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Transcription-replication encounters, consequences and genomic instability. Nat Struct Mol Biol 2013; 20:412-8. [PMID: 23552296 DOI: 10.1038/nsmb.2543] [Citation(s) in RCA: 201] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Accepted: 02/07/2013] [Indexed: 12/16/2022]
Abstract
To ensure accurate duplication of genetic material, the replication fork must overcome numerous natural obstacles on its way, including transcription complexes engaged along the same template. Here we review the various levels of interdependence between transcription and replication processes and how different types of encounters between RNA- and DNA-polymerase complexes may result in clashes of those machineries on the DNA template and thus increase genomic instability. In addition, we summarize strategies evolved in bacteria and eukaryotes to minimize the consequences of collisions, including R-loop formation and topological stresses.
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Wee KB, Yio WK, Surana U, Chiam KH. Transcription factor oscillations induce differential gene expressions. Biophys J 2012; 102:2413-23. [PMID: 22713556 DOI: 10.1016/j.bpj.2012.04.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2011] [Revised: 04/16/2012] [Accepted: 04/17/2012] [Indexed: 01/04/2023] Open
Abstract
Intracellular protein levels of diverse transcription factors (TFs) vary periodically with time. However, the effects of TF oscillations on gene expression, the primary role of TFs, are poorly understood. In this study, we determined these effects by comparing gene expression levels induced in the presence and in the absence of TF oscillations under same mean intracellular protein level of TF. For all the nonlinear TF transcription kinetics studied, an oscillatory TF is predicted to induce gene expression levels that are distinct from a nonoscillatory TF. The conditions dictating whether TF oscillations induce either higher or lower average gene expression levels were elucidated. Subsequently, the predicted effects from an oscillatory TF, which follows sigmoid transcription kinetics, were applied to demonstrate how oscillatory dynamics provide a mechanism for differential target gene transactivation. Generally, the mean TF concentration at which oscillations occur relative to the promoter binding affinity of a target gene determines whether the gene is up- or downregulated whereas the oscillation amplitude amplifies the magnitude of the differential regulation. Notably, the predicted trends of differential gene expressions induced by oscillatory NF-κB and glucocorticoid receptor match the reported experimental observations. Furthermore, the biological function of p53 oscillations is predicted to prime the cell for death upon DNA damage via differential upregulation of apoptotic genes. Lastly, given N target genes, an oscillatory TF can generate between (N-1) and (2N-1) distinct patterns of differential transactivation. This study provides insights into the mechanism for TF oscillations to induce differential gene expressions, and underscores the importance of TF oscillations in biological regulations.
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Affiliation(s)
- Keng Boon Wee
- A∗STAR Institute of High Performance Computing, Connexis, Singapore.
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Antico Arciuch VG, Elguero ME, Poderoso JJ, Carreras MC. Mitochondrial regulation of cell cycle and proliferation. Antioxid Redox Signal 2012; 16:1150-80. [PMID: 21967640 PMCID: PMC3315176 DOI: 10.1089/ars.2011.4085] [Citation(s) in RCA: 294] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Revised: 10/03/2011] [Accepted: 10/03/2011] [Indexed: 01/01/2023]
Abstract
Eukaryotic mitochondria resulted from symbiotic incorporation of α-proteobacteria into ancient archaea species. During evolution, mitochondria lost most of the prokaryotic bacterial genes and only conserved a small fraction including those encoding 13 proteins of the respiratory chain. In this process, many functions were transferred to the host cells, but mitochondria gained a central role in the regulation of cell proliferation and apoptosis, and in the modulation of metabolism; accordingly, defective organelles contribute to cell transformation and cancer, diabetes, and neurodegenerative diseases. Most cell and transcriptional effects of mitochondria depend on the modulation of respiratory rate and on the production of hydrogen peroxide released into the cytosol. The mitochondrial oxidative rate has to remain depressed for cell proliferation; even in the presence of O₂, energy is preferentially obtained from increased glycolysis (Warburg effect). In response to stress signals, traffic of pro- and antiapoptotic mitochondrial proteins in the intermembrane space (B-cell lymphoma-extra large, Bcl-2-associated death promoter, Bcl-2 associated X-protein and cytochrome c) is modulated by the redox condition determined by mitochondrial O₂ utilization and mitochondrial nitric oxide metabolism. In this article, we highlight the traffic of the different canonical signaling pathways to mitochondria and the contributions of organelles to redox regulation of kinases. Finally, we analyze the dynamics of the mitochondrial population in cell cycle and apoptosis.
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Affiliation(s)
| | - María Eugenia Elguero
- Laboratory of Oxygen Metabolism, University of Buenos Aires, University Hospital, Buenos Aires, Argentina
| | - Juan José Poderoso
- Laboratory of Oxygen Metabolism, University of Buenos Aires, University Hospital, Buenos Aires, Argentina
- Department of Internal Medicine, School of Medicine, University of Buenos Aires, Buenos Aires, Argentina
- CONICET, Buenos Aires, Argentina
| | - María Cecilia Carreras
- Laboratory of Oxygen Metabolism, University of Buenos Aires, University Hospital, Buenos Aires, Argentina
- CONICET, Buenos Aires, Argentina
- Department of Clinical Biochemistry, INFIBIOC and School of Pharmacy and Biochemistry, University of Buenos Aires, Buenos Aires, Argentina
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Neelamegham S, Liu G. Systems glycobiology: biochemical reaction networks regulating glycan structure and function. Glycobiology 2011; 21:1541-53. [PMID: 21436236 DOI: 10.1093/glycob/cwr036] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
There is a growing use of bioinformatics based methods in the field of Glycobiology. These have been used largely to curate glycan structures, organize array-based experimental data and display existing knowledge of glycosylation-related pathways in silico. Although the cataloging of vast amounts of data is beneficial, it is often a challenge to gain meaningful mechanistic insight from this exercise alone. The development of specific analysis tools to query the database is necessary. If these queries can integrate existing knowledge of glycobiology, new insights may be gained. Such queries that couple biochemical knowledge and mathematics have been developed in the field of Systems Biology. The current review summarizes the current state of the art in the application of computational modeling in the field of Glycobiology. It provides (i) an overview of experimental and online resources that can be used to construct glycosylation reaction networks, (ii) mathematical methods to formulate the problem including a description of ordinary differential equation and logic-based reaction networks, (iii) optimization techniques that can be applied to fit experimental data for the purpose of model reconstruction and for evaluating unknown model parameters, (iv) post-simulation analysis methods that yield experimentally testable hypotheses and (v) a summary of available software tools that can be used by non-specialists to perform many of the above functions.
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Affiliation(s)
- Sriram Neelamegham
- Department of Chemical and Biological Engineering, and The NY State Center for Excellence in Bioinformatics and Life Sciences, State University of New York, Buffalo, NY 14260, USA.
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Marín-Navarro J, Jauhiainen A, Moreno J, Alepuz P, Pérez-Ortín JE, Sunnerhagen P. Global estimation of mRNA stability in yeast. Methods Mol Biol 2011; 734:3-23. [PMID: 21468982 DOI: 10.1007/978-1-61779-086-7_1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Turnover of mRNA is an important level of gene regulation. Individual mRNAs have different intrinsic stabilities. Moreover, mRNA stability changes dynamically with conditions such as hormonal stimulation or cellular stress. While accurate methods exist to measure the half-life of an individual transcript, global methods to estimate mRNA turnover have limitations in terms of resolution in time and precision. We describe and compare two complementary approaches to estimating global transcript stability: (1) direct measurement of decay rates; (2) indirect estimation of turnover from determination of mRNA synthesis rates and steady-state levels. Since the two approaches have distinct strengths yet confer different cellular perturbations, it is valuable to consider results obtained with both methods. The practical aspects of the chapter are written from a yeast perspective; the general considerations hold true for all eukaryotes, however.
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Affiliation(s)
- Julia Marín-Navarro
- Department of Cell and Molecular Biology, Lundberg Laboratory, University of Gothenburg, Gothenburg, Sweden
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Cell state switching factors and dynamical patterning modules: complementary mediators of plasticity in development and evolution. J Biosci 2009; 34:553-72. [DOI: 10.1007/s12038-009-0074-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Newman SA, Bhat R, Mezentseva NV. Cell state switching factors and dynamical patterning modules: complementary mediators of plasticity in development and evolution. J Biosci 2009. [DOI: 10.1007/s12038-009-0001-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Soranzo N, Zampieri M, Farina L, Altafini C. mRNA stability and the unfolding of gene expression in the long-period yeast metabolic cycle. BMC SYSTEMS BIOLOGY 2009; 3:18. [PMID: 19200359 PMCID: PMC2677395 DOI: 10.1186/1752-0509-3-18] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2008] [Accepted: 02/06/2009] [Indexed: 11/10/2022]
Abstract
Background In yeast, genome-wide periodic patterns associated with energy-metabolic oscillations have been shown recently for both short (approx. 40 min) and long (approx. 300 min) periods. Results The dynamical regulation due to mRNA stability is found to be an important aspect of the genome-wide coordination of the long-period yeast metabolic cycle. It is shown that for periodic genes, arranged in classes according either to expression profile or to function, the pulses of mRNA abundance have phase and width which are directly proportional to the corresponding turnover rates. Conclusion The cascade of events occurring during the yeast metabolic cycle (and their correlation with mRNA turnover) reflects to a large extent the gene expression program observable in other dynamical contexts such as the response to stresses/stimuli.
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Newman SA, Bhat R. Dynamical patterning modules: physico-genetic determinants of morphological development and evolution. Phys Biol 2008; 5:015008. [PMID: 18403826 DOI: 10.1088/1478-3975/5/1/015008] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The shapes and forms of multicellular organisms arise by the generation of new cell states and types and changes in the numbers and rearrangements of the various kinds of cells. While morphogenesis and pattern formation in all animal species are widely recognized to be mediated by the gene products of an evolutionarily conserved 'developmental-genetic toolkit', the link between these molecular players and the physics underlying these processes has been generally ignored. This paper introduces the concept of 'dynamical patterning modules' (DPMs), units consisting of one or more products of the 'toolkit' genes that mobilize physical processes characteristic of chemically and mechanically excitable meso- to macroscopic systems such as cell aggregates: cohesion, viscoelasticity, diffusion, spatiotemporal heterogeneity based on lateral inhibition and multistable and oscillatory dynamics. We suggest that ancient toolkit gene products, most predating the emergence of multicellularity, assumed novel morphogenetic functions due to change in the scale and context inherent to multicellularity. We show that DPMs, acting individually and in concert with each other, constitute a 'pattern language' capable of generating all metazoan body plans and organ forms. The physical dimension of developmental causation implies that multicellular forms during the explosive radiation of animal body plans in the middle Cambrian, approximately 530 million years ago, could have explored an extensive morphospace without concomitant genotypic change or selection for adaptation. The morphologically plastic body plans and organ forms generated by DPMs, and their ontogenetic trajectories, would subsequently have been stabilized and consolidated by natural selection and genetic drift. This perspective also solves the apparent 'molecular homology-analogy paradox', whereby widely divergent modern animal types utilize the same molecular toolkit during development by proposing, in contrast to the Neo-Darwinian principle, that phenotypic disparity early in evolution occurred in advance of, rather than closely tracked, genotypic change.
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Affiliation(s)
- Stuart A Newman
- Department of Cell Biology and Anatomy, New York Medical College, Valhalla, NY 10595, USA.
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Tsuchiya M, Tsuchyia M, Wong ST, Yeo ZX, Colosimo A, Palumbo MC, Farina L, Crescenzi M, Mazzola A, Negri R, Bianchi MM, Selvarajoo K, Tomita M, Giuliani A. Gene expression waves. Cell cycle independent collective dynamics in cultured cells. FEBS J 2007; 274:2878-86. [PMID: 17466018 DOI: 10.1111/j.1742-4658.2007.05822.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The ergodic hypothesis, which assumes the independence of each cell of the ensemble from all the others, is a necessary prerequisite to attach single cell based explanations to the grand averages taken from population data. This was the prevailing view about the interpretation of cellular biology experiments that typically are performed on colonies of billions of cells. By analysing gene expression data of different cells going from yeast to mammalian cell cultures, we demonstrate that cell cultures display a sort of "ecology-in-a-plate" giving rise to a rich dynamics of gene expression that are independent from reproductive cycles, hence contradicting simple ergodic assumptions The aspecific character of the observed coordinated gene expression activity inhibits any simple mechanistic hypothesis and highlights the need to consider population effects in the interpretation of data coming from cell cultures.
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Affiliation(s)
- Masa Tsuchiya
- Institute for Advanced Biosciences, Keio University, Yamagata, Japan
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Martínez-Diez M, Santamaría G, Ortega ÁD, Cuezva JM. Biogenesis and dynamics of mitochondria during the cell cycle: significance of 3'UTRs. PLoS One 2006; 1:e107. [PMID: 17205111 PMCID: PMC1762426 DOI: 10.1371/journal.pone.0000107] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2006] [Accepted: 11/24/2006] [Indexed: 11/18/2022] Open
Abstract
Nowadays, we are facing a renaissance of mitochondria in cancer biology. However, our knowledge of the basic cell biology and on the timing and mechanisms that control the biosynthesis of mitochondrial constituents during progression through the cell cycle of mammalian cells remain largely unknown. Herein, we document the in vivo changes on mitochondrial morphology and dynamics that accompany cellular mitosis, and illustrate the following key points of the biogenesis of mitochondria during progression of liver cells through the cycle: (i) the replication of nuclear and mitochondrial genomes is synchronized during cellular proliferation, (ii) the accretion of OXPHOS proteins is asynchronously regulated during proliferation being the synthesis of beta-F1-ATPase and Hsp60 carried out also at G2/M and, (iii) the biosynthesis of cardiolipin is achieved during the S phase, although full development of the mitochondrial membrane potential (DeltaPsim) is attained at G2/M. Furthermore, we demonstrate using reporter constructs that the mechanism regulating the accretion of beta-F1-ATPase during cellular proliferation is controlled at the level of mRNA translation by the 3'UTR of the transcript. The 3'UTR-driven synthesis of the protein at G2/M is essential for conferring to the daughter cells the original phenotype of the parental cell. Our findings suggest that alterations on this process may promote deregulated beta-F1-ATPase expression in human cancer.
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Current awareness on yeast. Yeast 2006. [DOI: 10.1002/yea.1321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Li CM, Klevecz RR. A rapid genome-scale response of the transcriptional oscillator to perturbation reveals a period-doubling path to phenotypic change. Proc Natl Acad Sci U S A 2006; 103:16254-9. [PMID: 17043222 PMCID: PMC1613231 DOI: 10.1073/pnas.0604860103] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Perturbation of the gated-synchrony system in yeast with phenelzine, an antidepressant drug used in the treatment of affective disorders in humans, leads to a rapid lengthening in the period of the genome-wide transcriptional oscillation. The effect is a concerted, genome-scale change in expression that is first seen in genes maximally expressed in the late-reductive phase of the cycle, doubling the length of the reductive phase within two cycles after treatment. Clustering of genes based on their temporal patterns of expression yielded just three super clusters whose trajectories through time could then be mapped into a simple 3D figure. In contrast to transcripts in the late-reductive phase, most transcripts do not show transients in expression relative to others in their temporal cluster but change their period in a concerted fashion. Mapping the trajectories of the transcripts into low-dimensional surfaces that can be represented by simple systems of differential equations provides a readily testable model of the dynamic architecture of phenotype. In this system, period doubling may be a preferred pathway for phenotypic change. As a practical matter, low-amplitude, genome-wide oscillations, a ubiquitous but often unrecognized attribute of phenotype, could be a source of seemingly intractable biological noise in microarray studies.
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Affiliation(s)
- Caroline M. Li
- Dynamic Systems Group, Department of Biology, Beckman Research Institute, City of Hope Medical Center, Duarte CA 91010
| | - Robert R. Klevecz
- Dynamic Systems Group, Department of Biology, Beckman Research Institute, City of Hope Medical Center, Duarte CA 91010
- *To whom correspondence should be addressed. E-mail:
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