1
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Dyer OT, Ball RC. Surfactancy in a tadpole model of proteins. J R Soc Interface 2022; 19:20220172. [PMID: 36195115 PMCID: PMC9532023 DOI: 10.1098/rsif.2022.0172] [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] [Indexed: 11/07/2022] Open
Abstract
We model the environment of eukaryotic nuclei by representing macromolecules by only their entropic properties, with globular molecules represented by spherical colloids and flexible molecules by polymers. We put particular focus on proteins with both globular and intrinsically disordered regions, which we represent with 'tadpole' constructed by grafting single polymers and colloids together. In Monte Carlo simulations, we find these tadpoles support phase separation via depletion flocculation, and demonstrate several surfactant behaviours, including being found preferentially at interfaces and forming micelles in single phase solution. Furthermore, the model parameters can be tuned to give a tadpole a preference for either bulk phase. However, we find entropy too weak to drive these behaviours by itself at likely biological concentrations.
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Affiliation(s)
- O. T. Dyer
- Department of Physics, University of Warwick, Coventry CV4 7AL, UK
| | - R. C. Ball
- Department of Physics, University of Warwick, Coventry CV4 7AL, UK
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2
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Kantidze OL, Razin SV. Weak interactions in higher-order chromatin organization. Nucleic Acids Res 2020; 48:4614-4626. [PMID: 32313950 PMCID: PMC7229822 DOI: 10.1093/nar/gkaa261] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/30/2020] [Accepted: 04/03/2020] [Indexed: 12/20/2022] Open
Abstract
The detailed principles of the hierarchical folding of eukaryotic chromosomes have been revealed during the last two decades. Along with structures composing three-dimensional (3D) genome organization (chromatin compartments, topologically associating domains, chromatin loops, etc.), the molecular mechanisms that are involved in their establishment and maintenance have been characterized. Generally, protein-protein and protein-DNA interactions underlie the spatial genome organization in eukaryotes. However, it is becoming increasingly evident that weak interactions, which exist in biological systems, also contribute to the 3D genome. Here, we provide a snapshot of our current understanding of the role of the weak interactions in the establishment and maintenance of the 3D genome organization. We discuss how weak biological forces, such as entropic forces operating in crowded solutions, electrostatic interactions of the biomolecules, liquid-liquid phase separation, DNA supercoiling, and RNA environment participate in chromosome segregation into structural and functional units and drive intranuclear functional compartmentalization.
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Affiliation(s)
- Omar L Kantidze
- Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia
| | - Sergey V Razin
- Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia
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3
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Ibragimov AN, Bylino OV, Shidlovskii YV. Molecular Basis of the Function of Transcriptional Enhancers. Cells 2020; 9:E1620. [PMID: 32635644 PMCID: PMC7407508 DOI: 10.3390/cells9071620] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 07/03/2020] [Accepted: 07/03/2020] [Indexed: 02/06/2023] Open
Abstract
Transcriptional enhancers are major genomic elements that control gene activity in eukaryotes. Recent studies provided deeper insight into the temporal and spatial organization of transcription in the nucleus, the role of non-coding RNAs in the process, and the epigenetic control of gene expression. Thus, multiple molecular details of enhancer functioning were revealed. Here, we describe the recent data and models of molecular organization of enhancer-driven transcription.
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Affiliation(s)
- Airat N. Ibragimov
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia; (A.N.I.); (O.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia
| | - Oleg V. Bylino
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia; (A.N.I.); (O.V.B.)
| | - Yulii V. Shidlovskii
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia; (A.N.I.); (O.V.B.)
- I.M. Sechenov First Moscow State Medical University, 8, bldg. 2 Trubetskaya St., 119048 Moscow, Russia
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4
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Soft culture substrates favor stem-like cellular phenotype and facilitate reprogramming of human mesenchymal stem/stromal cells (hMSCs) through mechanotransduction. Sci Rep 2019; 9:9086. [PMID: 31235788 PMCID: PMC6591285 DOI: 10.1038/s41598-019-45352-3] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 06/04/2019] [Indexed: 01/26/2023] Open
Abstract
Biophysical cues influence many aspects of cell behavior. Stiffness of the extracellular matrix is probed by cells and transduced into biochemical signals through mechanotransduction protein networks, strongly influencing stem cell behavior. Cellular stemness is intimately related with mechanical properties of the cell, like intracellular contractility and stiffness, which in turn are influenced by the microenvironment. Pluripotency is associated with soft and low-contractility cells. Hence, we postulated that soft cell culture substrates, presumably inducing low cellular contractility and stiffness, increase the reprogramming efficiency of mesenchymal stem/stromal cells (MSCs) into induced pluripotent stem cells (iPSCs). We demonstrate that soft substrates (1.5 or 15 kPa polydimethylsiloxane – PDMS) caused modulation of several cellular features of MSCs into a phenotype closer to pluripotent stem cells (PSCs). MSCs cultured on soft substrates presented more relaxed nuclei, lower maturation of focal adhesions and F-actin assembling, more euchromatic and less heterochromatic nuclear DNA regions, and increased expression of pluripotency-related genes. These changes correlate with the reprogramming of MSCs, with a positive impact on the kinetics, robustness of colony formation and reprogramming efficiency. Additionally, substrate stiffness influences several phenotypic features of iPS cells and colonies, and data indicates that soft substrates favor full iPSC reprogramming.
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5
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Tan ZW, Guarnera E, Berezovsky IN. Exploring chromatin hierarchical organization via Markov State Modelling. PLoS Comput Biol 2018; 14:e1006686. [PMID: 30596637 PMCID: PMC6355033 DOI: 10.1371/journal.pcbi.1006686] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 01/31/2019] [Accepted: 11/27/2018] [Indexed: 01/02/2023] Open
Abstract
We propose a new computational method for exploring chromatin structural organization based on Markov State Modelling of Hi-C data represented as an interaction network between genomic loci. A Markov process describes the random walk of a traveling probe in the corresponding energy landscape, mimicking the motion of a biomolecule involved in chromatin function. By studying the metastability of the associated Markov State Model upon annealing, the hierarchical structure of individual chromosomes is observed, and corresponding set of structural partitions is identified at each level of hierarchy. Then, the notion of effective interaction between partitions is derived, delineating the overall topology and architecture of chromosomes. Mapping epigenetic data on the graphs of intra-chromosomal effective interactions helps in understanding how chromosome organization facilitates its function. A sketch of whole-genome interactions obtained from the analysis of 539 partitions from all 23 chromosomes, complemented by distributions of gene expression regulators and epigenetic factors, sheds light on the structure-function relationships in chromatin, delineating chromosomal territories, as well as structural partitions analogous to topologically associating domains and active / passive epigenomic compartments. In addition to the overall genome architecture shown by effective interactions, the affinity between partitions of different chromosomes was analyzed as an indicator of the degree of association between partitions in functionally relevant genomic interactions. The overall static picture of whole-genome interactions obtained with the method presented in this work provides a foundation for chromatin structural reconstruction, for the modelling of chromatin dynamics, and for exploring the regulation of genome function. The algorithms used in this study are implemented in a freely available Python package ChromaWalker (https://bitbucket.org/ZhenWahTan/chromawalker).
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Affiliation(s)
- Zhen Wah Tan
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Matrix, Singapore
| | - Enrico Guarnera
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Matrix, Singapore
| | - Igor N. Berezovsky
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Matrix, Singapore
- Department of Biological Sciences (DBS), National University of Singapore (NUS), Singapore
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6
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Lima AF, May G, Díaz-Colunga J, Pedreiro S, Paiva A, Ferreira L, Enver T, Iborra FJ, Pires das Neves R. Osmotic modulation of chromatin impacts on efficiency and kinetics of cell fate modulation. Sci Rep 2018; 8:7210. [PMID: 29740078 PMCID: PMC5940679 DOI: 10.1038/s41598-018-25517-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 04/12/2018] [Indexed: 11/23/2022] Open
Abstract
Chromatin structure is a major regulator of transcription and gene expression. Herein we explore the use of osmotic modulation to modify the chromatin structure and reprogram gene expression. In this study we use the extracellular osmotic pressure as a chromatin structure and transcriptional modulator. Hyposmotic modulation promotes chromatin loosening and induces changes in RNA polymerase II (Pol II) activity. The chromatin decondensation opens space for higher amounts of DNA engaged RNA Pol II. Hyposmotic modulation constitutes an alternative route to manipulate cell fate decisions. This technology was tested in model protocols of induced pluripotency and transdifferentiation in cells growing in suspension and adherent to substrates, CD34+ umbilical-cord-blood (UCB), fibroblasts and B-cells. The efficiency and kinetics of these cell fate modulation processes were improved by transient hyposmotic modulation of the cell environment.
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Affiliation(s)
- A F Lima
- UC-Biotech, CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3060-197, Cantanhede, Portugal.,Faculty of Science and Technology, University Nova of Lisbon (MIT-Portugal PhD Program), 2829-516, Caparica, Portugal
| | - G May
- University College London, Gower Street, London, WC1E 6BT, UK
| | - J Díaz-Colunga
- Centro Nacional de Biotecnología, CSIC. Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain
| | - S Pedreiro
- Unidade de Gestão Operacional de Citometria, Centro Hospitalar e Universitário de Coimbra, 3000-075, Coimbra, Portugal
| | - A Paiva
- Unidade de Gestão Operacional de Citometria, Centro Hospitalar e Universitário de Coimbra, 3000-075, Coimbra, Portugal.,Coimbra Institute for Clinical and Biomedical Research, Faculty of Medicine,University of Coimbra, 3004-504, Coimbra, Portugal
| | - L Ferreira
- UC-Biotech, CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3060-197, Cantanhede, Portugal.,Faculty of Medicine, University of Coimbra, 3004-504, Coimbra, Portugal
| | - T Enver
- University College London, Gower Street, London, WC1E 6BT, UK
| | - F J Iborra
- Centro Nacional de Biotecnología, CSIC. Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain
| | - R Pires das Neves
- UC-Biotech, CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3060-197, Cantanhede, Portugal. .,Institute for Interdisciplinary Research, University of Coimbra, 3030-789, Coimbra, Portugal.
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7
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Liu Z, Tjian R. Visualizing transcription factor dynamics in living cells. J Cell Biol 2018; 217:1181-1191. [PMID: 29378780 PMCID: PMC5881510 DOI: 10.1083/jcb.201710038] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 01/03/2018] [Accepted: 01/16/2018] [Indexed: 12/16/2022] Open
Abstract
The assembly of sequence-specific enhancer-binding transcription factors (TFs) at cis-regulatory elements in the genome has long been regarded as the fundamental mechanism driving cell type-specific gene expression. However, despite extensive biochemical, genetic, and genomic studies in the past three decades, our understanding of molecular mechanisms underlying enhancer-mediated gene regulation remains incomplete. Recent advances in imaging technologies now enable direct visualization of TF-driven regulatory events and transcriptional activities at the single-cell, single-molecule level. The ability to observe the remarkably dynamic behavior of individual TFs in live cells at high spatiotemporal resolution has begun to provide novel mechanistic insights and promises new advances in deciphering causal-functional relationships of TF targeting, genome organization, and gene activation. In this review, we review current transcription imaging techniques and summarize converging results from various lines of research that may instigate a revision of models to describe key features of eukaryotic gene regulation.
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Affiliation(s)
- Zhe Liu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA
| | - Robert Tjian
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine Center of Excellence, University of California, Berkeley, Berkeley, CA
- Howard Hughes Medical Institute, Berkeley, CA
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8
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Pérez-Garrastachu M, Arluzea J, Andrade R, Díez-Torre A, Urtizberea M, Silió M, Aréchaga J. Nucleoporins redistribute inside the nucleus after cell cycle arrest induced by histone deacetylases inhibition. Nucleus 2017; 8:515-533. [PMID: 28696859 DOI: 10.1080/19491034.2017.1320001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Nucleoporins are the main components of the nuclear-pore complex (NPC) and were initially considered as mere structural elements embedded in the nuclear envelope, being responsible for nucleocytoplasmic transport. Nevertheless, several recent scientific reports have revealed that some nucleoporins participate in nuclear processes such as transcription, replication, DNA repair and chromosome segregation. Thus, the interaction of NPCs with chromatin could modulate the distribution of chromosome territories relying on the epigenetic state of DNA. In particular, the nuclear basket proteins Tpr and Nup153, and the FG-nucleoporin Nup98 seem to play key roles in all these novel functions. In this work, histone deacetylase inhibitors (HDACi) were used to induce a hyperacetylated state of chromatin and the behavior of the mentioned nucleoporins was studied. Our results show that, after HDACi treatment, Tpr, Nup153 and Nup98 are translocated from the nuclear pore toward the interior of the cell nucleus, accumulating as intranuclear nucleoporin clusters. These transitory structures are highly dynamic, and are mainly present in the population of cells arrested at the G0/G1 phase of the cell cycle. Our results indicate that the redistribution of these nucleoporins from the nuclear envelope to the nuclear interior may be implicated in the early events of cell cycle initialization, particularly during the G1 phase transition.
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Affiliation(s)
- Miguel Pérez-Garrastachu
- a Laboratory of Stem Cells, Development & Cancer, Department of Cell Biology and Histology, Faculty of Medicine and Nursing , University of the Basque Country (UPV/EHU) , Leioa , Biscay , Spain
| | - Jon Arluzea
- a Laboratory of Stem Cells, Development & Cancer, Department of Cell Biology and Histology, Faculty of Medicine and Nursing , University of the Basque Country (UPV/EHU) , Leioa , Biscay , Spain.,b High Resolution and Analytical Biomedical Microscopy Core Facility, SGIKer , University of the Basque Country (UPV/EHU) , Leioa , Biscay , Spain
| | - Ricardo Andrade
- b High Resolution and Analytical Biomedical Microscopy Core Facility, SGIKer , University of the Basque Country (UPV/EHU) , Leioa , Biscay , Spain
| | - Alejandro Díez-Torre
- b High Resolution and Analytical Biomedical Microscopy Core Facility, SGIKer , University of the Basque Country (UPV/EHU) , Leioa , Biscay , Spain
| | - Marta Urtizberea
- a Laboratory of Stem Cells, Development & Cancer, Department of Cell Biology and Histology, Faculty of Medicine and Nursing , University of the Basque Country (UPV/EHU) , Leioa , Biscay , Spain
| | - Margarita Silió
- a Laboratory of Stem Cells, Development & Cancer, Department of Cell Biology and Histology, Faculty of Medicine and Nursing , University of the Basque Country (UPV/EHU) , Leioa , Biscay , Spain
| | - Juan Aréchaga
- a Laboratory of Stem Cells, Development & Cancer, Department of Cell Biology and Histology, Faculty of Medicine and Nursing , University of the Basque Country (UPV/EHU) , Leioa , Biscay , Spain.,b High Resolution and Analytical Biomedical Microscopy Core Facility, SGIKer , University of the Basque Country (UPV/EHU) , Leioa , Biscay , Spain
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9
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Abstract
Gene expression control is a fundamental determinant of cellular life with transcription being the most important step. The spatial nuclear arrangement of the transcription process driven by RNA polymerases II and III is nonrandomly organized in foci, which is believed to add another regulatory layer on gene expression control. RNA polymerase I transcription takes place within a specialized organelle, the nucleolus. Transcription of ribosomal RNA directly responds to metabolic requirements, which in turn is reflected in the architecture of nucleoli. It differs from that of the other polymerases with respect to the gene template organization, transcription rate, and epigenetic expression control, whereas other features are shared like the formation of DNA loops bringing genes and components of the transcription machinery in close proximity. In recent years, significant advances have been made in the understanding of the structural prerequisites of nuclear transcription, of the arrangement in the nuclear volume, and of the dynamics of these entities. Here, we compare ribosomal RNA and mRNA transcription side by side and review the current understanding focusing on structural aspects of transcription foci, of their constituents, and of the dynamical behavior of these components with respect to foci formation, disassembly, and cell cycle.
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Affiliation(s)
- Klara Weipoltshammer
- Department for Cell and Developmental Biology, Medical University of Vienna, Schwarzspanierstr. 17, 1090, Vienna, Austria
| | - Christian Schöfer
- Department for Cell and Developmental Biology, Medical University of Vienna, Schwarzspanierstr. 17, 1090, Vienna, Austria.
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10
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Muir R, Diot A, Poulton J. Mitochondrial content is central to nuclear gene expression: Profound implications for human health. Bioessays 2016; 38:150-6. [PMID: 26725055 PMCID: PMC4819685 DOI: 10.1002/bies.201500105] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We review a recent paper in Genome Research by Guantes et al. showing that nuclear gene expression is influenced by the bioenergetic status of the mitochondria. The amount of energy that mitochondria make available for gene expression varies considerably. It depends on: the energetic demands of the tissue; the mitochondrial DNA (mtDNA) mutant load; the number of mitochondria; stressors present in the cell. Hence, when failing mitochondria place the cell in energy crisis there are major effects on gene expression affecting the risk of degenerative diseases, cancer and ageing. In 2015 the UK parliament approved a change in the regulation of IVF techniques, allowing "Mitochondrial replacement therapy" to become a reproductive choice for women at risk of transmitting mitochondrial disease to their children. This is the first time that this technique will be available. Therefore understanding the interaction between mitochondria and the nucleus has never been more important.
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Affiliation(s)
- Rebecca Muir
- Nuffield Department of Obstetrics and Gynaecology, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Alan Diot
- Nuffield Department of Obstetrics and Gynaecology, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Joanna Poulton
- Nuffield Department of Obstetrics and Gynaecology, University of Oxford, John Radcliffe Hospital, Oxford, UK
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11
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Casafont I, Palanca A, Lafarga V, Mata-Garrido J, Berciano MT, Lafarga M. Dynamic Behavior of the RNA Polymerase II and the Ubiquitin Proteasome System During the Neuronal DNA Damage Response to Ionizing Radiation. Mol Neurobiol 2015; 53:6799-6808. [PMID: 26660115 DOI: 10.1007/s12035-015-9565-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 11/29/2015] [Indexed: 12/20/2022]
Abstract
Neurons are highly vulnerable to genotoxic agents. To restore genome integrity upon DNA lesions, neurons trigger a DNA damage response (DDR) that requires chromatin modifications and transcriptional silencing at DNA damage sites. To study the reorganization of the active RNA polymerase II (Pol II), which transcribes all mRNA-encoding genes, and the participation of the ubiquitin-proteasome system (UPS) in the neuronal DDR, we have used rat sensory ganglion neurons exposed to X-rays (4 Gy) ionizing radiation (IR). In control neurons, Pol II appears concentrated in numerous chromatin microfoci identified as transcription factories by the incorporation of 5'-fluorouridine into nascent RNA. Upon IR treatment, numerous IR-induced foci (IRIF), which were immunoreactive for γH2AX and 53BP1, were observed as early as 30 min post-IR; their number progressively reduced at 3 h, 1 day, and 3 days post-IR. The formation of IRIF was associated with a decrease in Pol II levels by both immunofluorescence and Western blotting. Treatment with the proteasome inhibitor bortezomib strongly increased Pol II levels in both control and irradiated neurons, suggesting that proteasome plays a proteolytic role by clearing stalled Pol II complexes at DNA damage sites, as a prelude to DNA repair. Neuronal IRIF recruited ubiquitylated proteins, including ubiquitylated histone H2A (Ub-H2A), and the catalytic proteasome 20S. Ub-H2A has been associated with transcriptional silencing at DNA damage sites. On the other hand, the participation of UPS in neuronal DDR may be essential for the ubiquitylation of Pol II and other proteasome substrates of the DNA repair machinery and their subsequent proteasome-mediated degradation.
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Affiliation(s)
- Iñigo Casafont
- Department of Anatomy and Cell Biology and "Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED)", University of Cantabria-IDIVAL, Cardenal Herrera Oria s/N, Santander, 39011, Spain
| | - Ana Palanca
- Department of Anatomy and Cell Biology and "Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED)", University of Cantabria-IDIVAL, Cardenal Herrera Oria s/N, Santander, 39011, Spain
| | - Vanesa Lafarga
- Laboratorio de Inestabilidad Genómica, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
| | - Jorge Mata-Garrido
- Department of Anatomy and Cell Biology and "Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED)", University of Cantabria-IDIVAL, Cardenal Herrera Oria s/N, Santander, 39011, Spain
| | - Maria T Berciano
- Department of Anatomy and Cell Biology and "Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED)", University of Cantabria-IDIVAL, Cardenal Herrera Oria s/N, Santander, 39011, Spain
| | - Miguel Lafarga
- Department of Anatomy and Cell Biology and "Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED)", University of Cantabria-IDIVAL, Cardenal Herrera Oria s/N, Santander, 39011, Spain.
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12
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Guantes R, Rastrojo A, Neves R, Lima A, Aguado B, Iborra FJ. Global variability in gene expression and alternative splicing is modulated by mitochondrial content. Genome Res 2015; 25:633-44. [PMID: 25800673 PMCID: PMC4417112 DOI: 10.1101/gr.178426.114] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 03/16/2015] [Indexed: 11/24/2022]
Abstract
Noise in gene expression is a main determinant of phenotypic variability. Increasing experimental evidence suggests that genome-wide cellular constraints largely contribute to the heterogeneity observed in gene products. It is still unclear, however, which global factors affect gene expression noise and to what extent. Since eukaryotic gene expression is an energy demanding process, differences in the energy budget of each cell could determine gene expression differences. Here, we quantify the contribution of mitochondrial variability (a natural source of ATP variation) to global variability in gene expression. We find that changes in mitochondrial content can account for ∼50% of the variability observed in protein levels. This is the combined result of the effect of mitochondria dosage on transcription and translation apparatus content and activities. Moreover, we find that mitochondrial levels have a large impact on alternative splicing, thus modulating both the abundance and type of mRNAs. A simple mathematical model in which mitochondrial content simultaneously affects transcription rate and splicing site choice can explain the alternative splicing data. The results of this study show that mitochondrial content (and/or probably function) influences mRNA abundance, translation, and alternative splicing, which ultimately affects cellular phenotype.
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Affiliation(s)
- Raul Guantes
- Department of Condensed Matter Physics, Materials Science Institute "Nicolás Cabrera" and Institute of Condensed Matter Physics (IFIMAC), Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain
| | - Alberto Rastrojo
- Centro Biología Molecular "Severo Ochoa," CSIC-UAM, Campus de Cantoblanco, 28049 Madrid, Spain
| | - Ricardo Neves
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headington, Oxford OX3 9DS, United Kingdom
| | - Ana Lima
- UC Biotech, Center for Neuroscience and Cell Biology, Biocant, Center of Innovation in Biotechnology, 3060-197 Cantanhede, Portugal
| | - Begoña Aguado
- Centro Biología Molecular "Severo Ochoa," CSIC-UAM, Campus de Cantoblanco, 28049 Madrid, Spain
| | - Francisco J Iborra
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headington, Oxford OX3 9DS, United Kingdom; Centro Nacional de Biotecnología, CSIC, Campus de Cantoblanco, 28049 Madrid, Spain
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13
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Raulf A, Spahn CK, Zessin PJM, Finan K, Bernhardt S, Heckel A, Heilemann M. Click chemistry facilitates direct labelling and super-resolution imaging of nucleic acids and proteins†Electronic supplementary information (ESI) available. See DOI: 10.1039/c4ra01027bClick here for additional data file. RSC Adv 2014; 4:30462-30466. [PMID: 25580242 PMCID: PMC4285124 DOI: 10.1039/c4ra01027b] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 06/27/2014] [Indexed: 12/21/2022] Open
Abstract
We demonstrate high-density labelling of cellular DNA and RNA using click chemistry and perform confocal and super-resolution microscopy. We visualize the crescent and ring-like structure of densely packed RNA in nucleoli. We further demonstrate click chemistry with unnatural amino acids for super-resolution imaging of outer-membrane proteins of E. coli.
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Affiliation(s)
- Anika Raulf
- Institute of Physical & Theoretical Chemistry , Goethe-University Frankfurt , Max-von-Laue-Str. 7 , 60438 Frankfurt/Main , Germany .
| | - Christoph K Spahn
- Institute of Physical & Theoretical Chemistry , Goethe-University Frankfurt , Max-von-Laue-Str. 7 , 60438 Frankfurt/Main , Germany .
| | - Patrick J M Zessin
- Institute of Physical & Theoretical Chemistry , Goethe-University Frankfurt , Max-von-Laue-Str. 7 , 60438 Frankfurt/Main , Germany .
| | | | - Stefan Bernhardt
- Institute for Organic Chemistry and Chemical Biology , Goethe-University Frankfurt , Max-von-Laue-Str. 9 , 60438 Frankfurt/Main , Germany
| | - Alexander Heckel
- Institute for Organic Chemistry and Chemical Biology , Goethe-University Frankfurt , Max-von-Laue-Str. 9 , 60438 Frankfurt/Main , Germany
| | - Mike Heilemann
- Institute of Physical & Theoretical Chemistry , Goethe-University Frankfurt , Max-von-Laue-Str. 7 , 60438 Frankfurt/Main , Germany .
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14
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Abstract
This volume brings together a number of perspectives on how certain physical phenomena contribute to the functional design and operation of the nucleus. This collection could not be more timely, resonating with an increasing awareness of the opportunities that lie at the interface of cell biology and the physical sciences. For example, this was a major theme in the 2012 and 2013 annual meetings of the American Society for Cell Biology, and one that the Society aims to emphasize even further going forward. In addition, the emerging canonical relevance of the physical sciences to cell biology has in recent summers made a most conspicuous appearance in the curriculum (lectures and intense labs) of the famed Physiology Course at the Marine Biological Laboratory in Woods Hole. So, much credit is due to Ronald Hancock and Kwang Jeon, the coeditors of this volume, and all the authors for creating a work that is so au courant.
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Affiliation(s)
- Thoru Pederson
- Program in Cell and Developmental Dynamics, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA.
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Papantonis A, Cook PR. Transcription factories: genome organization and gene regulation. Chem Rev 2013; 113:8683-705. [PMID: 23597155 DOI: 10.1021/cr300513p] [Citation(s) in RCA: 162] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Argyris Papantonis
- Sir William Dunn School of Pathology, University of Oxford , South Parks Road, Oxford OX1 3RE, United Kingdom
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