1
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Gillis A, Berry S. Global control of RNA polymerase II. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195024. [PMID: 38552781 DOI: 10.1016/j.bbagrm.2024.195024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 04/11/2024]
Abstract
RNA polymerase II (Pol II) is the multi-protein complex responsible for transcribing all protein-coding messenger RNA (mRNA). Most research on gene regulation is focused on the mechanisms controlling which genes are transcribed when, or on the mechanics of transcription. How global Pol II activity is determined receives comparatively less attention. Here, we follow the life of a Pol II molecule from 'assembly of the complex' to nuclear import, enzymatic activity, and degradation. We focus on how Pol II spends its time in the nucleus, and on the two-way relationship between Pol II abundance and activity in the context of homeostasis and global transcriptional changes.
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Affiliation(s)
- Alexander Gillis
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Sydney, Australia; UNSW RNA Institute, University of New South Wales, Sydney, Australia; Department of Molecular Medicine, School of Biomedical Sciences, University of New South Wales, Sydney, Australia
| | - Scott Berry
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Sydney, Australia; UNSW RNA Institute, University of New South Wales, Sydney, Australia; Department of Molecular Medicine, School of Biomedical Sciences, University of New South Wales, Sydney, Australia
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2
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Nicholson MD, Anderson CJ, Odom DT, Aitken SJ, Taylor MS. DNA lesion bypass and the stochastic dynamics of transcription-coupled repair. Proc Natl Acad Sci U S A 2024; 121:e2403871121. [PMID: 38717857 PMCID: PMC11098089 DOI: 10.1073/pnas.2403871121] [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: 02/23/2024] [Accepted: 04/09/2024] [Indexed: 05/18/2024] Open
Abstract
DNA base damage is a major source of oncogenic mutations and disruption to gene expression. The stalling of RNA polymerase II (RNAP) at sites of DNA damage and the subsequent triggering of repair processes have major roles in shaping the genome-wide distribution of mutations, clearing barriers to transcription, and minimizing the production of miscoded gene products. Despite its importance for genetic integrity, key mechanistic features of this transcription-coupled repair (TCR) process are controversial or unknown. Here, we exploited a well-powered in vivo mammalian model system to explore the mechanistic properties and parameters of TCR for alkylation damage at fine spatial resolution and with discrimination of the damaged DNA strand. For rigorous interpretation, a generalizable mathematical model of DNA damage and TCR was developed. Fitting experimental data to the model and simulation revealed that RNA polymerases frequently bypass lesions without triggering repair, indicating that small alkylation adducts are unlikely to be an efficient barrier to gene expression. Following a burst of damage, the efficiency of transcription-coupled repair gradually decays through gene bodies with implications for the occurrence and accurate inference of driver mutations in cancer. The reinitation of transcription from the repair site is not a general feature of transcription-coupled repair, and the observed data is consistent with reinitiation never taking place. Collectively, these results reveal how the directional but stochastic activity of TCR shapes the distribution of mutations following DNA damage.
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Affiliation(s)
- Michael D. Nicholson
- Cancer Research United Kingdom Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, EdinburghEH4 2XU, United Kingdom
| | - Craig J. Anderson
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, EdinburghEH4 2XU, United Kingdom
| | - Duncan T. Odom
- Division of Regulatory Genomics and Cancer Evolution (B270), German Cancer Research Center, Heidelberg69120, Germany
- Cancer Research United Kingdom Cambridge Institute, University of Cambridge, CambridgeCB2 0RE, United Kingdom
| | - Sarah J. Aitken
- Cancer Research United Kingdom Cambridge Institute, University of Cambridge, CambridgeCB2 0RE, United Kingdom
- Medical Research Council Toxicology Unit, University of Cambridge, CambridgeCB2 1QR, United Kingdom
- Department of Histopathology, Cambridge University Hospitals National Health Service Foundation Trust, CambridgeCB2 0QQ, United Kingdom
| | - Martin S. Taylor
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, EdinburghEH4 2XU, United Kingdom
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3
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Sugaya K. Characterization of cells expressing lipocalin-2 (LCN2) as a reporter. Biochem Cell Biol 2024. [PMID: 38696838 DOI: 10.1139/bcb-2024-0013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2024] Open
Abstract
Lipocalin-2 (LCN2), an effector molecule of the innate immune system that is small enough to be tagged as a reporter molecule, can be coupled with the ferric ion through a siderophore such as enterobactin (Ent). Mintbody (modification-specific intracellular antibody) can track a posttranslational protein modification in epigenetics. We constructed plasmids expressing the LCN2 hybrid of mintbody to examine the potential of LCN2 as a novel reporter for magnetic resonance imaging (MRI). Cells expressing the LCN2 hybrid of mintbody showed proper expression and localization of the hybrid and responded reasonably to Ent, suggesting their potential for in vivo study by MRI.
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Affiliation(s)
- Kimihiko Sugaya
- Department of Molecular Imaging and Theranostics, Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology (QST), Chiba, Japan
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4
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Pérez-Ortín JE, García-Marcelo MJ, Delgado-Román I, Muñoz-Centeno MC, Chávez S. Influence of cell volume on the gene transcription rate. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195008. [PMID: 38246270 DOI: 10.1016/j.bbagrm.2024.195008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 01/14/2024] [Accepted: 01/15/2024] [Indexed: 01/23/2024]
Abstract
Cells vary in volume throughout their life cycle and in many other circumstances, while their genome remains identical. Hence, the RNA production factory must adapt to changing needs, while maintaining the same production lines. This paradox is resolved by different mechanisms in distinct cells and circumstances. RNA polymerases have evolved to cope with the particular circumstances of each case and the different characteristics of the several RNA molecule types, especially their stabilities. Here we review current knowledge on these issues. We focus on the yeast Saccharomyces cerevisiae, where many of the studies have been performed, although we compare and discuss the results obtained in other eukaryotes and propose several ideas and questions to be tested and solved in the future. TAKE AWAY.
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Affiliation(s)
- José E Pérez-Ortín
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Facultad de Biológicas, Universitat de València, C/ Dr. Moliner 50, E46100 Burjassot, Spain.
| | - María J García-Marcelo
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Facultad de Biológicas, Universitat de València, C/ Dr. Moliner 50, E46100 Burjassot, Spain; Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville 41012, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Irene Delgado-Román
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville 41012, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - María C Muñoz-Centeno
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville 41012, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Sebastián Chávez
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville 41012, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
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5
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Stein J, Ericsson M, Nofal M, Magni L, Aufmkolk S, McMillan RB, Breimann L, Herlihy CP, Lee SD, Willemin A, Wohlmann J, Arguedas-Jimenez L, Yin P, Pombo A, Church GM, Wu CK. Cryosectioning-enabled super-resolution microscopy for studying nuclear architecture at the single protein level. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.05.576943. [PMID: 38370628 PMCID: PMC10871237 DOI: 10.1101/2024.02.05.576943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
DNA-PAINT combined with total Internal Reflection Fluorescence (TIRF) microscopy enables the highest localization precisions, down to single nanometers in thin biological samples, due to TIRF's unique method for optical sectioning and attaining high contrast. However, most cellular targets elude the accessible TIRF range close to the cover glass and thus require alternative imaging conditions, affecting resolution and image quality. Here, we address this limitation by applying ultrathin physical cryosectioning in combination with DNA-PAINT. With "tomographic & kinetically-enhanced" DNA-PAINT (tokPAINT), we demonstrate the imaging of nuclear proteins with sub-3 nanometer localization precision, advancing the quantitative study of nuclear organization within fixed cells and mouse tissues at the level of single antibodies. We believe that ultrathin sectioning combined with the versatility and multiplexing capabilities of DNA-PAINT will be a powerful addition to the toolbox of quantitative DNA-based super-resolution microscopy in intracellular structural analyses of proteins, RNA and DNA in situ.
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Affiliation(s)
- Johannes Stein
- Wyss Institute of Biologically Inspired Engineering, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Maria Ericsson
- Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Michel Nofal
- Wyss Institute of Biologically Inspired Engineering, Boston, MA, USA
| | - Lorenzo Magni
- Wyss Institute of Biologically Inspired Engineering, Boston, MA, USA
| | - Sarah Aufmkolk
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Ryan B. McMillan
- Wyss Institute of Biologically Inspired Engineering, Boston, MA, USA
| | - Laura Breimann
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | | | - S. Dean Lee
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Andréa Willemin
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany
- Humboldt-Universität zu Berlin, Institute for Biology, Berlin, Germany
| | - Jens Wohlmann
- Department of Biosciences, University of Oslo, Norway
| | - Laura Arguedas-Jimenez
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany
| | - Peng Yin
- Wyss Institute of Biologically Inspired Engineering, Boston, MA, USA
| | - Ana Pombo
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany
- Humboldt-Universität zu Berlin, Institute for Biology, Berlin, Germany
| | - George M. Church
- Wyss Institute of Biologically Inspired Engineering, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Chao-Kng Wu
- Department of Genetics, Harvard Medical School, Boston, MA, USA
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6
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Saxton MN, Morisaki T, Krapf D, Kimura H, Stasevich TJ. Live-cell imaging uncovers the relationship between histone acetylation, transcription initiation, and nucleosome mobility. SCIENCE ADVANCES 2023; 9:eadh4819. [PMID: 37792937 PMCID: PMC10550241 DOI: 10.1126/sciadv.adh4819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 09/01/2023] [Indexed: 10/06/2023]
Abstract
Histone acetylation and RNA polymerase II phosphorylation are associated with transcriptionally active chromatin, but their spatiotemporal relationship in live cells remains poorly understood. To address this problem, we combine Fab-based labeling of endogenous protein modifications with single-molecule tracking to quantify the dynamics of chromatin enriched with histone H3 lysine-27 acetylation (H3K27ac) and RNA polymerase II serine-5 phosphorylation (RNAP2-Ser5ph). Our analysis reveals that chromatin enriched with these two modifications is generally separate. In these separated sites, we show that the two modifications are inversely correlated with one another on the minutes time scale and that single nucleosomes within each region display distinct and opposing dynamics on the subsecond time scale. While nucleosomes diffuse ~15% faster in chromatin enriched with H3K27ac, they diffuse ~15% slower in chromatin enriched with RNAP2-Ser5ph. These results argue that high levels of H3K27ac and RNAP2-Ser5ph are not often present together at the same place and time, but rather each marks distinct transcriptionally poised or active sites, respectively.
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Affiliation(s)
- Matthew N. Saxton
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Tatsuya Morisaki
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Diego Krapf
- Department of Electrical and Computer Engineering, and School of Biomedical Engineering, Colorado State University, Fort Collins, CO, USA
| | - Hiroshi Kimura
- Cell Biology Center and World Research Hub Initiative, Tokyo Institute of Technology, Yokohama, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Timothy J. Stasevich
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
- Cell Biology Center and World Research Hub Initiative, Tokyo Institute of Technology, Yokohama, Japan
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7
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Eshghi I, Zidovska A, Grosberg AY. Model chromatin flows: numerical analysis of linear and nonlinear hydrodynamics inside a sphere. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2023; 46:69. [PMID: 37540478 DOI: 10.1140/epje/s10189-023-00327-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/25/2023] [Indexed: 08/05/2023]
Abstract
We solve a hydrodynamic model of active chromatin dynamics, within a confined geometry simulating the cell nucleus. Using both analytical and numerical methods, we describe the behavior of the chromatin polymer driven by the activity of motors having polar symmetry, both in the linear response regime as well as in the long-term, fully nonlinear regime of the flows. The introduction of a boundary induces a particular geometry in the flows of chromatin, which we describe using vector spherical harmonics, a tool which greatly simplifies both our analytical and numerical approaches. We find that the long-term behavior of this model in confinement is dominated by steady, transverse flows of chromatin which circulate around the spherical domain. These circulating flows are found to be robust to perturbations, and their characteristic size is set by the size of the domain. This gives us further insight into active chromatin dynamics in the cell nucleus, and provides a foundation for development of further, more complex models of active chromatin dynamics.
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Affiliation(s)
- Iraj Eshghi
- Center for Soft Matter Research, Department of Physics, New York University, New York, NY, 10003, USA
| | - Alexandra Zidovska
- Center for Soft Matter Research, Department of Physics, New York University, New York, NY, 10003, USA
| | - Alexander Y Grosberg
- Center for Soft Matter Research, Department of Physics, New York University, New York, NY, 10003, USA.
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8
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Cavallaro M, Wang Y, Hebenstreit D, Dutta R. Bayesian inference of polymerase dynamics over the exclusion process. ROYAL SOCIETY OPEN SCIENCE 2023; 10:221469. [PMID: 37538742 PMCID: PMC10394410 DOI: 10.1098/rsos.221469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 07/12/2023] [Indexed: 08/05/2023]
Abstract
Transcription is a complex phenomenon that permits the conversion of genetic information into phenotype by means of an enzyme called RNA polymerase, which erratically moves along and scans the DNA template. We perform Bayesian inference over a paradigmatic mechanistic model of non-equilibrium statistical physics, i.e. the asymmetric exclusion processes in the hydrodynamic limit, assuming a Gaussian process prior for the polymerase progression rate as a latent variable. Our framework allows us to infer the speed of polymerases during transcription given their spatial distribution, while avoiding the explicit inversion of the system's dynamics. The results, which show processing rates strongly varying with genomic position and minor role of traffic-like congestion, may have strong implications for the understanding of gene expression.
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Affiliation(s)
- Massimo Cavallaro
- Mathematics Institute, University of Warwick, Coventry, UK
- School of Life Sciences, University of Warwick, Coventry, UK
- Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, University of Warwick, Coventry, UK
| | - Yuexuan Wang
- Institute of Applied Statistics, Johannes Kepler Universität, Linz, Austria
| | | | - Ritabrata Dutta
- Department of Statistics, University of Warwick, Coventry, UK
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9
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Eshghi I, Zidovska A, Grosberg AY. Activity-Driven Phase Transition Causes Coherent Flows of Chromatin. PHYSICAL REVIEW LETTERS 2023; 131:048401. [PMID: 37566839 DOI: 10.1103/physrevlett.131.048401] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 06/23/2023] [Indexed: 08/13/2023]
Abstract
We discover a new type of nonequilibrium phase transition in a model of chromatin dynamics, which accounts for the coherent motions that have been observed in experiment. The coherent motion is due to the long-range cooperation of molecular motors tethered to chromatin. Cooperation occurs if each motor acts simultaneously on the polymer and the surrounding solvent, exerting on them equal and opposite forces. This drives the flow of solvent past the polymer, which in turn affects the orientation of nearby motors and, if the drive is strong enough, an active polar ("ferromagnetic") phase of motors can spontaneously form. Depending on boundary conditions, either transverse flows or sustained longitudinal oscillations and waves are possible. Predicted length scales are consistent with experiments. We now have in hand a coarse-grained description of chromatin dynamics which reproduces the directed coherent flows of chromatin seen in experiments. This field-theoretic description can be analytically coupled to other features of the nuclear environment such as fluctuating or porous boundaries, local heterogeneities in the distribution of chromatin or its activity, leading to insights on the effects of activity on the cell nucleus and its contents.
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Affiliation(s)
- Iraj Eshghi
- Center for Soft Matter Research, Department of Physics, New York University, New York, New York 10003, USA
| | - Alexandra Zidovska
- Center for Soft Matter Research, Department of Physics, New York University, New York, New York 10003, USA
| | - Alexander Y Grosberg
- Center for Soft Matter Research, Department of Physics, New York University, New York, New York 10003, USA
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10
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Eshghi I, Zidovska A, Grosberg AY. Symmetry-based classification of forces driving chromatin dynamics. SOFT MATTER 2022; 18:8134-8146. [PMID: 36239271 DOI: 10.1039/d2sm00840h] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Chromatin - the functional form of DNA in the cell - exists in the form of a polymer immersed in a nucleoplasmic fluid inside the cell nucleus. Both chromatin and nucleoplasm are subject to active forces resulting from local biological processes. This activity leads to non-equilibrium phenomena, affecting chromatin organization and dynamics, yet the underlying physics is far from understood. Here, we expand upon a previously developed two-fluid model of chromatin and nucleoplasm by considering three types of activity in the form of force dipoles - two with both forces of the dipole acting on the same fluid (either polymer or nucleoplasm) and a third, with two forces pushing chromatin and solvent in opposite directions. We find that this latter type results in the most significant flows, dominating over most length scales of interest. Due to the friction between the fluids and their viscosity, we observe emergent screening length scales in the active flows of this system. We predict that the presence of different activity types and their relative strengths can be inferred from observing the power spectra of hydrodynamic fluctuations in the chromatin and the nucleoplasm.
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Affiliation(s)
- Iraj Eshghi
- Center for Soft Matter Research, Department of Physics, New York University, New York, NY 10003, USA.
| | - Alexandra Zidovska
- Center for Soft Matter Research, Department of Physics, New York University, New York, NY 10003, USA.
| | - Alexander Y Grosberg
- Center for Soft Matter Research, Department of Physics, New York University, New York, NY 10003, USA.
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11
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Todorovic M, Rivollier P, Wong AAWL, Wang Z, Pryyma A, Nguyen TT, Newell KC, Froelich J, Perrin DM. Rationally Designed Amanitins Achieve Enhanced Cytotoxicity. J Med Chem 2022; 65:10357-10376. [PMID: 35696491 DOI: 10.1021/acs.jmedchem.1c02226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
For 70 years, α-amanitin, the most cytotoxic peptide in its class, has been without a synthetic rival; through synthesis, we address the structure-activity relationships to inform the design of new amatoxins and disclose analogues that are more cytotoxic than the natural product when evaluated on CHO, HEK293, and HeLa cells, whereas on liver-derived HepG2 cells, the same toxins show diminished cytotoxicity.
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Affiliation(s)
- Mihajlo Todorovic
- Chemistry Department, 2036 Main Mall, The University of British Columbia, 2036 Main Mall, Vancouver, BC V6T-1Z1, Canada
| | - Paul Rivollier
- Chemistry Department, 2036 Main Mall, The University of British Columbia, 2036 Main Mall, Vancouver, BC V6T-1Z1, Canada
| | - Antonio A W L Wong
- Chemistry Department, 2036 Main Mall, The University of British Columbia, 2036 Main Mall, Vancouver, BC V6T-1Z1, Canada
| | - Zhou Wang
- Chemistry Department, 2036 Main Mall, The University of British Columbia, 2036 Main Mall, Vancouver, BC V6T-1Z1, Canada
| | - Alla Pryyma
- Chemistry Department, 2036 Main Mall, The University of British Columbia, 2036 Main Mall, Vancouver, BC V6T-1Z1, Canada
| | - Tuan Trung Nguyen
- Chemistry Department, 2036 Main Mall, The University of British Columbia, 2036 Main Mall, Vancouver, BC V6T-1Z1, Canada
| | - Kayla C Newell
- Chemistry Department, 2036 Main Mall, The University of British Columbia, 2036 Main Mall, Vancouver, BC V6T-1Z1, Canada
| | - Juliette Froelich
- Chemistry Department, 2036 Main Mall, The University of British Columbia, 2036 Main Mall, Vancouver, BC V6T-1Z1, Canada
| | - David M Perrin
- Chemistry Department, 2036 Main Mall, The University of British Columbia, 2036 Main Mall, Vancouver, BC V6T-1Z1, Canada
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12
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Olson SW, Turner AMW, Arney JW, Saleem I, Weidmann CA, Margolis DM, Weeks KM, Mustoe AM. Discovery of a large-scale, cell-state-responsive allosteric switch in the 7SK RNA using DANCE-MaP. Mol Cell 2022; 82:1708-1723.e10. [PMID: 35320755 PMCID: PMC9081252 DOI: 10.1016/j.molcel.2022.02.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/29/2021] [Accepted: 02/02/2022] [Indexed: 12/17/2022]
Abstract
7SK is a conserved noncoding RNA that regulates transcription by sequestering the transcription factor P-TEFb. 7SK function entails complex changes in RNA structure, but characterizing RNA dynamics in cells remains an unsolved challenge. We developed a single-molecule chemical probing strategy, DANCE-MaP (deconvolution and annotation of ribonucleic conformational ensembles), that defines per-nucleotide reactivity, direct base pairing interactions, tertiary interactions, and thermodynamic populations for each state in RNA structural ensembles from a single experiment. DANCE-MaP reveals that 7SK RNA encodes a large-scale structural switch that couples dissolution of the P-TEFb binding site to structural remodeling at distal release factor binding sites. The 7SK structural equilibrium shifts in response to cell growth and stress and can be targeted to modulate expression of P-TEFbresponsive genes. Our study reveals that RNA structural dynamics underlie 7SK function as an integrator of diverse cellular signals to control transcription and establishes the power of DANCE-MaP to define RNA dynamics in cells.
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Affiliation(s)
- Samuel W Olson
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA
| | - Anne-Marie W Turner
- Department of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; UNC HIV Cure Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - J Winston Arney
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA
| | - Irfana Saleem
- Verna and Marrs McClean Department of Biochemistry and Molecular Biology, Therapeutic Innovation Center (THINC), Baylor College of Medicine, Houston, TX 77030, USA
| | - Chase A Weidmann
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA
| | - David M Margolis
- Department of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; UNC HIV Cure Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA.
| | - Anthony M Mustoe
- Verna and Marrs McClean Department of Biochemistry and Molecular Biology, Therapeutic Innovation Center (THINC), Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
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13
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Li J, Feng H, Liu S, Liu P, Chen X, Yang J, He L, Yang J, Chen J. Phosphorylated viral protein evades plant immunity through interfering the function of RNA-binding protein. PLoS Pathog 2022; 18:e1010412. [PMID: 35294497 PMCID: PMC8959173 DOI: 10.1371/journal.ppat.1010412] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 03/28/2022] [Accepted: 03/01/2022] [Indexed: 12/31/2022] Open
Abstract
Successful pathogen infection in plant depends on a proper interaction between the invading pathogen and its host. Post-translational modification (PTM) plays critical role(s) in plant-pathogen interaction. However, how PTM of viral protein regulates plant immunity remains poorly understood. Here, we found that S162 and S165 of Chinese wheat mosaic virus (CWMV) cysteine-rich protein (CRP) are phosphorylated by SAPK7 and play key roles in CWMV infection. Furthermore, the phosphorylation-mimic mutant of CRP (CRPS162/165D) but not the non-phosphorylatable mutant of CRP (CRPS162/165A) interacts with RNA-binding protein UBP1-associated protein 2C (TaUBA2C). Silencing of TaUBA2C expression in wheat plants enhanced CWMV infection. In contrast, overexpression of TaUBA2C in wheat plants inhibited CWMV infection. TaUBA2C inhibits CWMV infection through recruiting the pre-mRNA of TaNPR1, TaPR1 and TaRBOHD to induce cell death and H2O2 production. This effect can be supressed by CRPS162/165D through changing TaUBA2C chromatin-bound status and attenuating it’s the RNA- or DNA-binding activities. Taken together, our findings provide new knowledge on how CRP phosphorylation affects CWMV infection as well as the arms race between virus and wheat plants. Chinese wheat mosaic virus (CWMV) causes a damaging disease in cereal plants. However, CWMV interacts with host factors to facilitate virus infection is not clear yet. Here, we found that S162 and S165 of CWMV cysteine-rich protein (CRP) are phosphorylated by SAPK7 in vivo and in vitro. Mutational analyses have indicated that these two phosphorylation sites of CRP (CRPS162/165D) promoting CWMV infection in plants, due to the supressed cell death and H2O2 production. Further investigations found the CRPS162/165D can interact with TaUBA2C, while the non-phosphorylatable mutant of CRP (CRPS162/165A) does not. Futhermore, we have determined that CRPS162/165D and TaUBA2C interaction inhibited the formation of TaUBA2C speckles in nucleus to attenuate its RNA- and DNA-binding activity. We also showed that TaUBA2C recruit the pre-mRNA of TaNPR1, TaPR1 and TaRBOHD to up-regulated these genes expressions and then induce cell death and H2O2 production in plant. This effect can be supressed by the expression of CRPS162/165D, in a dose-dependent manner. Taken together, our discovery may provide a new sight for the arms race between virus and its host plants.
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Affiliation(s)
- Juan Li
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Huimin Feng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Shuang Liu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Peng Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Xuan Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Jin Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Long He
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Jian Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
- * E-mail: (JY); (JC)
| | - Jianping Chen
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
- * E-mail: (JY); (JC)
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14
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Uchino S, Ito Y, Sato Y, Handa T, Ohkawa Y, Tokunaga M, Kimura H. Live imaging of transcription sites using an elongating RNA polymerase II-specific probe. J Cell Biol 2022; 221:212888. [PMID: 34854870 PMCID: PMC8647360 DOI: 10.1083/jcb.202104134] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 10/12/2021] [Accepted: 11/10/2021] [Indexed: 12/15/2022] Open
Abstract
In eukaryotic nuclei, most genes are transcribed by RNA polymerase II (RNAP2), whose regulation is a key to understanding the genome and cell function. RNAP2 has a long heptapeptide repeat (Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7), and Ser2 is phosphorylated on an elongation form. To detect RNAP2 Ser2 phosphorylation (RNAP2 Ser2ph) in living cells, we developed a genetically encoded modification-specific intracellular antibody (mintbody) probe. The RNAP2 Ser2ph-mintbody exhibited numerous foci, possibly representing transcription “factories,” and foci were diminished during mitosis and in a Ser2 kinase inhibitor. An in vitro binding assay using phosphopeptides confirmed the mintbody’s specificity. RNAP2 Ser2ph-mintbody foci were colocalized with proteins associated with elongating RNAP2 compared with factors involved in the initiation. These results support the view that mintbody localization represents the sites of RNAP2 Ser2ph in living cells. RNAP2 Ser2ph-mintbody foci showed constrained diffusional motion like chromatin, but they were more mobile than DNA replication domains and p300-enriched foci, suggesting that the elongating RNAP2 complexes are separated from more confined chromatin domains.
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Affiliation(s)
- Satoshi Uchino
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Yuma Ito
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Yuko Sato
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.,Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Tetsuya Handa
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Makio Tokunaga
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Hiroshi Kimura
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.,Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
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15
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Sugaya K. Characterization of cells expressing MRI reporters for the analysis of epigenetics. Anal Biochem 2021; 633:114395. [PMID: 34600867 DOI: 10.1016/j.ab.2021.114395] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 09/25/2021] [Indexed: 11/17/2022]
Abstract
Epigenetics is thought to be involved in highly advanced life phenomena, and its regulation has created new opportunities in regenerative medicine. Mintbody (modification-specific intracellular antibody) can track a posttranslational protein modification in epigenetics using a genetic system encoded within a single chain of variable fragments tagged with a fluorescent protein. Magnetic resonance imaging (MRI) is a technique that allows observation of specific molecules in living organisms. The ferritin heavy chain (FTH1) is one of the MRI reporters used in mammals. The combination of FTH1 with mintbody may show remarkable ability as a reporter for MRI to investigate epigenetics in the deep part of a living organism. This article discusses the suitability and safety of FTH1 for use in the analysis of epigenetics by MRI. Cells expressing the FTH1 hybrid of mintbody showed insufficiently increased sensitivity by MRI even in the presence of excess iron. After incubation with ferric ammonium citrate, DNA damage was found in cells expressing the FTH1 hybrid of mintbody. The use of FTH1 as a genetically encoded reporter for MRI appears to be limited by the requirement of metal and its relatively low sensitivity. These results suggest future directionality and the possibility of studying epigenetics in vivo.
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Affiliation(s)
- Kimihiko Sugaya
- Department of Molecular Imaging and Theranostics, National Institute of Radiological Sciences (NIRS), National Institute for Quantum and Radiological Science and Technology (QST), Chiba, Japan.
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16
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Nguyen VQ, Ranjan A, Liu S, Tang X, Ling YH, Wisniewski J, Mizuguchi G, Li KY, Jou V, Zheng Q, Lavis LD, Lionnet T, Wu C. Spatiotemporal coordination of transcription preinitiation complex assembly in live cells. Mol Cell 2021; 81:3560-3575.e6. [PMID: 34375585 PMCID: PMC8420877 DOI: 10.1016/j.molcel.2021.07.022] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 05/18/2021] [Accepted: 07/16/2021] [Indexed: 12/17/2022]
Abstract
Transcription initiation by RNA polymerase II (RNA Pol II) requires preinitiation complex (PIC) assembly at gene promoters. In the dynamic nucleus, where thousands of promoters are broadly distributed in chromatin, it is unclear how multiple individual components converge on any target to establish the PIC. Here we use live-cell, single-molecule tracking in S. cerevisiae to visualize constrained exploration of the nucleoplasm by PIC components and Mediator's key role in guiding this process. On chromatin, TFIID/TATA-binding protein (TBP), Mediator, and RNA Pol II instruct assembly of a short-lived PIC, which occurs infrequently but efficiently within a few seconds on average. Moreover, PIC exclusion by nucleosome encroachment underscores regulated promoter accessibility by chromatin remodeling. Thus, coordinated nuclear exploration and recruitment to accessible targets underlies dynamic PIC establishment in yeast. Our study provides a global spatiotemporal model for transcription initiation in live cells.
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Affiliation(s)
- Vu Q Nguyen
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Anand Ranjan
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Sheng Liu
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Xiaona Tang
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Yick Hin Ling
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jan Wisniewski
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA; Experimental Immunology Branch, National Cancer Institute, Bethesda, MD 20892, USA
| | - Gaku Mizuguchi
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Kai Yu Li
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Vivian Jou
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Qinsi Zheng
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Timothée Lionnet
- Institute of Systems Genetics, Langone Medical Center, New York University, New York, NY 10016, USA
| | - Carl Wu
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA.
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17
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Live-cell imaging reveals the spatiotemporal organization of endogenous RNA polymerase II phosphorylation at a single gene. Nat Commun 2021; 12:3158. [PMID: 34039974 PMCID: PMC8155019 DOI: 10.1038/s41467-021-23417-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 04/16/2021] [Indexed: 02/07/2023] Open
Abstract
The carboxyl-terminal domain of RNA polymerase II (RNAP2) is phosphorylated during transcription in eukaryotic cells. While residue-specific phosphorylation has been mapped with exquisite spatial resolution along the 1D genome in a population of fixed cells using immunoprecipitation-based assays, the timing, kinetics, and spatial organization of phosphorylation along a single-copy gene have not yet been measured in living cells. Here, we achieve this by combining multi-color, single-molecule microscopy with fluorescent antibody-based probes that specifically bind to different phosphorylated forms of endogenous RNAP2 in living cells. Applying this methodology to a single-copy HIV-1 reporter gene provides live-cell evidence for heterogeneity in the distribution of RNAP2 along the length of the gene as well as Serine 5 phosphorylated RNAP2 clusters that remain separated in both space and time from nascent mRNA synthesis. Computational models determine that 5 to 40 RNAP2 cluster around the promoter during a typical transcriptional burst, with most phosphorylated at Serine 5 within 6 seconds of arrival and roughly half escaping the promoter in ~1.5 minutes. Taken together, our data provide live-cell support for the notion of efficient transcription clusters that transiently form around promoters and contain high concentrations of RNAP2 phosphorylated at Serine 5.
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18
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Mei Y, Wang Y, Li F, Zhou X. The C4 protein encoded by tomato leaf curl Yunnan virus reverses transcriptional gene silencing by interacting with NbDRM2 and impairing its DNA-binding ability. PLoS Pathog 2020; 16:e1008829. [PMID: 33002088 PMCID: PMC7529289 DOI: 10.1371/journal.ppat.1008829] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 07/22/2020] [Indexed: 12/19/2022] Open
Abstract
In plants, cytosine DNA methylation is an efficient defense mechanism against geminiviruses, since methylation of the viral genome results in transcriptional gene silencing (TGS). As a counter-defense mechanism, geminiviruses encode viral proteins to suppress viral DNA methylation and TGS. However, the molecular mechanisms by which viral proteins contribute to TGS suppression remain incompletely understood. In this study, we found that the C4 protein encoded by tomato leaf curl Yunnan virus (TLCYnV) suppresses methylation of the viral genome through interacting with and impairing the DNA-binding ability of NbDRM2, a pivotal DNA methyltransferase in the methyl cycle. We show that NbDRM2 catalyzes the addition of methyl groups on specific cytosine sites of the viral genome, hence playing an important role in anti-viral defense. Underscoring the relevance of the C4-mediated suppression of NbDRM2 activity, plants infected by TLCYnV producing C4(S43A), a point mutant version of C4 unable to interact with NbDRM2, display milder symptoms and lower virus accumulation, concomitant with enhanced viral DNA methylation, than plants infected by wild-type TLCYnV. Expression of TLCYnV C4, but not of the NbDRM2-interaction compromised C4(S43A) mutant, in 16c-TGS Nicotiana benthamiana plants results in the recovery of GFP, a proxy for suppression of TGS. This study provides new insights into the molecular mechanisms by which geminiviruses suppress TGS, and uncovers a new viral strategy based on the inactivation of the methyltransferase NbDRM2.
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Affiliation(s)
- Yuzhen Mei
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yaqin Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Fangfang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xueping Zhou
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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19
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Prudêncio P, Rebelo K, Grosso AR, Martinho RG, Carmo-Fonseca M. Analysis of Mammalian Native Elongating Transcript sequencing (mNET-seq) high-throughput data. Methods 2020; 178:89-95. [PMID: 31493517 DOI: 10.1016/j.ymeth.2019.09.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 07/17/2019] [Accepted: 09/01/2019] [Indexed: 11/28/2022] Open
Abstract
Mammalian Native Elongating Transcript sequencing (mNET-seq) is a recently developed technique that generates genome-wide profiles of nascent transcripts associated with RNA polymerase II (Pol II) elongation complexes. The ternary transcription complexes formed by Pol II, DNA template and nascent RNA are first isolated, without crosslinking, by immunoprecipitation with antibodies that specifically recognize the different phosphorylation states of the polymerase large subunit C-terminal domain (CTD). The coordinate of the 3' end of the RNA in the complexes is then identified by high-throughput sequencing. The main advantage of mNET-seq is that it provides global, bidirectional maps of Pol II CTD phosphorylation-specific nascent transcripts and coupled RNA processing at single nucleotide resolution. Here we describe the general pipeline to prepare and analyse high-throughput data from mNET-seq experiments.
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Affiliation(s)
- Pedro Prudêncio
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal; Center for Biomedical Research, Universidade do Algarve, Faro, Portugal.
| | - Kenny Rebelo
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Ana Rita Grosso
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal; UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Rui Gonçalo Martinho
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal; Center for Biomedical Research, Universidade do Algarve, Faro, Portugal; iBiMED, Departamento de Ciências Médicas, Universidade de Aveiro, Aveiro, Portugal
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
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20
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Mizi A, Gade Gusmao E, Papantonis A. iHi-C 2.0: A simple approach for mapping native spatial chromatin organisation from low cell numbers. Methods 2020; 170:33-37. [DOI: 10.1016/j.ymeth.2019.07.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 07/04/2019] [Indexed: 01/05/2023] Open
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21
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Cook PR, Marenduzzo D. Transcription-driven genome organization: a model for chromosome structure and the regulation of gene expression tested through simulations. Nucleic Acids Res 2019; 46:9895-9906. [PMID: 30239812 PMCID: PMC6212781 DOI: 10.1093/nar/gky763] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 09/14/2018] [Indexed: 12/29/2022] Open
Abstract
Current models for the folding of the human genome see a hierarchy stretching down from chromosome territories, through A/B compartments and topologically-associating domains (TADs), to contact domains stabilized by cohesin and CTCF. However, molecular mechanisms underlying this folding, and the way folding affects transcriptional activity, remain obscure. Here we review physical principles driving proteins bound to long polymers into clusters surrounded by loops, and present a parsimonious yet comprehensive model for the way the organization determines function. We argue that clusters of active RNA polymerases and their transcription factors are major architectural features; then, contact domains, TADs and compartments just reflect one or more loops and clusters. We suggest tethering a gene close to a cluster containing appropriate factors—a transcription factory—increases the firing frequency, and offer solutions to many current puzzles concerning the actions of enhancers, super-enhancers, boundaries and eQTLs (expression quantitative trait loci). As a result, the activity of any gene is directly influenced by the activity of other transcription units around it in 3D space, and this is supported by Brownian-dynamics simulations of transcription factors binding to cognate sites on long polymers.
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Affiliation(s)
- Peter R Cook
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Davide Marenduzzo
- SUPA, School of Physics, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK
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22
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Morisaki T, Stasevich TJ. Quantifying Single mRNA Translation Kinetics in Living Cells. Cold Spring Harb Perspect Biol 2018; 10:a032078. [PMID: 30385605 PMCID: PMC6211384 DOI: 10.1101/cshperspect.a032078] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
One of the last hurdles to quantifying the full central dogma of molecular biology in living cells with single-molecule resolution has been the imaging of single messenger RNA (mRNA) translation. Here we describe how recent advances in protein tagging and imaging technologies are being used to precisely visualize and quantify the synthesis of nascent polypeptide chains from single mRNA in living cells. We focus on recent applications of repeat-epitope tags and describe how they enable quantification of single mRNA ribosomal densities, translation initiation and elongation rates, and translation site mobility and higher-order structure. Together with complementary live-cell assays to monitor translation using fast-maturing fluorophores and mRNA-binding protein knockoff, single-molecule studies are beginning to uncover striking and unexpected heterogeneity in gene expression at the level of translation.
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Affiliation(s)
- Tatsuya Morisaki
- Institute of Genome Architecture and Function and Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523
| | - Timothy J Stasevich
- Institute of Genome Architecture and Function and Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523
- Cell Biology Unit, Institute of Innovative Research, Tokyo Institute of Technology, Midori-ku, Yokohama, Kanagawa, 226-8503, Japan
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23
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Sugaya K. Let's think again about using mammalian temperature-sensitive mutants to investigate functional molecules-The perspectives from the studies on three mutants showing chromosome instability. J Cell Biochem 2018; 119:7143-7150. [PMID: 29943840 DOI: 10.1002/jcb.27205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 05/24/2018] [Indexed: 11/06/2022]
Abstract
This review evaluates the use of temperature-sensitive (ts) mutants to investigate functional molecules in mammalian cells. A series of studies were performed in which mammalian cells expressing functional molecules were isolated from ts mutants using complementation by the introduction and expression of the responsible protein tagged with the green fluorescent protein. The results showed that chromosome instability and cell-cycle arrest were caused by ts defects in the following three molecules: the largest subunit of RNA polymerase II, a protein involved in splicing, and ubiquitin-activating enzyme. The cells expressing functional protein were then isolated by introducing the responsible gene tagged with the green fluorescent protein to complement the ts phenotype. These cells proved to be useful in analyzing the dynamics of RNA polymerase II in living cells. Analyses of the functional interaction between proteins involved in splicing were also useful in the investigation of ts mutants and their derivatives. In addition, these cells demonstrated the functional localization of ubiquitin-activating enzyme in the nucleus. Mammalian ts mutants continue to show great potential to aid in understanding the functions of the essential molecules in cells. Therefore, it is highly important that studies on the identification and characterization of the genes responsible for the phenotype of a mutant are carried out.
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Affiliation(s)
- Kimihiko Sugaya
- Department of Molecular Imaging and Theranostics, National Institute of Radiological Sciences (NIRS), National Institutes for Quantum and Radiological Science and Technology (QST), Chiba, Japan.,Group of Quantum-state Controlled MRI, National Institutes for Quantum and Radiological Science and Technology (QST), Chiba, Japan
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24
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Conic S, Desplancq D, Ferrand A, Fischer V, Heyer V, Reina San Martin B, Pontabry J, Oulad-Abdelghani M, Babu N K, Wright GD, Molina N, Weiss E, Tora L. Imaging of native transcription factors and histone phosphorylation at high resolution in live cells. J Cell Biol 2018; 217:1537-1552. [PMID: 29440513 PMCID: PMC5881509 DOI: 10.1083/jcb.201709153] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 12/15/2017] [Accepted: 01/18/2018] [Indexed: 01/16/2023] Open
Abstract
Conic et al. introduce a versatile antibody-based imaging approach to track endogenous nuclear factors in living cells. It allows efficient intracellular delivery of any fluorescent dye–conjugated antibody, or Fab fragment, into a variety of cell types. The dynamics of nuclear targets or posttranslational modifications can be monitored with high precision using confocal and super-resolution microscopy. Fluorescent labeling of endogenous proteins for live-cell imaging without exogenous expression of tagged proteins or genetic manipulations has not been routinely possible. We describe a simple versatile antibody-based imaging approach (VANIMA) for the precise localization and tracking of endogenous nuclear factors. Our protocol can be implemented in every laboratory allowing the efficient and nonharmful delivery of organic dye-conjugated antibodies, or antibody fragments, into different metazoan cell types. Live-cell imaging permits following the labeled probes bound to their endogenous targets. By using conventional and super-resolution imaging we show dynamic changes in the distribution of several nuclear transcription factors (i.e., RNA polymerase II or TAF10), and specific phosphorylated histones (γH2AX), upon distinct biological stimuli at the nanometer scale. Hence, considering the large panel of available antibodies and the simplicity of their implementation, VANIMA can be used to uncover novel biological information based on the dynamic behavior of transcription factors or posttranslational modifications in the nucleus of single live cells.
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Affiliation(s)
- Sascha Conic
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | | | - Alexia Ferrand
- Imaging Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Veronique Fischer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Vincent Heyer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Bernardo Reina San Martin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Julien Pontabry
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France.,Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Institute of Epigenetics and Stem Cells, München, Germany
| | - Mustapha Oulad-Abdelghani
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Kishore Babu N
- School of Biological Sciences, Nanyang Technological University, Singapore
| | | | - Nacho Molina
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Etienne Weiss
- Institut de Recherche de l'ESBS, UMR 7242, Illkirch, France
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France .,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France.,School of Biological Sciences, Nanyang Technological University, Singapore
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25
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Vosnakis N, Koch M, Scheer E, Kessler P, Mély Y, Didier P, Tora L. Coactivators and general transcription factors have two distinct dynamic populations dependent on transcription. EMBO J 2017; 36:2710-2725. [PMID: 28724529 PMCID: PMC5599802 DOI: 10.15252/embj.201696035] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 06/08/2017] [Accepted: 06/15/2017] [Indexed: 12/29/2022] Open
Abstract
SAGA and ATAC are two distinct chromatin modifying co‐activator complexes with distinct enzymatic activities involved in RNA polymerase II (Pol II) transcription regulation. To investigate the mobility of co‐activator complexes and general transcription factors in live‐cell nuclei, we performed imaging experiments based on photobleaching. SAGA and ATAC, but also two general transcription factors (TFIID and TFIIB), were highly dynamic, exhibiting mainly transient associations with chromatin, contrary to Pol II, which formed more stable chromatin interactions. Fluorescence correlation spectroscopy analyses revealed that the mobile pool of the two co‐activators, as well as that of TFIID and TFIIB, can be subdivided into “fast” (free) and “slow” (chromatin‐interacting) populations. Inhibiting transcription elongation decreased H3K4 trimethylation and reduced the “slow” population of SAGA, ATAC, TFIIB and TFIID. In addition, inhibiting histone H3K4 trimethylation also reduced the “slow” populations of SAGA and ATAC. Thus, our results demonstrate that in the nuclei of live cells the equilibrium between fast and slow population of SAGA or ATAC complexes is regulated by active transcription via changes in the abundance of H3K4me3 on chromatin.
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Affiliation(s)
- Nikolaos Vosnakis
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Marc Koch
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Elisabeth Scheer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Pascal Kessler
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Yves Mély
- Université de Strasbourg, Illkirch, France.,Laboratoire de Biophotonique et Pharmacologie, Illkirch, France
| | - Pascal Didier
- Université de Strasbourg, Illkirch, France.,Laboratoire de Biophotonique et Pharmacologie, Illkirch, France
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France .,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
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26
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Brant L, Georgomanolis T, Nikolic M, Brackley CA, Kolovos P, van Ijcken W, Grosveld FG, Marenduzzo D, Papantonis A. Exploiting native forces to capture chromosome conformation in mammalian cell nuclei. Mol Syst Biol 2016; 12:891. [PMID: 27940490 PMCID: PMC5199122 DOI: 10.15252/msb.20167311] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Mammalian interphase chromosomes fold into a multitude of loops to fit the confines of cell nuclei, and looping is tightly linked to regulated function. Chromosome conformation capture (3C) technology has significantly advanced our understanding of this structure‐to‐function relationship. However, all 3C‐based methods rely on chemical cross‐linking to stabilize spatial interactions. This step remains a “black box” as regards the biases it may introduce, and some discrepancies between microscopy and 3C studies have now been reported. To address these concerns, we developed “i3C”, a novel approach for capturing spatial interactions without a need for cross‐linking. We apply i3C to intact nuclei of living cells and exploit native forces that stabilize chromatin folding. Using different cell types and loci, computational modeling, and a methylation‐based orthogonal validation method, “TALE‐iD”, we show that native interactions resemble cross‐linked ones, but display improved signal‐to‐noise ratios and are more focal on regulatory elements and CTCF sites, while strictly abiding to topologically associating domain restrictions.
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Affiliation(s)
- Lilija Brant
- Center for Molecular Medicine, University of Cologne, Cologne, Germany
| | | | - Milos Nikolic
- Center for Molecular Medicine, University of Cologne, Cologne, Germany
| | - Chris A Brackley
- School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Petros Kolovos
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Frank G Grosveld
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Davide Marenduzzo
- School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
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27
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Melnik S, Caudron-Herger M, Brant L, Carr IM, Rippe K, Cook PR, Papantonis A. Isolation of the protein and RNA content of active sites of transcription from mammalian cells. Nat Protoc 2016; 11:553-65. [DOI: 10.1038/nprot.2016.032] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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28
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Wu Z, Zhu D, Lin X, Miao J, Gu L, Deng X, Yang Q, Sun K, Zhu D, Cao X, Tsuge T, Dean C, Aoyama T, Gu H, Qu LJ. RNA Binding Proteins RZ-1B and RZ-1C Play Critical Roles in Regulating Pre-mRNA Splicing and Gene Expression during Development in Arabidopsis. THE PLANT CELL 2016; 28:55-73. [PMID: 26721863 PMCID: PMC4746689 DOI: 10.1105/tpc.15.00949] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 12/18/2015] [Accepted: 12/28/2015] [Indexed: 05/19/2023]
Abstract
Nuclear-localized RNA binding proteins are involved in various aspects of RNA metabolism, which in turn modulates gene expression. However, the functions of nuclear-localized RNA binding proteins in plants are poorly understood. Here, we report the functions of two proteins containing RNA recognition motifs, RZ-1B and RZ-1C, in Arabidopsis thaliana. RZ-1B and RZ-1C were localized to nuclear speckles and interacted with a spectrum of serine/arginine-rich (SR) proteins through their C termini. RZ-1C preferentially bound to purine-rich RNA sequences in vitro through its N-terminal RNA recognition motif. Disrupting the RNA binding activity of RZ-1C with SR proteins through overexpression of the C terminus of RZ-1C conferred defective phenotypes similar to those observed in rz-1b rz-1c double mutants, including delayed seed germination, reduced stature, and serrated leaves. Loss of function of RZ-1B and RZ-1C was accompanied by defective splicing of many genes and global perturbation of gene expression. In addition, we found that RZ-1C directly targeted FLOWERING LOCUS C (FLC), promoting efficient splicing of FLC introns and likely also repressing FLC transcription. Our findings highlight the critical role of RZ-1B/1C in regulating RNA splicing, gene expression, and many key aspects of plant development via interaction with proteins including SR proteins.
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Affiliation(s)
- Zhe Wu
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing 100871, China Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom Institute for Chemical Research, Kyoto University, Gokasho Uji, Kyoto 611-0011, Japan
| | - Danling Zhu
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing 100871, China
| | - Xiaoya Lin
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing 100871, China
| | - Jin Miao
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing 100871, China
| | - Lianfeng Gu
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fujian 350002, China
| | - Xian Deng
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qian Yang
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing 100871, China
| | - Kangtai Sun
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing 100871, China
| | - Danmeng Zhu
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing 100871, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Tomohiko Tsuge
- Institute for Chemical Research, Kyoto University, Gokasho Uji, Kyoto 611-0011, Japan
| | - Caroline Dean
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Takashi Aoyama
- Institute for Chemical Research, Kyoto University, Gokasho Uji, Kyoto 611-0011, Japan
| | - Hongya Gu
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing 100871, China National Plant Gene Research Center, Beijing 100101, China
| | - Li-Jia Qu
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing 100871, China National Plant Gene Research Center, Beijing 100101, China
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29
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Wiśniewski JR, Duś-Szachniewicz K, Ostasiewicz P, Ziółkowski P, Rakus D, Mann M. Absolute Proteome Analysis of Colorectal Mucosa, Adenoma, and Cancer Reveals Drastic Changes in Fatty Acid Metabolism and Plasma Membrane Transporters. J Proteome Res 2015; 14:4005-18. [PMID: 26245529 DOI: 10.1021/acs.jproteome.5b00523] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Colorectal cancer is a leading cause of cancer-related death. It develops from normal enterocytes, through a benign adenoma stage, into the cancer and finally into the metastatic form. We previously compared the proteomes of normal colorectal enterocytes, cancer and nodal metastasis to a depth of 8100 proteins and found extensive quantitative remodeling between normal and cancer tissues but not cancer and metastasis (Wiśniewski et al. PMID 22968445). Here we utilize advances in the proteomic workflow to perform an in depth analysis of the normal tissue (N), the adenoma (A), and the cancer (C). Absolute proteomics of 10 000 proteins per patient from microdissected formalin-fixed and paraffin-embedded clinical material established a quantitative protein repository of the disease. Between N and A, 23% of all proteins changed significantly, 17.8% from A to C and 21.6% from N to C. Together with principal component analysis of the patient groups, this suggests that N, A, and C are equidistant but not on one developmental line. Our proteomics approach allowed us to assess changes in varied cell size, the composition of different subcellular components, and alterations in basic biological processes including the energy metabolism, plasma membrane transport, DNA replication, and transcription. This revealed several-fold higher concentrations of enzymes in fatty acid metabolism in C compared with N, and unexpectedly, the same held true of plasma membrane transporters.
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Affiliation(s)
- Jacek R Wiśniewski
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry , Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Kamila Duś-Szachniewicz
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry , Am Klopferspitz 18, 82152 Martinsried, Germany.,Department of Pathology, Wrocław Medical University , 50-368 Wrocław, Poland
| | - Paweł Ostasiewicz
- Department of Pathology, Wrocław Medical University , 50-368 Wrocław, Poland
| | - Piotr Ziółkowski
- Department of Pathology, Wrocław Medical University , 50-368 Wrocław, Poland
| | - Dariusz Rakus
- Department of Animal Molecular Physiology, Wroclaw University , 50-205 Wrocław, Poland
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry , Am Klopferspitz 18, 82152 Martinsried, Germany
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30
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Werner MS, Ruthenburg AJ. Nuclear Fractionation Reveals Thousands of Chromatin-Tethered Noncoding RNAs Adjacent to Active Genes. Cell Rep 2015; 12:1089-98. [PMID: 26257179 DOI: 10.1016/j.celrep.2015.07.033] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 07/02/2015] [Accepted: 07/14/2015] [Indexed: 01/09/2023] Open
Abstract
A number of long noncoding RNAs (lncRNAs) have been reported to regulate transcription via recruitment of chromatin modifiers or bridging distal enhancer elements to gene promoters. However, the generality of these modes of regulation and the mechanisms of chromatin attachment for thousands of unstudied human lncRNAs remain unclear. To address these questions, we performed stringent nuclear fractionation coupled to RNA sequencing. We provide genome-wide identification of human chromatin-associated lncRNAs and demonstrate tethering of RNA to chromatin by RNAPII is a pervasive mechanism of attachment. We also uncovered thousands of chromatin-enriched RNAs (cheRNAs) that share molecular properties with known lncRNAs. Although distinct from eRNAs derived from active prototypical enhancers, the production of cheRNAs is strongly correlated with the expression of neighboring protein-coding genes. This work provides an updated framework for nuclear RNA organization that includes a large chromatin-associated transcript population correlated with active genes and may prove useful in de novo enhancer annotation.
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Affiliation(s)
- Michael S Werner
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Alexander J Ruthenburg
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA; Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA.
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31
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Kimura H, Hayashi-Takanaka Y, Stasevich TJ, Sato Y. Visualizing posttranslational and epigenetic modifications of endogenous proteins in vivo. Histochem Cell Biol 2015; 144:101-9. [PMID: 26138929 PMCID: PMC4522274 DOI: 10.1007/s00418-015-1344-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2015] [Indexed: 01/29/2023]
Abstract
Protein localization and dynamics can now be visualized in living cells using the fluorescent protein fusion technique, but it is still difficult to selectively detect molecules with a specific function. As a posttranslational protein modification is often associated with a specific function, marking specifically modified protein molecules in living cells is a way to track an important fraction of protein. In the nucleus, histones are subjected to a variety of modifications such as acetylation and methylation that are associated with epigenetic gene regulation. RNA polymerase II, an enzyme that transcribes genes, is also differentially phosphorylated during the initiation and elongation of transcription. To understand the mechanism of gene regulation in vivo, we have developed methods to track histone and RNA polymerase II modifications using probes derived from modification-specific monoclonal antibodies. In Fab-based live endogenous modification labeling (FabLEM), fluorescently labeled antigen-binding fragments (Fabs) are loaded into cells. Fabs bind to target modifications in the nucleus with a binding time of a second to tens of seconds, and so the modification can be tracked without disturbing cell function. For tracking over longer periods of time or in living animals, we have also developed a genetically encoded system to express a modification-specific intracellular antibody (mintbody). Transgenic fruit fly and zebrafish that express histone H3 Lys9 acetylation-specific mintbody developed normally and remain fertile, suggesting that visualizing histone modifications in any tissue in live animals has become possible. These live cell modification tracking techniques will facilitate future studies on epigenetic regulation related to development, differentiation, and disease. Moreover, these techniques can be applied to any other protein modification, opening up new avenues in broad areas in biology and medicine.
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Affiliation(s)
- Hiroshi Kimura
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8501, Japan,
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32
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Sugaya K, Ishihara Y, Inoue S. Nuclear localization of ubiquitin-activating enzyme Uba1 is characterized in its mammalian temperature-sensitive mutant. Genes Cells 2015; 20:659-66. [PMID: 26059705 DOI: 10.1111/gtc.12257] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 05/12/2015] [Indexed: 11/26/2022]
Abstract
In our previous study, a point mutation in Uba1, the gene encoding ubiquitin-activating enzyme, was identified in temperature-sensitive (ts) CHO-K1 mutant tsTM3 cells, which led to a Met-to-Ile substitution at amino acid 256 in Uba1 protein. Characterization of this mutant revealed a deficiency of nuclear Uba1 and impaired ubiquitination in the nucleus. The ts defects in tsTM3 were complemented by the expression of the wild-type Uba1 tagged with green fluorescent protein (GFP). In this study, the expression and localization of Uba1 were investigated using the various forms of Uba1 tagged with GFP. Western blot analysis and confocal microscopy revealed that nuclear localization of Uba1, as well as even the modified and truncated forms of Uba1, appears to be essential to rescue tsTM3 cells. The localization of Uba1 in the nucleus, even if it was a small amount, was proportional to the efficiency of complementation of tsTM3 cells. Uba1 plays an important role in the nucleus, and a ts mutation found in tsTM3 cells appears to result in the loss of localization of Uba1 in the nucleus.
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Affiliation(s)
- Kimihiko Sugaya
- Research Center for Radiation Protection and Fukushima Project Headquarters, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba, 263-8555, Japan
| | - Yoshie Ishihara
- Research Center for Radiation Protection and Fukushima Project Headquarters, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba, 263-8555, Japan
| | - Sonoe Inoue
- Research Center for Radiation Protection and Fukushima Project Headquarters, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba, 263-8555, Japan
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33
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Simon TW, Budinsky RA, Rowlands JC. A model for aryl hydrocarbon receptor-activated gene expression shows potency and efficacy changes and predicts squelching due to competition for transcription co-activators. PLoS One 2015; 10:e0127952. [PMID: 26039703 PMCID: PMC4454675 DOI: 10.1371/journal.pone.0127952] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 04/22/2015] [Indexed: 12/17/2022] Open
Abstract
A stochastic model of nuclear receptor-mediated transcription was developed based on activation of the aryl hydrocarbon receptor (AHR) by 2,3,7,8-tetrachlorodibenzodioxin (TCDD) and subsequent binding the activated AHR to xenobiotic response elements (XREs) on DNA. The model was based on effects observed in cells lines commonly used as in vitro experimental systems. Following ligand binding, the AHR moves into the cell nucleus and forms a heterodimer with the aryl hydrocarbon nuclear translocator (ARNT). In the model, a requirement for binding to DNA is that a generic coregulatory protein is subsequently bound to the AHR-ARNT dimer. Varying the amount of coregulator available within the nucleus altered both the potency and efficacy of TCDD for inducing for transcription of CYP1A1 mRNA, a commonly used marker for activation of the AHR. Lowering the amount of available cofactor slightly increased the EC50 for the transcriptional response without changing the efficacy or maximal response. Further reduction in the amount of cofactor reduced the efficacy and produced non-monotonic dose-response curves (NMDRCs) at higher ligand concentrations. The shapes of these NMDRCs were reminiscent of the phenomenon of squelching. Resource limitations for transcriptional machinery are becoming apparent in eukaryotic cells. Within single cells, nuclear receptor-mediated gene expression appears to be a stochastic process; however, intercellular communication and other aspects of tissue coordination may represent a compensatory process to maintain an organism’s ability to respond on a phenotypic level to various stimuli within an inconstant environment.
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Affiliation(s)
- Ted W. Simon
- Ted Simon LLC, Winston, GA, United States of America
- * E-mail:
| | - Robert A. Budinsky
- The Dow Chemical Company, Toxicology and Environmental Research & Consulting. Midland, MI, United States of America
| | - J. Craig Rowlands
- The Dow Chemical Company, Toxicology and Environmental Research & Consulting. Midland, MI, United States of America
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34
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Padovan-Merhar O, Nair GP, Biaesch AG, Mayer A, Scarfone S, Foley SW, Wu AR, Churchman LS, Singh A, Raj A. Single mammalian cells compensate for differences in cellular volume and DNA copy number through independent global transcriptional mechanisms. Mol Cell 2015; 58:339-52. [PMID: 25866248 DOI: 10.1016/j.molcel.2015.03.005] [Citation(s) in RCA: 289] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 01/16/2015] [Accepted: 03/04/2015] [Indexed: 10/23/2022]
Abstract
Individual mammalian cells exhibit large variability in cellular volume, even with the same absolute DNA content, and so must compensate for differences in DNA concentration in order to maintain constant concentration of gene expression products. Using single-molecule counting and computational image analysis, we show that transcript abundance correlates with cellular volume at the single-cell level due to increased global transcription in larger cells. Cell fusion experiments establish that increased cellular content itself can directly increase transcription. Quantitative analysis shows that this mechanism measures the ratio of cellular volume to DNA content, most likely through sequestration of a transcriptional factor to DNA. Analysis of transcriptional bursts reveals a separate mechanism for gene dosage compensation after DNA replication that enables proper transcriptional output during early and late S phase. Our results provide a framework for quantitatively understanding the relationships among DNA content, cell size, and gene expression variability in single cells.
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Affiliation(s)
- Olivia Padovan-Merhar
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gautham P Nair
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrew G Biaesch
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andreas Mayer
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Steven Scarfone
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shawn W Foley
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Angela R Wu
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | | | - Abhyudai Singh
- Department of Electrical and Computer Engineering, University of Delaware, Newark, DE 19716, USA
| | - Arjun Raj
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA.
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35
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Abstract
The different cell types of an organism share the same DNA, but during cell differentiation their genomes undergo diverse structural and organizational changes that affect gene expression and other cellular functions. These can range from large-scale folding of whole chromosomes or of smaller genomic regions, to the re-organization of local interactions between enhancers and promoters, mediated by the binding of transcription factors and chromatin looping. The higher-order organization of chromatin is also influenced by the specificity of the contacts that it makes with nuclear structures such as the lamina. Sophisticated methods for mapping chromatin contacts are generating genome-wide data that provide deep insights into the formation of chromatin interactions, and into their roles in the organization and function of the eukaryotic cell nucleus.
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36
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Roy AL, Singer DS. Core promoters in transcription: old problem, new insights. Trends Biochem Sci 2015; 40:165-71. [PMID: 25680757 DOI: 10.1016/j.tibs.2015.01.007] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 01/09/2015] [Accepted: 01/15/2015] [Indexed: 12/11/2022]
Abstract
Early studies established that transcription initiates within an approximately 50 bp DNA segment capable of nucleating the assembly of RNA polymerase II (Pol II) and associated general transcription factors (GTFs) necessary for transcriptional initiation; this region is called a core promoter. Subsequent analyses identified a series of conserved DNA sequence elements, present in various combinations or not at all, in core promoters. Recent genome-wide analyses have provided further insights into the complexity of core promoter architecture and function. Here we review recent studies that delineate the active role of core promoters in the transcriptional regulation of diverse physiological systems.
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Affiliation(s)
- Ananda L Roy
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, MA, USA.
| | - Dinah S Singer
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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37
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Stasevich TJ, Hayashi-Takanaka Y, Sato Y, Maehara K, Ohkawa Y, Sakata-Sogawa K, Tokunaga M, Nagase T, Nozaki N, McNally JG, Kimura H. Regulation of RNA polymerase II activation by histone acetylation in single living cells. Nature 2014; 516:272-5. [PMID: 25252976 DOI: 10.1038/nature13714] [Citation(s) in RCA: 191] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 07/25/2014] [Indexed: 12/31/2022]
Abstract
In eukaryotic cells, post-translational histone modifications have an important role in gene regulation. Starting with early work on histone acetylation, a variety of residue-specific modifications have now been linked to RNA polymerase II (RNAP2) activity, but it remains unclear if these markers are active regulators of transcription or just passive byproducts. This is because studies have traditionally relied on fixed cell populations, meaning temporal resolution is limited to minutes at best, and correlated factors may not actually be present in the same cell at the same time. Complementary approaches are therefore needed to probe the dynamic interplay of histone modifications and RNAP2 with higher temporal resolution in single living cells. Here we address this problem by developing a system to track residue-specific histone modifications and RNAP2 phosphorylation in living cells by fluorescence microscopy. This increases temporal resolution to the tens-of-seconds range. Our single-cell analysis reveals histone H3 lysine-27 acetylation at a gene locus can alter downstream transcription kinetics by as much as 50%, affecting two temporally separate events. First acetylation enhances the search kinetics of transcriptional activators, and later the acetylation accelerates the transition of RNAP2 from initiation to elongation. Signatures of the latter can be found genome-wide using chromatin immunoprecipitation followed by sequencing. We argue that this regulation leads to a robust and potentially tunable transcriptional response.
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Affiliation(s)
- Timothy J Stasevich
- 1] Graduate School of Frontier Biosciences, Osaka University, Osaka, 565-0871, Japan [2] Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, USA [3] Transcription Imaging Consortium, Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA
| | - Yoko Hayashi-Takanaka
- 1] Graduate School of Frontier Biosciences, Osaka University, Osaka, 565-0871, Japan [2] Japan Science and Technology Agency (JST), Core Research for Evolutional Science and Technology (CREST), Kawaguchi, Saitama, 332-0012, Japan [3] Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Yuko Sato
- 1] Graduate School of Frontier Biosciences, Osaka University, Osaka, 565-0871, Japan [2] Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Kazumitsu Maehara
- Department of Advanced Medical Initiatives, Faculty of Medicine, Kyushu University, Fukuoka, 812-8582, Japan
| | - Yasuyuki Ohkawa
- 1] Japan Science and Technology Agency (JST), Core Research for Evolutional Science and Technology (CREST), Kawaguchi, Saitama, 332-0012, Japan [2] Department of Advanced Medical Initiatives, Faculty of Medicine, Kyushu University, Fukuoka, 812-8582, Japan
| | - Kumiko Sakata-Sogawa
- 1] Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan [2] RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, 230-0045, Japan
| | - Makio Tokunaga
- 1] Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan [2] RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, 230-0045, Japan
| | - Takahiro Nagase
- Department of Biotechnology Research, Kazusa DNA Research Institute, Chiba, 292-0818, Japan
| | | | - James G McNally
- 1] Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA [2] Institute for Soft Matter and Functional Materials, Helmholtz Zentrum Berlin, Berlin, 14109, Germany
| | - Hiroshi Kimura
- 1] Graduate School of Frontier Biosciences, Osaka University, Osaka, 565-0871, Japan [2] Japan Science and Technology Agency (JST), Core Research for Evolutional Science and Technology (CREST), Kawaguchi, Saitama, 332-0012, Japan [3] Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
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Stasevich TJ, Sato Y, Nozaki N, Kimura H. Quantifying histone and RNA polymerase II post-translational modification dynamics in mother and daughter cells. Methods 2014; 70:77-88. [PMID: 25131722 DOI: 10.1016/j.ymeth.2014.08.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 07/18/2014] [Accepted: 08/04/2014] [Indexed: 01/21/2023] Open
Abstract
Post-translational histone modifications are highly correlated with transcriptional activity, but the relative timing of these marks and their dynamic interplay during gene regulation remains controversial. To shed light on this problem and clarify the connections between histone modifications and transcription, we demonstrate how FabLEM (Fab-based Live Endogenous Modification labeling) can be used to simultaneously track histone H3 Lysine 9 acetylation (H3K9ac) together with RNA polymerase II Serine 2 and Serine 5 phosphorylation (RNAP2 Ser2ph/Ser5ph) in single living cells and their progeny. We provide a detailed description of the FabLEM methodology, including helpful tips for preparing and loading fluorescently conjugated antigen binding fragments (Fab) into cells for optimal results. We also introduce simple procedures for analyzing and visualizing FabLEM data, including color-coded scatterplots to track correlations between modifications through the cell cycle and temporal cross-correlation analysis to dissect modification dynamics. Using these methods, we find significant correlations that span cell generations, with a relatively strong correlation between H3K9ac and Ser5ph that appears to peak a few hours before mitosis and may reflect the bookmarking of genes for efficient re-initiation following mitosis. The techniques we have developed are broadly applicable and should help clarify how histone modifications dynamically contribute to gene regulation.
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Affiliation(s)
- Timothy J Stasevich
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan; Dept. of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA; Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA.
| | - Yuko Sato
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
| | | | - Hiroshi Kimura
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan; Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan.
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Sugaya K, Ishihara Y, Inoue S, Tsuji H. Characterization of ubiquitin-activating enzyme Uba1 in the nucleus by its mammalian temperature-sensitive mutant. PLoS One 2014; 9:e96666. [PMID: 24805847 PMCID: PMC4013028 DOI: 10.1371/journal.pone.0096666] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2013] [Accepted: 04/10/2014] [Indexed: 12/16/2022] Open
Abstract
Temperature-sensitive (ts) CHO-K1 mutant tsTM3 exhibits chromosomal instability and cell-cycle arrest in the S to G2 phases with decreased DNA synthesis at the nonpermissive temperature, 39°C. Previously, complementation tests with other mutants showed that tsTM3 harbors a genetic defect in the ubiquitin-activating enzyme Uba1. Sequence comparison of the Uba1 gene between wild-type and mutant cells in this study revealed that the mutant phenotype is caused by a G-to-A transition that yields a Met-to-Ile substitution at position 256 in hamster Uba1. The ts defects in tsTM3 were complemented by expression of the wild-type Uba1 tagged with green fluorescent protein. Expression of the Uba1 primarily in the nucleus appeared to rescue tsTM3 cells. Incubation at 39°C resulted in a decrease of nuclear Uba1 in tsTM3 cells, suggesting that loss of Uba1 in the nucleus may lead to the ts defects. Analyses with the fluorescent ubiquitination-based cell cycle indicator revealed that loss of function of Uba1 leads to failure of the ubiquitin system in the nucleus. Incubation at 39°C caused an increase in endogenous geminin in tsTM3 cells. A ts mutation of Uba1 found in tsTM3 cells appears to be a novel mutation reflecting the important roles of Uba1 in nucleus.
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Affiliation(s)
- Kimihiko Sugaya
- Research Center for Radiation Protection, National Institute of Radiological Sciences, Chiba, Japan
- Fukushima Project Headquarters, National Institute of Radiological Sciences, Chiba, Japan
- * E-mail:
| | - Yoshie Ishihara
- Research Center for Radiation Protection, National Institute of Radiological Sciences, Chiba, Japan
- Fukushima Project Headquarters, National Institute of Radiological Sciences, Chiba, Japan
| | - Sonoe Inoue
- Research Center for Radiation Protection, National Institute of Radiological Sciences, Chiba, Japan
- Fukushima Project Headquarters, National Institute of Radiological Sciences, Chiba, Japan
| | - Hideo Tsuji
- Fukushima Project Headquarters, National Institute of Radiological Sciences, Chiba, Japan
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40
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Weber CM, Ramachandran S, Henikoff S. Nucleosomes are context-specific, H2A.Z-modulated barriers to RNA polymerase. Mol Cell 2014; 53:819-30. [PMID: 24606920 DOI: 10.1016/j.molcel.2014.02.014] [Citation(s) in RCA: 263] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 11/04/2013] [Accepted: 01/28/2014] [Indexed: 01/03/2023]
Abstract
Nucleosomes are barriers to transcription in vitro; however, their effects on RNA polymerase in vivo are unknown. Here we describe a simple and general strategy to comprehensively map the positions of elongating and arrested RNA polymerase II (RNAPII) at nucleotide resolution. We find that the entry site of the first (+1) nucleosome is a barrier to RNAPII for essentially all genes, including those undergoing regulated pausing farther upstream. In contrast to the +1 nucleosome, gene body nucleosomes are low barriers and cause RNAPII stalling both at the entry site and near the dyad axis. The extent of the +1 nucleosome barrier correlates with nucleosome occupancy but anticorrelates with enrichment of histone variant H2A.Z. Importantly, depletion of H2A.Z from a nucleosome position results in a higher barrier to RNAPII. Our results suggest that nucleosomes present significant, context-specific barriers to RNAPII in vivo that can be tuned by the incorporation of H2A.Z.
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Affiliation(s)
- Christopher M Weber
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Srinivas Ramachandran
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Steven Henikoff
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
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41
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Li JJ, Bickel PJ, Biggin MD. System wide analyses have underestimated protein abundances and the importance of transcription in mammals. PeerJ 2014; 2:e270. [PMID: 24688849 PMCID: PMC3940484 DOI: 10.7717/peerj.270] [Citation(s) in RCA: 207] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 01/22/2014] [Indexed: 12/17/2022] Open
Abstract
Large scale surveys in mammalian tissue culture cells suggest that the protein expressed at the median abundance is present at 8,000–16,000 molecules per cell and that differences in mRNA expression between genes explain only 10–40% of the differences in protein levels. We find, however, that these surveys have significantly underestimated protein abundances and the relative importance of transcription. Using individual measurements for 61 housekeeping proteins to rescale whole proteome data from Schwanhausser et al. (2011), we find that the median protein detected is expressed at 170,000 molecules per cell and that our corrected protein abundance estimates show a higher correlation with mRNA abundances than do the uncorrected protein data. In addition, we estimated the impact of further errors in mRNA and protein abundances using direct experimental measurements of these errors. The resulting analysis suggests that mRNA levels explain at least 56% of the differences in protein abundance for the 4,212 genes detected by Schwanhausser et al. (2011), though because one major source of error could not be estimated the true percent contribution should be higher. We also employed a second, independent strategy to determine the contribution of mRNA levels to protein expression. We show that the variance in translation rates directly measured by ribosome profiling is only 12% of that inferred by Schwanhausser et al. (2011), and that the measured and inferred translation rates correlate poorly (R2 = 0.13). Based on this, our second strategy suggests that mRNA levels explain ∼81% of the variance in protein levels. We also determined the percent contributions of transcription, RNA degradation, translation and protein degradation to the variance in protein abundances using both of our strategies. While the magnitudes of the two estimates vary, they both suggest that transcription plays a more important role than the earlier studies implied and translation a much smaller role. Finally, the above estimates only apply to those genes whose mRNA and protein expression was detected. Based on a detailed analysis by Hebenstreit et al. (2012), we estimate that approximately 40% of genes in a given cell within a population express no mRNA. Since there can be no translation in the absence of mRNA, we argue that differences in translation rates can play no role in determining the expression levels for the ∼40% of genes that are non-expressed.
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Affiliation(s)
- Jingyi Jessica Li
- Department of Statistics, University of California , Berkeley, CA , USA ; Departments of Statistics and Human Genetics, University of California , Los Angeles, CA , USA
| | - Peter J Bickel
- Department of Statistics, University of California , Berkeley, CA , USA
| | - Mark D Biggin
- Genomics Division, Lawrence Berkeley National Laboratory , Berkeley, CA , USA
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42
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Corden JL. RNA polymerase II C-terminal domain: Tethering transcription to transcript and template. Chem Rev 2013; 113:8423-55. [PMID: 24040939 PMCID: PMC3988834 DOI: 10.1021/cr400158h] [Citation(s) in RCA: 126] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jeffry L Corden
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine , 725 North Wolfe Street, Baltimore Maryland 21205, United States
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43
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Papantonis A, Cook PR. Transcription factories: genome organization and gene regulation. Chem Rev 2013; 113:8683-705. [PMID: 23597155 DOI: 10.1021/cr300513p] [Citation(s) in RCA: 159] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Argyris Papantonis
- Sir William Dunn School of Pathology, University of Oxford , South Parks Road, Oxford OX1 3RE, United Kingdom
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44
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Ghamari A, van de Corput MP, Thongjuea S, van Cappellen WA, van IJcken W, van Haren J, Soler E, Eick D, Lenhard B, Grosveld FG. In vivo live imaging of RNA polymerase II transcription factories in primary cells. Genes Dev 2013; 27:767-77. [PMID: 23592796 PMCID: PMC3639417 DOI: 10.1101/gad.216200.113] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 03/18/2013] [Indexed: 11/24/2022]
Abstract
Transcription steps are marked by different modifications of the C-terminal domain of RNA polymerase II (RNAPII). Phosphorylation of Ser5 and Ser7 by cyclin-dependent kinase 7 (CDK7) as part of TFIIH marks initiation, whereas phosphorylation of Ser2 by CDK9 marks elongation. These processes are thought to take place in localized transcription foci in the nucleus, known as "transcription factories," but it has been argued that the observed clusters/foci are mere fixation or labeling artifacts. We show that transcription factories exist in living cells as distinct foci by live-imaging fluorescently labeled CDK9, a kinase known to associate with active RNAPII. These foci were observed in different cell types derived from CDK9-mCherry knock-in mice. We show that these foci are very stable while highly dynamic in exchanging CDK9. Chromatin immunoprecipitation (ChIP) coupled with deep sequencing (ChIP-seq) data show that the genome-wide binding sites of CDK9 and initiating RNAPII overlap on transcribed genes. Immunostaining shows that CDK9-mCherry foci colocalize with RNAPII-Ser5P, much less with RNAPII-Ser2P, and not with CDK12 (a kinase reported to be involved in the Ser2 phosphorylation) or with splicing factor SC35. In conclusion, transcription factories exist in living cells, and initiation and elongation of transcripts takes place in different nuclear compartments.
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Affiliation(s)
- Alireza Ghamari
- Department of Cell Biology, Erasmus Medical Center, 3015GE Rotterdam, the Netherlands
| | | | - Supat Thongjuea
- Computational Biology Unit-Bergen Centre for Computational Science
- Sars Centre for Marine Molecular Biology, University of Bergen, N-5008 Bergen, Norway
| | - Wiggert A. van Cappellen
- Department of Reproduction and Development, Erasmus Medical Center, 3015GE Rotterdam, the Netherlands
| | - Wilfred van IJcken
- Biomics Department, Erasmus Medical Center, 3015GE, Rotterdam, the Netherlands
| | - Jeffrey van Haren
- Department of Cell Biology, Erasmus Medical Center, 3015GE Rotterdam, the Netherlands
| | - Eric Soler
- Department of Cell Biology, Erasmus Medical Center, 3015GE Rotterdam, the Netherlands
| | - Dirk Eick
- Department of Molecular Epigenetics, Helmholtz Zentrum München, Center of Integrated Protein Science (CIPSM), D-81377 Munich, Germany
| | - Boris Lenhard
- Computational Biology Unit-Bergen Centre for Computational Science
- Sars Centre for Marine Molecular Biology, University of Bergen, N-5008 Bergen, Norway
| | - Frank G. Grosveld
- Department of Cell Biology, Erasmus Medical Center, 3015GE Rotterdam, the Netherlands
- Centre for Biomedical Genetics, 3015GE Rotterdam, the Netherlands
- Cancer Genomics Centre, 3015GE Rotterdam, the Netherlands
- Netherlands Consortium for Systems Biology, 3015GE Rotterdam, the Netherlands
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45
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RNA polymerase II acts as an RNA-dependent RNA polymerase to extend and destabilize a non-coding RNA. EMBO J 2013; 32:781-90. [PMID: 23395899 DOI: 10.1038/emboj.2013.18] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Accepted: 01/03/2013] [Indexed: 11/09/2022] Open
Abstract
RNA polymerase II (Pol II) is a well-characterized DNA-dependent RNA polymerase, which has also been reported to have RNA-dependent RNA polymerase (RdRP) activity. Natural cellular RNA substrates of mammalian Pol II, however, have not been identified and the cellular function of the Pol II RdRP activity is unknown. We found that Pol II can use a non-coding RNA, B2 RNA, as both a substrate and a template for its RdRP activity. Pol II extends B2 RNA by 18 nt on its 3'-end in an internally templated reaction. The RNA product resulting from extension of B2 RNA by the Pol II RdRP can be removed from Pol II by a factor present in nuclear extracts. Treatment of cells with α-amanitin or actinomycin D revealed that extension of B2 RNA by Pol II destabilizes the RNA. Our studies provide compelling evidence that mammalian Pol II acts as an RdRP to control the stability of a cellular RNA by extending its 3'-end.
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46
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Davidson S, Macpherson N, Mitchell JA. Nuclear organization of RNA polymerase II transcription. Biochem Cell Biol 2013; 91:22-30. [PMID: 23442138 DOI: 10.1139/bcb-2012-0059] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Transcription occurs at distinct nuclear compartments termed transcription factories that are specialized for transcription by 1 of the 3 polymerase complexes (I, II, or III). Protein-coding genes appear to move in and out of RNA polymerase II (RNAPII) compartments as they are expressed and silenced. In addition, transcription factories are sites where several transcription units, either from the same chromosome or different chromosomes, are transcribed. Chromosomes occupy distinct territories in the interphase nucleus with active genes preferentially positioned on the periphery or even looped out of the territory. These chromosome territories have been observed to intermingle in the nucleus, and multiple interactions among different chromosomes have been identified in genome-wide studies. Deep sequencing of the transcriptome and RNAPII associated on DNA obtained by chromatin immunoprecipitation have revealed a plethora of noncoding transcription and intergenic accumulations of RNAPII that must also be considered in models of genome function. The organization of transcription into distinct regions of the nucleus has changed the way we view transcription with the evolving model for silencing or activation of gene expression involving physical relocation of the transcription unit to a silencing or activation compartment, thus, highlighting the need to consider the process of transcription in the 3-dimensional nuclear space.
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Affiliation(s)
- Scott Davidson
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON M5S 3G5, Canada
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47
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Osakabe A, Tachiwana H, Takaku M, Hori T, Obuse C, Kimura H, Fukagawa T, Kurumizaka H. Vertebrate Spt2 is a novel nucleolar histone chaperone that assists in ribosomal DNA transcription. J Cell Sci 2013; 126:1323-32. [PMID: 23378026 DOI: 10.1242/jcs.112623] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In eukaryotes, transcription occurs in the chromatin context with the assistance of histone-binding proteins, such as chromatin/nucleosome remodeling factors and histone chaperones. However, it is unclear how each remodeling factor or histone chaperone functions in transcription. Here, we identify a novel histone-binding protein, Spt2, in higher eukaryotes. Recombinant human Spt2 binds to histones and DNA, and promotes nucleosome assembly in vitro. Spt2 accumulates in nucleoli and interacts with RNA polymerase I in chicken DT40 cells, suggesting its involvement in ribosomal RNA transcription. Consistently, Spt2-deficient chicken DT40 cells are sensitive to RNA polymerase I inhibitors and exhibit decreased transcription activity, as shown by a transcription run-on assay. Domain analyses of Spt2 revealed that the C-terminal region, containing the region homologous to yeast Spt2, is responsible for histone binding, while the central region is essential for nucleolar localization and DNA binding. Based on these results, we conclude that vertebrate Spt2 is a novel histone chaperone with a separate DNA-binding domain that facilitates ribosomal DNA transcription through chromatin remodeling during transcription.
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Affiliation(s)
- Akihisa Osakabe
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
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48
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Extensive quantitative remodeling of the proteome between normal colon tissue and adenocarcinoma. Mol Syst Biol 2013; 8:611. [PMID: 22968445 PMCID: PMC3472694 DOI: 10.1038/msb.2012.44] [Citation(s) in RCA: 181] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Accepted: 08/08/2012] [Indexed: 12/15/2022] Open
Abstract
In-depth proteomic analysis of microdissected colorectal cancer identifies extensive alterations in the cell-surface and nuclear proteomes between normal mucosa and adenocarcinoma, but observes strikingly little proteomic change between cancer and metastases. ![]()
First large-scale proteomic analysis of microdissected tissue from archival formalin-fixed and paraffin-embedded material. Quantitation of 7576 proteins between patient-matched samples of normal colonic mucosa, primary cancer, and nodal metastasis. Expression levels of 1808 proteins changed significantly between normal and cancer tissues. Total Protein Approach (TPA)—a new way to determine protein copy numbers per cell without protein standards.
We report a proteomic analysis of microdissected material from formalin-fixed and paraffin-embedded colorectal cancer, quantifying >7500 proteins between patient matched normal mucosa, primary carcinoma, and nodal metastases. Expression levels of 1808 proteins changed significantly between normal and cancer tissues, a much larger fraction than that reported in transcript-based studies. Tumor cells exhibit extensive alterations in the cell-surface and nuclear proteomes. Functionally similar changes in the proteome were observed comparing rapidly growing and differentiated CaCo-2 cells. In contrast, there was minimal proteomic remodeling between primary cancer and metastases, suggesting that no drastic proteome changes are necessary for the tumor to propagate in a different tissue context. Additionally, we introduce a new way to determine protein copy numbers per cell without protein standards. Copy numbers estimated in enterocytes and cancer cells are in good agreement with CaCo-2 and HeLa cells and with the literature data. Our proteomic data set furthermore allows mapping quantitative changes of functional protein classes, enabling novel insights into the biology of colon cancer.
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49
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Steffen PA, Fonseca JP, Ringrose L. Epigenetics meets mathematics: towards a quantitative understanding of chromatin biology. Bioessays 2012; 34:901-13. [PMID: 22911103 DOI: 10.1002/bies.201200076] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
How fast? How strong? How many? So what? Why do numbers matter in biology? Chromatin binding proteins are forever in motion, exchanging rapidly between bound and free pools. How do regulatory systems whose components are in constant flux ensure stability and flexibility? This review explores the application of quantitative and mathematical approaches to mechanisms of epigenetic regulation. We discuss methods for measuring kinetic parameters and protein quantities in living cells, and explore the insights that have been gained by quantifying and modelling dynamics of chromatin binding proteins.
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50
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Möller A, Xie SQ, Hosp F, Lang B, Phatnani HP, James S, Ramirez F, Collin GB, Naggert JK, Babu MM, Greenleaf AL, Selbach M, Pombo A. Proteomic analysis of mitotic RNA polymerase II reveals novel interactors and association with proteins dysfunctional in disease. Mol Cell Proteomics 2012; 11:M111.011767. [PMID: 22199231 PMCID: PMC3433901 DOI: 10.1074/mcp.m111.011767] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Revised: 11/19/2011] [Indexed: 11/06/2022] Open
Abstract
RNA polymerase II (RNAPII) transcribes protein-coding genes in eukaryotes and interacts with factors involved in chromatin remodeling, transcriptional activation, elongation, and RNA processing. Here, we present the isolation of native RNAPII complexes using mild extraction conditions and immunoaffinity purification. RNAPII complexes were extracted from mitotic cells, where they exist dissociated from chromatin. The proteomic content of native complexes in total and size-fractionated extracts was determined using highly sensitive LC-MS/MS. Protein associations with RNAPII were validated by high-resolution immunolocalization experiments in both mitotic cells and in interphase nuclei. Functional assays of transcriptional activity were performed after siRNA-mediated knockdown. We identify >400 RNAPII associated proteins in mitosis, among these previously uncharacterized proteins for which we show roles in transcriptional elongation. We also identify, as novel functional RNAPII interactors, two proteins involved in human disease, ALMS1 and TFG, emphasizing the importance of gene regulation for normal development and physiology.
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Affiliation(s)
- André Möller
- From the ‡MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital Campus, London W12 0NN, United Kingdom
| | - Sheila Q. Xie
- From the ‡MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital Campus, London W12 0NN, United Kingdom
| | - Fabian Hosp
- §Max-Delbrück Center for Molecular Medicine, 13092 Berlin, Germany
| | - Benjamin Lang
- ¶MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Hemali P. Phatnani
- ‖Department of Biochemistry, Duke University, Medical Center, Durham, North Carolina 27710
| | - Sonya James
- From the ‡MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital Campus, London W12 0NN, United Kingdom
| | | | | | | | - M. Madan Babu
- ¶MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Arno L. Greenleaf
- ‖Department of Biochemistry, Duke University, Medical Center, Durham, North Carolina 27710
| | - Matthias Selbach
- §Max-Delbrück Center for Molecular Medicine, 13092 Berlin, Germany
| | - Ana Pombo
- From the ‡MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital Campus, London W12 0NN, United Kingdom
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