1
|
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.
Collapse
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
| |
Collapse
|
2
|
Willemin A, Szabó D, Pombo A. Epigenetic regulatory layers in the 3D nucleus. Mol Cell 2024; 84:415-428. [PMID: 38242127 PMCID: PMC10872226 DOI: 10.1016/j.molcel.2023.12.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 11/21/2023] [Accepted: 12/15/2023] [Indexed: 01/21/2024]
Abstract
Nearly 7 decades have elapsed since Francis Crick introduced the central dogma of molecular biology, as part of his ideas on protein synthesis, setting the fundamental rules of sequence information transfer from DNA to RNAs and proteins. We have since learned that gene expression is finely tuned in time and space, due to the activities of RNAs and proteins on regulatory DNA elements, and through cell-type-specific three-dimensional conformations of the genome. Here, we review major advances in genome biology and discuss a set of ideas on gene regulation and highlight how various biomolecular assemblies lead to the formation of structural and regulatory features within the nucleus, with roles in transcriptional control. We conclude by suggesting further developments that will help capture the complex, dynamic, and often spatially restricted events that govern gene expression in mammalian cells.
Collapse
Affiliation(s)
- 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.
| | - Dominik Szabó
- 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
| | - 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.
| |
Collapse
|
3
|
Belmont AS. Nuclear Compartments: An Incomplete Primer to Nuclear Compartments, Bodies, and Genome Organization Relative to Nuclear Architecture. Cold Spring Harb Perspect Biol 2022; 14:a041268. [PMID: 34400557 PMCID: PMC9248822 DOI: 10.1101/cshperspect.a041268] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
This work reviews nuclear compartments, defined broadly to include distinct nuclear structures, bodies, and chromosome domains. It first summarizes original cytological observations before comparing concepts of nuclear compartments emerging from microscopy versus genomic approaches and then introducing new multiplexed imaging approaches that promise in the future to meld both approaches. I discuss how previous models of radial distribution of chromosomes or the binary division of the genome into A and B compartments are now being refined by the recognition of more complex nuclear compartmentalization. The poorly understood question of how these nuclear compartments are established and maintained is then discussed, including through the modern perspective of phase separation, before moving on to address possible functions of nuclear compartments, using the possible role of nuclear speckles in modulating gene expression as an example. Finally, the review concludes with a discussion of future questions for this field.
Collapse
Affiliation(s)
- Andrew S Belmont
- Department of Cell and Developmental Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801, USA
| |
Collapse
|
4
|
Kimura H, Sato Y. Imaging transcription elongation dynamics by new technologies unveils the organization of initiation and elongation in transcription factories. Curr Opin Cell Biol 2022; 74:71-79. [DOI: 10.1016/j.ceb.2022.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 01/05/2022] [Accepted: 01/10/2022] [Indexed: 11/27/2022]
|
5
|
Pancholi A, Klingberg T, Zhang W, Prizak R, Mamontova I, Noa A, Sobucki M, Kobitski AY, Nienhaus GU, Zaburdaev V, Hilbert L. RNA polymerase II clusters form in line with surface condensation on regulatory chromatin. Mol Syst Biol 2021; 17:e10272. [PMID: 34569155 PMCID: PMC8474054 DOI: 10.15252/msb.202110272] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 08/26/2021] [Accepted: 09/10/2021] [Indexed: 12/15/2022] Open
Abstract
It is essential for cells to control which genes are transcribed into RNA. In eukaryotes, two major control points are recruitment of RNA polymerase II (Pol II) into a paused state, and subsequent pause release toward transcription. Pol II recruitment and pause release occur in association with macromolecular clusters, which were proposed to be formed by a liquid-liquid phase separation mechanism. How such a phase separation mechanism relates to the interaction of Pol II with DNA during recruitment and transcription, however, remains poorly understood. Here, we use live and super-resolution microscopy in zebrafish embryos to reveal Pol II clusters with a large variety of shapes, which can be explained by a theoretical model in which regulatory chromatin regions provide surfaces for liquid-phase condensation at concentrations that are too low for canonical liquid-liquid phase separation. Model simulations and chemical perturbation experiments indicate that recruited Pol II contributes to the formation of these surface-associated condensates, whereas elongating Pol II is excluded from these condensates and thereby drives their unfolding.
Collapse
Affiliation(s)
- Agnieszka Pancholi
- Zoological InstituteDepartment of Systems Biology and BioinformaticsKarlsruhe Institute of TechnologyKarlsruheGermany
- Institute of Biological and Chemical Systems—Biological Information ProcessingKarlsruhe Institute of TechnologyEggenstein‐LeopoldshafenGermany
| | - Tim Klingberg
- Department of BiologyFriedrich‐Alexander‐Universität Erlangen‐NürnbergErlangenGermany
- Max‐Planck‐Zentrum für Physik und MedizinErlangenGermany
| | - Weichun Zhang
- Institute of Applied PhysicsKarlsruhe Institute of TechnologyKarlsruheGermany
- Institute of NanotechnologyKarlsruhe Institute of TechnologyEggenstein‐LeopoldshafenGermany
| | - Roshan Prizak
- Institute of Biological and Chemical Systems—Biological Information ProcessingKarlsruhe Institute of TechnologyEggenstein‐LeopoldshafenGermany
| | - Irina Mamontova
- Institute of Biological and Chemical Systems—Biological Information ProcessingKarlsruhe Institute of TechnologyEggenstein‐LeopoldshafenGermany
| | - Amra Noa
- Institute of Biological and Chemical Systems—Biological Information ProcessingKarlsruhe Institute of TechnologyEggenstein‐LeopoldshafenGermany
| | - Marcel Sobucki
- Institute of Biological and Chemical Systems—Biological Information ProcessingKarlsruhe Institute of TechnologyEggenstein‐LeopoldshafenGermany
| | - Andrei Yu Kobitski
- Institute of Applied PhysicsKarlsruhe Institute of TechnologyKarlsruheGermany
| | - Gerd Ulrich Nienhaus
- Institute of Biological and Chemical Systems—Biological Information ProcessingKarlsruhe Institute of TechnologyEggenstein‐LeopoldshafenGermany
- Institute of Applied PhysicsKarlsruhe Institute of TechnologyKarlsruheGermany
- Institute of NanotechnologyKarlsruhe Institute of TechnologyEggenstein‐LeopoldshafenGermany
- Department of PhysicsUniversity of Illinois at Urbana‐ChampaignUrbanaILUSA
| | - Vasily Zaburdaev
- Department of BiologyFriedrich‐Alexander‐Universität Erlangen‐NürnbergErlangenGermany
- Max‐Planck‐Zentrum für Physik und MedizinErlangenGermany
| | - Lennart Hilbert
- Zoological InstituteDepartment of Systems Biology and BioinformaticsKarlsruhe Institute of TechnologyKarlsruheGermany
- Institute of Biological and Chemical Systems—Biological Information ProcessingKarlsruhe Institute of TechnologyEggenstein‐LeopoldshafenGermany
| |
Collapse
|
6
|
Jerkovic I, Cavalli G. Understanding 3D genome organization by multidisciplinary methods. Nat Rev Mol Cell Biol 2021; 22:511-528. [PMID: 33953379 DOI: 10.1038/s41580-021-00362-w] [Citation(s) in RCA: 160] [Impact Index Per Article: 53.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/16/2021] [Indexed: 02/03/2023]
Abstract
Understanding how chromatin is folded in the nucleus is fundamental to understanding its function. Although 3D genome organization has been historically difficult to study owing to a lack of relevant methodologies, major technological breakthroughs in genome-wide mapping of chromatin contacts and advances in imaging technologies in the twenty-first century considerably improved our understanding of chromosome conformation and nuclear architecture. In this Review, we discuss methods of 3D genome organization analysis, including sequencing-based techniques, such as Hi-C and its derivatives, Micro-C, DamID and others; microscopy-based techniques, such as super-resolution imaging coupled with fluorescence in situ hybridization (FISH), multiplex FISH, in situ genome sequencing and live microscopy methods; and computational and modelling approaches. We describe the most commonly used techniques and their contribution to our current knowledge of nuclear architecture and, finally, we provide a perspective on up-and-coming methods that open possibilities for future major discoveries.
Collapse
Affiliation(s)
- Ivana Jerkovic
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France
| | - Giacomo Cavalli
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France.
| |
Collapse
|
7
|
Enhancer-gene rewiring in the pathogenesis of Quebec platelet disorder. Blood 2021; 136:2679-2690. [PMID: 32663239 DOI: 10.1182/blood.2020005394] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/06/2020] [Indexed: 12/12/2022] Open
Abstract
Quebec platelet disorder (QPD) is an autosomal dominant bleeding disorder with a unique, platelet-dependent, gain-of-function defect in fibrinolysis, without systemic fibrinolysis. The hallmark feature of QPD is a >100-fold overexpression of PLAU, specifically in megakaryocytes. This overexpression leads to a >100-fold increase in platelet stores of urokinase plasminogen activator (PLAU/uPA); subsequent plasmin-mediated degradation of diverse α-granule proteins; and platelet-dependent, accelerated fibrinolysis. The causative mutation is a 78-kb tandem duplication of PLAU. How this duplication causes megakaryocyte-specific PLAU overexpression is unknown. To investigate the mechanism that causes QPD, we used epigenomic profiling, comparative genomics, and chromatin conformation capture approaches to study PLAU regulation in cultured megakaryocytes from participants with QPD and unaffected controls. QPD duplication led to ectopic interactions between PLAU and a conserved megakaryocyte enhancer found within the same topologically associating domain (TAD). Our results support a unique disease mechanism whereby the reorganization of sub-TAD genome architecture results in a dramatic, cell-type-specific blood disorder phenotype.
Collapse
|
8
|
Dai EN, Heo S, Mauck RL. "Looping In" Mechanics: Mechanobiologic Regulation of the Nucleus and the Epigenome. Adv Healthc Mater 2020; 9:e2000030. [PMID: 32285630 DOI: 10.1002/adhm.202000030] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 02/17/2020] [Accepted: 02/18/2020] [Indexed: 12/11/2022]
Abstract
Cells respond to physical cues in their microenvironment. These cues result in changes in cell behavior, some of which are transient, and others of which are permanent. Understanding and leveraging permanent alteration of cell behavior induced by mechanical cues, or "mechanical memories," is an important aim in cell and tissue engineering. Herein, this paper reviews the existing literature outlining how cells may store memories of biophysical cues with a specific focus on the nucleus, the storehouse of information in eukaryotic cells. In particular, this review details mechanically driven adaptations in nuclear structure and genome organization and outlines potential mechanisms by which mechanical memories may be encoded within the structure and organization of the nucleus and chromatin.
Collapse
Affiliation(s)
- Eric N. Dai
- Departments of Orthopaedic Surgery and Bioengineering University of Pennsylvania Philadelphia PA 19104 USA
- Translational Musculoskeletal Research Center Corporal Michael J. Crescenz VA Medical Center Philadelphia PA 19104 USA
| | - Su‐Jin Heo
- Departments of Orthopaedic Surgery and Bioengineering University of Pennsylvania Philadelphia PA 19104 USA
- Translational Musculoskeletal Research Center Corporal Michael J. Crescenz VA Medical Center Philadelphia PA 19104 USA
| | - Robert L. Mauck
- Departments of Orthopaedic Surgery and Bioengineering University of Pennsylvania Philadelphia PA 19104 USA
- Translational Musculoskeletal Research Center Corporal Michael J. Crescenz VA Medical Center Philadelphia PA 19104 USA
- McKay Orthopaedic Research Laboratory University of Pennsylvania Philadelphia PA 19104‐6081 USA
| |
Collapse
|
9
|
|
10
|
Methods for mapping three-dimensional genome architecture. Methods 2020; 170:1-3. [PMID: 31669352 DOI: 10.1016/j.ymeth.2019.10.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
11
|
Kempfer R, Pombo A. Methods for mapping 3D chromosome architecture. Nat Rev Genet 2019; 21:207-226. [PMID: 31848476 DOI: 10.1038/s41576-019-0195-2] [Citation(s) in RCA: 288] [Impact Index Per Article: 57.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2019] [Indexed: 12/12/2022]
Abstract
Determining how chromosomes are positioned and folded within the nucleus is critical to understanding the role of chromatin topology in gene regulation. Several methods are available for studying chromosome architecture, each with different strengths and limitations. Established imaging approaches and proximity ligation-based chromosome conformation capture (3C) techniques (such as DNA-FISH and Hi-C, respectively) have revealed the existence of chromosome territories, functional nuclear landmarks (such as splicing speckles and the nuclear lamina) and topologically associating domains. Improvements to these methods and the recent development of ligation-free approaches, including GAM, SPRITE and ChIA-Drop, are now helping to uncover new aspects of 3D genome topology that confirm the nucleus to be a complex, highly organized organelle.
Collapse
Affiliation(s)
- Rieke Kempfer
- Epigenetic Regulation and Chromatin Architecture Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, Berlin, Germany. .,Institute for Biology, Humboldt University of Berlin, Berlin, Germany.
| | - Ana Pombo
- Epigenetic Regulation and Chromatin Architecture Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, Berlin, Germany. .,Institute for Biology, Humboldt University of Berlin, Berlin, Germany.
| |
Collapse
|
12
|
Szczepińska T, Rusek AM, Plewczynski D. Intermingling of chromosome territories. Genes Chromosomes Cancer 2019; 58:500-506. [DOI: 10.1002/gcc.22736] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 01/08/2019] [Accepted: 01/08/2019] [Indexed: 02/01/2023] Open
Affiliation(s)
| | - Anna Maria Rusek
- Centre of New TechnologiesUniversity of Warsaw Warsaw Poland
- Clinical Molecular Biology DepartmentMedical University of Bialystok Bialystok Poland
| | - Dariusz Plewczynski
- Centre of New TechnologiesUniversity of Warsaw Warsaw Poland
- Faculty of Mathematics and Information ScienceWarsaw University of Technology Warsaw Poland
| |
Collapse
|
13
|
Ferrai C, Torlai Triglia E, Risner-Janiczek JR, Rito T, Rackham OJ, de Santiago I, Kukalev A, Nicodemi M, Akalin A, Li M, Ungless MA, Pombo A. RNA polymerase II primes Polycomb-repressed developmental genes throughout terminal neuronal differentiation. Mol Syst Biol 2017; 13:946. [PMID: 29038337 PMCID: PMC5658700 DOI: 10.15252/msb.20177754] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Polycomb repression in mouse embryonic stem cells (ESCs) is tightly associated with promoter co‐occupancy of RNA polymerase II (RNAPII) which is thought to prime genes for activation during early development. However, it is unknown whether RNAPII poising is a general feature of Polycomb repression, or is lost during differentiation. Here, we map the genome‐wide occupancy of RNAPII and Polycomb from pluripotent ESCs to non‐dividing functional dopaminergic neurons. We find that poised RNAPII complexes are ubiquitously present at Polycomb‐repressed genes at all stages of neuronal differentiation. We observe both loss and acquisition of RNAPII and Polycomb at specific groups of genes reflecting their silencing or activation. Strikingly, RNAPII remains poised at transcription factor genes which are silenced in neurons through Polycomb repression, and have major roles in specifying other, non‐neuronal lineages. We conclude that RNAPII poising is intrinsically associated with Polycomb repression throughout differentiation. Our work suggests that the tight interplay between RNAPII poising and Polycomb repression not only instructs promoter state transitions, but also may enable promoter plasticity in differentiated cells.
Collapse
Affiliation(s)
- Carmelo Ferrai
- Epigenetic Regulation and Chromatin Architecture, Max Delbrück Center for Molecular Medicine, Berlin, Germany .,Genome Function, MRC London Institute of Medical Sciences (previously MRC Clinical Sciences Centre), London, UK.,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK
| | - Elena Torlai Triglia
- Epigenetic Regulation and Chromatin Architecture, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Jessica R Risner-Janiczek
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK.,Stem Cell Neurogenesis, MRC London Institute of Medical Sciences (previously MRC Clinical Sciences Centre), London, UK.,Neurophysiology Group, MRC London Institute of Medical Sciences (previously MRC Clinical Sciences Centre), London, UK
| | - Tiago Rito
- Epigenetic Regulation and Chromatin Architecture, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | | | - Inês de Santiago
- Genome Function, MRC London Institute of Medical Sciences (previously MRC Clinical Sciences Centre), London, UK.,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK
| | - Alexander Kukalev
- Epigenetic Regulation and Chromatin Architecture, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Mario Nicodemi
- Dipartimento di Fisica, Università di Napoli Federico II and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, Naples, Italy
| | - Altuna Akalin
- Scientific Bioinformatics Platform, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Meng Li
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK.,Stem Cell Neurogenesis, MRC London Institute of Medical Sciences (previously MRC Clinical Sciences Centre), London, UK
| | - Mark A Ungless
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK .,Neurophysiology Group, MRC London Institute of Medical Sciences (previously MRC Clinical Sciences Centre), London, UK
| | - Ana Pombo
- Epigenetic Regulation and Chromatin Architecture, Max Delbrück Center for Molecular Medicine, Berlin, Germany .,Genome Function, MRC London Institute of Medical Sciences (previously MRC Clinical Sciences Centre), London, UK.,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK.,Institute for Biology, Humboldt-Universität zu Berlin, Berlin Germany
| |
Collapse
|
14
|
Kar G, Kim JK, Kolodziejczyk AA, Natarajan KN, Torlai Triglia E, Mifsud B, Elderkin S, Marioni JC, Pombo A, Teichmann SA. Flipping between Polycomb repressed and active transcriptional states introduces noise in gene expression. Nat Commun 2017; 8:36. [PMID: 28652613 PMCID: PMC5484669 DOI: 10.1038/s41467-017-00052-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 04/28/2017] [Indexed: 11/09/2022] Open
Abstract
Polycomb repressive complexes (PRCs) are important histone modifiers, which silence gene expression; yet, there exists a subset of PRC-bound genes actively transcribed by RNA polymerase II (RNAPII). It is likely that the role of Polycomb repressive complex is to dampen expression of these PRC-active genes. However, it is unclear how this flipping between chromatin states alters the kinetics of transcription. Here, we integrate histone modifications and RNAPII states derived from bulk ChIP-seq data with single-cell RNA-sequencing data. We find that Polycomb repressive complex-active genes have greater cell-to-cell variation in expression than active genes, and these results are validated by knockout experiments. We also show that PRC-active genes are clustered on chromosomes in both two and three dimensions, and interactions with active enhancers promote a stabilization of gene expression noise. These findings provide new insights into how chromatin regulation modulates stochastic gene expression and transcriptional bursting, with implications for regulation of pluripotency and development.Polycomb repressive complexes modify histones but it is unclear how changes in chromatin states alter kinetics of transcription. Here, the authors use single-cell RNAseq and ChIPseq to find that actively transcribed genes with Polycomb marks have greater cell-to-cell variation in expression.
Collapse
Affiliation(s)
- Gozde Kar
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Jong Kyoung Kim
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
- Department of New Biology, DGIST, Daegu, 42988, Republic of Korea
| | - Aleksandra A Kolodziejczyk
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Kedar Nath Natarajan
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Elena Torlai Triglia
- Epigenetic Regulation and Chromatin Architecture Group, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Robert Roessle Strasse, Berlin-Buch, 13125, Germany
| | - Borbala Mifsud
- Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London, WC2A 3LY, UK
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, UK
- William Harvey Research Institute, Queen Mary University London, Charterhouse Square, London, EC1M 6BQ, UK
| | - Sarah Elderkin
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - John C Marioni
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Ana Pombo
- Epigenetic Regulation and Chromatin Architecture Group, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Robert Roessle Strasse, Berlin-Buch, 13125, Germany
| | - Sarah A Teichmann
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
| |
Collapse
|
15
|
Active and poised promoter states drive folding of the extended HoxB locus in mouse embryonic stem cells. Nat Struct Mol Biol 2017; 24:515-524. [DOI: 10.1038/nsmb.3402] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 03/27/2017] [Indexed: 12/30/2022]
|
16
|
Complex multi-enhancer contacts captured by Genome Architecture Mapping (GAM). Nature 2017; 543:519-524. [PMID: 28273065 PMCID: PMC5366070 DOI: 10.1038/nature21411] [Citation(s) in RCA: 450] [Impact Index Per Article: 64.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Accepted: 01/18/2017] [Indexed: 12/22/2022]
Abstract
The organization of the genome in the nucleus and the interactions of genes with their regulatory elements are key features of transcriptional control and their disruption can cause disease. We developed a novel genome-wide method, Genome Architecture Mapping (GAM), for measuring chromatin contacts, and other features of three-dimensional chromatin topology, based on sequencing DNA from a large collection of thin nuclear sections. We apply GAM to mouse embryonic stem cells and identify an enrichment for specific interactions between active genes and enhancers across very large genomic distances, using a mathematical model ‘SLICE’ (Statistical Inference of Co-segregation). GAM also reveals an abundance of three-way contacts genome-wide, especially between regions that are highly transcribed or contain super-enhancers, highlighting a previously inaccessible complexity in genome architecture and a major role for gene-expression specific contacts in organizing the genome in mammalian nuclei.
Collapse
|
17
|
Abstract
Gene expression control is a fundamental determinant of cellular life with transcription being the most important step. The spatial nuclear arrangement of the transcription process driven by RNA polymerases II and III is nonrandomly organized in foci, which is believed to add another regulatory layer on gene expression control. RNA polymerase I transcription takes place within a specialized organelle, the nucleolus. Transcription of ribosomal RNA directly responds to metabolic requirements, which in turn is reflected in the architecture of nucleoli. It differs from that of the other polymerases with respect to the gene template organization, transcription rate, and epigenetic expression control, whereas other features are shared like the formation of DNA loops bringing genes and components of the transcription machinery in close proximity. In recent years, significant advances have been made in the understanding of the structural prerequisites of nuclear transcription, of the arrangement in the nuclear volume, and of the dynamics of these entities. Here, we compare ribosomal RNA and mRNA transcription side by side and review the current understanding focusing on structural aspects of transcription foci, of their constituents, and of the dynamical behavior of these components with respect to foci formation, disassembly, and cell cycle.
Collapse
Affiliation(s)
- Klara Weipoltshammer
- Department for Cell and Developmental Biology, Medical University of Vienna, Schwarzspanierstr. 17, 1090, Vienna, Austria
| | - Christian Schöfer
- Department for Cell and Developmental Biology, Medical University of Vienna, Schwarzspanierstr. 17, 1090, Vienna, Austria.
| |
Collapse
|
18
|
Affiliation(s)
- Huy Q. Nguyen
- Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire 03755;
| | - Giovanni Bosco
- Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire 03755;
| |
Collapse
|
19
|
Cai M, Gao F, Zhang P, An W, Shi J, Wang K, Lu W. Analysis of a transgenic Oct4 enhancer reveals high fidelity long-range chromosomal interactions. Sci Rep 2015; 5:14558. [PMID: 26435056 PMCID: PMC4592970 DOI: 10.1038/srep14558] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 08/27/2015] [Indexed: 12/14/2022] Open
Abstract
Genome structure or nuclear organization has fascinated researchers investigating genome function. Recently, much effort has gone into defining relationships between specific genome structures and gene expression in pluripotent cells. We previously analyzed chromosomal interactions of the endogenous Oct4 distal enhancer in pluripotent cells. Here, we derive ES and iPS cells from a transgenic Oct4 distal enhancer reporter mouse. Using sonication-based Circularized Chromosome Conformation Capture (4C) coupled with next generation sequencing, we determined and compared the genome-wide interactome of the endogenous and transgenic Oct4 distal enhancers. Integrative genomic analysis indicated that the transgenic enhancer binds to a similar set of loci and shares similar key enrichment profiles with its endogenous counterpart. Both the endogenous and transgenic Oct4 enhancer interacting loci were enriched in the open nucleus compartment, which is associated with active histone marks (H3K4me1, H3K27ac, H3K4me3 and H3K9ac), active cis-regulatory sequences (DNA hypersensitivity sites (DHS)), 5-hydroxymethylcytosine (5-hmc), and early DNA replication domains. In addition, binding of some pluripotency-related transcription factors was consistently enriched in our 4C sites, and genes in those sites were generally more highly expressed. Overall, our work reveals critical features that may function in gene expression regulation in mouse pluripotent cells.
Collapse
Affiliation(s)
- Mingyang Cai
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA 90033, USA.,Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, CA 90033, USA.,Division of Biostatistics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Fan Gao
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA 90033, USA.,Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, CA 90033, USA
| | - Peilin Zhang
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA 90033, USA
| | - Woojin An
- Department of Biochemistry and Molecular Biology, Norris Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Jiandang Shi
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Kai Wang
- Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, CA 90033, USA.,Division of Biostatistics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90033, USA.,Department of Psychiatry, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Wange Lu
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA 90033, USA.,Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| |
Collapse
|
20
|
Lopes Novo C, Rugg-Gunn PJ. Chromatin organization in pluripotent cells: emerging approaches to study and disrupt function. Brief Funct Genomics 2015. [PMID: 26206085 PMCID: PMC4958138 DOI: 10.1093/bfgp/elv029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Translating the vast amounts of genomic and epigenomic information accumulated on the linear genome into three-dimensional models of nuclear organization is a current major challenge. In response to this challenge, recent technological innovations based on chromosome conformation capture methods in combination with increasingly powerful functional approaches have revealed exciting insights into key aspects of genome regulation. These findings have led to an emerging model where the genome is folded and compartmentalized into highly conserved topological domains that are further divided into functional subdomains containing physical loops that bring cis-regulatory elements to close proximity. Targeted functional experiments, largely based on designable DNA-binding proteins, have begun to define the major architectural proteins required to establish and maintain appropriate genome regulation. Here, we focus on the accessible and well-characterized system of pluripotent cells to review the functional role of chromatin organization in regulating pluripotency, differentiation and reprogramming.
Collapse
|
21
|
Myosin VI regulates gene pairing and transcriptional pause release in T cells. Proc Natl Acad Sci U S A 2015; 112:E1587-93. [PMID: 25770220 DOI: 10.1073/pnas.1502461112] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Naive CD4 T cells differentiate into several effector lineages, which generate a stronger and more rapid response to previously encountered immunological challenges. Although effector function is a key feature of adaptive immunity, the molecular basis of this process is poorly understood. Here, we investigated the spatiotemporal regulation of cytokine gene expression in resting and restimulated effector T helper 1 (Th1) cells. We found that the Lymphotoxin (LT)/TNF alleles, which encode TNF-α, were closely juxtaposed shortly after T-cell receptor (TCR) engagement, when transcription factors are limiting. Allelic pairing required a nuclear myosin, myosin VI, which is rapidly recruited to the LT/TNF locus upon restimulation. Furthermore, transcription was paused at the TNF locus and other related genes in resting Th1 cells and released in a myosin VI-dependent manner following activation. We propose that homologous pairing and myosin VI-mediated transcriptional pause release account for the rapid and efficient expression of genes induced by an external stimulus.
Collapse
|
22
|
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.
Collapse
|
23
|
Schubert V, Weisshart K. Abundance and distribution of RNA polymerase II in Arabidopsis interphase nuclei. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:1687-98. [PMID: 25740920 PMCID: PMC4357323 DOI: 10.1093/jxb/erv091] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
RNA polymerase II (RNAPII) is responsible for the transcription of most eukaryotic protein-coding genes. Analysing the topological distribution and quantification of RNAPII can contribute to understanding its function in interphase nuclei. Previously it was shown that RNAPII molecules in plant nuclei form reticulate structures within euchromatin of differentiated Arabidopsis thaliana nuclei rather than being organized in distinct 'transcription factories' as observed in mammalian nuclei. Immunosignal intensity measurements based on specific antibody labelling in maximum intensity projections of image stacks acquired by structured illumination microscopy (SIM) suggested a relative proportional increase of RNAPII in endopolyploid plant nuclei. Here, photoactivated localization microscopy (PALM) was applied to determine the absolute number and distribution of active and inactive RNAPII molecules in differentiated A. thaliana nuclei. The proportional increase of RNAPII during endopolyploidization is confirmed, but it is also shown that PALM measurements are more reliable than those based on SIM in terms of quantification. The single molecule localization results show that, although RNAPII molecules are globally dispersed within plant euchromatin, they also aggregate within smaller distances as described for mammalian transcription factories.
Collapse
Affiliation(s)
- Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466 Stadt Seeland, Germany
| | | |
Collapse
|
24
|
Chakraborty S, Mehta I, Kulashreshtha M, Rao BJ. Quantitative analysis of chromosome localization in the nucleus. Methods Mol Biol 2015; 1228:223-33. [PMID: 25311133 DOI: 10.1007/978-1-4939-1680-1_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The spatial organization of the genome within the interphase nucleus is important for mediating genome functions. The radial organization of chromosome territories has been studied traditionally using two-dimensional fluorescence in situ hybridization (FISH) using labeled whole chromosome probes. Information from 2D-FISH images is analyzed quantitatively and is depicted in the form of the spatial distribution of chromosomes territories. However, to the best of our knowledge no open-access tools are available to delineate the position of chromosome territories from 2D-FISH images. In this chapter we present a methodology termed Image Analysis of Chromosomes for computing their localization (IMACULAT). IMACULAT is an open-access, automated tool that partitions the cell nucleus into shells of equal area or volume and computes the spatial distribution of chromosome territories.
Collapse
Affiliation(s)
- Sandeep Chakraborty
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, Maharashtra, India,
| | | | | | | |
Collapse
|
25
|
Schubert V, Rudnik R, Schubert I. Chromatin associations in Arabidopsis interphase nuclei. Front Genet 2014; 5:389. [PMID: 25431580 PMCID: PMC4230181 DOI: 10.3389/fgene.2014.00389] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 10/23/2014] [Indexed: 11/30/2022] Open
Abstract
The arrangement of chromatin within interphase nuclei seems to be caused by topological constraints and related to gene expression depending on tissue and developmental stage. In yeast and animals it was found that homologous and heterologous chromatin association are required to realize faithful expression and DNA repair. To test whether such associations are present in plants we analyzed Arabidopsis thaliana interphase nuclei by FISH using probes from different chromosomes. We found that chromatin fiber movement and variable associations, although in general relatively seldom, may occur between euchromatin segments along chromosomes, sometimes even over large distances. The combination of euchromatin segments bearing high or low co-expressing genes did not reveal different association frequencies probably due to adjacent genes of deviating expression patterns. Based on previous data and on FISH analyses presented here, we conclude that the global interphase chromatin organization in A. thaliana is relatively stable, due to the location of its 10 centromeres at the nuclear periphery and of the telomeres mainly at the centrally localized nucleolus. Nevertheless, chromatin movement enables a flexible spatial genome arrangement in plant nuclei.
Collapse
Affiliation(s)
- Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben Stadt Seeland, Germany
| | - Radoslaw Rudnik
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben Stadt Seeland, Germany
| | - Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben Stadt Seeland, Germany ; Faculty of Science and Central European Institute of Technology, Masaryk University Brno, Czech Republic
| |
Collapse
|
26
|
Sun J, Li W, Sun Y, Yu D, Wen X, Wang H, Cui J, Wang G, Hoffman AR, Hu JF. A novel antisense long noncoding RNA within the IGF1R gene locus is imprinted in hematopoietic malignancies. Nucleic Acids Res 2014; 42:9588-601. [PMID: 25092925 PMCID: PMC4150754 DOI: 10.1093/nar/gku549] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Dysregulation of the insulin-like growth factor type I receptor (IGF1R) has been implicated in the progression and therapeutic resistance of malignancies. In acute myeloid leukemia (AML) cells, IGF1R is one of the most abundantly phosphorylated receptor tyrosine kinases, promoting cell growth through the PI3K/Akt signaling pathway. However, little is known regarding the molecular mechanisms underlying IGF1R gene dysregulation in cancer. We discovered a novel intragenic long noncoding RNA (lncRNA) within the IGF1R locus, named IRAIN, which is transcribed in an antisense direction from an intronic promoter. The IRAIN lncRNA was expressed exclusively from the paternal allele, with the maternal counterpart being silenced. Using both reverse transcription-associated trap and chromatin conformation capture assays, we demonstrate that this lncRNA interacts with chromatin DNA and is involved in the formation of an intrachromosomal enhancer/promoter loop. Knockdown of IRAIN lncRNA with shRNA abolishes this intrachromosomal interaction. In addition, IRAIN was downregulated both in leukemia cell lines and in blood obtained from high-risk AML patients. These data identify IRAIN as a new imprinted lncRNA that is involved in long-range DNA interactions.
Collapse
Affiliation(s)
- Jingnan Sun
- Stem Cell and Cancer Center, First Affiliated Hospital, Jilin University, Changchun, Jilin 130061, PR China Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Wei Li
- Stem Cell and Cancer Center, First Affiliated Hospital, Jilin University, Changchun, Jilin 130061, PR China
| | - Yunpeng Sun
- Stem Cell and Cancer Center, First Affiliated Hospital, Jilin University, Changchun, Jilin 130061, PR China
| | - Dehai Yu
- Stem Cell and Cancer Center, First Affiliated Hospital, Jilin University, Changchun, Jilin 130061, PR China Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Xue Wen
- Stem Cell and Cancer Center, First Affiliated Hospital, Jilin University, Changchun, Jilin 130061, PR China
| | - Hong Wang
- Stem Cell and Cancer Center, First Affiliated Hospital, Jilin University, Changchun, Jilin 130061, PR China Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Jiuwei Cui
- Stem Cell and Cancer Center, First Affiliated Hospital, Jilin University, Changchun, Jilin 130061, PR China
| | - Guanjun Wang
- Stem Cell and Cancer Center, First Affiliated Hospital, Jilin University, Changchun, Jilin 130061, PR China
| | - Andrew R Hoffman
- Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Ji-Fan Hu
- Stem Cell and Cancer Center, First Affiliated Hospital, Jilin University, Changchun, Jilin 130061, PR China Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| |
Collapse
|
27
|
Schubert V. RNA polymerase II forms transcription networks in rye and Arabidopsis nuclei and its amount increases with endopolyploidy. Cytogenet Genome Res 2014; 143:69-77. [PMID: 25060696 DOI: 10.1159/000365233] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
RNA polymerase II (RNAPII) is responsible for the transcription of most eukaryotic genes. In mammalian nuclei, RNAPII is mainly localized in relatively few distinct transcription factories. In this study--applying super-resolution microscopy--it is shown that in plants, inactive (non-phosphorylated) and active (phosphorylated) RNAPII modifications compose distinct 'transcription networks' within the euchromatin. These reticulate structures sometimes attach to each other, but they are absent from heterochromatin and nucleoli. The global RNAPII distribution within nuclei is not influenced by interphase chromatin organization such as Rabl (rye) versus non-Rabl (Arabidopsis thaliana) orientation. Replication of sister chromatids without cell division causes endopolyploidy, a phenomenon widespread in plants and animals. Endopolyploidy raises the number of gene copies per nucleus. Here, it is shown that the amounts of active and inactive RNAPII enzymes in differentiated 2-32C leaf nuclei of A. thaliana proportionally increase with rising endopolyploidy. Thus, increasing the transcriptional activity of cells and tissues seems to be an important function of endopolyploidy.
Collapse
Affiliation(s)
- Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| |
Collapse
|
28
|
Abstract
This review summarizes the current understanding of the role of nuclear bodies in regulating gene expression. The compartmentalization of cellular processes, such as ribosome biogenesis, RNA processing, cellular response to stress, transcription, modification and assembly of spliceosomal snRNPs, histone gene synthesis and nuclear RNA retention, has significant implications for gene regulation. These functional nuclear domains include the nucleolus, nuclear speckle, nuclear stress body, transcription factory, Cajal body, Gemini of Cajal body, histone locus body and paraspeckle. We herein review the roles of nuclear bodies in regulating gene expression and their relation to human health and disease.
Collapse
Affiliation(s)
| | - Cornelius F. Boerkoel
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-604-875-2157; Fax: +1-604-875-2376
| |
Collapse
|
29
|
Nicodemi M, Pombo A. Models of chromosome structure. Curr Opin Cell Biol 2014; 28:90-5. [PMID: 24804566 DOI: 10.1016/j.ceb.2014.04.004] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 04/11/2014] [Indexed: 10/25/2022]
Abstract
Understanding the mechanisms that control chromosome folding in the nucleus of eukaryotes and their contribution to gene regulation is a key open issue in molecular biology. Microscopy and chromatin-capture techniques have shown that chromatin has a complex organization, which dynamically changes across organisms and cell types. The need to make sense of such a fascinating complexity has prompted the development of quantitative models from physics, to find the principles of chromosome folding, its origin and function. Here, we concisely review recent advances in chromosome modeling, focusing on a recently proposed framework, the Strings & Binders Switch (SBS) model, which recapitulates key features of chromosome organization in space and time.
Collapse
Affiliation(s)
- Mario Nicodemi
- Universita' di Napoli "Federico II", Dipartimento di Fisica, INFN Sezione di Napoli, CNR-SPIN, Complesso Universitario di Monte S. Angelo, Via Cintia, 80126 Napoli, Italy.
| | - Ana Pombo
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Robert Rössle Strasse 10, 13125 Berlin-Buch, Germany.
| |
Collapse
|
30
|
Mardaryev AN, Gdula MR, Yarker JL, Emelianov VU, Emelianov VN, Poterlowicz K, Sharov AA, Sharova TY, Scarpa JA, Joffe B, Solovei I, Chambon P, Botchkarev VA, Fessing MY. p63 and Brg1 control developmentally regulated higher-order chromatin remodelling at the epidermal differentiation complex locus in epidermal progenitor cells. Development 2014; 141:101-11. [PMID: 24346698 DOI: 10.1242/dev.103200] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Chromatin structural states and their remodelling, including higher-order chromatin folding and three-dimensional (3D) genome organisation, play an important role in the control of gene expression. The role of 3D genome organisation in the control and execution of lineage-specific transcription programmes during the development and differentiation of multipotent stem cells into specialised cell types remains poorly understood. Here, we show that substantial remodelling of the higher-order chromatin structure of the epidermal differentiation complex (EDC), a keratinocyte lineage-specific gene locus on mouse chromosome 3, occurs during epidermal morphogenesis. During epidermal development, the locus relocates away from the nuclear periphery towards the nuclear interior into a compartment enriched in SC35-positive nuclear speckles. Relocation of the EDC locus occurs prior to the full activation of EDC genes involved in controlling terminal keratinocyte differentiation and is a lineage-specific, developmentally regulated event controlled by transcription factor p63, a master regulator of epidermal development. We also show that, in epidermal progenitor cells, p63 directly regulates the expression of the ATP-dependent chromatin remodeller Brg1, which binds to distinct domains within the EDC and is required for relocation of the EDC towards the nuclear interior. Furthermore, Brg1 also regulates gene expression within the EDC locus during epidermal morphogenesis. Thus, p63 and its direct target Brg1 play an essential role in remodelling the higher-order chromatin structure of the EDC and in the specific positioning of this locus within the landscape of the 3D nuclear space, as required for the efficient expression of EDC genes in epidermal progenitor cells during skin development.
Collapse
|
31
|
Schierding W, Cutfield WS, O'Sullivan JM. The missing story behind Genome Wide Association Studies: single nucleotide polymorphisms in gene deserts have a story to tell. Front Genet 2014; 5:39. [PMID: 24600475 PMCID: PMC3927098 DOI: 10.3389/fgene.2014.00039] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 01/31/2014] [Indexed: 11/13/2022] Open
Abstract
Genome wide association studies are central to the evolution of personalized medicine. However, the propensity for single nucleotide polymorphisms (SNPs) to fall outside of genes means that understanding how these polymorphisms alter cellular function requires an expanded view of human genetics. Integrating the study of genome structure (chromosome conformation capture) into its function opens up new avenues of exploration. Changes in the epigenome associated with SNPs in gene deserts will allow us to define complex diseases in a much clearer manner, and usher in a new era of disease pathway exploration.
Collapse
Affiliation(s)
| | - Wayne S. Cutfield
- Liggins Institute, University of AucklandAuckland, New Zealand
- Gravida – National Centre for Growth and DevelopmentAuckland, New Zealand
| | - Justin M. O'Sullivan
- Liggins Institute, University of AucklandAuckland, New Zealand
- Gravida – National Centre for Growth and DevelopmentAuckland, New Zealand
| |
Collapse
|
32
|
Affiliation(s)
- Jiannan Guo
- Biochemistry Department, University of Iowa , Iowa City, Iowa 52242, United States
| | | |
Collapse
|
33
|
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: 127] [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
| |
Collapse
|
34
|
Rieder D, Ploner C, Krogsdam AM, Stocker G, Fischer M, Scheideler M, Dani C, Amri EZ, Müller WG, McNally JG, Trajanoski Z. Co-expressed genes prepositioned in spatial neighborhoods stochastically associate with SC35 speckles and RNA polymerase II factories. Cell Mol Life Sci 2013; 71:1741-59. [PMID: 24026398 DOI: 10.1007/s00018-013-1465-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 08/02/2013] [Accepted: 08/28/2013] [Indexed: 11/26/2022]
Abstract
Chromosomally separated, co-expressed genes can be in spatial proximity, but there is still debate about how this nuclear organization is achieved. Proposed mechanisms include global genome organization, preferential positioning of chromosome territories, or gene-gene sharing of various nuclear bodies. To investigate this question, we selected a set of genes that were co-expressed upon differentiation of human multipotent stem cells. We applied a novel multi-dimensional analysis procedure which revealed that prior to gene expression, the relative position of these genes was conserved in nuclei. Upon stem cell differentiation and concomitant gene expression, we found that co-expressed genes were closer together. In addition, we found that genes in the same 1-μm-diameter neighborhood associated with either the same splicing speckle or to a lesser extent with the same transcription factory. Dispersal of speckles by overexpression of the serine-arginine (SR) protein kinase cdc2-like kinase Clk2 led to a significant drop in the number of genes in shared neighborhoods. We demonstrate quantitatively that the frequencies of speckle and factory sharing can be explained by assuming stochastic selection of a nuclear body within a restricted sub-volume defined by the original global gene positioning present prior to gene expression. We conclude that the spatial organization of these genes is a two-step process in which transcription-induced association with nuclear bodies enhances and refines a pre-existing global organization.
Collapse
Affiliation(s)
- Dietmar Rieder
- Division of Bioinformatics, Biocenter, Innsbruck Medical University, Innrain 80, 6020, Innsbruck, Austria
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Barbieri M, Fraser J, Lavitas LM, Chotalia M, Dostie J, Pombo A, Nicodemi M. A polymer model explains the complexity of large-scale chromatin folding. Nucleus 2013; 4:267-73. [PMID: 23823730 DOI: 10.4161/nucl.25432] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The underlying global organization of chromatin within the cell nucleus has been the focus of intense recent research. Hi-C methods have allowed for the detection of genome-wide chromatin interactions, revealing a complex large-scale organization where chromosomes tend to partition into megabase-sized "topological domains" of local chromatin interactions and intra-chromosomal contacts extends over much longer scales, in a cell-type and chromosome specific manner. Until recently, the distinct chromatin folding properties observed experimentally have been difficult to explain in a single conceptual framework. We reported that a simple polymer-physics model of chromatin, the strings and binders switch (SBS) model, succeeds in describing the full range of chromatin configurations observed in vivo. The SBS model simulates the interactions between randomly diffusing binding molecules and binding sites on a polymer chain. It explains how polymer architectural patterns can be established, how different stable conformations can be produced and how conformational changes can be reliably regulated by simple strategies, such as protein upregulation or epigenetic modifications, via fundamental thermodynamics mechanisms.
Collapse
Affiliation(s)
- Mariano Barbieri
- Universita' di Napoli "Federico II"; Dipartimento di Fisica; INFN Sezione di Napoli; CNR-SPIN, Complesso Universitario di Monte S. Angelo; Napoli, Italy; Department of Biochemistry and Goodman Cancer Research Center; McGill University; Montréal, Québec Canada; Berlin Institute for Medical Systems Biology; Max Delbrück Center for Molecular Medicine; Berlin-Buch, Germany; Genome Function Group; MRC Clinical Sciences Centre; Imperial College London; Hammersmith Hospital Campus; London, UK
| | | | | | | | | | | | | |
Collapse
|
36
|
Wei Z, Huang D, Gao F, Chang WH, An W, Coetzee GA, Wang K, Lu W. Biological implications and regulatory mechanisms of long-range chromosomal interactions. J Biol Chem 2013; 288:22369-77. [PMID: 23779110 DOI: 10.1074/jbc.r113.485292] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Development of high-throughput sequencing-based methods has enabled us to examine nuclear architecture at unprecedented resolution, allowing further examination of the function of long-range chromosomal interactions. Here, we review methods used to investigate novel long-range chromosomal interactions and genome-wide organization of chromatin. We further discuss transcriptional activation and silencing in relation to organization and positioning of gene loci and regulation of chromatin organization through protein complexes and noncoding RNAs.
Collapse
Affiliation(s)
- Zong Wei
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA
| | | | | | | | | | | | | | | |
Collapse
|
37
|
Abstract
Allostery is largely associated with conformational and functional transitions in individual proteins. This concept can be extended to consider the impact of conformational perturbations on cellular function and disease states. Here, we clarify the concept of allostery and how it controls physiological activities. We focus on the challenging questions of how allostery can both cause disease and contribute to development of new therapeutics. We aim to increase the awareness of the linkage between disease symptoms on the cellular level and specific aberrant allosteric actions on the molecular level and to emphasize the potential of allosteric drugs in innovative therapies.
Collapse
|
38
|
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: 162] [Impact Index Per Article: 14.7] [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
| | | |
Collapse
|
39
|
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.
Collapse
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
| |
Collapse
|
40
|
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.
Collapse
Affiliation(s)
- Scott Davidson
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON M5S 3G5, Canada
| | | | | |
Collapse
|
41
|
Nussinov R, Ma B, Tsai CJ. A broad view of scaffolding suggests that scaffolding proteins can actively control regulation and signaling of multienzyme complexes through allostery. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:820-9. [PMID: 23291467 DOI: 10.1016/j.bbapap.2012.12.014] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 12/19/2012] [Accepted: 12/21/2012] [Indexed: 10/27/2022]
Abstract
Enzymes often work sequentially in pathways; and consecutive reaction steps are typically carried out by molecules associated in the same multienzyme complex. Localization confines the enzymes; anchors them; increases the effective concentration of substrates and products; and shortens pathway timescales; however, it does not explain enzyme coordination or pathway branching. Here, we distinguish between metabolic and signaling multienzyme complexes. We argue for a central role of scaffolding proteins in regulating multienzyme complexes signaling and suggest that metabolic multienzyme complexes are less dependent on scaffolding because they undergo conformational control through direct subunit-subunit contacts. In particular, we propose that scaffolding proteins have an essential function in controlling branching in signaling pathways. This new broadened definition of scaffolding proteins goes beyond cases such as the classic yeast mitogen-activated protein kinase Ste5 and encompasses proteins such as E3 ligases which lack active sites and work via allostery. With this definition, we classify the mechanisms of multienzyme complexes based on whether the substrates are transferred through the involvement of scaffolding proteins, and outline the functional merits to metabolic or signaling pathways. Overall, while co-localization topography helps multistep pathways non-specifically, allosteric regulation requires precise multienzyme organization and interactions and works via population shift, either through direct enzyme subunit-subunit interactions or through active involvement of scaffolding proteins. This article is part of a Special Issue entitled: The emerging dynamic view of proteins: Protein plasticity in allostery, evolution and self-assembly.
Collapse
Affiliation(s)
- Ruth Nussinov
- Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
| | | | | |
Collapse
|
42
|
Papantonis A, Kohro T, Baboo S, Larkin JD, Deng B, Short P, Tsutsumi S, Taylor S, Kanki Y, Kobayashi M, Li G, Poh HM, Ruan X, Aburatani H, Ruan Y, Kodama T, Wada Y, Cook PR. TNFα signals through specialized factories where responsive coding and miRNA genes are transcribed. EMBO J 2012; 31:4404-14. [PMID: 23103767 PMCID: PMC3512387 DOI: 10.1038/emboj.2012.288] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 09/24/2012] [Indexed: 11/09/2022] Open
Abstract
Tumour necrosis factor alpha (TNFα) is a potent cytokine that signals through nuclear factor kappa B (NFκB) to activate a subset of human genes. It is usually assumed that this involves RNA polymerases transcribing responsive genes wherever they might be in the nucleus. Using primary human endothelial cells, variants of chromosome conformation capture (including 4C and chromatin interaction analysis with paired-end tag sequencing), and fluorescence in situ hybridization to detect single nascent transcripts, we show that TNFα induces responsive genes to congregate in discrete 'NFκB factories'. Some factories further specialize in transcribing responsive genes encoding micro-RNAs that target downregulated mRNAs. We expect all signalling pathways to contain this extra leg, where responding genes are transcribed in analogous specialized factories.
Collapse
Affiliation(s)
- Argyris Papantonis
- The Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Abstract
There is considerable evidence that transcription does not occur homogeneously or diffusely throughout the nucleus, but rather at a number of specialized, discrete sites termed transcription factories. The factories are composed of ~4–30 RNA polymerase molecules, and are associated with many other molecules involved in transcriptional activation and mRNA processing. Some data suggest that the polymerase molecules within a factory remain stationary relative to the transcribed DNA, which is thought to be reeled through the factory site. There is also some evidence that transcription factories could help organize chromatin and nuclear structure, contributing to both the formation of chromatin loops and the clustering of active and co-regulated genes.
Collapse
Affiliation(s)
- Dietmar Rieder
- Division of Bioinformatics, Biocenter, Innsbruck Medical University Innsbruck, Austria
| | | | | |
Collapse
|
44
|
Papantonis A, Cook PR. Fixing the model for transcription: the DNA moves, not the polymerase. Transcription 2012; 2:41-4. [PMID: 21326910 DOI: 10.4161/trns.2.1.14275] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Revised: 11/23/2010] [Accepted: 11/23/2010] [Indexed: 11/19/2022] Open
Abstract
The traditional model for transcription sees active polymerases tracking along their templates. An alternative (controversial) model has active enzymes immobilized in "factories." Recent evidence supports the idea that the DNA moves, not the polymerase, and points to alternative explanations of how regulatory motifs like enhancers and silencers work.
Collapse
|
45
|
Polycomb associates genome-wide with a specific RNA polymerase II variant, and regulates metabolic genes in ESCs. Cell Stem Cell 2012; 10:157-70. [PMID: 22305566 PMCID: PMC3682187 DOI: 10.1016/j.stem.2011.12.017] [Citation(s) in RCA: 225] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2011] [Revised: 11/09/2011] [Accepted: 12/22/2011] [Indexed: 11/25/2022]
Abstract
Polycomb repressor complexes (PRCs) are important chromatin modifiers fundamentally implicated in pluripotency and cancer. Polycomb silencing in embryonic stem cells (ESCs) can be accompanied by active chromatin and primed RNA polymerase II (RNAPII), but the relationship between PRCs and RNAPII remains unclear genome-wide. We mapped PRC repression markers and four RNAPII states in ESCs using ChIP-seq, and found that PRC targets exhibit a range of RNAPII variants. First, developmental PRC targets are bound by unproductive RNAPII (S5p+S7p−S2p−) genome-wide. Sequential ChIP, Ring1B depletion, and genome-wide correlations show that PRCs and RNAPII-S5p physically bind to the same chromatin and functionally synergize. Second, we identify a cohort of genes marked by PRC and elongating RNAPII (S5p+S7p+S2p+); they produce mRNA and protein, and their expression increases upon PRC1 knockdown. We show that this group of PRC targets switches between active and PRC-repressed states within the ESC population, and that many have roles in metabolism.
Collapse
|
46
|
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: 12] [Impact Index Per Article: 1.0] [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.
Collapse
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
| |
Collapse
|
47
|
Abstract
We analyzed three human genes that were >200 kbp in length as they are switched on rapidly and synchronously by tumor necrosis factor alpha and obtained new insights into the transcription cycle that are difficult to obtain using continuously active, short, genes. First, a preexisting "whole-gene" loop in one gene disappears on stimulation; it is stabilized by CCCTC-binding factor and TFIIB and poises the gene for a prompt response. Second, "subgene" loops (detected using chromosome conformation capture) develop and enlarge, a result that is simply explained if elongating polymerases become immobilized in transcription factories, where they reel in their templates. Third, high-resolution localization confirms that relevant nascent transcripts (detected using RNA fluorescence in situ hybridization) lie close enough to be present on the surface of one factory. These dynamics underscore the complex transitions between the poised, initiating, and elongating transcriptional states.
Collapse
|
48
|
Metazoan promoters: emerging characteristics and insights into transcriptional regulation. Nat Rev Genet 2012; 13:233-45. [PMID: 22392219 DOI: 10.1038/nrg3163] [Citation(s) in RCA: 340] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Promoters are crucial for gene regulation. They vary greatly in terms of associated regulatory elements, sequence motifs, the choice of transcription start sites and other features. Several technologies that harness next-generation sequencing have enabled recent advances in identifying promoters and their features, helping researchers who are investigating functional categories of promoters and their modes of regulation. Additional features of promoters that are being characterized include types of histone modifications, nucleosome positioning, RNA polymerase pausing and novel small RNAs. In this Review, we discuss recent findings relating to metazoan promoters and how these findings are leading to a revised picture of what a gene promoter is and how it works.
Collapse
|
49
|
Sas-Chen A, Avraham R, Yarden Y. A crossroad of microRNAs and immediate early genes (IEGs) encoding oncogenic transcription factors in breast cancer. J Mammary Gland Biol Neoplasia 2012; 17:3-14. [PMID: 22327345 DOI: 10.1007/s10911-012-9243-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Accepted: 01/26/2012] [Indexed: 02/07/2023] Open
Abstract
Signaling networks are involved in development, as well as in malignancy of the mammary gland. Distinct external stimuli activate intricate signaling cascades, which culminate in the activation of specific transcriptional programs. These signal-specific transcriptional programs are instigated by transcription factors (TFs) encoded by the immediate early genes (IEGs), and they lead to diverse cellular outcomes, including oncogenesis. Hence, regulating the expression of IEGs is of great importance, and involves several complementary transcriptional and posttranscriptional mechanisms, the latter entails also microRNAs (miRNAs). miRNAs are a class of non-coding RNAs, which have been implicated in regulation of various aspects of signaling networks. Through examination of the basic characteristics of miRNA function, we highlight the benefits of using miRNAs as regulators of early TFs and signaling networks. We further focus on the role of miRNAs as regulators of IEGs, which shape the initial steps of signaling-induced transcription. We especially emphasize the role of miRNAs in buffering external noise and maintaining low basal activation of IEGs in the absence of proper stimuli.
Collapse
Affiliation(s)
- Aldema Sas-Chen
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, 76100, Israel
| | | | | |
Collapse
|
50
|
Deng B, Melnik S, Cook PR. Transcription factories, chromatin loops, and the dysregulation of gene expression in malignancy. Semin Cancer Biol 2012; 23:65-71. [PMID: 22285981 DOI: 10.1016/j.semcancer.2012.01.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Accepted: 01/03/2012] [Indexed: 02/02/2023]
Abstract
Pathologists recognize and classify cancers according to nuclear morphology, but there remains little scientific explanation of why malignant nuclei possess their characteristic features, or how those features are related to dysregulated function. This essay will discuss a basic structure-function axis that connects one central architectural motif in the nucleus-the chromatin loop-to the vital nuclear function of transcription. The loop is attached to a "transcription factory" through components of the transcription machinery (either polymerases or transcriptional activators/repressors), and the position of a gene within a loop determines how often that gene is transcribed. Then, dysregulated transcription is tightly coupled to alterations in structure, and vice versa. We also speculate on how the experimental approaches being used to analyze loops and factories might be applied to study the problems of tumour initiation and progression.
Collapse
Affiliation(s)
- Binwei Deng
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | | | | |
Collapse
|