/17/2022] [Indexed: 12/14/2022]
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10
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Patange S, Ball DA, Wan Y, Karpova TS, Girvan M, Levens D, Larson DR. MYC amplifies gene expression through global changes in transcription factor dynamics. Cell Rep 2022; 38:110292. [PMID: 35081348 DOI: 10.1016/j.celrep.2021.110292] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/16/2021] [Accepted: 12/30/2021] [Indexed: 12/14/2022] Open
Abstract
The MYC oncogene has been studied for decades, yet there is still intense debate over how this transcription factor controls gene expression. Here, we seek to answer these questions with an in vivo readout of discrete events of gene expression in single cells. We engineered an optogenetic variant of MYC (Pi-MYC) and combined this tool with single-molecule RNA and protein imaging techniques to investigate the role of MYC in modulating transcriptional bursting and transcription factor binding dynamics in human cells. We find that the immediate consequence of MYC overexpression is an increase in the duration rather than in the frequency of bursts, a functional role that is different from the majority of human transcription factors. We further propose that the mechanism by which MYC exerts global effects on the active period of genes is by altering the binding dynamics of transcription factors involved in RNA polymerase II complex assembly and productive elongation.
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Affiliation(s)
- Simona Patange
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA; Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
| | - David A Ball
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Yihan Wan
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Tatiana S Karpova
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Michelle Girvan
- Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
| | - David Levens
- Laboratory of Pathology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Daniel R Larson
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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Palacio M, Taatjes DJ. Merging Established Mechanisms with New Insights: Condensates, Hubs, and the Regulation of RNA Polymerase II Transcription. J Mol Biol 2022; 434:167216. [PMID: 34474085 PMCID: PMC8748285 DOI: 10.1016/j.jmb.2021.167216] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/16/2021] [Accepted: 08/19/2021] [Indexed: 01/17/2023]
Abstract
The regulation of RNA polymerase II (pol II) transcription requires a complex and context-specific array of proteins and protein complexes, as well as nucleic acids and metabolites. Every major physiological process requires coordinated transcription of specific sets of genes at the appropriate time, and a breakdown in this regulation is a hallmark of human disease. A proliferation of recent studies has revealed that many general transcription components, including sequence-specific, DNA-binding transcription factors, Mediator, and pol II itself, are capable of liquid-liquid phase separation, to form condensates that partition these factors away from the bulk aqueous phase. These findings hold great promise for next-level understanding of pol II transcription; however, many mechanistic aspects align with more conventional models, and whether phase separation per se regulates pol II activity in cells remains controversial. In this review, we describe the conventional and condensate-dependent models, and why their similarities and differences are important. We also compare and contrast these models in the context of genome organization and pol II transcription (initiation, elongation, and termination), and highlight the central role of RNA in these processes. Finally, we discuss mutations that disrupt normal partitioning of transcription factors, and how this may contribute to disease.
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Affiliation(s)
- Megan Palacio
- Dept. of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Dylan J. Taatjes
- Dept. of Biochemistry, University of Colorado, Boulder, CO, USA,corresponding author;
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12
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Affiliation(s)
- Dylan J Taatjes
- Dept. of Biochemistry, University of Colorado, Boulder, CO, USA.
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