1
|
Solovei I, Mirny L. Spandrels of the cell nucleus. Curr Opin Cell Biol 2024; 90:102421. [PMID: 39180905 DOI: 10.1016/j.ceb.2024.102421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Revised: 07/18/2024] [Accepted: 08/02/2024] [Indexed: 08/27/2024]
Abstract
S.J. Gould and R. Lewontin in their famous "Spandrels paper" (1979) argued that many anatomical elements arise in evolution not due to their "current utility" but rather due to other "reasons for origin", such as other developmental processes, physical constraints and mechanical forces. Here, in the same spirit, we argue that a variety of molecular processes, physical constraints, and mechanical forces, alone or together, generate structures that are detectable in the cell nucleus, yet these structures themselves may not carry any specific function, being a mere reflection of processes that produced them.
Collapse
Affiliation(s)
- Irina Solovei
- Biocenter, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany.
| | - Leonid Mirny
- Institute for Medical Engineering and Science, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA.
| |
Collapse
|
2
|
Vilar JMG, Saiz L. The unreasonable effectiveness of equilibrium gene regulation through the cell cycle. Cell Syst 2024; 15:639-648.e2. [PMID: 38981487 DOI: 10.1016/j.cels.2024.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 06/19/2023] [Accepted: 06/14/2024] [Indexed: 07/11/2024]
Abstract
Systems like the prototypical lac operon can reliably hold repression of transcription upon DNA replication across cell cycles with just 10 repressor molecules per cell and behave as if they were at equilibrium. The origin of this phenomenology is still an unresolved question. Here, we develop a general theory to analyze strong perturbations in quasi-equilibrium systems and use it to quantify the effects of DNA replication in gene regulation. We find a scaling law linking actual with predicted equilibrium transcription via a single kinetic parameter. We show that even the lac operon functions beyond the physical limits of naive regulation through compensatory mechanisms that suppress non-equilibrium effects. Synthetic systems without adjuvant activators, such as the cAMP receptor protein (CRP), lack this reliability. Our results provide a rationale for the function of CRP, beyond just being a tunable activator, as a mitigator of cell cycle perturbations.
Collapse
Affiliation(s)
- Jose M G Vilar
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country (UPV/EHU), P.O. Box 644, 48080 Bilbao, Spain; IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain.
| | - Leonor Saiz
- Department of Biomedical Engineering, University of California, 451 E. Health Sciences Drive, Davis, CA 95616, USA; Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany; Center for Systems Biology Dresden, 01307 Dresden, Germany.
| |
Collapse
|
3
|
Kupkova K, Shetty SJ, Hoffman EA, Bekiranov S, Auble DT. Genome-scale chromatin binding dynamics of RNA Polymerase II general transcription machinery components. EMBO J 2024; 43:1799-1821. [PMID: 38565951 PMCID: PMC11066129 DOI: 10.1038/s44318-024-00089-2] [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: 08/02/2023] [Revised: 02/20/2024] [Accepted: 02/28/2024] [Indexed: 04/04/2024] Open
Abstract
A great deal of work has revealed, in structural detail, the components of the preinitiation complex (PIC) machinery required for initiation of mRNA gene transcription by RNA polymerase II (Pol II). However, less-well understood are the in vivo PIC assembly pathways and their kinetics, an understanding of which is vital for determining how rates of in vivo RNA synthesis are established. We used competition ChIP in budding yeast to obtain genome-scale estimates of the residence times for five general transcription factors (GTFs): TBP, TFIIA, TFIIB, TFIIE and TFIIF. While many GTF-chromatin interactions were short-lived ( < 1 min), there were numerous interactions with residence times in the range of several minutes. Sets of genes with a shared function also shared similar patterns of GTF kinetic behavior. TFIIE, a GTF that enters the PIC late in the assembly process, had residence times correlated with RNA synthesis rates. The datasets and results reported here provide kinetic information for most of the Pol II-driven genes in this organism, offering a rich resource for exploring the mechanistic relationships between PIC assembly, gene regulation, and transcription.
Collapse
Affiliation(s)
- Kristyna Kupkova
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA, 22908, USA
- Center for Public Health Genomics, University of Virginia Health System, Charlottesville, VA, 22908, USA
| | - Savera J Shetty
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA, 22908, USA
| | - Elizabeth A Hoffman
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA, 22908, USA
| | - Stefan Bekiranov
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA, 22908, USA
| | - David T Auble
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA, 22908, USA.
| |
Collapse
|
4
|
Dixit S, Middelkoop TC, Choubey S. Governing principles of transcriptional logic out of equilibrium. Biophys J 2024; 123:1015-1029. [PMID: 38486450 PMCID: PMC11052701 DOI: 10.1016/j.bpj.2024.03.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 03/04/2024] [Accepted: 03/11/2024] [Indexed: 03/24/2024] Open
Abstract
To survive, adapt, and develop, cells respond to external and internal stimuli by tightly regulating transcription. Transcriptional regulation involves the combinatorial binding of a repertoire of transcription factors to DNA, which often results in switch-like binary outputs akin to Boolean logic gates. Recent experimental studies have demonstrated that in eukaryotes, transcription factor binding to DNA often involves energy expenditure, thereby driving the system out of equilibrium. The governing principles of transcriptional logic operations out of equilibrium remain unexplored. Here, we employ a simple two-input, single-locus model of transcription that can accommodate both equilibrium and nonequilibrium mechanisms. Using this model, we find that nonequilibrium regimes can give rise to all the logic operations accessible in equilibrium. Strikingly, energy expenditure alters the regulatory function of the two transcription factors in a mutually exclusive manner. This allows for the emergence of new logic operations that are inaccessible in equilibrium. Overall, our results show that energy expenditure can expand the range of cellular decision-making without the need for more complex promoter architectures.
Collapse
Affiliation(s)
- Smruti Dixit
- The Institute of Mathematical Sciences, CIT Campus, Chennai, India.
| | - Teije C Middelkoop
- Laboratory of Developmental Mechanobiology, Division BIOCEV, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Sandeep Choubey
- The Institute of Mathematical Sciences, CIT Campus, Chennai, India; Homi Bhabha National Institute, Training School Complex, Mumbai, India.
| |
Collapse
|
5
|
Hwang DW, Maekiniemi A, Singer RH, Sato H. Real-time single-molecule imaging of transcriptional regulatory networks in living cells. Nat Rev Genet 2024; 25:272-285. [PMID: 38195868 DOI: 10.1038/s41576-023-00684-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/27/2023] [Indexed: 01/11/2024]
Abstract
Gene regulatory networks drive the specific transcriptional programmes responsible for the diversification of cell types during the development of multicellular organisms. Although our knowledge of the genes involved in these dynamic networks has expanded rapidly, our understanding of how transcription is spatiotemporally regulated at the molecular level over a wide range of timescales in the small volume of the nucleus remains limited. Over the past few decades, advances in the field of single-molecule fluorescence imaging have enabled real-time behaviours of individual transcriptional components to be measured in living cells and organisms. These efforts are now shedding light on the dynamic mechanisms of transcription, revealing not only the temporal rules but also the spatial coordination of underlying molecular interactions during various biological events.
Collapse
Affiliation(s)
- Dong-Woo Hwang
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Anna Maekiniemi
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Robert H Singer
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Hanae Sato
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA.
- Nano Life Science Institute (WPI-Nano LSI), Kanazawa University, Kakuma-machi, Kanazawa, Japan.
| |
Collapse
|
6
|
Stortz M, Presman DM, Levi V. Transcriptional condensates: a blessing or a curse for gene regulation? Commun Biol 2024; 7:187. [PMID: 38365945 PMCID: PMC10873363 DOI: 10.1038/s42003-024-05892-5] [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: 10/26/2023] [Accepted: 02/06/2024] [Indexed: 02/18/2024] Open
Abstract
Whether phase-separation is involved in the organization of the transcriptional machinery and if it aids or inhibits the transcriptional process is a matter of intense debate. In this Mini Review, we will cover the current knowledge regarding the role of transcriptional condensates on gene expression regulation. We will summarize the latest discoveries on the relationship between condensate formation, genome organization, and transcriptional activity, focusing on the strengths and weaknesses of the experimental approaches used to interrogate these aspects of transcription in living cells. Finally, we will discuss the challenges for future research.
Collapse
Grants
- PICT 2020-00818 Ministry of Science, Technology and Productive Innovation, Argentina | Agencia Nacional de Promoción Científica y Tecnológica (National Agency for Science and Technology, Argentina)
- PICT-2018-1921 Ministry of Science, Technology and Productive Innovation, Argentina | Agencia Nacional de Promoción Científica y Tecnológica (National Agency for Science and Technology, Argentina)
- PICT 2019-0397 Ministry of Science, Technology and Productive Innovation, Argentina | Agencia Nacional de Promoción Científica y Tecnológica (National Agency for Science and Technology, Argentina)
- 20020190100101BA University of Buenos Aires | Secretaría de Ciencia y Técnica, Universidad de Buenos Aires (Secretaría de Ciencia y Técnica de la Universidad de Buenos Aires)
- 2022-11220210100212CO Consejo Nacional de Investigaciones Científicas y Técnicas (National Scientific and Technical Research Council)
Collapse
Affiliation(s)
- Martin Stortz
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET-Universidad de Buenos Aires, Buenos Aires, C1428EGA, Argentina
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Diego M Presman
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires, C1428EGA, Argentina.
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, C1428EGA, Argentina.
| | - Valeria Levi
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET-Universidad de Buenos Aires, Buenos Aires, C1428EGA, Argentina.
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, C1428EGA, Argentina.
| |
Collapse
|
7
|
Meeussen JVW, Lenstra TL. Time will tell: comparing timescales to gain insight into transcriptional bursting. Trends Genet 2024; 40:160-174. [PMID: 38216391 PMCID: PMC10860890 DOI: 10.1016/j.tig.2023.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/27/2023] [Accepted: 11/27/2023] [Indexed: 01/14/2024]
Abstract
Recent imaging studies have captured the dynamics of regulatory events of transcription inside living cells. These events include transcription factor (TF) DNA binding, chromatin remodeling and modification, enhancer-promoter (E-P) proximity, cluster formation, and preinitiation complex (PIC) assembly. Together, these molecular events culminate in stochastic bursts of RNA synthesis, but their kinetic relationship remains largely unclear. In this review, we compare the timescales of upstream regulatory steps (input) with the kinetics of transcriptional bursting (output) to generate mechanistic models of transcription dynamics in single cells. We highlight open questions and potential technical advances to guide future endeavors toward a quantitative and kinetic understanding of transcription regulation.
Collapse
Affiliation(s)
- Joseph V W Meeussen
- Division of Gene Regulation, The Netherlands Cancer Institute, Oncode Institute, Amsterdam 1066CX, The Netherlands
| | - Tineke L Lenstra
- Division of Gene Regulation, The Netherlands Cancer Institute, Oncode Institute, Amsterdam 1066CX, The Netherlands.
| |
Collapse
|
8
|
Du M, Stitzinger SH, Spille JH, Cho WK, Lee C, Hijaz M, Quintana A, Cissé II. Direct observation of a condensate effect on super-enhancer controlled gene bursting. Cell 2024; 187:331-344.e17. [PMID: 38194964 DOI: 10.1016/j.cell.2023.12.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 10/29/2023] [Accepted: 12/04/2023] [Indexed: 01/11/2024]
Abstract
Enhancers are distal DNA elements believed to loop and contact promoters to control gene expression. Recently, we found diffraction-sized transcriptional condensates at genes controlled by clusters of enhancers (super-enhancers). However, a direct function of endogenous condensates in controlling gene expression remains elusive. Here, we develop live-cell super-resolution and multi-color 3D-imaging approaches to investigate putative roles of endogenous condensates in the regulation of super-enhancer controlled gene Sox2. In contrast to enhancer distance, we find instead that the condensate's positional dynamics are a better predictor of gene expression. A basal gene bursting occurs when the condensate is far (>1 μm), but burst size and frequency are enhanced when the condensate moves in proximity (<1 μm). Perturbations of cohesin and local DNA elements do not prevent basal bursting but affect the condensate and its burst enhancement. We propose a three-way kissing model whereby the condensate interacts transiently with gene locus and regulatory DNA elements to control gene bursting.
Collapse
Affiliation(s)
- Manyu Du
- Department of Biological Physics, Max Planck Institute for Immunobiology and Epigenetics, Freiburg im Breisgau, Baden-Württemberg 79108, Germany
| | - Simon Hendrik Stitzinger
- Department of Biological Physics, Max Planck Institute for Immunobiology and Epigenetics, Freiburg im Breisgau, Baden-Württemberg 79108, Germany
| | - Jan-Hendrik Spille
- Department of Biological Physics, Max Planck Institute for Immunobiology and Epigenetics, Freiburg im Breisgau, Baden-Württemberg 79108, Germany
| | - Won-Ki Cho
- Department of Biological Physics, Max Planck Institute for Immunobiology and Epigenetics, Freiburg im Breisgau, Baden-Württemberg 79108, Germany
| | - Choongman Lee
- Department of Biological Physics, Max Planck Institute for Immunobiology and Epigenetics, Freiburg im Breisgau, Baden-Württemberg 79108, Germany
| | - Mohammed Hijaz
- Department of Biological Physics, Max Planck Institute for Immunobiology and Epigenetics, Freiburg im Breisgau, Baden-Württemberg 79108, Germany
| | - Andrea Quintana
- Department of Biological Physics, Max Planck Institute for Immunobiology and Epigenetics, Freiburg im Breisgau, Baden-Württemberg 79108, Germany
| | - Ibrahim I Cissé
- Department of Biological Physics, Max Planck Institute for Immunobiology and Epigenetics, Freiburg im Breisgau, Baden-Württemberg 79108, Germany.
| |
Collapse
|
9
|
Syed S, Lim B. Multi-labeling Live Imaging to Quantify Gene Expression Dynamics During Drosophila Embryonic Development. Methods Mol Biol 2024; 2805:137-151. [PMID: 39008179 DOI: 10.1007/978-1-0716-3854-5_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Transcription in developing metazoans is inherently stochastic, involving transient and dynamic interactions among transcriptional machinery. A fundamental challenge with traditional techniques, including fixed-tissue protein and RNA staining, is the lack of temporal resolution. Quantifying kinetic changes in transcription can elucidate underlying mechanisms of interaction among regulatory modules. In this protocol, we describe the successful implementation of a combination of MS2/MCP and PP7/PCP systems in living Drosophila embryos to further our understanding of transcriptional dynamics during development. Our technique can be extended to visualize transcriptional activities of multiple genes or alleles simultaneously, characterize allele-specific expression of a target gene, and quantitatively analyze RNA polymerase II activity in a single-cell resolution.
Collapse
Affiliation(s)
- Sahla Syed
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Bomyi Lim
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
10
|
Yavuz S, Kabbech H, van Staalduinen J, Linder S, van Cappellen W, Nigg A, Abraham T, Slotman J, Quevedo M, Poot R, Zwart W, van Royen M, Grosveld F, Smal I, Houtsmuller A. Compartmentalization of androgen receptors at endogenous genes in living cells. Nucleic Acids Res 2023; 51:10992-11009. [PMID: 37791849 PMCID: PMC10639085 DOI: 10.1093/nar/gkad803] [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: 04/14/2023] [Revised: 09/06/2023] [Accepted: 09/20/2023] [Indexed: 10/05/2023] Open
Abstract
A wide range of nuclear proteins are involved in the spatio-temporal organization of the genome through diverse biological processes such as gene transcription and DNA replication. Upon stimulation by testosterone and translocation to the nucleus, multiple androgen receptors (ARs) accumulate in microscopically discernable foci which are irregularly distributed in the nucleus. Here, we investigated the formation and physical nature of these foci, by combining novel fluorescent labeling techniques to visualize a defined chromatin locus of AR-regulated genes-PTPRN2 or BANP-simultaneously with either AR foci or individual AR molecules. Quantitative colocalization analysis showed evidence of AR foci formation induced by R1881 at both PTPRN2 and BANP loci. Furthermore, single-particle tracking (SPT) revealed three distinct subdiffusive fractional Brownian motion (fBm) states: immobilized ARs were observed near the labeled genes likely as a consequence of DNA-binding, while the intermediate confined state showed a similar spatial behavior but with larger displacements, suggesting compartmentalization by liquid-liquid phase separation (LLPS), while freely mobile ARs were diffusing in the nuclear environment. All together, we show for the first time in living cells the presence of AR-regulated genes in AR foci.
Collapse
Affiliation(s)
- Selçuk Yavuz
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Hélène Kabbech
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jente van Staalduinen
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Simon Linder
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Wiggert A van Cappellen
- Erasmus Optical Imaging Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Alex L Nigg
- Erasmus Optical Imaging Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Tsion E Abraham
- Erasmus Optical Imaging Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Johan A Slotman
- Erasmus Optical Imaging Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marti Quevedo
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Raymond A Poot
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Wilbert Zwart
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Martin E van Royen
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Frank G Grosveld
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Ihor Smal
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Adriaan B Houtsmuller
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Erasmus Optical Imaging Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| |
Collapse
|
11
|
Keller SH, Deng H, Lim B. Regulation of the dynamic RNA Pol II elongation rate in Drosophila embryos. Cell Rep 2023; 42:113225. [PMID: 37837623 PMCID: PMC10842316 DOI: 10.1016/j.celrep.2023.113225] [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: 06/29/2022] [Revised: 08/20/2023] [Accepted: 09/22/2023] [Indexed: 10/16/2023] Open
Abstract
An increasing number of studies have shown the key role that RNA polymerase II (RNA Pol II) elongation plays in gene regulation. We systematically examine how various enhancers, promoters, and gene body composition influence the RNA Pol II elongation rate through a single-cell-resolution live imaging assay. By using reporter constructs containing 5' MS2 and 3' PP7 repeating stem loops, we quantify the rate of RNA Pol II elongation in live Drosophila embryos. We find that promoters and exonic gene lengths have no effect on elongation rate, while enhancers and the presence of long introns may significantly change how quickly RNA Pol II moves across a gene. Furthermore, we observe in multiple constructs that the RNA Pol II elongation rate accelerates after the transcriptional onset of nuclear cycle 14 in Drosophila embryos. Our study provides a single-cell view of various mechanisms that affect the dynamic RNA Pol II elongation rate, ultimately affecting the rate of mRNA production.
Collapse
Affiliation(s)
- Samuel H Keller
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hao Deng
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Bomyi Lim
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA.
| |
Collapse
|
12
|
Junier I, Ghobadpour E, Espeli O, Everaers R. DNA supercoiling in bacteria: state of play and challenges from a viewpoint of physics based modeling. Front Microbiol 2023; 14:1192831. [PMID: 37965550 PMCID: PMC10642903 DOI: 10.3389/fmicb.2023.1192831] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 09/25/2023] [Indexed: 11/16/2023] Open
Abstract
DNA supercoiling is central to many fundamental processes of living organisms. Its average level along the chromosome and over time reflects the dynamic equilibrium of opposite activities of topoisomerases, which are required to relax mechanical stresses that are inevitably produced during DNA replication and gene transcription. Supercoiling affects all scales of the spatio-temporal organization of bacterial DNA, from the base pair to the large scale chromosome conformation. Highlighted in vitro and in vivo in the 1960s and 1970s, respectively, the first physical models were proposed concomitantly in order to predict the deformation properties of the double helix. About fifteen years later, polymer physics models demonstrated on larger scales the plectonemic nature and the tree-like organization of supercoiled DNA. Since then, many works have tried to establish a better understanding of the multiple structuring and physiological properties of bacterial DNA in thermodynamic equilibrium and far from equilibrium. The purpose of this essay is to address upcoming challenges by thoroughly exploring the relevance, predictive capacity, and limitations of current physical models, with a specific focus on structural properties beyond the scale of the double helix. We discuss more particularly the problem of DNA conformations, the interplay between DNA supercoiling with gene transcription and DNA replication, its role on nucleoid formation and, finally, the problem of scaling up models. Our primary objective is to foster increased collaboration between physicists and biologists. To achieve this, we have reduced the respective jargon to a minimum and we provide some explanatory background material for the two communities.
Collapse
Affiliation(s)
- Ivan Junier
- CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, Université Grenoble Alpes, Grenoble, France
| | - Elham Ghobadpour
- CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, Université Grenoble Alpes, Grenoble, France
- École Normale Supérieure (ENS) de Lyon, CNRS, Laboratoire de Physique and Centre Blaise Pascal de l'ENS de Lyon, Lyon, France
| | - Olivier Espeli
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Ralf Everaers
- École Normale Supérieure (ENS) de Lyon, CNRS, Laboratoire de Physique and Centre Blaise Pascal de l'ENS de Lyon, Lyon, France
| |
Collapse
|
13
|
Wang Y, He S, Fang X. Emerging roles of phase separation in plant transcription and chromatin organization. CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102387. [PMID: 37311366 DOI: 10.1016/j.pbi.2023.102387] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/07/2023] [Accepted: 05/10/2023] [Indexed: 06/15/2023]
Abstract
Transcription is a core step in gene expression. Regulation of transcription is achieved at the level of transcription machinery, local chromatin environment as well as higher-order chromatin organization. Our understanding of transcriptional regulation was advanced by recent introduction of transcription and chromatin-associated condensates, which typically arise via phase separation of proteins and nucleic acids. While studies from mammalian cells are unveiling the mechanisms of phase separation in transcription regulation, those in plants further broaden and deepen our understanding of this process. In this review, we discuss recent progress in plants how phase separation operates in RNA-mediated chromatin silencing, transcription activity, and chromatin compartmentalization.
Collapse
Affiliation(s)
- Yunhe Wang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Shengbo He
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China.
| | - Xiaofeng Fang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| |
Collapse
|
14
|
Mahat DB, Tippens ND, Martin-Rufino JD, Waterton SK, Fu J, Blatt SE, Sharp PA. Single-cell nascent RNA sequencing using click-chemistry unveils coordinated transcription. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.15.558015. [PMID: 37745427 PMCID: PMC10516050 DOI: 10.1101/2023.09.15.558015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Transcription is the primary regulatory step in gene expression. Divergent transcription initiation from promoters and enhancers produces stable RNAs from genes and unstable RNAs from enhancers1-5. Nascent RNA capture and sequencing assays simultaneously measure gene and enhancer activity in cell populations6-9. However, fundamental questions in the temporal regulation of transcription and enhancer-gene synchrony remain unanswered primarily due to the absence of a single-cell perspective on active transcription. In this study, we present scGRO-seq - a novel single-cell nascent RNA sequencing assay using click-chemistry - and unveil the coordinated transcription throughout the genome. scGRO-seq demonstrates the episodic nature of transcription, and estimates burst size and frequency by directly quantifying transcribing RNA polymerases in individual cells. It reveals the co-transcription of functionally related genes and leverages the replication-dependent non-polyadenylated histone genes transcription to elucidate cell-cycle dynamics. The single-nucleotide spatial and temporal resolution of scGRO-seq identifies networks of enhancers and genes and indicates that the bursting of transcription at super-enhancers precedes the burst from associated genes. By imparting insights into the dynamic nature of transcription and the origin and propagation of transcription signals, scGRO-seq demonstrates its unique ability to investigate the mechanisms of transcription regulation and the role of enhancers in gene expression.
Collapse
Affiliation(s)
- Dig B. Mahat
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Nathaniel D. Tippens
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | | | - Sean K. Waterton
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
- Current address: Department of Biology, Stanford University, Stanford, CA 94305
| | - Jiayu Fu
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
- Current address: Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL 60208
| | - Sarah E. Blatt
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
- Current address: Exact Sciences Corporation, Madison, WI 53719
| | - Phillip A. Sharp
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
- Lead Contact
| |
Collapse
|
15
|
Kleiner RE. Chemical Approaches To Investigate Post-transcriptional RNA Regulation. ACS Chem Biol 2023; 18:1684-1697. [PMID: 37540831 PMCID: PMC11031734 DOI: 10.1021/acschembio.3c00406] [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] [Indexed: 08/06/2023]
Abstract
RNA plays a central role in biological processes, and its activity is regulated by a host of diverse chemical and biochemical mechanisms including post-transcriptional modification and interactions with RNA-binding proteins. Here, we describe our efforts to illuminate RNA biology through the application of chemical tools, focusing on post-transcriptional regulatory mechanisms. We describe the development of an activity-based protein profiling approach for discovery and characterization of RNA-modifying enzymes. Next, we highlight novel approaches for RNA imaging based upon metabolic labeling with modified nucleosides and engineering of the nucleotide salvage pathway. Finally, we discuss profiling RNA-protein interactions using small molecule-dependent RNA editing and synthetic photo-cross-linkable oligonucleotide probes. Our work provides enabling technologies for deciphering the complexity of RNA and its diverse functions in biology.
Collapse
Affiliation(s)
- Ralph E. Kleiner
- Department of Chemistry, Princeton University, Princeton, NJ, USA 08544
| |
Collapse
|
16
|
Kupkova K, Shetty SJ, Hoffman EA, Bekiranov S, Auble DT. Genome-scale chromatin interaction dynamic measurements for key components of the RNA Pol II general transcription machinery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.25.550532. [PMID: 37546819 PMCID: PMC10402067 DOI: 10.1101/2023.07.25.550532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Background A great deal of work has revealed in structural detail the components of the machinery responsible for mRNA gene transcription initiation. These include the general transcription factors (GTFs), which assemble at promoters along with RNA Polymerase II (Pol II) to form a preinitiation complex (PIC) aided by the activities of cofactors and site-specific transcription factors (TFs). However, less well understood are the in vivo PIC assembly pathways and their kinetics, an understanding of which is vital for determining on a mechanistic level how rates of in vivo RNA synthesis are established and how cofactors and TFs impact them. Results We used competition ChIP to obtain genome-scale estimates of the residence times for five GTFs: TBP, TFIIA, TFIIB, TFIIE and TFIIF in budding yeast. While many GTF-chromatin interactions were short-lived (< 1 min), there were numerous interactions with residence times in the several minutes range. Sets of genes with a shared function also shared similar patterns of GTF kinetic behavior. TFIIE, a GTF that enters the PIC late in the assembly process, had residence times correlated with RNA synthesis rates. Conclusions The datasets and results reported here provide kinetic information for most of the Pol II-driven genes in this organism and therefore offer a rich resource for exploring the mechanistic relationships between PIC assembly, gene regulation, and transcription. The relationships between gene function and GTF dynamics suggest that shared sets of TFs tune PIC assembly kinetics to ensure appropriate levels of expression.
Collapse
Affiliation(s)
- Kristyna Kupkova
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908
- Center for Public Health Genomics, University of Virginia Health System, Charlottesville, VA 22908
| | - Savera J. Shetty
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908
| | - Elizabeth A. Hoffman
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908
| | - Stefan Bekiranov
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908
| | - David T. Auble
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908
| |
Collapse
|
17
|
Pownall ME, Miao L, Vejnar CE, M’Saad O, Sherrard A, Frederick MA, Benitez MD, Boswell CW, Zaret KS, Bewersdorf J, Giraldez AJ. Chromatin expansion microscopy reveals nanoscale organization of transcription and chromatin. Science 2023; 381:92-100. [PMID: 37410825 PMCID: PMC10372697 DOI: 10.1126/science.ade5308] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 05/17/2023] [Indexed: 07/08/2023]
Abstract
Nanoscale chromatin organization regulates gene expression. Although chromatin is notably reprogrammed during zygotic genome activation (ZGA), the organization of chromatin regulatory factors during this universal process remains unclear. In this work, we developed chromatin expansion microscopy (ChromExM) to visualize chromatin, transcription, and transcription factors in vivo. ChromExM of embryos during ZGA revealed how the pioneer factor Nanog interacts with nucleosomes and RNA polymerase II (Pol II), providing direct visualization of transcriptional elongation as string-like nanostructures. Blocking elongation led to more Pol II particles clustered around Nanog, with Pol II stalled at promoters and Nanog-bound enhancers. This led to a new model termed "kiss and kick", in which enhancer-promoter contacts are transient and released by transcriptional elongation. Our results demonstrate that ChromExM is broadly applicable to study nanoscale nuclear organization.
Collapse
Affiliation(s)
- Mark E. Pownall
- Department of Genetics, Yale University School of Medicine; New Haven, CT 06510, USA
| | - Liyun Miao
- Department of Genetics, Yale University School of Medicine; New Haven, CT 06510, USA
| | - Charles E. Vejnar
- Department of Genetics, Yale University School of Medicine; New Haven, CT 06510, USA
| | - Ons M’Saad
- Department of Cell Biology, Yale University School of Medicine; New Haven, CT 06510, USA
- Department of Biomedical Engineering, Yale University; New Haven, CT 06510, USA
| | - Alice Sherrard
- Department of Genetics, Yale University School of Medicine; New Haven, CT 06510, USA
| | - Megan A. Frederick
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Maria D.J. Benitez
- Department of Genetics, Yale University School of Medicine; New Haven, CT 06510, USA
| | - Curtis W. Boswell
- Department of Genetics, Yale University School of Medicine; New Haven, CT 06510, USA
| | - Kenneth S. Zaret
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale University School of Medicine; New Haven, CT 06510, USA
- Kavli Institute for Neuroscience, Yale University School of Medicine; New Haven, CT 06510, USA
- Department of Biomedical Engineering, Yale University; New Haven, CT 06510, USA
- Department of Physics, Yale University; New Haven, CT 06510, USA
- Nanobiology Institute, Yale University; West Haven, CT 06477, USA
| | - Antonio J. Giraldez
- Department of Genetics, Yale University School of Medicine; New Haven, CT 06510, USA
- Yale Stem Cell Center, Yale University School of Medicine; New Haven, CT 06510, USA
- Yale Cancer Center, Yale University School of Medicine; New Haven, CT 06510, USA
| |
Collapse
|
18
|
Mach P, Giorgetti L. Integrative approaches to study enhancer-promoter communication. Curr Opin Genet Dev 2023; 80:102052. [PMID: 37257410 PMCID: PMC10293802 DOI: 10.1016/j.gde.2023.102052] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/21/2023] [Accepted: 04/22/2023] [Indexed: 06/02/2023]
Abstract
The spatiotemporal control of gene expression in complex multicellular organisms relies on noncoding regulatory sequences such as enhancers, which activate transcription of target genes often over large genomic distances. Despite the advances in the identification and characterization of enhancers, the principles and mechanisms by which enhancers select and control their target genes remain largely unknown. Here, we review recent interdisciplinary and quantitative approaches based on emerging techniques that aim to address open questions in the field, notably how regulatory information is encoded in the DNA sequence, how this information is transferred from enhancers to promoters, and how these processes are regulated in time.
Collapse
Affiliation(s)
- Pia Mach
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; University of Basel, Basel, Switzerland. https://twitter.com/@MachPia
| | - Luca Giorgetti
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
| |
Collapse
|
19
|
Langenbacher AD, Lu F, Crisman L, Huang ZYS, Chapski DJ, Vondriska TM, Wang Y, Gao C, Chen JN. Rtf1 Transcriptionally Regulates Neonatal and Adult Cardiomyocyte Biology. J Cardiovasc Dev Dis 2023; 10:221. [PMID: 37233188 PMCID: PMC10219292 DOI: 10.3390/jcdd10050221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/16/2023] [Accepted: 05/18/2023] [Indexed: 05/27/2023] Open
Abstract
The PAF1 complex component Rtf1 is an RNA Polymerase II-interacting transcription regulatory protein that promotes transcription elongation and the co-transcriptional monoubiquitination of histone 2B. Rtf1 plays an essential role in the specification of cardiac progenitors from the lateral plate mesoderm during early embryogenesis, but its requirement in mature cardiac cells is unknown. Here, we investigate the importance of Rtf1 in neonatal and adult cardiomyocytes using knockdown and knockout approaches. We demonstrate that loss of Rtf1 activity in neonatal cardiomyocytes disrupts cell morphology and results in a breakdown of sarcomeres. Similarly, Rtf1 ablation in mature cardiomyocytes of the adult mouse heart leads to myofibril disorganization, disrupted cell-cell junctions, fibrosis, and systolic dysfunction. Rtf1 knockout hearts eventually fail and exhibit structural and gene expression defects resembling dilated cardiomyopathy. Intriguingly, we observed that loss of Rtf1 activity causes a rapid change in the expression of key cardiac structural and functional genes in both neonatal and adult cardiomyocytes, suggesting that Rtf1 is continuously required to support expression of the cardiac gene program.
Collapse
Affiliation(s)
- Adam D Langenbacher
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90025, USA
| | - Fei Lu
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90025, USA
| | - Lauren Crisman
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90025, USA
| | - Zi Yi Stephanie Huang
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90025, USA
| | - Douglas J Chapski
- Departments of Anesthesiology, Medicine, and Physiology, David Geffen School of Medicine, University of California, Los Angeles, CA 90025, USA
| | - Thomas M Vondriska
- Departments of Anesthesiology, Medicine, and Physiology, David Geffen School of Medicine, University of California, Los Angeles, CA 90025, USA
| | - Yibin Wang
- Departments of Anesthesiology, Medicine, and Physiology, David Geffen School of Medicine, University of California, Los Angeles, CA 90025, USA
- Signature Research Program in Cardiovascular and Metabolic Diseases, Duke-NUS School of Medicine and National Heart Center of Singapore, Singapore 169857, Singapore
| | - Chen Gao
- Departments of Anesthesiology, Medicine, and Physiology, David Geffen School of Medicine, University of California, Los Angeles, CA 90025, USA
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Jau-Nian Chen
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90025, USA
| |
Collapse
|
20
|
Goychuk A, Kannan D, Chakraborty AK, Kardar M. Polymer folding through active processes recreates features of genome organization. Proc Natl Acad Sci U S A 2023; 120:e2221726120. [PMID: 37155885 PMCID: PMC10194017 DOI: 10.1073/pnas.2221726120] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 04/02/2023] [Indexed: 05/10/2023] Open
Abstract
From proteins to chromosomes, polymers fold into specific conformations that control their biological function. Polymer folding has long been studied with equilibrium thermodynamics, yet intracellular organization and regulation involve energy-consuming, active processes. Signatures of activity have been measured in the context of chromatin motion, which shows spatial correlations and enhanced subdiffusion only in the presence of adenosine triphosphate. Moreover, chromatin motion varies with genomic coordinate, pointing toward a heterogeneous pattern of active processes along the sequence. How do such patterns of activity affect the conformation of a polymer such as chromatin? We address this question by combining analytical theory and simulations to study a polymer subjected to sequence-dependent correlated active forces. Our analysis shows that a local increase in activity (larger active forces) can cause the polymer backbone to bend and expand, while less active segments straighten out and condense. Our simulations further predict that modest activity differences can drive compartmentalization of the polymer consistent with the patterns observed in chromosome conformation capture experiments. Moreover, segments of the polymer that show correlated active (sub)diffusion attract each other through effective long-ranged harmonic interactions, whereas anticorrelations lead to effective repulsions. Thus, our theory offers nonequilibrium mechanisms for forming genomic compartments, which cannot be distinguished from affinity-based folding using structural data alone. As a first step toward exploring whether active mechanisms contribute to shaping genome conformations, we discuss a data-driven approach.
Collapse
Affiliation(s)
- Andriy Goychuk
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Deepti Kannan
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Arup K. Chakraborty
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA02139
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Mehran Kardar
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA02139
| |
Collapse
|
21
|
Mahdavi S, Salmon GL, Daghlian P, Garcia HG, Phillips R. Flexibility and sensitivity in gene regulation out of equilibrium. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.11.536490. [PMID: 37090612 PMCID: PMC10120662 DOI: 10.1101/2023.04.11.536490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Cells adapt to environments and tune gene expression by controlling the concentrations of proteins and their kinetics in regulatory networks. In both eukaryotes and prokaryotes, experiments and theory increasingly attest that these networks can and do consume bio-chemical energy. How does this dissipation enable cellular behaviors unobtainable in equilibrium? This open question demands quantitative models that transcend thermodynamic equilibrium. Here we study the control of a simple, ubiquitous gene regulatory motif to explore the consequences of departing equilibrium in kinetic cycles. Employing graph theory, we find that dissipation unlocks nonmonotonicity and enhanced sensitivity of gene expression with respect to a transcription factor's concentration. These features allow a single transcription factor to act as both a repressor and activator at different levels or achieve outputs with multiple concentration regions of locally-enhanced sensitivity. We systematically dissect how energetically-driving individual transitions within regulatory networks, or pairs of transitions, generates more adjustable and sensitive phenotypic responses. Our findings quantify necessary conditions and detectable consequences of energy expenditure. These richer mathematical behaviors-feasibly accessed using biological energy budgets and rates-may empower cells to accomplish sophisticated regulation with simpler architectures than those required at equilibrium. Significance Statement Growing theoretical and experimental evidence demonstrates that cells can (and do) spend biochemical energy while regulating their genes. Here we explore the impact of departing from equilibrium in simple regulatory cycles, and learn that beyond increasing sensitivity, dissipation can unlock more flexible input-output behaviors that are otherwise forbidden without spending energy. These more complex behaviors could enable cells to perform more sophisticated functions using simpler systems than those needed at equilibrium.
Collapse
|
22
|
Competing constraints shape the nonequilibrium limits of cellular decision-making. Proc Natl Acad Sci U S A 2023; 120:e2211203120. [PMID: 36862689 PMCID: PMC10013869 DOI: 10.1073/pnas.2211203120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Abstract
Gene regulation is central to cellular function. Yet, despite decades of work, we lack quantitative models that can predict how transcriptional control emerges from molecular interactions at the gene locus. Thermodynamic models of transcription, which assume that gene circuits operate at equilibrium, have previously been employed with considerable success in the context of bacterial systems. However, the presence of ATP-dependent processes within the eukaryotic transcriptional cycle suggests that equilibrium models may be insufficient to capture how eukaryotic gene circuits sense and respond to input transcription factor concentrations. Here, we employ simple kinetic models of transcription to investigate how energy dissipation within the transcriptional cycle impacts the rate at which genes transmit information and drive cellular decisions. We find that biologically plausible levels of energy input can lead to significant gains in how rapidly gene loci transmit information but discover that the regulatory mechanisms underlying these gains change depending on the level of interference from noncognate activator binding. When interference is low, information is maximized by harnessing energy to push the sensitivity of the transcriptional response to input transcription factors beyond its equilibrium limits. Conversely, when interference is high, conditions favor genes that harness energy to increase transcriptional specificity by proofreading activator identity. Our analysis further reveals that equilibrium gene regulatory mechanisms break down as transcriptional interference increases, suggesting that energy dissipation may be indispensable in systems where noncognate factor interference is sufficiently large.
Collapse
|
23
|
Das SK, Lewis BA, Levens D. MYC: a complex problem. Trends Cell Biol 2023; 33:235-246. [PMID: 35963793 PMCID: PMC9911561 DOI: 10.1016/j.tcb.2022.07.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 07/11/2022] [Accepted: 07/13/2022] [Indexed: 12/22/2022]
Abstract
The MYC protooncogene functions as a universal amplifier of transcription through interaction with numerous factors and complexes that regulate almost every cellular process. However, a comprehensive model that explains MYC's actions and the interplay governing the complicated dynamics of components of the transcription and replication machinery is still lacking. Here, we review the potency of MYC as an oncogenic driver and how it regulates the broad spectrum of complexes (effectors and regulators). We propose a 'hand-over model' for differential partitioning and trafficking of unstructured MYC via a loose interaction network between various gene-regulatory complexes and factors. Additionally, the article discusses how unstructured-MYC energetically favors efficient modulation of the energy landscape of the transcription cycle.
Collapse
Affiliation(s)
- Subhendu K Das
- Gene Regulation Section, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute (NCI), Bethesda, MD 20892-1500, USA
| | - Brian A Lewis
- Gene Regulation Section, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute (NCI), Bethesda, MD 20892-1500, USA
| | - David Levens
- Gene Regulation Section, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute (NCI), Bethesda, MD 20892-1500, USA.
| |
Collapse
|
24
|
Itani A, Shida Y, Ogasawara W. A microfluidic device for simultaneous detection of enzyme secretion and elongation of a single hypha. Front Microbiol 2023; 14:1125760. [PMID: 36937311 PMCID: PMC10020217 DOI: 10.3389/fmicb.2023.1125760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 02/16/2023] [Indexed: 03/06/2023] Open
Abstract
Filamentous fungi grow through elongation of their apical region by exocytosis and secrete enzymes that can be of commercial or industrial importance. Their hyphae exhibit extensive branching, making it difficult to control hyphal growth for observation and analysis. Therefore, although hyphal morphology and productivity are closely related, the relationship between the two has not yet been clarified. Conventional morphology and productivity studies have only compared the results of macro imaging of fungal pellets cultured in bulk with the averaged products in the culture medium. Filamentous fungi are multicellular and their expression differs between different hyphae. To truly understand the relationship between morphology and productivity, it is necessary to compare the morphology and productivity of individual hyphae. To achieve this, we developed a microfluidic system that confines hyphae to individual channels for observation and investigated the relationship between their growth, morphology, and enzyme productivity. Furthermore, using Trichoderma reesei, a potent cellulase-producing fungus, as a model, we developed a cellulase detection assay with 4-MUC substrate to detect hyphal growth and enzyme secretion in a microfluidic device in real time. Using a strain that expresses cellobiohydrolase I (CBH I) fused with AcGFP1, we compared fluorescence from the detection assay with GFP fluorescence intensity, which showed a strong correlation between the two. These results indicate that extracellular enzymes can be easily detected in the microfluidic device in real time because the production of cellulase is synchronized in T. reesei. This microfluidic system enables real-time visualization of the dynamics of hypha and enzymes during carbon source exchange and the quantitative dynamics of gene expression. This technology can be applied to many biosystems from bioenergy production to human health.
Collapse
Affiliation(s)
- Ayaka Itani
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Japan
| | - Yosuke Shida
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Japan
- *Correspondence: Yosuke Shida,
| | - Wataru Ogasawara
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Japan
- Department of Science of Technology Innovation, Nagaoka University of Technology, Nagaoka, Japan
- Wataru Ogasawara,
| |
Collapse
|
25
|
Wang K, Escobar M, Li J, Mahata B, Goell J, Shah S, Cluck M, Hilton I. Systematic comparison of CRISPR-based transcriptional activators uncovers gene-regulatory features of enhancer-promoter interactions. Nucleic Acids Res 2022; 50:7842-7855. [PMID: 35849129 PMCID: PMC9371918 DOI: 10.1093/nar/gkac582] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 06/19/2022] [Accepted: 06/24/2022] [Indexed: 12/29/2022] Open
Abstract
Nuclease-inactivated CRISPR/Cas-based (dCas-based) systems have emerged as powerful technologies to synthetically reshape the human epigenome and gene expression. Despite the increasing adoption of these platforms, their relative potencies and mechanistic differences are incompletely characterized, particularly at human enhancer-promoter pairs. Here, we systematically compared the most widely adopted dCas9-based transcriptional activators, as well as an activator consisting of dCas9 fused to the catalytic core of the human CBP protein, at human enhancer-promoter pairs. We find that these platforms display variable relative expression levels in different human cell types and that their transactivation efficacies vary based upon the effector domain, effector recruitment architecture, targeted locus and cell type. We also show that each dCas9-based activator can induce the production of enhancer RNAs (eRNAs) and that this eRNA induction is positively correlated with downstream mRNA expression from a cognate promoter. Additionally, we use dCas9-based activators to demonstrate that an intrinsic transcriptional and epigenetic reciprocity can exist between human enhancers and promoters and that enhancer-mediated tracking and engagement of a downstream promoter can be synthetically driven by targeting dCas9-based transcriptional activators to an enhancer. Collectively, our study provides new insights into the enhancer-mediated control of human gene expression and the use of dCas9-based activators.
Collapse
Affiliation(s)
- Kaiyuan Wang
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - Mario Escobar
- Department of BioSciences, Rice University, Houston, TX 77005, USA
| | - Jing Li
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - Barun Mahata
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - Jacob Goell
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - Spencer Shah
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - Madeleine Cluck
- Department of BioSciences, Rice University, Houston, TX 77005, USA
| | - Isaac B Hilton
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
- Department of BioSciences, Rice University, Houston, TX 77005, USA
| |
Collapse
|
26
|
Forero-Quintero LS, Raymond W, Munsky B, Stasevich TJ. Visualization, Quantification, and Modeling of Endogenous RNA Polymerase II Phosphorylation at a Single-copy Gene in Living Cells. Bio Protoc 2022; 12:e4482. [PMID: 36082371 PMCID: PMC9411018 DOI: 10.21769/bioprotoc.4482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 06/12/2022] [Accepted: 06/14/2022] [Indexed: 01/05/2023] Open
Abstract
In eukaryotic cells, RNA Polymerase II (RNAP2) is the enzyme in charge of transcribing mRNA from DNA. RNAP2 possesses an extended carboxy-terminal domain (CTD) that gets dynamically phosphorylated as RNAP2 progresses through the transcription cycle, therefore regulating each step of transcription from recruitment to termination. Although RNAP2 residue-specific phosphorylation has been characterized in fixed cells by immunoprecipitation-based assays, or in live cells by using tandem gene arrays, these assays can mask heterogeneity and limit temporal and spatial resolution. Our protocol employs multi-colored complementary fluorescent antibody-based (Fab) probes to specifically detect the CTD of the RNAP2 (CTD-RNAP2), and its phosphorylated form at the serine 5 residue (Ser5ph-RNAP2) at a single-copy HIV-1 reporter gene. Together with high-resolution fluorescence microscopy, single-molecule tracking analysis, and rigorous computational modeling, our system allows us to visualize, quantify, and predict endogenous RNAP2 phosphorylation dynamics and mRNA synthesis at a single-copy gene, in living cells, and throughout the transcription cycle. Graphical abstract: Schematic of the steps for visualizing, quantifying, and predicting RNAP2 phosphorylation at a single-copy gene.
Collapse
Affiliation(s)
- Linda S. Forero-Quintero
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80523, USA
,
*For correspondence:
| | - William Raymond
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523, USA
| | - Brian Munsky
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80523, USA
,
School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523, USA
| | - Timothy J. Stasevich
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
,
Cell Biology Center and World Research Hub Initiative, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8503, Japan
| |
Collapse
|
27
|
Deng H, Lim B. Shared Transcriptional Machinery at Homologous Alleles Leads to Reduced Transcription in Early Drosophila Embryos. Front Cell Dev Biol 2022; 10:912838. [PMID: 35898395 PMCID: PMC9311490 DOI: 10.3389/fcell.2022.912838] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 06/21/2022] [Indexed: 02/05/2023] Open
Abstract
The mechanism by which transcriptional machinery is recruited to enhancers and promoters to regulate gene expression is one of the most challenging and extensively studied questions in modern biology. We explored the possibility that interallelic interactions between two homologous alleles might affect gene regulation. Using an MS2- and PP7-based, allele-specific live imaging assay, we visualized de novo transcripts of a reporter gene in hemizygous and homozygous Drosophila embryos. Surprisingly, each homozygous allele produced fewer RNAs than the corresponding hemizygous allele, suggesting the possibility of allelic competition in homozygotes. However, the competition was not observed when the enhancer-promoter interaction was weakened by placing the reporter construct in a different chromosome location or by moving the enhancer further away from the promoter. Moreover, the reporter gene showed reduced transcriptional activity when a partial transcription unit (either an enhancer or reporter gene only) was in the homologous position. We propose that the transcriptional machinery that binds both the enhancer and promoter regions, such as RNA Pol II or preinitiation complexes, may be responsible for the allelic competition. We showed that the degree of allelic interference increased over developmental time as more Pol II was needed to activate zygotic genes. Such allelic competition was observed for an endogenous gene as well. Our study provides new insights into the role of 3D interallelic interactions in gene regulation.
Collapse
|
28
|
Guo X, Tang T, Duan M, Zhang L, Ge H. The nonequilibrium mechanism of noise-enhanced drug synergy in HIV latency reactivation. iScience 2022; 25:104358. [PMID: 35620426 PMCID: PMC9127169 DOI: 10.1016/j.isci.2022.104358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 03/04/2022] [Accepted: 04/29/2022] [Indexed: 11/29/2022] Open
Abstract
Noise-modulating chemicals can synergize with transcriptional activators in reactivating latent HIV to eliminate latent HIV reservoirs. To understand the underlying biomolecular mechanism, we investigate a previous two-gene-state model and identify two necessary conditions for the synergy: an assumption of the inhibition effect of transcription activators on noise enhancers; and frequent transitions to the gene non-transcription-permissive state. We then develop a loop-four-gene-state model with Tat transcription/translation and find that drug synergy is mainly determined by the magnitude and direction of energy input into the genetic regulatory kinetics of the HIV promoter. The inhibition effect of transcription activators is actually a phenomenon of energy dissipation in the nonequilibrium gene transition system. Overall, the loop-four-state model demonstrates that energy dissipation plays a crucial role in HIV latency reactivation, which might be useful for improving drug effects and identifying other synergies on lentivirus latency reactivation. The inhibition of Activator on Noise enhancer is necessary for their synergy in reactivating HIV The drug synergy is a nonequilibrium phenomenon in the gene regulatory system The magnitude and direction of energy input determine the drug synergy This nonequilibrium mechanism is general without regarding molecular details
Collapse
|
29
|
Wu J, Chen B, Liu Y, Ma L, Huang W, Lin Y. Modulating gene regulation function by chemically controlled transcription factor clustering. Nat Commun 2022; 13:2663. [PMID: 35562359 PMCID: PMC9106659 DOI: 10.1038/s41467-022-30397-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 04/29/2022] [Indexed: 12/21/2022] Open
Abstract
Recent studies have suggested that transcriptional protein condensates (or clusters) may play key roles in gene regulation and cell fate determination. However, it remains largely unclear how the gene regulation function is quantitatively tuned by transcription factor (TF) clustering and whether TF clustering may confer emergent behaviors as in cell fate control systems. Here, to address this, we construct synthetic TFs whose clustering behavior can be chemically controlled. Through single-parameter tuning of the system (i.e., TF clustering propensity), we provide lines of evidence supporting the direct transcriptional activation and amplification of target genes by TF clustering. Single-gene imaging suggests that such amplification results from the modulation of transcriptional dynamics. Importantly, TF clustering propensity modulates the gene regulation function by significantly tuning the effective TF binding affinity and to a lesser extent the ultrasensitivity, contributing to bimodality and sustained response behavior that are reminiscent of canonical cell fate control systems. Collectively, these results demonstrate that TF clustering can modulate the gene regulation function to enable emergent behaviors, and highlight the potential applications of chemically controlled protein clustering. Transcription factor (TF) condensates appear to be pervasive, yet their roles remain debated. Here, the authors use a synthetic biology approach to show that TF clusters causally amplify transcription and can confer bimodality and “memory”.
Collapse
Affiliation(s)
- Jiegen Wu
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China.,The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, 100871, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China.,School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Baoqiang Chen
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Yadi Liu
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China.,The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, 100871, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China
| | - Liang Ma
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China.,The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, 100871, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China
| | - Wen Huang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China.,The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, 100871, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China
| | - Yihan Lin
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China. .,The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, 100871, Beijing, China. .,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China.
| |
Collapse
|
30
|
Feric M, Misteli T. Function moves biomolecular condensates in phase space. Bioessays 2022; 44:e2200001. [PMID: 35243657 PMCID: PMC9277701 DOI: 10.1002/bies.202200001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/19/2022] [Accepted: 02/22/2022] [Indexed: 11/08/2022]
Abstract
Phase separation underlies the formation of biomolecular condensates. We hypothesize the cellular processes that occur within condensates shape their structural features. We use the example of transcription to discuss structure-function relationships in condensates. Various types of transcriptional condensates have been reported across the evolutionary spectrum in the cell nucleus as well as in mitochondrial and bacterial nucleoids. In vitro and in vivo observations suggest that transcriptional activity of condensates influences their supramolecular structure, which in turn affects their function. Condensate organization thus becomes driven by differences in miscibility among the DNA and proteins of the transcription machinery and the RNA transcripts they generate. These considerations are in line with the notion that cellular processes shape the structural properties of condensates, leading to a dynamic, mutual interplay between structure and function in the cell.
Collapse
Affiliation(s)
- Marina Feric
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Tom Misteli
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| |
Collapse
|
31
|
Johari YB, Scarrott JM, Pohle TH, Liu P, Mayer A, Brown AJ, James DC. Engineering of the CMV promoter for controlled expression of recombinant genes in HEK293 cells. Biotechnol J 2022; 17:e2200062. [PMID: 35482470 DOI: 10.1002/biot.202200062] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/07/2022] [Accepted: 04/23/2022] [Indexed: 11/08/2022]
Abstract
Expression of recombinant genes in HEK293 cells is frequently utilized for production of recombinant proteins and viral vectors. These systems frequently employ the cytomegalovirus (CMV) promoter to drive recombinant gene transcription. However, the mechanistic basis of CMV-mediated transcriptional activation in HEK293 cells is unknown and consequently there are no strategies to engineer CMV for controlled expression of recombinant genes. Extensive bioinformatic analyses of transcription factor regulatory elements (TFREs) within the human CMV sequence and transcription factor mRNAs within the HEK293 transcriptome revealed 80 possible regulatory interactions. Through in vitro functional testing using reporter constructs harboring discrete TFREs or CMV deletion variants we identified key TFRE components and clusters of TFREs (cis-regulatory modules) within the CMV sequence. Our data reveal that CMV activity in HEK293 cells is a function of the promoters various constituent TFREs including AhR:ARNT, CREB, E4F, Sp1, ZBED1, JunB, c-Rel, and NF-κB. We also identified critical Sp1-dependent upstream activator elements near the transcriptional start site that were required for efficient transcription and YY1 and RBP-Jκ binding sites that mediate transrepression. Our study shows for the first time that novel, compact CMV-derived promoters can be engineered that exhibit up to 50% higher transcriptional efficiency (activity per unit DNA sequence) or 14% increase in total activity compared to the wild-type counterpart.
Collapse
Affiliation(s)
- Yusuf B Johari
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
| | - Joseph M Scarrott
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
| | - Thilo H Pohle
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
| | - Ping Liu
- Cell Line Development, REGENXBIO Inc., Rockville, Maryland, USA
| | - Ayda Mayer
- Cell Line Development, REGENXBIO Inc., Rockville, Maryland, USA
| | - Adam J Brown
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK.,Syngensys Ltd., Sheffield, UK
| | - David C James
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK.,Syngensys Ltd., Sheffield, UK
| |
Collapse
|
32
|
Zuin J, Roth G, Zhan Y, Cramard J, Redolfi J, Piskadlo E, Mach P, Kryzhanovska M, Tihanyi G, Kohler H, Eder M, Leemans C, van Steensel B, Meister P, Smallwood S, Giorgetti L. Nonlinear control of transcription through enhancer-promoter interactions. Nature 2022; 604:571-577. [PMID: 35418676 PMCID: PMC9021019 DOI: 10.1038/s41586-022-04570-y] [Citation(s) in RCA: 159] [Impact Index Per Article: 79.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 02/21/2022] [Indexed: 12/19/2022]
Abstract
Chromosome structure in mammals is thought to regulate transcription by modulating three-dimensional interactions between enhancers and promoters, notably through CTCF-mediated loops and topologically associating domains (TADs)1-4. However, how chromosome interactions are actually translated into transcriptional outputs remains unclear. Here, to address this question, we use an assay to position an enhancer at large numbers of densely spaced chromosomal locations relative to a fixed promoter, and measure promoter output and interactions within a genomic region with minimal regulatory and structural complexity. A quantitative analysis of hundreds of cell lines reveals that the transcriptional effect of an enhancer depends on its contact probabilities with the promoter through a nonlinear relationship. Mathematical modelling suggests that nonlinearity might arise from transient enhancer-promoter interactions being translated into slower promoter bursting dynamics in individual cells, therefore uncoupling the temporal dynamics of interactions from those of transcription. This uncovers a potential mechanism of how distal enhancers act from large genomic distances, and of how topologically associating domain boundaries block distal enhancers. Finally, we show that enhancer strength also determines absolute transcription levels as well as the sensitivity of a promoter to CTCF-mediated transcriptional insulation. Our measurements establish general principles for the context-dependent role of chromosome structure in long-range transcriptional regulation.
Collapse
Affiliation(s)
- Jessica Zuin
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Gregory Roth
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Yinxiu Zhan
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Julie Cramard
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Josef Redolfi
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Ewa Piskadlo
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Pia Mach
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | | | - Gergely Tihanyi
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Hubertus Kohler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Mathias Eder
- Division of Gene Regulation and Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Christ Leemans
- Division of Gene Regulation and Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Bas van Steensel
- Division of Gene Regulation and Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | | | - Luca Giorgetti
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
| |
Collapse
|
33
|
Bowles JR, Hoppe C, Ashe HL, Rattray M. Scalable inference of transcriptional kinetic parameters from MS2 time series data. Bioinformatics 2022; 38:1030-1036. [PMID: 34788793 PMCID: PMC8796374 DOI: 10.1093/bioinformatics/btab765] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 07/22/2021] [Accepted: 11/03/2021] [Indexed: 02/04/2023] Open
Abstract
MOTIVATION The MS2-MCP (MS2 coat protein) live imaging system allows for visualization of transcription dynamics through the introduction of hairpin stem-loop sequences into a gene. A fluorescent signal at the site of nascent transcription in the nucleus quantifies mRNA production. Computational modelling can be used to infer the promoter states along with the kinetic parameters governing transcription, such as promoter switching frequency and polymerase loading rate. However, modelling of the fluorescent trace presents a challenge due its persistence; the observed fluorescence at a given time point depends on both current and previous promoter states. A compound state Hidden Markov Model (cpHMM) was recently introduced to allow inference of promoter activity from MS2-MCP data. However, the computational time for inference scales exponentially with gene length and the cpHMM is therefore not currently practical for application to many eukaryotic genes. RESULTS We present a scalable implementation of the cpHMM for fast inference of promoter activity and transcriptional kinetic parameters. This new method can model genes of arbitrary length through the use of a time-adaptive truncated compound state space. The truncated state space provides a good approximation to the full state space by retaining the most likely set of states at each time during the forward pass of the algorithm. Testing on MS2-MCP fluorescent data collected from early Drosophila melanogaster embryos indicates that the method provides accurate inference of kinetic parameters within a computationally feasible timeframe. The inferred promoter traces generated by the model can also be used to infer single-cell transcriptional parameters. AVAILABILITY AND IMPLEMENTATION Python implementation is available at https://github.com/ManchesterBioinference/burstInfer, along with code to reproduce the examples presented here. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Jonathan R Bowles
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, UK
| | - Caroline Hoppe
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, UK
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Hilary L Ashe
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, UK
| | - Magnus Rattray
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, UK
| |
Collapse
|
34
|
Shang J, He L, Wang J, Tong A, Xiang Y. In Situ Visualizing Nascent RNA by Exploring DNA-Templated Oxidative Amination of 4-Thiouridine. Bioconjug Chem 2022; 33:164-171. [PMID: 34910465 DOI: 10.1021/acs.bioconjchem.1c00524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tracking and mapping the nascent RNA molecules in cells is essential for deciphering embryonic development and neuronal differentiation. Here, we utilized 4-thiouridine (s4U) as a metabolic tag to label nascent RNA and developed a fluorescence imaging method based on the DNA-templated oxidative amination (DTOA) reaction of s4U. The DTOA reaction occurred between amine-modified DNA and s4U-containing RNA with high sequence specificity and chemical selectivity. Target nascent mRNAs in HeLa cells, including those encoding green fluorescent proteins (GFPs) and endogenous BAG-1, were thus lit up selectively by DTOA-based fluorescence in situ hybridization (DTOA FISH). We believe the DTOA conjugation chemistry shown in this study could be generally applied to investigate the spatial distribution of nascent transcription dynamics in cellular processes.
Collapse
Affiliation(s)
- Jiachen Shang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Luo He
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Jingyi Wang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Aijun Tong
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Yu Xiang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| |
Collapse
|
35
|
Yang X, Luo S, Zhang Z, Wang Z, Zhou T, Zhang J. Silent transcription intervals and translational bursting lead to diverse phenotypic switching. Phys Chem Chem Phys 2022; 24:26600-26608. [DOI: 10.1039/d2cp03703c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
For complex process of gene expression, we use theoretical analysis and stochastic simulations to study the phenotypic diversity induced by silent transcription intervals and translational bursting.
Collapse
Affiliation(s)
- Xiyan Yang
- School of Financial Mathematics and Statistics, Guangdong University of Finance, Guangzhou 510521, P. R. China
| | - Songhao Luo
- School of Mathematics, Sun Yat-Sen University, Guangzhou 510275, P. R. China
- Guangdong Province Key Laboratory of Computational Science, Guangzhou 510275, P. R. China
| | - Zhenquan Zhang
- School of Mathematics, Sun Yat-Sen University, Guangzhou 510275, P. R. China
- Guangdong Province Key Laboratory of Computational Science, Guangzhou 510275, P. R. China
| | - Zihao Wang
- School of Mathematics, Sun Yat-Sen University, Guangzhou 510275, P. R. China
- Guangdong Province Key Laboratory of Computational Science, Guangzhou 510275, P. R. China
| | - Tianshou Zhou
- School of Mathematics, Sun Yat-Sen University, Guangzhou 510275, P. R. China
- Guangdong Province Key Laboratory of Computational Science, Guangzhou 510275, P. R. China
| | - Jiajun Zhang
- School of Mathematics, Sun Yat-Sen University, Guangzhou 510275, P. R. China
- Guangdong Province Key Laboratory of Computational Science, Guangzhou 510275, P. R. China
| |
Collapse
|
36
|
Chen M, Luo S, Cao M, Guo C, Zhou T, Zhang J. Exact distributions for stochastic gene expression models with arbitrary promoter architecture and translational bursting. Phys Rev E 2022; 105:014405. [PMID: 35193181 DOI: 10.1103/physreve.105.014405] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/14/2021] [Indexed: 11/07/2022]
Abstract
Gene expression in individual cells is inherently variable and sporadic, leading to cell-to-cell variability in mRNA and protein levels. Recent single-cell and single-molecule experiments indicate that promoter architecture and translational bursting play significant roles in controlling gene expression noise and generating the phenotypic diversity that life exhibits. To quantitatively understand the impact of these factors, it is essential to construct an accurate mathematical description of stochastic gene expression and find the exact analytical results, which is a formidable task. Here, we develop a stochastic model of bursty gene expression, which considers the complex promoter architecture governing the variability in mRNA expression and a general distribution characterizing translational burst. We derive the analytical expression for the corresponding protein steady-state distribution and all moment statistics of protein counts. We show that the total protein noise can be decomposed into three parts: the low-copy noise of protein due to probabilistic individual birth and death events, the noise due to stochastic switching between promoter states, and the noise resulting from translational busting. The theoretical results derived provide quantitative insights into the biochemical mechanisms of stochastic gene expression.
Collapse
Affiliation(s)
- Meiling Chen
- Guangdong Province Key Laboratory of Computational Science, Guangzhou 510275, People's Republic of China.,School of Mathematics, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China
| | - Songhao Luo
- Guangdong Province Key Laboratory of Computational Science, Guangzhou 510275, People's Republic of China.,School of Mathematics, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China
| | - Mengfang Cao
- Guangdong Province Key Laboratory of Computational Science, Guangzhou 510275, People's Republic of China.,School of Mathematics, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China
| | - Chengjun Guo
- School of Mathematics and Statistics, Guangdong University of Technology, Guangzhou 510275, People's Republic of China
| | - Tianshou Zhou
- Guangdong Province Key Laboratory of Computational Science, Guangzhou 510275, People's Republic of China.,School of Mathematics, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China
| | - Jiajun Zhang
- Guangdong Province Key Laboratory of Computational Science, Guangzhou 510275, People's Republic of China.,School of Mathematics, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China
| |
Collapse
|
37
|
Jordán-Pla A, Pérez-Ortín JE. High-Resolution Deep Sequencing of Nascent Transcription in Yeast with BioGRO-seq. Methods Mol Biol 2022; 2477:57-70. [PMID: 35524111 DOI: 10.1007/978-1-0716-2257-5_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
RNA biogenesis in eukaryotic cells is a tightly regulated multilayered process in which a diverse set of players act in an orchestrated manner via complex molecular interactions to secure the initial flow of gene expression. Transcription from DNA to RNA is the essential first step in RNA biogenesis, and consists of three main phases: initiation, elongation, and termination. In each phase, transcription factors act on RNA polymerases to modulate their passage along the DNA template in a very precise manner, governed by molecular mechanisms, some of which are not yet fully understood. Genome-scale run-on-based methodologies have been developed with the aim of mapping the position of transcriptionally engaged RNA polymerases. Among them, the BioGRO methodology has been instrumental in advancing our understanding of the transcriptional dynamics in yeast. Here we take the previously known BioGRO method further by coupling it with deep sequencing. BioGRO-seq maps elongating RNA polymerases along the genome with strand specificity and single-nucleotide resolution. BioGRO-seq profiling provides insights into the biogenesis and regulation of not just the canonical protein-coding transcriptome, but also into the often more challenging to study noncoding and unstable transcriptome.
Collapse
Affiliation(s)
- Antonio Jordán-Pla
- Facultad de Biológicas, Departamento de Bioquímica y Biología Molecular, Institut de Biotecnología i Biomedicina (Biotecmed), Universitat de València, Burjassot, Valencia, Spain.
| | - José E Pérez-Ortín
- Facultad de Biológicas, Departamento de Bioquímica y Biología Molecular, Institut de Biotecnología i Biomedicina (Biotecmed), Universitat de València, Burjassot, Valencia, Spain
| |
Collapse
|
38
|
Schweizer G, Wagner A. Both Binding Strength and Evolutionary Accessibility Affect the Population Frequency of Transcription Factor Binding Sequences in Arabidopsis thaliana. Genome Biol Evol 2021; 13:6459646. [PMID: 34894231 PMCID: PMC8712246 DOI: 10.1093/gbe/evab273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2021] [Indexed: 11/22/2022] Open
Abstract
Mutations in DNA sequences that bind transcription factors and thus modulate gene expression are a source of adaptive variation in gene expression. To understand how transcription factor binding sequences evolve in natural populations of the thale cress Arabidopsis thaliana, we integrated genomic polymorphism data for loci bound by transcription factors with in vitro data on binding affinity for these transcription factors. Specifically, we studied 19 different transcription factors, and the allele frequencies of 8,333 genomic loci bound in vivo by these transcription factors in 1,135 A. thaliana accessions. We find that transcription factor binding sequences show very low genetic diversity, suggesting that they are subject to purifying selection. High frequency alleles of such binding sequences tend to bind transcription factors strongly. Conversely, alleles that are absent from the population tend to bind them weakly. In addition, alleles with high frequencies also tend to be the endpoints of many accessible evolutionary paths leading to these alleles. We show that both high affinity and high evolutionary accessibility contribute to high allele frequency for at least some transcription factors. Although binding sequences with stronger affinity are more frequent, we did not find them to be associated with higher gene expression levels. Epistatic interactions among individual mutations that alter binding affinity are pervasive and can help explain variation in accessibility among binding sequences. In summary, combining in vitro binding affinity data with in vivo binding sequence data can help understand the forces that affect the evolution of transcription factor binding sequences in natural populations.
Collapse
Affiliation(s)
- Gabriel Schweizer
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge-Batiment Genopode, Lausanne, Switzerland
| | - Andreas Wagner
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge-Batiment Genopode, Lausanne, Switzerland.,Santa Fe Institute, Santa Fe, New Mexico, USA.,Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, South Africa
| |
Collapse
|
39
|
Hu F, Zhu T, Guo X, Yu K, Ma X, Liu C, Liu L, Gao Y, Song M, Wu J, Huang B, Li Y. Generation of duck Tembusu virus using a simple reverse genetic system in duck embryo fibroblast cells. J Virol Methods 2021; 300:114385. [PMID: 34843824 DOI: 10.1016/j.jviromet.2021.114385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 09/04/2021] [Accepted: 11/25/2021] [Indexed: 11/25/2022]
Abstract
Outbreaks of duck Tembusu virus (DTMUV) have caused serious economic losses in China since 2010. In this study, an infectious clone of the DTMUV BZ-2010strain, isolated from layer cherry duck in China, was constructed using the bacterium-free infectious subgenomic-amplicons method. The subgenomic-amplicons of the human cytomegalovirus promoter (pCMV) at the 5' terminus of the first DNA fragment, the entire genome of DTMUV, and the hepatitis delta ribozyme followed by the simian virus 40 polyadenylation signal (HDR/SV40pA) at the 3' terminus of the last DNA fragment were synthesized and amplified by PCR in three DNA fragments. The pCMV and HDR/SV40pA were used to drive the viral RNA transcription and generate a full-length RNA transcript of the virus, and were found to be effective in reassembling DTMUV in duck embryo fibroblast cells. The RNA transcripts from the infection clone were infectious in duck embryo fibroblast cells, generating the reconstituted DTMUV. This study provided a valuable reverse genetic tool for the further study DTMUV pathogenesis.
Collapse
Affiliation(s)
- Feng Hu
- Institute of Poultry Science, Shandong Academy of Agricultural Sciences / Shandong Provincial Key Laboratory of Immunity and Diagnosis of Poultry Diseases, No. 1 Jiaoxiao Road, Jinan, Shandong, 250023, China.
| | - Tong Zhu
- Institute of Poultry Science, Shandong Academy of Agricultural Sciences / Shandong Provincial Key Laboratory of Immunity and Diagnosis of Poultry Diseases, No. 1 Jiaoxiao Road, Jinan, Shandong, 250023, China.
| | - Xiaozhen Guo
- Institute of Poultry Science, Shandong Academy of Agricultural Sciences / Shandong Provincial Key Laboratory of Immunity and Diagnosis of Poultry Diseases, No. 1 Jiaoxiao Road, Jinan, Shandong, 250023, China.
| | - Kexiang Yu
- Institute of Poultry Science, Shandong Academy of Agricultural Sciences / Shandong Provincial Key Laboratory of Immunity and Diagnosis of Poultry Diseases, No. 1 Jiaoxiao Road, Jinan, Shandong, 250023, China.
| | - Xiuli Ma
- Institute of Poultry Science, Shandong Academy of Agricultural Sciences / Shandong Provincial Key Laboratory of Immunity and Diagnosis of Poultry Diseases, No. 1 Jiaoxiao Road, Jinan, Shandong, 250023, China.
| | - Cunxia Liu
- Institute of Poultry Science, Shandong Academy of Agricultural Sciences / Shandong Provincial Key Laboratory of Immunity and Diagnosis of Poultry Diseases, No. 1 Jiaoxiao Road, Jinan, Shandong, 250023, China.
| | - Liping Liu
- Institute of Poultry Science, Shandong Academy of Agricultural Sciences / Shandong Provincial Key Laboratory of Immunity and Diagnosis of Poultry Diseases, No. 1 Jiaoxiao Road, Jinan, Shandong, 250023, China.
| | - Yuehua Gao
- Institute of Poultry Science, Shandong Academy of Agricultural Sciences / Shandong Provincial Key Laboratory of Immunity and Diagnosis of Poultry Diseases, No. 1 Jiaoxiao Road, Jinan, Shandong, 250023, China.
| | - Minxun Song
- Institute of Poultry Science, Shandong Academy of Agricultural Sciences / Shandong Provincial Key Laboratory of Immunity and Diagnosis of Poultry Diseases, No. 1 Jiaoxiao Road, Jinan, Shandong, 250023, China.
| | - Jiaqiang Wu
- Institute of Poultry Science, Shandong Academy of Agricultural Sciences / Shandong Provincial Key Laboratory of Immunity and Diagnosis of Poultry Diseases, No. 1 Jiaoxiao Road, Jinan, Shandong, 250023, China.
| | - Bing Huang
- Institute of Poultry Science, Shandong Academy of Agricultural Sciences / Shandong Provincial Key Laboratory of Immunity and Diagnosis of Poultry Diseases, No. 1 Jiaoxiao Road, Jinan, Shandong, 250023, China.
| | - Yufeng Li
- Institute of Poultry Science, Shandong Academy of Agricultural Sciences / Shandong Provincial Key Laboratory of Immunity and Diagnosis of Poultry Diseases, No. 1 Jiaoxiao Road, Jinan, Shandong, 250023, China.
| |
Collapse
|
40
|
Garbuzov FE, Gursky VV. Nonequilibrium model of short-range repression in gene transcription regulation. Phys Rev E 2021; 104:014407. [PMID: 34412298 DOI: 10.1103/physreve.104.014407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 06/24/2021] [Indexed: 11/07/2022]
Abstract
Transcription factors are proteins that regulate gene activity by activating or repressing gene transcription. A special class of transcriptional repressors operates via a short-range mechanism, making local DNA regions inaccessible to binding by activators, and thus providing an indirect repressive action on the target gene. This mechanism is commonly modeled assuming that repressors interact with DNA under thermodynamic equilibrium and neglecting some configurations of the gene regulatory region. We elaborate on a more general nonequilibrium model of short-range repression using the graph formalism for transitions between gene states, and we apply analytical calculations to compare it with the equilibrium model in terms of the repression strength and expression noise. In contrast to the equilibrium approach, the new model allows us to separate two basic mechanisms of short-range repression. The first mechanism is associated with the recruiting of factors that mediate chromatin condensation, and the second one concerns the blocking of factors that mediate chromatin loosening. The nonequilibrium model demonstrates better performance on previously published gene expression data obtained for transcription factors controlling Drosophila development, and furthermore it predicts that the first repression mechanism is the most favorable in this system. The presented approach can be scaled to larger gene networks and can be used to infer specific modes and parameters of transcriptional regulation from gene expression data.
Collapse
Affiliation(s)
- F E Garbuzov
- Ioffe Institute, 26 Polytekhnicheskaya, St. Petersburg 194021, Russia
| | - V V Gursky
- Ioffe Institute, 26 Polytekhnicheskaya, St. Petersburg 194021, Russia
| |
Collapse
|
41
|
Garcia DA, Fettweis G, Presman DM, Paakinaho V, Jarzynski C, Upadhyaya A, Hager GL. Power-law behavior of transcription factor dynamics at the single-molecule level implies a continuum affinity model. Nucleic Acids Res 2021; 49:6605-6620. [PMID: 33592625 DOI: 10.1093/nar/gkab072] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 01/13/2021] [Accepted: 02/11/2021] [Indexed: 12/11/2022] Open
Abstract
Single-molecule tracking (SMT) allows the study of transcription factor (TF) dynamics in the nucleus, giving important information regarding the diffusion and binding behavior of these proteins in the nuclear environment. Dwell time distributions obtained by SMT for most TFs appear to follow bi-exponential behavior. This has been ascribed to two discrete populations of TFs-one non-specifically bound to chromatin and another specifically bound to target sites, as implied by decades of biochemical studies. However, emerging studies suggest alternate models for dwell-time distributions, indicating the existence of more than two populations of TFs (multi-exponential distribution), or even the absence of discrete states altogether (power-law distribution). Here, we present an analytical pipeline to evaluate which model best explains SMT data. We find that a broad spectrum of TFs (including glucocorticoid receptor, oestrogen receptor, FOXA1, CTCF) follow a power-law distribution of dwell-times, blurring the temporal line between non-specific and specific binding, suggesting that productive binding may involve longer binding events than previously believed. From these observations, we propose a continuum of affinities model to explain TF dynamics, that is consistent with complex interactions of TFs with multiple nuclear domains as well as binding and searching on the chromatin template.
Collapse
Affiliation(s)
- David A Garcia
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA.,Department of Physics, University of Maryland, College Park, MD 20742, USA
| | - Gregory Fettweis
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA
| | - Diego M Presman
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA.,Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, C1428EGA, Buenos Aires, Argentina
| | - Ville Paakinaho
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA.,Institute of Biomedicine, University of Eastern Finland, Kuopio, PO Box 1627, FI-70211 Kuopio, Finland
| | - Christopher Jarzynski
- Department of Physics, University of Maryland, College Park, MD 20742, USA.,Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA.,Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
| | - Arpita Upadhyaya
- Department of Physics, University of Maryland, College Park, MD 20742, USA.,Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA
| |
Collapse
|
42
|
Koch AL, Morisaki T, Stasevich TJ. A Multi-color Bicistronic Biosensor to Compare the Translation Dynamics of Different Open Reading Frames at Single-molecule Resolution in Live Cells. Bio Protoc 2021; 11:e4096. [PMID: 34395732 DOI: 10.21769/bioprotoc.4096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/29/2021] [Accepted: 05/16/2021] [Indexed: 11/02/2022] Open
Abstract
Here, we describe how to image and quantitate the translation dynamics of a bicistronic biosensor that we recently created to fairly compare cap-dependent and IRES-mediated translation at single-molecule resolution in live human cells. This technique employs a pair of complementary intrabodies loaded into living cells that co-translationally bind complementary epitopes in the two separate ORFs of the bicistronic biosensor. This causes the biosensor to fluoresce in different colors depending on which ORF/epitopes are translated. Using the biosensor together with high-resolution fluorescence microscopy and single-molecule tracking analysis allows for the quantitative comparison of translation dynamics between the two ORFs at a resolution of tens-of-nanometers in space and sub-seconds in time, which is not possible with more traditional GFP or luciferase reporters. Since both ORFs are on the same biosensor, they experience the same microenvironment, allowing a fair comparison of their relative translational activities. In this protocol, we describe how to get this assay up and running in cultured human cells so that translation dynamics can be studied under both normal and stressful cellular conditions. We also provide a number of useful tips and notes to help express components at appropriate levels inside cells for optimal live cell imaging. Graphical abstract: Steps required for 3-color single-molecule translation imaging and analysis.
Collapse
Affiliation(s)
- Amanda L Koch
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Tatsuya Morisaki
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Timothy J Stasevich
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA.,Cell Biology Center and World Research Hub Initiative, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8503, Japan
| |
Collapse
|
43
|
Gene Expression at a Single Molecule Level: Implications for MDS and AML. Blood 2021; 138:625-636. [PMID: 34157070 DOI: 10.1182/blood.2019004261] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/03/2020] [Indexed: 12/11/2022] Open
Abstract
Non-genetic heterogeneity, or gene expression stochasticity, is an important source of variability in biological systems. With the advent and improvement of single molecule resolution technologies, it has been shown that transcription dynamics and resultant transcript number fluctuations generate significant cell-to-cell variability that has important biological effects and may contribute substantially to both tissue homeostasis and disease. In this respect, the pathophysiology of stem cell-derived malignancies such as AML and MDS, which has historically been studied at the ensemble level, may require re-evaluation. To that end, it is our aim in this review to highlight the results of recent single-molecule, biophysical, and systems studies of gene expression dynamics, with the explicit purpose of demonstrating how the insights from these basic science studies may help inform and progress the field of leukemia biology and, ultimately, research into novel therapies.
Collapse
|
44
|
Forero-Quintero LS, Raymond W, Handa T, Saxton MN, Morisaki T, Kimura H, Bertrand E, Munsky B, Stasevich TJ. 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: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [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.
Collapse
Affiliation(s)
- Linda S Forero-Quintero
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - William Raymond
- Department of Chemical and Biological Engineering and School of Biomedical Engineering, Colorado State University, Fort Collins, CO, USA
| | - Tetsuya Handa
- Cell Biology Center and World Research Hub Initiative, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE, UK
| | - 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
| | - Hiroshi Kimura
- Cell Biology Center and World Research Hub Initiative, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
- Institut de Génétique Moléculaire de Montpellier, Montpellier, France
| | - Edouard Bertrand
- World Research Hub Initiative, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Brian Munsky
- Department of Chemical and Biological Engineering and School of Biomedical Engineering, Colorado State University, Fort Collins, CO, USA.
| | - Timothy J Stasevich
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA.
- Institut de Génétique Moléculaire de Montpellier, Montpellier, France.
| |
Collapse
|
45
|
Liu J, Hansen D, Eck E, Kim YJ, Turner M, Alamos S, Garcia HG. Real-time single-cell characterization of the eukaryotic transcription cycle reveals correlations between RNA initiation, elongation, and cleavage. PLoS Comput Biol 2021; 17:e1008999. [PMID: 34003867 PMCID: PMC8162642 DOI: 10.1371/journal.pcbi.1008999] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 05/28/2021] [Accepted: 04/23/2021] [Indexed: 12/23/2022] Open
Abstract
The eukaryotic transcription cycle consists of three main steps: initiation, elongation, and cleavage of the nascent RNA transcript. Although each of these steps can be regulated as well as coupled with each other, their in vivo dissection has remained challenging because available experimental readouts lack sufficient spatiotemporal resolution to separate the contributions from each of these steps. Here, we describe a novel application of Bayesian inference techniques to simultaneously infer the effective parameters of the transcription cycle in real time and at the single-cell level using a two-color MS2/PP7 reporter gene and the developing fruit fly embryo as a case study. Our method enables detailed investigations into cell-to-cell variability in transcription-cycle parameters as well as single-cell correlations between these parameters. These measurements, combined with theoretical modeling, suggest a substantial variability in the elongation rate of individual RNA polymerase molecules. We further illustrate the power of this technique by uncovering a novel mechanistic connection between RNA polymerase density and nascent RNA cleavage efficiency. Thus, our approach makes it possible to shed light on the regulatory mechanisms in play during each step of the transcription cycle in individual, living cells at high spatiotemporal resolution.
Collapse
Affiliation(s)
- Jonathan Liu
- Department of Physics, University of California at Berkeley, Berkeley, California, United States of America
| | - Donald Hansen
- Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Heidelberg, Germany
| | - Elizabeth Eck
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, California, United States of America
| | - Yang Joon Kim
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, California, United States of America
| | - Meghan Turner
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, California, United States of America
| | - Simon Alamos
- Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, California, United States of America
| | - Hernan G. Garcia
- Department of Physics, University of California at Berkeley, Berkeley, California, United States of America
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, California, United States of America
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California, United States of America
- Institute for Quantitative Biosciences-QB3, University of California at Berkeley, Berkeley, California, United States of America
| |
Collapse
|
46
|
Cvekl A, Eliscovich C. Crystallin gene expression: Insights from studies of transcriptional bursting. Exp Eye Res 2021; 207:108564. [PMID: 33894228 DOI: 10.1016/j.exer.2021.108564] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 03/05/2021] [Accepted: 03/22/2021] [Indexed: 01/26/2023]
Abstract
Cellular differentiation is marked by temporally and spatially regulated gene expression. The ocular lens is one of the most powerful mammalian model system since it is composed from only two cell subtypes, called lens epithelial and fiber cells. Lens epithelial cells differentiate into fiber cells through a series of spatially and temporally orchestrated processes, including massive production of crystallins, cellular elongation and the coordinated degradation of nuclei and other organelles. Studies of transcriptional and posttranscriptional gene regulatory mechanisms in lens provide a wide range of opportunities to understand global molecular mechanisms of gene expression as steady-state levels of crystallin mRNAs reach very high levels comparable to globin genes in erythrocytes. Importantly, dysregulation of crystallin gene expression results in lens structural abnormalities and cataracts. The mRNA life cycle is comprised of multiple stages, including transcription, splicing, nuclear export into cytoplasm, stabilization, localization, translation and ultimate decay. In recent years, development of modern mRNA detection methods with single molecule and single cell resolution enabled transformative studies to visualize the mRNA life cycle to generate novel insights into the sequential regulatory mechanisms of gene expression during embryogenesis. This review is focused on recent major advancements in studies of transcriptional bursting in differentiating lens fiber cells, analysis of nascent mRNA expression from bi-directional promoters, transient nuclear accumulation of specific mRNAs, condensation of chromatin prior lens fiber cell denucleation, and outlines future studies to probe the interactions of individual mRNAs with specific RNA-binding proteins (RBPs) in the cytoplasm and regulation of translation and mRNA decay.
Collapse
Affiliation(s)
- Ales Cvekl
- Department of Ophthalmology and VIsual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
| | - Carolina Eliscovich
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| |
Collapse
|
47
|
McNamara AV, Awais R, Momiji H, Dunham L, Featherstone K, Harper CV, Adamson AA, Semprini S, Jones NA, Spiller DG, Mullins JJ, Finkenstädt BF, Rand D, White MRH, Davis JRE. Transcription Factor Pit-1 Affects Transcriptional Timing in the Dual-Promoter Human Prolactin Gene. Endocrinology 2021; 162:6060060. [PMID: 33388754 PMCID: PMC7871365 DOI: 10.1210/endocr/bqaa249] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Indexed: 12/31/2022]
Abstract
Gene transcription occurs in short bursts interspersed with silent periods, and these kinetics can be altered by promoter structure. The effect of alternate promoter architecture on transcription bursting is not known. We studied the human prolactin (hPRL) gene that contains 2 promoters, a pituitary-specific promoter that requires the transcription factor Pit-1 and displays dramatic transcriptional bursting activity and an alternate upstream promoter that is active in nonpituitary tissues. We studied large hPRL genomic fragments with luciferase reporters, and used bacterial artificial chromosome recombineering to manipulate critical promoter regions. Stochastic switch mathematical modelling of single-cell time-lapse luminescence image data revealed that the Pit-1-dependent promoter showed longer, higher-amplitude transcriptional bursts. Knockdown studies confirmed that the presence of Pit-1 stabilized and prolonged periods of active transcription. Pit-1 therefore plays an active role in establishing the timing of transcription cycles, in addition to its cell-specific functions.
Collapse
Affiliation(s)
- Anne V McNamara
- Systems Microscopy Centre, Division of Molecular and Cellular Function, School of Biological Sciences, Faculty Biology, Medicine & Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
| | - Raheela Awais
- School of Life Sciences, University of Liverpool, Liverpool, UK
| | - Hiroshi Momiji
- Mathematics Institute & Zeeman Institute for Systems Biology, and Infectious Epidemiology Research, University of Warwick, Senate House Coventry, UK
| | - Lee Dunham
- Division of Diabetes, Endocrinology & Gastroenterology, School of Medical Sciences, Faculty of Biology, Medicine & Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
| | - Karen Featherstone
- Division of Diabetes, Endocrinology & Gastroenterology, School of Medical Sciences, Faculty of Biology, Medicine & Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
| | - Claire V Harper
- Department of Biology, Edge Hill University, Ormskirk, Lancashire, UK
| | - Antony A Adamson
- Genome Editing Unit, Faculty of Biology, Medicine & Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
| | - Sabrina Semprini
- University/BHF Centre for Cardiovascular Science, The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Nicholas A Jones
- Systems Microscopy Centre, Division of Molecular and Cellular Function, School of Biological Sciences, Faculty Biology, Medicine & Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
| | - David G Spiller
- Systems Microscopy Centre, Division of Molecular and Cellular Function, School of Biological Sciences, Faculty Biology, Medicine & Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
| | - John J Mullins
- University/BHF Centre for Cardiovascular Science, The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Bärbel F Finkenstädt
- Mathematics Institute & Zeeman Institute for Systems Biology, and Infectious Epidemiology Research, University of Warwick, Senate House Coventry, UK
| | - David Rand
- Mathematics Institute & Zeeman Institute for Systems Biology, and Infectious Epidemiology Research, University of Warwick, Senate House Coventry, UK
| | - Michael R H White
- Systems Microscopy Centre, Division of Molecular and Cellular Function, School of Biological Sciences, Faculty Biology, Medicine & Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
- Correspondence: Professor Michael R. H. White, Systems Microscopy Centre, Division of Molecular and Cellular Function, Faculty of Biology, Medicine & Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, M13 9PT, UK. E-mail: ; or Professor Julian R. E. Davis, Division of Diabetes, Endocrinology & Gastroenterology, Faculty of Biology, Medicine & Health, Manchester Academic Health Sciences Centre, University of Manchester, M13 9PT, UK. E-mail:
| | - Julian R E Davis
- Division of Diabetes, Endocrinology & Gastroenterology, School of Medical Sciences, Faculty of Biology, Medicine & Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
- Correspondence: Professor Michael R. H. White, Systems Microscopy Centre, Division of Molecular and Cellular Function, Faculty of Biology, Medicine & Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, M13 9PT, UK. E-mail: ; or Professor Julian R. E. Davis, Division of Diabetes, Endocrinology & Gastroenterology, Faculty of Biology, Medicine & Health, Manchester Academic Health Sciences Centre, University of Manchester, M13 9PT, UK. E-mail:
| |
Collapse
|
48
|
Liou SH, Singh SK, Singer RH, Coleman RA, Liu WL. Structure of the p53/RNA polymerase II assembly. Commun Biol 2021; 4:397. [PMID: 33767390 PMCID: PMC7994806 DOI: 10.1038/s42003-021-01934-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 03/02/2021] [Indexed: 02/07/2023] Open
Abstract
The tumor suppressor p53 protein activates expression of a vast gene network in response to stress stimuli for cellular integrity. The molecular mechanism underlying how p53 targets RNA polymerase II (Pol II) to regulate transcription remains unclear. To elucidate the p53/Pol II interaction, we have determined a 4.6 Å resolution structure of the human p53/Pol II assembly via single particle cryo-electron microscopy. Our structure reveals that p53's DNA binding domain targets the upstream DNA binding site within Pol II. This association introduces conformational changes of the Pol II clamp into a further-closed state. A cavity was identified between p53 and Pol II that could possibly host DNA. The transactivation domain of p53 binds the surface of Pol II's jaw that contacts downstream DNA. These findings suggest that p53's functional domains directly regulate DNA binding activity of Pol II to mediate transcription, thereby providing insights into p53-regulated gene expression.
Collapse
Affiliation(s)
- Shu-Hao Liou
- Gruss-Lipper Biophotonics Center, Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Sameer K Singh
- Gruss-Lipper Biophotonics Center, Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Robert H Singer
- Gruss-Lipper Biophotonics Center, Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY, USA
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Robert A Coleman
- Gruss-Lipper Biophotonics Center, Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY, USA.
| | - Wei-Li Liu
- Gruss-Lipper Biophotonics Center, Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY, USA.
| |
Collapse
|
49
|
A hierarchical regulatory network analysis of the vitamin D induced transcriptome reveals novel regulators and complete VDR dependency in monocytes. Sci Rep 2021; 11:6518. [PMID: 33753848 PMCID: PMC7985518 DOI: 10.1038/s41598-021-86032-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 02/04/2021] [Indexed: 11/11/2022] Open
Abstract
The transcription factor vitamin D receptor (VDR) is the high affinity nuclear target of the biologically active form of vitamin D3 (1,25(OH)2D3). In order to identify pure genomic transcriptional effects of 1,25(OH)2D3, we used VDR cistrome, transcriptome and open chromatin data, obtained from the human monocytic cell line THP-1, for a novel hierarchical analysis applying three bioinformatics approaches. We predicted 75.6% of all early 1,25(OH)2D3-responding (2.5 or 4 h) and 57.4% of the late differentially expressed genes (24 h) to be primary VDR target genes. VDR knockout led to a complete loss of 1,25(OH)2D3–induced genome-wide gene regulation. Thus, there was no indication of any VDR-independent non-genomic actions of 1,25(OH)2D3 modulating its transcriptional response. Among the predicted primary VDR target genes, 47 were coding for transcription factors and thus may mediate secondary 1,25(OH)2D3 responses. CEBPA and ETS1 ChIP-seq data and RNA-seq following CEBPA knockdown were used to validate the predicted regulation of secondary vitamin D target genes by both transcription factors. In conclusion, a directional network containing 47 partly novel primary VDR target transcription factors describes secondary responses in a highly complex vitamin D signaling cascade. The central transcription factor VDR is indispensable for all transcriptome-wide effects of the nuclear hormone.
Collapse
|
50
|
Larke MSC, Schwessinger R, Nojima T, Telenius J, Beagrie RA, Downes DJ, Oudelaar AM, Truch J, Graham B, Bender MA, Proudfoot NJ, Higgs DR, Hughes JR. Enhancers predominantly regulate gene expression during differentiation via transcription initiation. Mol Cell 2021; 81:983-997.e7. [PMID: 33539786 PMCID: PMC7612206 DOI: 10.1016/j.molcel.2021.01.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 09/25/2020] [Accepted: 01/02/2021] [Indexed: 12/16/2022]
Abstract
Gene transcription occurs via a cycle of linked events, including initiation, promoter-proximal pausing, and elongation of RNA polymerase II (Pol II). A key question is how transcriptional enhancers influence these events to control gene expression. Here, we present an approach that evaluates the level and change in promoter-proximal transcription (initiation and pausing) in the context of differential gene expression, genome-wide. This combinatorial approach shows that in primary cells, control of gene expression during differentiation is achieved predominantly via changes in transcription initiation rather than via release of Pol II pausing. Using genetically engineered mouse models, deleted for functionally validated enhancers of the α- and β-globin loci, we confirm that these elements regulate Pol II recruitment and/or initiation to modulate gene expression. Together, our data show that gene expression during differentiation is regulated predominantly at the level of initiation and that enhancers are key effectors of this process.
Collapse
Affiliation(s)
- Martin S C Larke
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK; MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Ron Schwessinger
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK; MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Takayuki Nojima
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Jelena Telenius
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Robert A Beagrie
- Laboratory of Gene Regulation, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Damien J Downes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - A Marieke Oudelaar
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK; MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Julia Truch
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Bryony Graham
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - M A Bender
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Nicholas J Proudfoot
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Douglas R Higgs
- Laboratory of Gene Regulation, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
| | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK; MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
| |
Collapse
|