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Singh A. Negative feedback through mRNA provides the best control of gene-expression noise. IEEE Trans Nanobioscience 2012; 10:194-200. [PMID: 22020106 DOI: 10.1109/tnb.2011.2168826] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Genetically identical cell populations exposed to the same environment can exhibit considerable cell-to-cell variation in the levels of specific proteins. This variation or expression noise arises from the inherent stochastic nature of biochemical reactions that constitute gene expression. Negative feedback loops are common motifs in gene networks that reduce expression noise and intercellular variability in protein levels. Using stochastic models of gene expression we here compare different feedback architectures in their ability to reduce stochasticity in protein levels. A mathematically controlled comparison shows that in physiologically relevant parameter regimes, feedback regulation through the mRNA provides the best suppression of expression noise. Consistent with our theoretical results we find negative feedback loops though the mRNA in essential eukaryotic genes, where feedback is mediated via intron-derived microRNAs. Finally, we find that contrary to previous results, protein-mediated translational regulation may not always provide significantly better noise suppression than protein-mediated transcriptional regulation.
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Affiliation(s)
- Abhyudai Singh
- Department of Electrical and Computer Engineering, University of Delaware, Newark, DE 19716, USA.
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52
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Pir P, Gutteridge A, Wu J, Rash B, Kell DB, Zhang N, Oliver SG. The genetic control of growth rate: a systems biology study in yeast. BMC SYSTEMS BIOLOGY 2012; 6:4. [PMID: 22244311 PMCID: PMC3398284 DOI: 10.1186/1752-0509-6-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Accepted: 01/13/2012] [Indexed: 11/10/2022]
Abstract
BACKGROUND Control of growth rate is mediated by tight regulation mechanisms in all free-living organisms since long-term survival depends on adaptation to diverse environmental conditions. The yeast, Saccharomyces cerevisiae, when growing under nutrient-limited conditions, controls its growth rate via both nutrient-specific and nutrient-independent gene sets. At slow growth rates, at least, it has been found that the expression of the genes that exert significant control over growth rate (high flux control or HFC genes) is not necessarily regulated by growth rate itself. It has not been determined whether the set of HFC genes is the same at all growth rates or whether it is the same in conditions of nutrient limitation or excess. RESULTS HFC genes were identified in competition experiments in which a population of hemizygous diploid yeast deletants were grown at, or close to, the maximum specific growth rate in either nutrient-limiting or nutrient-sufficient conditions. A hemizygous mutant is one in which one of any pair of homologous genes is deleted in a diploid, These HFC genes divided into two classes: a haploinsufficient (HI) set, where the hemizygous mutants grow slower than the wild type, and a haploproficient (HP) set, which comprises hemizygotes that grow faster than the wild type. The HI set was found to be enriched for genes involved in the processes of gene expression, while the HP set was enriched for genes concerned with the cell cycle and genome integrity. CONCLUSION A subset of growth-regulated genes have HFC characteristics when grown in conditions where there are few, or no, external constraints on the rate of growth that cells may attain. This subset is enriched for genes that participate in the processes of gene expression, itself (i.e. transcription and translation). The fact that haploproficiency is exhibited by mutants grown at the previously determined maximum rate implies that the control of growth rate in this simple eukaryote represents a trade-off between the selective advantages of rapid growth and the need to maintain the integrity of the genome.
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Affiliation(s)
- Pınar Pir
- Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK
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Singh A, Razooky BS, Dar RD, Weinberger LS. Dynamics of protein noise can distinguish between alternate sources of gene-expression variability. Mol Syst Biol 2012; 8:607. [PMID: 22929617 PMCID: PMC3435505 DOI: 10.1038/msb.2012.38] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Accepted: 07/30/2012] [Indexed: 12/19/2022] Open
Abstract
Within individual cells, two molecular processes have been implicated as sources of noise in gene expression: (i) Poisson fluctuations in mRNA abundance arising from random birth and death of individual mRNA transcripts or (ii) promoter fluctuations arising from stochastic promoter transitions between different transcriptional states. Steady-state measurements of variance in protein levels are insufficient to discriminate between these two mechanisms, and mRNA single-molecule fluorescence in situ hybridization (smFISH) is challenging when cellular mRNA concentrations are high. Here, we present a perturbation method that discriminates mRNA birth/death fluctuations from promoter fluctuations by measuring transient changes in protein variance and that can operate in the regime of high molecular numbers. Conceptually, the method exploits the fact that transcriptional blockage results in more rapid increases in protein variability when mRNA birth/death fluctuations dominate over promoter fluctuations. We experimentally demonstrate the utility of this perturbation approach in the HIV-1 model system. Our results support promoter fluctuations as the primary noise source in HIV-1 expression. This study illustrates a relatively simple method that complements mRNA smFISH hybridization and can be used with existing GFP-tagged libraries to include or exclude alternate sources of noise in gene expression.
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Affiliation(s)
- Abhyudai Singh
- Department of Chemistry and Biochemistry, University of California, San Diego, CA, USA
- Department of Electrical and Computer Engineering, University of Delaware, Newark, DE, USA
| | - Brandon S Razooky
- Department of Chemistry and Biochemistry, University of California, San Diego, CA, USA
- Biophysics Graduate Group, University of California, San Francisco, CA, USA
- The Gladstone Institute of Virology and Immunology, San Francisco, CA, USA
| | - Roy D Dar
- The Gladstone Institute of Virology and Immunology, San Francisco, CA, USA
- Center for Systems and Synthetic Biology, University of California, San Francisco, CA, USA
| | - Leor S Weinberger
- Department of Chemistry and Biochemistry, University of California, San Diego, CA, USA
- The Gladstone Institute of Virology and Immunology, San Francisco, CA, USA
- Center for Systems and Synthetic Biology, University of California, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
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Error prevention and mitigation as forces in the evolution of genes and genomes. Nat Rev Genet 2011; 12:875-81. [PMID: 22094950 DOI: 10.1038/nrg3092] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Why are short introns rarely a multiple of three nucleotides long? Why do essential genes cluster? Why are genes in operons often lined up in the order in which they are needed in the encoded pathway? In this Opinion article, we argue that these and many other - ostensibly disparate - observations are all pieces of an emerging picture in which multiple aspects of gene anatomy and genome architecture have evolved in response to error-prone gene expression.
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Gijsbers ACJ, Schoumans J, Ruivenkamp CAL. Interpretation of array comparative genome hybridization data: a major challenge. Cytogenet Genome Res 2011; 135:222-7. [PMID: 22086107 DOI: 10.1159/000334066] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The advent and application of high-resolution array-based comparative genome hybridization (array CGH) has led to the detection of large numbers of copy number variants (CNVs) in patients with developmental delay and/or multiple congenital anomalies as well as in healthy individuals. The notion that CNVs are also abundantly present in the normal population challenges the interpretation of the clinical significance of detected CNVs in patients. In this review we will illustrate a general clinical workflow based on our own experience that can be used in routine diagnostics for the interpretation of CNVs.
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Affiliation(s)
- A C J Gijsbers
- Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
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Abstract
Synpolydactyly 1 (SPD1; OMIM 186000), also known as type II syndactyly, is a dominantly inherited limb malformation that is characterized by an increased number of digits. SPD1 is most commonly caused by polyalanine repeat expansions in the coding region of the HOXD13 gene, which are believed to show a dominant-negative effect. In addition, missense and out-of-frame deletion mutations in the HOXD13 gene are also known to cause SPD, and the mechanism responsible for the phenotype appears to be haploinsufficiency. Here, we analyzed a large consanguineous family from Pakistan with SPD showing a wide variation in phenotype among affected individuals. We performed genetic linkage analysis, which identified a region on chromosome 2 containing the HOXD13 gene. Haplotype analysis with microsatellite markers suggested segregation of the phenotype with HOXD13 gene with incomplete penetrance. Direct sequencing analysis of HOXD13 gene revealed a nonsense mutation, designated Q248X. All affected individuals with the severe SPD phenotype are homozygous for the mutation, while those with the mild SPD phenotype are heterozygous for the mutation. Furthermore, some unaffected individuals also carry the mutation in the heterozygous state, showing incomplete penetrance. Our results demonstrate the first nonsense mutation in the HOXD13 gene underlying a severe form of SPD in the homozygous state, and a milder form of SPD with approximately 50% penetrance in the heterozygous state, most likely due to the production of 50% of protein compared to normal individuals..
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Alvarado DM, McCall K, Aferol H, Silva MJ, Garbow JR, Spees WM, Patel T, Siegel M, Dobbs MB, Gurnett CA. Pitx1 haploinsufficiency causes clubfoot in humans and a clubfoot-like phenotype in mice. Hum Mol Genet 2011; 20:3943-52. [PMID: 21775501 DOI: 10.1093/hmg/ddr313] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Clubfoot affects 1 in 1000 live births, although little is known about its genetic or developmental basis. We recently identified a missense mutation in the PITX1 bicoid homeodomain transcription factor in a family with a spectrum of lower extremity abnormalities, including clubfoot. Because the E130K mutation reduced PITX1 activity, we hypothesized that PITX1 haploinsufficiency could also cause clubfoot. Using copy number analysis, we identified a 241 kb chromosome 5q31 microdeletion involving PITX1 in a patient with isolated familial clubfoot. The PITX1 deletion segregated with autosomal dominant clubfoot over three generations. To study the role of PITX1 haploinsufficiency in clubfoot pathogenesis, we began to breed Pitx1 knockout mice. Although Pitx1(+/-) mice were previously reported to be normal, clubfoot was observed in 20 of 225 Pitx1(+/-) mice, resulting in an 8.9% penetrance. Clubfoot was unilateral in 16 of the 20 affected Pitx1(+/-) mice, with the right and left limbs equally affected, in contrast to right-sided predominant hindlimb abnormalities previously noted with complete loss of Pitx1. Peroneal artery hypoplasia occurred in the clubfoot limb and corresponded spatially with small lateral muscle compartments. Tibial and fibular bone volumes were also reduced. Skeletal muscle gene expression was significantly reduced in Pitx1(-/-) E12.5 hindlimb buds compared with the wild-type, suggesting that muscle hypoplasia was due to abnormal early muscle development and not disuse atrophy. Our morphological data suggest that PITX1 haploinsufficiency may cause a developmental field defect preferentially affecting the lateral lower leg, a theory that accounts for similar findings in human clubfoot.
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Affiliation(s)
- David M Alvarado
- Department of Orthopaedic Surgery, Washington University School of Medicine, St Louis, MO 63110, USA
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58
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Saka Y, Lhoussaine C, Kuttler C, Ullner E, Thiel M. Theoretical basis of the community effect in development. BMC SYSTEMS BIOLOGY 2011; 5:54. [PMID: 21496342 PMCID: PMC3105943 DOI: 10.1186/1752-0509-5-54] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Accepted: 04/17/2011] [Indexed: 02/06/2023]
Abstract
BACKGROUND Genetically identical cells often show significant variation in gene expression profile and behaviour even in the same physiological condition. Notably, embryonic cells destined to the same tissue maintain a uniform transcriptional regulatory state and form a homogeneous cell group. One mechanism to keep the homogeneity within embryonic tissues is the so-called community effect in animal development. The community effect is an interaction among a group of many nearby precursor cells, and is necessary for them to maintain tissue-specific gene expression and differentiate in a coordinated manner. Although it has been shown that the cell-cell communication by a diffusible factor plays a crucial role, it is not immediately obvious why a community effect needs many cells. RESULTS In this work, we propose a model of the community effect in development, which consists in a linear gene cascade and cell-cell communication. We examined the properties of the model theoretically using a combination of stochastic and deterministic modelling methods. We have derived the analytical formula for the threshold size of a cell population that is necessary for a community effect, which is in good agreement with stochastic simulation results. CONCLUSIONS Our theoretical analysis indicates that a simple model with a linear gene cascade and cell-cell communication is sufficient to reproduce the community effect in development. The model explains why a community needs many cells. It suggests that the community's long-term behaviour is independent of the initial induction level, although the initiation of a community effect requires a sufficient amount of inducing signal. The mechanism of the community effect revealed by our theoretical analysis is analogous to that of quorum sensing in bacteria. The community effect may underlie the size control in animal development and also the genesis of autosomal dominant diseases including tumorigenesis.
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Affiliation(s)
- Yasushi Saka
- School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Cédric Lhoussaine
- LIFL, UMR Université Lille 1/CNRS 8022, Cité Scientifique, Bat M3, 59655 Villeneuve d'Ascq, Cedex France
- Interdisciplinary Research Institute, CNRS USR3078, Parc de la Haute Borne, 50 avenue Halley, BP70478, 59658 Villeneuve d'Ascq, France
| | - Celine Kuttler
- LIFL, UMR Université Lille 1/CNRS 8022, Cité Scientifique, Bat M3, 59655 Villeneuve d'Ascq, Cedex France
- Interdisciplinary Research Institute, CNRS USR3078, Parc de la Haute Borne, 50 avenue Halley, BP70478, 59658 Villeneuve d'Ascq, France
| | - Ekkehard Ullner
- School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
- Department of Physics, Institute for Complex Systems and Mathematical Biology, SUPA, University of Aberdeen, Old Aberdeen, Aberdeen AB24 3UE, UK
| | - Marco Thiel
- Department of Physics, Institute for Complex Systems and Mathematical Biology, SUPA, University of Aberdeen, Old Aberdeen, Aberdeen AB24 3UE, UK
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Bhat PJ, Darunte L, Kareenhalli V, Dandekar J, Kumar A. Can metabolic plasticity be a cause for cancer? Warburg-Waddington legacy revisited. Clin Epigenetics 2011; 2:113-22. [PMID: 22704333 PMCID: PMC3365601 DOI: 10.1007/s13148-011-0030-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Accepted: 03/15/2011] [Indexed: 01/06/2023] Open
Abstract
UNLABELLED Fermentation of glucose to lactate in the presence of sufficient oxygen, known as aerobic glycolysis or Warburg effect, is a universal phenotype of cancer cells. Understanding its origin and role in cellular immortalization and transformation has attracted considerable attention in the recent past. Intriguingly, while we now know that Warburg effect is essential for tumor growth and development, it is thought to arise because of genetic and/or epigenetic changes. In contrast to the above, we propose that Warburg effect can also arise due to normal biochemical fluctuations, independent of genetic and epigenetic changes. Cells that have acquired Warburg effect proliferate rapidly to give rise to a population of heterogeneous progenitors of cancer cells. Such cells also generate more lactate and alter the fitness landscape. This dynamic fitness landscape facilitates evolution of cancer cells from its progenitors, in a fashion analogous to Darwinian evolution. Thus, sporadic cancer can also occur first by the acquisition of Warburg effect, then followed by mutation and selection. The idea proposed here circumvents the inherent difficulties associated with the current understanding of tumorigenesis, and is also consistent with many experimental and epidemiological observations. We discuss this model in the context of epigenetics as originally enunciated by Waddington. ELECTRONIC SUPPLEMENTARY MATERIAL The online version of this article (doi:10.1007/s13148-011-0030-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Paike Jayadeva Bhat
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 40076 India
| | - Lalit Darunte
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 40076 India
| | - Venkatesh Kareenhalli
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 40076 India
| | - Jaswandi Dandekar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 40076 India
| | - Abhay Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 40076 India
- Department of Biotechnology, Lovely School of Sciences, Lovely Professional University, Phagwara, Punjab 144402 India
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Wang GZ, Lercher MJ, Hurst LD. Transcriptional coupling of neighboring genes and gene expression noise: evidence that gene orientation and noncoding transcripts are modulators of noise. Genome Biol Evol 2011; 3:320-31. [PMID: 21402863 PMCID: PMC5654408 DOI: 10.1093/gbe/evr025] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
How is noise in gene expression modulated? Do mechanisms of noise control impact genome organization? In yeast, the expression of one gene can affect that of a very close neighbor. As the effect is highly regionalized, we hypothesize that genes in different orientations will have differing degrees of coupled expression and, in turn, different noise levels. Divergently organized gene pairs, in particular those with bidirectional promoters, have close promoters, maximizing the likelihood that expression of one gene affects the neighbor. With more distant promoters, the same is less likely to hold for gene pairs in nondivergent orientation. Stochastic models suggest that coupled chromatin dynamics will typically result in low abundance-corrected noise (ACN). Transcription of noncoding RNA (ncRNA) from a bidirectional promoter, we thus hypothesize to be a noise-reduction, expression-priming, mechanism. The hypothesis correctly predicts that protein-coding genes with a bidirectional promoter, including those with a ncRNA partner, have lower ACN than other genes and divergent gene pairs uniquely have correlated ACN. Moreover, as predicted, ACN increases with the distance between promoters. The model also correctly predicts ncRNA transcripts to be often divergently transcribed from genes that a priori would be under selection for low noise (essential genes, protein complex genes) and that the latter genes should commonly reside in divergent orientation. Likewise, that genes with bidirectional promoters are rare subtelomerically, cluster together, and are enriched in essential gene clusters is expected and observed. We conclude that gene orientation and transcription of ncRNAs are candidate modulators of noise.
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Affiliation(s)
- Guang-Zhong Wang
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom
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61
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Abstract
Bimodality of gene expression, as a mechanism contributing to phenotypic diversity, enhances the survival of cells in a fluctuating environment. To date, the bimodal response of a gene regulatory system has been attributed to the cooperativity of transcription factor binding or to feedback loops. It has remained unclear whether noncooperative binding of transcription factors can give rise to bimodality in an open-loop system. We study a theoretical model of gene expression in a two-step cascade (a deterministically monostable system) in which the regulatory gene produces transcription factors that have a nonlinear effect on the activity of the target gene. We show that a unimodal distribution of transcription factors over the cell population can generate a bimodal steady-state output without cooperative transcription factor binding. We introduce a simple method of geometric construction that allows one to predict the onset of bimodality. The construction only involves the parameters of bursting of the regulatory gene and the dose-response curve of the target gene. Using this method, we show that the gene expression may switch between unimodal and bimodal as the concentration of inducers or corepressors is varied. These findings may explain the experimentally observed bimodal response of cascades consisting of a fluorescent protein reporter controlled by the tetracycline repressor. The geometric construction provides a useful tool for designing experiments and for interpretation of their results. Our findings may have important implications for understanding the strategies adopted by cell populations to survive in changing environments.
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Dauwerse JG, Dixon J, Seland S, Ruivenkamp CAL, van Haeringen A, Hoefsloot LH, Peters DJM, Boers ACD, Daumer-Haas C, Maiwald R, Zweier C, Kerr B, Cobo AM, Toral JF, Hoogeboom AJM, Lohmann DR, Hehr U, Dixon MJ, Breuning MH, Wieczorek D. Mutations in genes encoding subunits of RNA polymerases I and III cause Treacher Collins syndrome. Nat Genet 2010; 43:20-2. [PMID: 21131976 DOI: 10.1038/ng.724] [Citation(s) in RCA: 235] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2010] [Accepted: 10/29/2010] [Indexed: 12/19/2022]
Abstract
We identified a deletion of a gene encoding a subunit of RNA polymerases I and III, POLR1D, in an individual with Treacher Collins syndrome (TCS). Subsequently, we detected 20 additional heterozygous mutations of POLR1D in 252 individuals with TCS. Furthermore, we discovered mutations in both alleles of POLR1C in three individuals with TCS. These findings identify two additional genes involved in TCS, confirm the genetic heterogeneity of TCS and support the hypothesis that TCS is a ribosomopathy.
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Affiliation(s)
- Johannes G Dauwerse
- Center for Human and Clinical Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands.
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63
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Abstract
Gene expression responds to changes in conditions but also stochastically among individuals. In budding yeast, both expression responsiveness across conditions ("plasticity") and cell-to-cell variation ("noise") have been quantified for thousands of genes and found to correlate across genes. It has been argued therefore that noise and plasticity may be strongly coupled and mechanistically linked. This is consistent with some theoretical ideas, but a strong coupling between noise and plasticity also has the potential to introduce cost-benefit conflicts during evolution. For example, if high plasticity is beneficial (genes need to respond to the environment), but noise is detrimental (fluctuations are harmful), then strong coupling should be disfavored. Here, evidence is presented that cost-benefit conflicts do occur and that they constrain the evolution of gene expression and promoter usage. In contrast to recent assertions, coupling between noise and plasticity is not a general property, but one associated with particular mechanisms of transcription initiation. Further, promoter architectures associated with coupling are avoided when noise is most likely to be detrimental, and noise and plasticity are largely independent traits for core cellular components. In contrast, when genes are duplicated noise-plasticity coupling increases, consistent with reduced detrimental affects of expression variation. Noise-plasticity coupling is, therefore, an evolvable trait that may constrain the emergence of highly responsive gene expression and be selected against during evolution. Further, the global quantitative data in yeast suggest that one mechanism that relieves the constraints imposed by noise-plasticity coupling is gene duplication, providing an example of how duplication can facilitate escape from adaptive conflicts.
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Affiliation(s)
- Ben Lehner
- Genetic Systems Laboratory, EMBL-CRG Systems Biology Unit and ICREA, CRG, UPF, Barcelona, Spain.
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SOYER OS, CREEVEY CJ. Duplicate retention in signalling proteins and constraints from network dynamics. J Evol Biol 2010; 23:2410-21. [DOI: 10.1111/j.1420-9101.2010.02101.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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65
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Bosl WJ, Li R. The role of noise and positive feedback in the onset of autosomal dominant diseases. BMC SYSTEMS BIOLOGY 2010; 4:93. [PMID: 20587063 PMCID: PMC2902440 DOI: 10.1186/1752-0509-4-93] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2009] [Accepted: 06/29/2010] [Indexed: 01/26/2023]
Abstract
Background Autosomal dominant (AD) diseases result when a single mutant or non-functioning gene is present on an autosomal chromosome. These diseases often do not emerge at birth. There are presently two prevailing theories explaining the expression of AD diseases. One explanation originates from the Knudson two-hit theory of hereditary cancers, where loss of heterozygosity or occurrence of somatic mutations impairs the function of the wild-type copy. While these somatic second hits may be sufficient for stable disease states, it is often difficult to determine if their occurrence necessarily marks the initiation of disease progression. A more direct consequence of a heterozygous genetic background is haploinsufficiency, referring to a lack of sufficient gene function due to reduced wild-type gene copy number; however, haploinsufficiency can involve a variety of additional mechanisms, such as noise in gene expression or protein levels, injury and second hit mutations in other genes. In this study, we explore the possible contribution to the onset of autosomal dominant diseases from intrinsic factors, such as those determined by the structure of the molecular networks governing normal cellular physiology. Results First, simple models of single gene insufficiency using the positive feedback loops that may be derived from a three-component network were studied by computer simulation using Bionet software. The network structure is shown to affect the dynamics considerably; some networks are relatively stable even when large stochastic variations in are present, while others exhibit switch-like dynamics. In the latter cases, once the network switches over to the disease state it remains in that state permanently. Model pathways for two autosomal dominant diseases, AD polycystic kidney disease and mature onset diabetes of youth (MODY) were simulated and the results are compared to known disease characteristics. Conclusions By identifying the intrinsic mechanisms involved in the onset of AD diseases, it may be possible to better assess risk factors as well as lead to potential new drug targets. To illustrate the applicability of this study of pathway dynamics, we simulated the primary pathways involved in two autosomal dominant diseases, Polycystic Kidney Disease (PKD) and mature onset diabetes of youth (MODY). Simulations demonstrate that some of the primary disease characteristics are consistent with the positive feedback - stochastic variation theory presented here. This has implications for new drug targets to control these diseases by blocking the positive feedback loop in the relevant pathways.
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Wang D, Pezo RC, Corner G, Sison C, Lesser ML, Shenoy SM, Mariadason JM, Singer RH, Augenlicht LH. Altered dynamics of intestinal cell maturation in Apc1638N/+ mice. Cancer Res 2010; 70:5348-57. [PMID: 20570902 DOI: 10.1158/0008-5472.can-09-4593] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Novel imaging of active transcription sites in interphase nuclei of intestinal epithelial cells in situ showed that key genes associated with Wnt and Notch signaling were dynamically regulated as the cells underwent normal maturation during their migration along the mouse crypt-villus axis (CVA). However, oscillating patterns of activation of these genes were displaced along this axis in the histologically normal intestinal mucosa of Apc(1638N/+) mice before tumor development. Gene expression profiling then showed that the normal reprogramming of cells along the CVA was dampened in the Apc(1638N/+) mice, with an overrepresentation of c-myc target genes among those loci affected in the mutant mice. Moreover, in the Apc(1638N/+) mice, there was a perturbed pattern of expression of lineage-specific markers along the CVA consistent with transcription site repression of the Math1 gene, and genes encoding enzymes of every step of the tricarboxylic acid cycle were downregulated in the crypt of Apc(1638N/+) mice compared with WT, but not in the villus. These changes may alter energy metabolism and generate a pseudohypoxic state, suggested by elevated expression of Hif1alpha and its target genes. Thus, although intestinal tumors develop in Apc(1638N/+) mice on focal loss or inactivation of the WT allele, our results show that in the Apc(1638N/+) mouse, inheritance of only a single WT Apc allele perturbs the dynamic and complex reprogramming underlying normal cell maturation, which links epithelial function and homeostasis with architectural organization of the intestine.
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Affiliation(s)
- Donghai Wang
- Department of Medicine, Montefiore Medical Center, Bronx, New York 10467, USA
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67
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Proulx SR, Smiley MW. The evolutionary origins of gene regulation. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2010; 314:327-40. [PMID: 20095005 DOI: 10.1002/jez.b.21339] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
One way that organisms cope with constantly changing physical and biological conditions is by regulating the expression of genes and thereby altering protein production. Clearly, altering the protein production to match the environmental demands can be adaptive, but there may be evolutionary barriers to the transition from constitutive expression to regulated expression. In particular, down-regulating a gene when it is not needed means that there will necessarily be a delay in protein production when the protein is up-regulated in the future. We develop a model of simple gene regulation in response to randomly changing environmental conditions. We calculate the long-term behavior of gene expression and determine the fitness consequences of changes in the gene regulation. We then embed this model into a population genetic framework in order to determine the conditions that allow populations to evolve environment-specific transcription rates. The population genetic model follows the evolutionary transition from constitutive expression to regulated expression. There are three distinct possible evolutionary outcomes. The gene may be stuck in the always on position, the gene may first evolve to an intermediate constitutive expression level and then evolve regulation, or regulation can evolve directly from the ancestral state in a smooth fashion. Regulation is most likely to evolve when the costs of mis-expression are low and the transcript decay rate is high. This suggests that genes that have less severe reductions in fitness when mis-expressed are more likely to initially evolve regulation.
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Affiliation(s)
- Stephen R Proulx
- Ecology, Evolution and Marine Biology Department, UC Santa Barbara, Santa Barbara, California 93106-9620, USA.
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68
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Subramanian K, Gadgil C. Robustness of the Drosophila segment polarity network to transient perturbations. IET Syst Biol 2010; 4:169-76. [PMID: 20232996 DOI: 10.1049/iet-syb.2009.0036] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Continuous and Boolean models for the Drosophila segment polarity network have shown that the system is able to maintain the wild-type pattern when subjected to sustained changes in the interaction parameters and initial conditions. Embryo development is likely to occur under fluctuating environmental conditions. Here, a well-established Boolean model is used to explore the ability of the segment polarity network to resist transient changes. Paths along which alternate unviable states are reached, and hence critical nodes whose state changes lead the system away from the wild-type state, are identified. It is found that the system appears to be more sensitive to changes that involve activation of normally inactive nodes. Through a simulation of the heat shock response, it is shown how a localised perturbation in one parasegment is more deleterious than a global perturbation affecting all parasegments. The sequence of events involved in the recovery of the system from a global transient heat shock condition is identified. Finally, these results are discussed in terms of the robustness of the system response.
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Affiliation(s)
- K Subramanian
- National Chemical Laboratory, Chemical Engineering and Process Development Division, Pune, India
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69
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Rajala T, Häkkinen A, Healy S, Yli-Harja O, Ribeiro AS. Effects of transcriptional pausing on gene expression dynamics. PLoS Comput Biol 2010; 6:e1000704. [PMID: 20300642 PMCID: PMC2837387 DOI: 10.1371/journal.pcbi.1000704] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2009] [Accepted: 02/04/2010] [Indexed: 11/19/2022] Open
Abstract
Stochasticity in gene expression affects many cellular processes and is a source of phenotypic diversity between genetically identical individuals. Events in elongation, particularly RNA polymerase pausing, are a source of this noise. Since the rate and duration of pausing are sequence-dependent, this regulatory mechanism of transcriptional dynamics is evolvable. The dependency of pause propensity on regulatory molecules makes pausing a response mechanism to external stress. Using a delayed stochastic model of bacterial transcription at the single nucleotide level that includes the promoter open complex formation, pausing, arrest, misincorporation and editing, pyrophosphorolysis, and premature termination, we investigate how RNA polymerase pausing affects a gene's transcriptional dynamics and gene networks. We show that pauses' duration and rate of occurrence affect the bursting in RNA production, transcriptional and translational noise, and the transient to reach mean RNA and protein levels. In a genetic repressilator, increasing the pausing rate and the duration of pausing events increases the period length but does not affect the robustness of the periodicity. We conclude that RNA polymerase pausing might be an important evolvable feature of genetic networks.
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Affiliation(s)
- Tiina Rajala
- Computational Systems Biology Research Group, Department of Signal Processing, Tampere University of Technology, Tampere, Finland
| | - Antti Häkkinen
- Computational Systems Biology Research Group, Department of Signal Processing, Tampere University of Technology, Tampere, Finland
| | - Shannon Healy
- Computational Systems Biology Research Group, Department of Signal Processing, Tampere University of Technology, Tampere, Finland
| | - Olli Yli-Harja
- Computational Systems Biology Research Group, Department of Signal Processing, Tampere University of Technology, Tampere, Finland
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Andre S. Ribeiro
- Computational Systems Biology Research Group, Department of Signal Processing, Tampere University of Technology, Tampere, Finland
- * E-mail:
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70
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Murphy KF, Adams RM, Wang X, Balázsi G, Collins JJ. Tuning and controlling gene expression noise in synthetic gene networks. Nucleic Acids Res 2010; 38:2712-26. [PMID: 20211838 PMCID: PMC2860118 DOI: 10.1093/nar/gkq091] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Synthetic gene networks can be used to control gene expression and cellular phenotypes in a variety of applications. In many instances, however, such networks can behave unreliably due to gene expression noise. Accordingly, there is a need to develop systematic means to tune gene expression noise, so that it can be suppressed in some cases and harnessed in others, e.g. in cellular differentiation to create population-wide heterogeneity. Here, we present a method for controlling noise in synthetic eukaryotic gene expression systems, utilizing reduction of noise levels by TATA box mutations and noise propagation in transcriptional cascades. Specifically, we introduce TATA box mutations into promoters driving TetR expression and show that these mutations can be used to effectively tune the noise of a target gene while decoupling it from the mean, with negligible effects on the dynamic range and basal expression. We apply mathematical and computational modeling to explain the experimentally observed effects of TATA box mutations. This work, which highlights some important aspects of noise propagation in gene regulatory cascades, has practical implications for implementing gene expression control in synthetic gene networks.
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Affiliation(s)
- Kevin F Murphy
- Department of Biomedical Engineering, Howard Hughes Medical Institute, Center for BioDynamics & Center for Advanced Biotechnology, Department of Biology, Boston University, Boston, MA 02215, USA
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71
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Ribeiro AS, Häkkinen A, Mannerström H, Lloyd-Price J, Yli-Harja O. Effects of the promoter open complex formation on gene expression dynamics. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 81:011912. [PMID: 20365404 DOI: 10.1103/physreve.81.011912] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2009] [Revised: 12/11/2009] [Indexed: 05/29/2023]
Abstract
Little is known about the biological mechanisms that shape the distribution of intervals between the completion of RNA molecules (T(p)RNA) , and thus transcriptional noise. We characterize numerically and analytically how the promoter open complex delay (tau(P)) and the transcription initiation rate (k(t)) shape T(p)RNA. From this, we assess the noise and mean of transcript levels and show that these can be tuned both independently and simultaneously by tau(P) and k(t). Finally, we characterize how tau(P) affects bursting in RNA production and show that the tau(P) measured for a lac promoter best fits independent measurements of the burst distribution of the same promoter. Since tau(P) affects noise in gene expression, and given that it is sequence dependent, it is likely to be evolvable.
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Affiliation(s)
- Andre S Ribeiro
- Computational Systems Biology Research Group, Department of Signal Processing, Tampere University of Technology, FI-33101 Tampere, Finland
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72
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Pilbrough W, Munro TP, Gray P. Intraclonal protein expression heterogeneity in recombinant CHO cells. PLoS One 2009; 4:e8432. [PMID: 20037651 PMCID: PMC2793030 DOI: 10.1371/journal.pone.0008432] [Citation(s) in RCA: 137] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2009] [Accepted: 12/02/2009] [Indexed: 11/19/2022] Open
Abstract
Therapeutic glycoproteins have played a major role in the commercial success of biotechnology in the post-genomic era. But isolating recombinant mammalian cell lines for large-scale production remains costly and time-consuming, due to substantial variation and unpredictable stability of expression amongst transfected cells, requiring extensive clone screening to identify suitable high producers. Streamlining this process is of considerable interest to industry yet the underlying phenomena are still not well understood. Here we examine an antibody-expressing Chinese hamster ovary (CHO) clone at single-cell resolution using flow cytometry and vectors, which couple light and heavy chain transcription to fluorescent markers. Expression variation has traditionally been attributed to genetic heterogeneity arising from random genomic integration of vector DNA. It follows that single cell cloning should yield a homogeneous cell population. We show, in fact, that expression in a clone can be surprisingly heterogeneous (standard deviation 50 to 70% of the mean), approaching the level of variation in mixed transfectant pools, and each antibody chain varies in tandem. Phenotypic variation is fully developed within just 18 days of cloning, yet is not entirely explained by measurement noise, cell size, or the cell cycle. By monitoring the dynamic response of subpopulations and subclones, we show that cells also undergo slow stochastic fluctuations in expression (half-life 2 to 11 generations). Non-genetic diversity may therefore play a greater role in clonal variation than previously thought. This also has unexpected implications for expression stability. Stochastic gene expression noise and selection bias lead to perturbations from steady state at the time of cloning. The resulting transient response as clones reestablish their expression distribution is not ordinarily accounted for but can contribute to declines in median expression over timescales of up to 50 days. Noise minimization may therefore be a novel strategy to reduce apparent expression instability and simplify cell line selection.
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Affiliation(s)
- Warren Pilbrough
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Queensland, Australia
| | - Trent P. Munro
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Queensland, Australia
- ACYTE Biotech Pty Ltd, Brisbane, Queensland, Australia
- * E-mail:
| | - Peter Gray
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Queensland, Australia
- ACYTE Biotech Pty Ltd, Brisbane, Queensland, Australia
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73
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Veitia RA, Birchler JA. Dominance and gene dosage balance in health and disease: why levels matter! J Pathol 2009; 220:174-85. [DOI: 10.1002/path.2623] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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74
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Smiley MW, Proulx SR. Gene expression dynamics in randomly varying environments. J Math Biol 2009; 61:231-251. [PMID: 19756606 DOI: 10.1007/s00285-009-0298-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2008] [Revised: 08/21/2009] [Indexed: 01/01/2023]
Abstract
A simple model of gene regulation in response to stochastically changing environmental conditions is developed and analyzed. The model consists of a differential equation driven by a continuous time 2-state Markov process. The density function of the resulting process converges to a beta distribution. We show that the moments converge to their stationary values exponentially in time. Simulations of a two-stage process where protein production depends on mRNA concentrations are also presented demonstrating that protein concentration tracks the environment whenever the rate of protein turnover is larger than the rate of environmental change. Single-celled organisms are therefore expected to have relatively high mRNA and protein turnover rates for genes that respond to environmental fluctuations.
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Affiliation(s)
- Michael W Smiley
- Department of Mathematics, Iowa State University, 396 Carver Hall, Ames, IA, 50011, USA
| | - Stephen R Proulx
- Ecology Evolution and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, 93106-9620, USA.
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75
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Crudu A, Debussche A, Radulescu O. Hybrid stochastic simplifications for multiscale gene networks. BMC SYSTEMS BIOLOGY 2009; 3:89. [PMID: 19735554 PMCID: PMC2761401 DOI: 10.1186/1752-0509-3-89] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2009] [Accepted: 09/07/2009] [Indexed: 01/06/2023]
Abstract
BACKGROUND Stochastic simulation of gene networks by Markov processes has important applications in molecular biology. The complexity of exact simulation algorithms scales with the number of discrete jumps to be performed. Approximate schemes reduce the computational time by reducing the number of simulated discrete events. Also, answering important questions about the relation between network topology and intrinsic noise generation and propagation should be based on general mathematical results. These general results are difficult to obtain for exact models. RESULTS We propose a unified framework for hybrid simplifications of Markov models of multiscale stochastic gene networks dynamics. We discuss several possible hybrid simplifications, and provide algorithms to obtain them from pure jump processes. In hybrid simplifications, some components are discrete and evolve by jumps, while other components are continuous. Hybrid simplifications are obtained by partial Kramers-Moyal expansion [1-3] which is equivalent to the application of the central limit theorem to a sub-model. By averaging and variable aggregation we drastically reduce simulation time and eliminate non-critical reactions. Hybrid and averaged simplifications can be used for more effective simulation algorithms and for obtaining general design principles relating noise to topology and time scales. The simplified models reproduce with good accuracy the stochastic properties of the gene networks, including waiting times in intermittence phenomena, fluctuation amplitudes and stationary distributions. The methods are illustrated on several gene network examples. CONCLUSION Hybrid simplifications can be used for onion-like (multi-layered) approaches to multi-scale biochemical systems, in which various descriptions are used at various scales. Sets of discrete and continuous variables are treated with different methods and are coupled together in a physically justified approach.
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Affiliation(s)
- Alina Crudu
- IRMAR UMR CNRS 6625 Université de Rennes1, Campus de Beaulieu, 35042 Rennes, France.
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76
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Positive selection for elevated gene expression noise in yeast. Mol Syst Biol 2009; 5:299. [PMID: 19690568 PMCID: PMC2736655 DOI: 10.1038/msb.2009.58] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2008] [Accepted: 07/09/2009] [Indexed: 11/26/2022] Open
Abstract
It is well known that the expression noise is lessened by natural selection for genes that are important for cell growth or are sensitive to dosage. In theory, expression noise can also be elevated by natural selection when noisy gene expression is advantageous. Here we analyze yeast genome-wide gene expression noise data and show that plasma-membrane transporters show significantly elevated expression noise after controlling all confounding factors. We propose a model that explains why and under what conditions elevated expression noise may be beneficial and subject to positive selection. Our model predicts and the simulation confirms that, under certain conditions, expression noise also increases the evolvability of gene expression by promoting the fixation of favorable expression level-altering mutations. Indeed, yeast genes with higher noise show greater between-strain and between-species divergences in expression, even when all confounding factors are excluded. Together, our theoretical model and empirical results suggest that, for yeast genes such as plasma-membrane transporters, elevated expression noise is advantageous, is subject to positive selection, and is a facilitator of adaptive gene expression evolution.
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77
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Wei G, Wang Z, Lam J, Fraser K, Rao GP, Liu X. Robust filtering for stochastic genetic regulatory networks with time-varying delay. Math Biosci 2009; 220:73-80. [DOI: 10.1016/j.mbs.2009.04.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2008] [Revised: 04/08/2009] [Accepted: 04/13/2009] [Indexed: 10/20/2022]
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78
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Taniguchi E, Cho MJ, Arenkiel BR, Hansen MS, Rivera OJ, McCleish AT, Qualman SJ, Guttridge DC, Scott MP, Capecchi MR, Keller C. Bortezomib reverses a post-translational mechanism of tumorigenesis for patched1 haploinsufficiency in medulloblastoma. Pediatr Blood Cancer 2009; 53:136-44. [PMID: 19213072 PMCID: PMC2850215 DOI: 10.1002/pbc.21968] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
BACKGROUND Tumor initiation has been attributed to haploinsufficiency at a single locus for a large number of cancers. Patched1 (Ptc1) was one of the first such loci, and Ptc1 haploinsufficiency has been asserted to lead to medulloblastoma and rhabdomyosarcoma in mice. PROCEDURE To study the role of Ptc1 in cerebellar tumor development and to create a preclinical therapeutic platform, we have generated a conditional Ptc1 haploinsufficiency model of medulloblastoma by inactivating Ptc1 in Pax7-expressing cells of the cerebellum. RESULTS These mice developed exclusively medulloblastoma. We show that despite the presence of transcription of Ptc1, Ptc1 protein is nearly undetectable or absent in tumors. Our results suggest that Ptc1 loss of function is complete, but achieved at the protein level rather than by the classic genetic two-hit mechanism or a strict half-dosage genetic haploinsufficiency mechanism. Furthermore, we found that bortezomib, a 26S proteasome inhibitor, had a significant anti-tumor activity in vitro and in vivo, which was accompanied by restoration of Ptc1 protein and downregulation of the hedgehog signaling pathway. The same effect was seen for both human and mouse medulloblastoma tumor cell growth. CONCLUSIONS These results suggest that proteasome inhibition is a potential new therapeutic approach in medulloblastoma.
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Affiliation(s)
- Eri Taniguchi
- Greehey Children’s Cancer Research Institute, Departments of Cellular & Structural Biology and Pediatrics, University of Texas Health Science Center, San Antonio, TX 78229 USA
| | - Min Jung Cho
- Greehey Children’s Cancer Research Institute, Departments of Cellular & Structural Biology and Pediatrics, University of Texas Health Science Center, San Antonio, TX 78229 USA
| | - Benjamin R. Arenkiel
- Howard Hughes Medical Institute and Department of Human Genetics, University of Utah, Salt Lake City, UT 84112 USA
| | - Mark S. Hansen
- Howard Hughes Medical Institute and Department of Human Genetics, University of Utah, Salt Lake City, UT 84112 USA
| | - Omar J. Rivera
- Greehey Children’s Cancer Research Institute, Departments of Cellular & Structural Biology and Pediatrics, University of Texas Health Science Center, San Antonio, TX 78229 USA
| | - Amanda T. McCleish
- Greehey Children’s Cancer Research Institute, Departments of Cellular & Structural Biology and Pediatrics, University of Texas Health Science Center, San Antonio, TX 78229 USA
| | - Stephen J. Qualman
- Children’s Research Institute, Department of Laboratory Medicine, Columbus Children’s Hospital, Columbus, OH 43205 USA
| | - Denis C. Guttridge
- Human Cancer Genetics Program, The Ohio State University College of Medicine, Columbus, OH 43210 USA
| | - Matthew P. Scott
- Howard Hughes Medical Institute and Departments of Developmental Biology, Genetics, and Bioengineering, Stanford University School of Medicine, Stanford, California 94305 USA
| | - Mario R. Capecchi
- Howard Hughes Medical Institute and Department of Human Genetics, University of Utah, Salt Lake City, UT 84112 USA
| | - Charles Keller
- Greehey Children’s Cancer Research Institute, Departments of Cellular & Structural Biology and Pediatrics, University of Texas Health Science Center, San Antonio, TX 78229 USA,Corresponding author: Greehey Children’s Cancer Research Institute, University of Texas Health Science Center, 8403 Floyd Curl Drive, MC-7784, San Antonio, TX 78229-3900 USA, Tel: (210)562-9062, Fax: (210)562-9014,
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79
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Yin S, Wang P, Deng W, Zheng H, Hu L, Hurst LD, Kong X. Dosage compensation on the active X chromosome minimizes transcriptional noise of X-linked genes in mammals. Genome Biol 2009; 10:R74. [PMID: 19594925 PMCID: PMC2728528 DOI: 10.1186/gb-2009-10-7-r74] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2009] [Revised: 06/13/2009] [Accepted: 07/13/2009] [Indexed: 01/14/2023] Open
Abstract
Comparison of gene expression variation in autosomal and X-linked genes reveals that high transcriptional noise is not a necessary consequence of haploid expression. Background Theory predicts that haploid-expressed genes should have noisier expression than comparable diploid-expressed ones with the same expression level. However, in mammals there are several classes of gene that are monoallelically expressed, including X-linked genes, imprinted genes and some other autosomal genes. Does it follow that the evolution of X chromosomes in eukaryotes comes at the cost of increased transcriptional noise in the heterogametic sex? Moreover, is escaping X-inactivation in mammalian females associated with an increase in transcriptional variation? To address these questions, we analyze gene expression variation between replicate samples of diverse mammalian cell lines in steady-state using microarray data. Results We observe that transcriptional variation of X-linked genes is no different to that of autosomal genes both before and after control for transcript abundance. By contrast, autosomal genes subject to allelic exclusion do have unusually high noise levels even allowing for their low transcript abundance. The prior theory we suggest was insufficient, at least as regards X-chromosomes, as it failed to appreciate the regulatory complexity of gene expression, not least the effects of genomic neighborhood. Conclusions These results suggest that high noise is not a necessary consequence of haploid expression and emphasize the primacy of expression level as a determinant of noise. The latter has consequences for understanding the etiology of haplo-insufficiency and the evolution of gene expression levels. Given the coupling between expression level and noise on the X-chromosome, we suggest that part of the selective advantage of dosage compensation is noise abatement of X-linked genes.
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Affiliation(s)
- Shanye Yin
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai JiaoTong University School of Medicine, South Chongqing Road, Shanghai 200025, PR China
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80
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Wang Z, Liu X, Liu Y, Liang J, Vinciotti V. An extended Kalman filtering approach to modeling nonlinear dynamic gene regulatory networks via short gene expression time series. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2009; 6:410-419. [PMID: 19644169 DOI: 10.1109/tcbb.2009.5] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
In this paper, the extended Kalman filter (EKF) algorithm is applied to model the gene regulatory network from gene time series data. The gene regulatory network is considered as a nonlinear dynamic stochastic model that consists of the gene measurement equation and the gene regulation equation. After specifying the model structure, we apply the EKF algorithm for identifying both the model parameters and the actual value of gene expression levels. It is shown that the EKF algorithm is an online estimation algorithm that can identify a large number of parameters (including parameters of nonlinear functions) through iterative procedure by using a small number of observations. Four real-world gene expression data sets are employed to demonstrate the effectiveness of the EKF algorithm, and the obtained models are evaluated from the viewpoint of bioinformatics.
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Affiliation(s)
- Zidong Wang
- Department of Information Systems and Computing, Brunel University, Uxbridge, Middlesex UB83PH, UK.
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81
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Mayburd AL. Expression variation: its relevance to emergence of chronic disease and to therapy. PLoS One 2009; 4:e5921. [PMID: 19526064 PMCID: PMC2692004 DOI: 10.1371/journal.pone.0005921] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2008] [Accepted: 05/13/2009] [Indexed: 12/05/2022] Open
Abstract
Background Stochastic fluctuations in the protein turnover underlie the random emergence of neural precursor cells from initially homogenous cell population. If stochastic alteration of the levels in signal transduction networks is sufficient to spontaneously alter a phenotype, can it cause a sporadic chronic disease as well – including cancer? Methods Expression in >80 disease-free tissue environments was measured using Affymetrix microarray platform comprising 54675 probe-sets. Steps were taken to suppress the technical noise inherent to microarray experiment. Next, the integrated expression and expression variability data were aligned with the mechanistic data covering major human chronic diseases. Results Measured as class average, variability of expression of disease associated genes measured in health was higher than variability of random genes for all chronic pathologies. Anti-cancer FDA approved targets were displaying much higher variability as a class compared to random genes. Same held for magnitude of gene expression. The genes known to participate in multiple chronic disorders demonstrated the highest variability. Disease-related gene categories displayed on average more intricate regulation of biological function vs random reference, were enriched in adaptive and transient functions as well as positive feedback relationships. Conclusions A possible causative link can be suggested between normal (healthy) state gene expression variation and inception of major human pathologies, including cancer. Study of variability profiles may lead to novel diagnostic methods, therapies and better drug target prioritization. The results of the study suggest the need to advance personalized therapy development.
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82
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Banerjee S, Bose I. Functional characteristics of a double positive feedback loop coupled with autorepression. Phys Biol 2008; 5:046008. [DOI: 10.1088/1478-3975/5/4/046008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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83
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Yang K, Kurihara N, Fan K, Newmark H, Rigas B, Bancroft L, Corner G, Livote E, Lesser M, Edelmann W, Velcich A, Lipkin M, Augenlicht L. Dietary induction of colonic tumors in a mouse model of sporadic colon cancer. Cancer Res 2008; 68:7803-10. [PMID: 18829535 DOI: 10.1158/0008-5472.can-08-1209] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A defined rodent "new Western diet" (NWD), which recapitulates intake levels of nutrients that are major dietary risk factors for human colon cancer, induced colonic tumors when fed to wild-type C57Bl/6 mice for 1.5 to 2 years from age 6 weeks (two-thirds of their life span). Colonic tumors were prevented by elevating dietary calcium and vitamin D(3) to levels comparable with upper levels consumed by humans, but tumorigenesis was not altered by similarly increasing folate, choline, methionine, or fiber, each of which was also at the lower levels in the NWD that are associated with risk for colon cancer. The NWD significantly altered profiles of gene expression in the flat colonic mucosa that exhibited heterogeneity among the mice, but unsupervised clustering of the data and novel statistical analyses showed reprogramming of colonic epithelial cells in the flat mucosa by the NWD was similar to that initiated by inheritance of a mutant Apc allele. The NWD also caused general down-regulation of genes encoding enzymes involved in lipid metabolism and the tricarboxylic acid cycle in colonic epithelial cells before tumor formation, which was prevented by the supplementation of the NWD with calcium and vitamin D(3) that prevented colon tumor development, demonstrating profound interaction among nutrients. This mouse model of dietary induction of colon cancer recapitulates levels and length of exposure to nutrients linked to relative risk for human sporadic colon cancer, which represents the etiology of >90% of colon cancer in the United States and other Western countries.
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Affiliation(s)
- Kan Yang
- Strang Cancer Research Laboratory, Department of Medicine, Gastroenterology and Hepatology, Weill Medical College of Cornell University, New York, New York 10467, USA
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84
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McKinney BA. Informatics approaches for identifying biologic relationships in time‐series data. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2008; 1:60-68. [DOI: 10.1002/wnan.12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Brett A. McKinney
- Department of Genetics, University of Alabama School of Medicine, Birmingham, AL, 35294 USA
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85
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Determining biological noise via single cell analysis. Anal Bioanal Chem 2008; 393:73-80. [PMID: 18958456 DOI: 10.1007/s00216-008-2431-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2008] [Revised: 09/16/2008] [Accepted: 09/23/2008] [Indexed: 10/21/2022]
Abstract
Single cell analysis techniques describe the cellular heterogeneity that originates from fundamental stochastic variations in each of the molecular processes underlying cell function. The quantitative description of this set of variations is called biological noise and includes intrinsic and extrinsic noise. The former refers to stochastic variations directly involved with a given process, while the latter is due to environmental factors associated with other processes. Mathematical models are successful in predicting noise trends in simple biological systems, but it takes single cell techniques such as flow cytometry and time lapse microscopy to determine and dissect biological noise. This review describes several approaches that have been successfully used to describe biological noise.
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86
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Lehner B. Selection to minimise noise in living systems and its implications for the evolution of gene expression. Mol Syst Biol 2008; 4:170. [PMID: 18319722 PMCID: PMC2290932 DOI: 10.1038/msb.2008.11] [Citation(s) in RCA: 185] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2007] [Accepted: 01/28/2008] [Indexed: 01/26/2023] Open
Abstract
Gene expression, like many biological processes, is subject to noise. This noise has been measured on a global scale, but its general importance to the fitness of an organism is unclear. Here, I show that noise in gene expression in yeast has evolved to prevent harmful stochastic variation in the levels of genes that reduce fitness when their expression levels change. Therefore, there has probably been widespread selection to minimise noise in gene expression. Selection to minimise noise, because it results in gene expression that is stable to stochastic variation in cellular components, may also constrain the ability of gene expression to respond to non-stochastic variation. I present evidence that this has indeed been the case in yeast. I therefore conclude that gene expression noise is an important biological trait, and one that probably limits the evolvability of complex living systems.
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Affiliation(s)
- Ben Lehner
- EMBL-CRG Systems Biology Unit, Barcelona, Spain.
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87
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Wang Z, Yang F, Ho DWC, Swift S, Tucker A, Liu X. Stochastic Dynamic Modeling of Short Gene Expression Time-Series Data. IEEE Trans Nanobioscience 2008; 7:44-55. [PMID: 18334455 DOI: 10.1109/tnb.2008.2000149] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Z Wang
- Department of Information Systems and Computing, Brunel University, Uxbridge, UK.
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88
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Kont V, Laan M, Kisand K, Merits A, Scott HS, Peterson P. Modulation of Aire regulates the expression of tissue-restricted antigens. Mol Immunol 2008; 45:25-33. [PMID: 17599412 PMCID: PMC1994210 DOI: 10.1016/j.molimm.2007.05.014] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2007] [Accepted: 05/15/2007] [Indexed: 12/17/2022]
Abstract
Intrathymic expression of tissue-restricted antigens (TRAs) has been viewed as the key element in the induction of central tolerance and recently, a central role for the autoimmune regulator (Aire) has been suggested in this process. The aim of this study was to establish whether down or up-regulation of Aire leads to alterations in TRA expression and whether this is limited to thymic epithelial cells. This study also characterized whether TRAs follow Aire expression during normal development, and whether thymic microenvironment plays a role in the expression of Aire and TRAs. We did several in vivo and in vitro experiments to manipulate Aire expression and measured expression of four TRAs (Trefoil factor-3, Insulin-2, Major urinary protein-1 and Salivary protein-1) by real-time RT-PCR. Aire had an allele dose-dependent effect on TRA expression in the thymuses of mice from two strains, C57BL/6J and Balb/c, but had no effect on TRA expression in the lymph nodes. In the thymus, Aire and TRAs were both localized in the medulla and were co-expressed during normal development and involution. In the primary stromal cells as well as thymic epithelial cell line, the adenoviral over-expression of Aire resulted in an increase in TRA expression. By manipulating in vitro organ-cultures we showed that thymic microenvironment plays a dominant role in Aire expression whereas TRAs follow the same pattern. The data underline a direct role for Aire in TRA expression and suggest that modulation of Aire has a potential to control central tolerance and autoimmunity.
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Affiliation(s)
- Vivian Kont
- Molecular Pathology, Biomedicum, Tartu University, Ravila 19, 50411 Tartu, Estonia
| | - Martti Laan
- Molecular Pathology, Biomedicum, Tartu University, Ravila 19, 50411 Tartu, Estonia
| | - Kai Kisand
- Molecular Pathology, Biomedicum, Tartu University, Ravila 19, 50411 Tartu, Estonia
| | - Andres Merits
- Institute of Technology, Tartu University, Tartu, Estonia
| | - Hamish S. Scott
- Division of Molecular Medicine, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Pärt Peterson
- Molecular Pathology, Biomedicum, Tartu University, Ravila 19, 50411 Tartu, Estonia
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89
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Batada NN, Hurst LD. Evolution of chromosome organization driven by selection for reduced gene expression noise. Nat Genet 2007; 39:945-9. [PMID: 17660811 DOI: 10.1038/ng2071] [Citation(s) in RCA: 176] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The distribution of genes on eukaryotic chromosomes is nonrandom, but the reasons behind this are not well understood. The commonly observed clustering of essential genes is a case in point. Here we model and test a new hypothesis. Essential proteins are unusual in that random fluctuations in abundance (noise) can be highly deleterious. We hypothesize that persistently open chromatin domains are sinks for essential genes, as they enable reduced noise by avoidance of transcriptional bursting associated with chromatin remodeling. Simulation of the model captures clustering and correctly predicts that (i) essential gene clusters are associated with low nucleosome occupancy (ii) noise-sensitive nonessential genes cluster with essential genes (iii) nonessential genes of similar knockout fitness are physically linked (iv) genes in domains rich in essential genes have low noise (v) essential genes are rare subtelomerically and (vi) essential gene clusters are preferentially conserved. We conclude that different noise characteristics of different genomic domains favors nonrandom gene positioning. This has implications for gene therapy and understanding transgenic phenotypes.
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Affiliation(s)
- Nizar N Batada
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK.
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90
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Abstract
Neurofibromatosis 2 (NF2) is a hereditary tumor disease characterized by bilateral vestibular schwannomas. Polyneuropathy seems to occur quite frequently in NF2 and in most cases, the etiology of this neuropathy is unclear, especially when the neuropathy is symmetric. NF2 is believed to follow the two-hit hypothesis. According to this, one allele is mutated in the germline, and the second hit is somatic and results in tumor formation. The second hit most frequently is a loss of the NF2 locus, often the entire chromosome 22. We set out to investigate the underlying genetics in peripheral nerve of NF2 patients with polyneuropathy. We identified NF2 patients with polyneuropathy in which we could detect the germline mutation and analyzed NF2 gene dosage in archived nerve biopsies from these patients using a newly developed method. We observed merlin haploinsufficiency in peripheral nerves of two different patients with NF2-related polyneuropathy. This finding was further supported by showing that approximately 50% merlin expression in a cell line using shRNA results in altered gene expression as previously shown in schwannomas. Thus, we suggest that reduced merlin gene dosage is relevant in NF2-associated polyneuropathy.
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Affiliation(s)
- Clemens O Hanemann
- Clinical Neurobiology, Inst. Biomedical and Clinical Science, Peninsula Medical School, The John Bull Building, Tamar Science Park, Research Way, Plymouth PL6 8BU, UK.
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91
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Mogal AP, van der Meer R, Crooke PS, Abdulkadir SA. Haploinsufficient prostate tumor suppression by Nkx3.1: a role for chromatin accessibility in dosage-sensitive gene regulation. J Biol Chem 2007; 282:25790-800. [PMID: 17602165 DOI: 10.1074/jbc.m702438200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Transcription factor haploinsufficiency plays a role in the pathogenesis of many diseases, including cancer. In a mouse model of prostate tumor initiation, loss of a single allele of the tumor suppressor Nkx3.1 stochastically inactivates the expression of a class of dosage-sensitive target genes. Here we show that dosage sensitivity is associated with the differential histone H3/H4 acetylation states of Nkx3.1 target genes. When histone acetylation is induced in Nkx3.1+/- mouse prostates with the histone deacetylase inhibitor Trichostatin A, Nkx3.1 can bind to and reactivate the expression of dosage-sensitive target genes. We incorporated our findings into a mathematical model that entails the association of Nkx3.1 with histone acetyltransferase activity. Subsequent experiments indicate that Nkx3.1 associates with and recruits the histone acetyltransferase p300/CREB-binding protein-associated factor to chromatin. Finally, we demonstrate a role for the dosage-sensitive target gene intelectin/omentin in suppressing prostate tumorigenicity. Our results reveal how the interplay between transcription factor dosage and chromatin affects target gene expression in tumor initiation.
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Affiliation(s)
- Ashish P Mogal
- Department of Pathology, Vanderbilt University Medical Center, Nashville 37232, USA
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92
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Innocentini GCP, Hornos JEM. Modeling stochastic gene expression under repression. J Math Biol 2007; 55:413-31. [PMID: 17516070 DOI: 10.1007/s00285-007-0090-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2006] [Revised: 03/14/2007] [Indexed: 11/26/2022]
Abstract
Intrinsic transcriptional noise induced by operator fluctuations is investigated with a simple spin-like stochastic model. The effects of transcriptional fluctuations in protein synthesis are probed by coupling transcription and translation by an amplificative interaction. In the presence of repression a new term contributes to the noise, which depends on the rate of mRNA production. If the switch decay time is small compared with the mRNA life time, the noise is also small. In general the damping of protein production by a repressive agent occurs linearly but fluctuations can show a maximum at intermediate repression. The discrepancy among the switch decay time, the mRNA degradation, and protein degradation is crucial for the repressive control in translation without large fluctuations. The noise profiles obtained here are in quantitative agreement with recent experiments.
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Affiliation(s)
- G C P Innocentini
- Instituto de Física de São Carlos, Universidade de São Paulo, Caixa Postal 369, 13560-970, São Carlos, SP, Brazil.
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93
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Paixão T, Carvalho TP, Calado DP, Carneiro J. Quantitative insights into stochastic monoallelic expression of cytokine genes. Immunol Cell Biol 2007; 85:315-22. [PMID: 17438562 DOI: 10.1038/sj.icb.7100057] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Gene expression from both parental alleles is beneficial by masking the effects of deleterious recessive mutations and by reducing the noise in gene expression in diploid organisms. However, a class of genes are expressed preferentially or strictly from a single allele. The selective advantage of avoiding biallelic expression is clear for allelic-excluded antigen receptor and odorant receptor genes, genes undergoing X-chromosome inactivation in females and parental genomic imprinted genes. In contrast, there is no clear biological rationale for the predominant and stochastic monoallelic expression of cytokine genes in the immune system, and the underlying mechanism is elusive and controversial. A clarification of the mechanism of predominant monoallelic expression would be instrumental in better understanding its eventual biological functional. This prompted the development of a quantitative framework that could describe the dynamics of the pattern of allele expression of the IL-10 gene, from which general quantitative insights could be gained. We report that the experimental observations on these patterns of allelic expression cannot be easily reconciled with a simple model of stochastic transcriptional activation, in which the two alleles are, at any time, equally competent for transcription. Instead, these observations call into action a general model of eukaryotic transcriptional regulation according to which the locus competence for transcription is dynamic, involving multiple, cooperative and stochastic modification steps. In this model, the probability that an allele becomes transcriptionally active is a function of the number of chromatin modifications that it accumulated. On the basis of the properties of this model, we argue that predominant monoallelic expression might have had no adaptive role, and may have evolved under indirect selection for low frequency of expressing cells.
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Affiliation(s)
- Tiago Paixão
- Instituto Gulbenkian de Ciência, 2781-901 Oeiras, Portugal.
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94
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Abstract
A single gene, regulating its own expression via a positive feedback loop, constitutes a common motif in gene regulatory networks and signalling cascades. Recent experiments on the development of competence in the bacterial population B. subtilis show that the autoregulatory genetic module by itself can give rise to two types of cellular states. The states correspond to the low and high expression states of the master regulator ComK. The high expression state is attained when the ComK protein level exceeds a threshold value leading to a full activation of the autostimulatory loop. Stochasticity in gene expression drives the transitions between the two stable states. In this paper, we explain the appearance of bimodal protein distributions in B. subtilis cell population in the framework of three possible scenarios. In two of the cases, bistability provides the basis for binary gene expression. In the third case, the system is monostable in a deterministic description and stochasticity in gene expression is solely responsible for the appearance of the two expression states.
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95
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Paszek P. Modeling stochasticity in gene regulation: characterization in the terms of the underlying distribution function. Bull Math Biol 2007; 69:1567-601. [PMID: 17361363 DOI: 10.1007/s11538-006-9176-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2005] [Accepted: 07/05/2006] [Indexed: 11/29/2022]
Abstract
Intrinsic stochasticity plays an essential role in gene regulation because of a small number of involved molecules of DNA, mRNA and protein of a given species. To better understand this phenomenon, small gene regulatory systems are mathematically modeled as systems of coupled chemical reactions, but the existing exact description utilizing a Chapman-Kolmogorov equation or simulation algorithms is limited and inefficient. The present work considers a much more efficient yet accurate modeling approach, which allows analyzing stochasticity in the system in the terms of the underlying distribution function. We depart from the analysis of a single gene regulatory module to find that the mRNA and protein variance is decomposable into additive terms resulting from respective sources of stochasticity. This variance decomposition is asserted by constructing two approximations to the exact stochastic description: First, the continuous approximation, which considers only the stochasticity due to the intermittent gene activity. Second, the mixed approximation, which in addition attributes stochasticity to the mRNA transcription/decay process. Considered approximations yield systems of first order partial differential equations for the underlying distribution function, which can be efficiently solved using developed numerical methods. Single cell simulations and numerical two-dimensional mRNA-protein stationary distribution functions are presented to confirm accuracy of approximating models.
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Affiliation(s)
- Pawel Paszek
- Department of Statistics, Rice University, 6100 Main St. MS-138, Houston, TX 77005, USA.
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96
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Tan C, Song H, Niemi J, You L. A synthetic biology challenge: making cells compute. MOLECULAR BIOSYSTEMS 2007; 3:343-53. [PMID: 17460793 DOI: 10.1039/b618473c] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Advances in biology and engineering have enabled the reprogramming of cells with well-defined functions, leading to the emergence of synthetic biology. Early successes in this nascent field suggest its potential to impact diverse areas. Here, we examine the feasibility of engineering circuits for cell-based computation. We illustrate the basic concepts by describing the mapping of several computational problems to engineered gene circuits. Revolving around these examples and past studies, we discuss technologies and computational methods available to design, test, and optimize gene circuits. We conclude with discussion of challenges involved in a typical design cycle, as well as those specific to cellular computation.
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Affiliation(s)
- Cheemeng Tan
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
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97
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Jay PY, Bielinska M, Erlich JM, Mannisto S, Pu WT, Heikinheimo M, Wilson DB. Impaired mesenchymal cell function in Gata4 mutant mice leads to diaphragmatic hernias and primary lung defects. Dev Biol 2007; 301:602-14. [PMID: 17069789 PMCID: PMC1808541 DOI: 10.1016/j.ydbio.2006.09.050] [Citation(s) in RCA: 133] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2006] [Revised: 09/08/2006] [Accepted: 09/29/2006] [Indexed: 01/13/2023]
Abstract
Congenital diaphragmatic hernia (CDH) is an often fatal birth defect that is commonly associated with pulmonary hypoplasia and cardiac malformations. Some investigators hypothesize that this constellation of defects results from genetic or environmental triggers that disrupt mesenchymal cell function in not only the primordial diaphragm but also the thoracic organs. The alternative hypothesis is that the displacement of the abdominal viscera in the chest secondarily perturbs the development of the heart and lungs. Recently, loss-of-function mutations in the gene encoding FOG-2, a transcriptional co-regulator, have been linked to CDH and pulmonary hypoplasia in humans and mice. Here we show that mutagenesis of the gene for GATA-4, a transcription factor known to functionally interact with FOG-2, predisposes inbred mice to a similar set of birth defects. Analysis of wild-type mouse embryos demonstrated co-expression of Gata4 and Fog2 in mesenchymal cells of the developing diaphragm, lungs, and heart. A significant fraction of C57Bl/6 mice heterozygous for a Gata4 deletion mutation died within 1 day of birth. Developmental defects in the heterozygotes included midline diaphragmatic hernias, dilated distal airways, and cardiac malformations. Heterozygotes had any combination of these defects or none. In chimeric mice, Gata4(-/-) cells retained the capacity to contribute to cells in the diaphragmatic central tendon and lung mesenchyme, indicating that GATA-4 is not required for differentiation of these lineages. We conclude that GATA-4, like its co-regulator FOG-2, is required for proper mesenchymal cell function in the developing diaphragm, lungs, and heart.
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Affiliation(s)
- Patrick Y. Jay
- Department of Pediatrics, Washington University and St. Louis Children’s Hospital, St. Louis, MO 63110
- Department of Genetics, Washington University and St. Louis Children’s Hospital, St. Louis, MO 63110
| | - Malgorzata Bielinska
- Department of Pediatrics, Washington University and St. Louis Children’s Hospital, St. Louis, MO 63110
| | - Jonathan M. Erlich
- Department of Pediatrics, Washington University and St. Louis Children’s Hospital, St. Louis, MO 63110
| | - Susanna Mannisto
- Program for Developmental & Reproductive Biology, Biomedicum Helsinki and Children’s Hospital, University of Helsinki, 00290 Helsinki, Finland
| | - William T. Pu
- Departments of Cardiology, Pediatrics, & Genetics, Children’s Hospital Boston and Harvard Medical School, Boston, MA 02115
| | - Markku Heikinheimo
- Department of Pediatrics, Washington University and St. Louis Children’s Hospital, St. Louis, MO 63110
- Program for Developmental & Reproductive Biology, Biomedicum Helsinki and Children’s Hospital, University of Helsinki, 00290 Helsinki, Finland
| | - David B. Wilson
- Department of Pediatrics, Washington University and St. Louis Children’s Hospital, St. Louis, MO 63110
- Departments of Molecular Biology & Pharmacology, Washington University and St. Louis Children’s Hospital, St. Louis, MO 63110
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98
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Bielinska M, Jay PY, Erlich JM, Mannisto S, Urban Z, Heikinheimo M, Wilson DB. Molecular genetics of congenital diaphragmatic defects. Ann Med 2007; 39:261-74. [PMID: 17558598 PMCID: PMC2174621 DOI: 10.1080/07853890701326883] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Congenital diaphragmatic hernia (CDH) is a severe birth defect that is accompanied by malformations of the lung, heart, testis, and other organs. Patients with CDH may have any combination of these extradiaphragmatic defects, suggesting that CDH is often a manifestation of a global embryopathy. This review highlights recent advances in human and mouse genetics that have led to the identification of genes involved in CDH. These include genes for transcription factors, molecules involved in cell migration, and extracellular matrix components. The expression patterns of these genes in the developing embryo suggest that mesenchymal cell function is compromised in the diaphragm and other affected organs in patients with CDH. We discuss potential mechanisms underlying the seemingly random combination of diaphragmatic, pulmonary, cardiovascular, and gonadal defects in these patients.
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Affiliation(s)
- Malgorzata Bielinska
- Department of Pediatrics, Washington University and St. Louis Children's Hospital, St. Louis, MO 63110 USA
| | - Patrick Y. Jay
- Department of Pediatrics, Washington University and St. Louis Children's Hospital, St. Louis, MO 63110 USA
- Department of Genetics, Washington University and St. Louis Children's Hospital, St. Louis, MO 63110 USA
| | - Jonathan M. Erlich
- Department of Pediatrics, Washington University and St. Louis Children's Hospital, St. Louis, MO 63110 USA
| | - Susanna Mannisto
- Program for Developmental & Reproductive Biology, Biomedicum Helsinki and Children's Hospital, University of Helsinki, 00290 Helsinki, Finland
| | - Zsolt Urban
- Department of Pediatrics, Washington University and St. Louis Children's Hospital, St. Louis, MO 63110 USA
- Department of Genetics, Washington University and St. Louis Children's Hospital, St. Louis, MO 63110 USA
| | - Markku Heikinheimo
- Department of Pediatrics, Washington University and St. Louis Children's Hospital, St. Louis, MO 63110 USA
- Program for Developmental & Reproductive Biology, Biomedicum Helsinki and Children's Hospital, University of Helsinki, 00290 Helsinki, Finland
| | - David B. Wilson
- Department of Pediatrics, Washington University and St. Louis Children's Hospital, St. Louis, MO 63110 USA
- Department of Molecular Biology & Pharmacology, Washington University and St. Louis Children's Hospital, St. Louis, MO 63110 USA
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99
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Wang CL, Yang DC, Wabl M. Slow, stochastic transgene repression with properties of a timer. Genome Biol 2006; 7:R47. [PMID: 16764729 PMCID: PMC1779533 DOI: 10.1186/gb-2006-7-6-r47] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2006] [Revised: 03/30/2006] [Accepted: 05/08/2006] [Indexed: 11/30/2022] Open
Abstract
The dynamics of retroviral transgene repression were analyzed in several clones; repression was found to be slow and different genomic positions showed different dynamics. Background When gene expression varies unpredictably between genetically identical organisms, this is sometimes ascribed as stochastic. With the prevalence of retroviral vectors, stochastic repression is often observed and can complicate the interpretation of outcomes. But it may also faithfully reflect characteristics of sites in the genome. Results We created and identified several cell clones in which, within a given cell, retroviral transcription of a transgene was repressed heritably and essentially irreversibly. This repression was relatively slow; total repression in all cells took months. We observed the dynamics of repression and found that they were ergodic, that is, tending with a probability to a final state independent of previous conditions. Different positions of the transgene in the genome demonstrated different dynamics. At a position on mouse chromosome 9, repression abided by near perfect first-order kinetics and was highly reproducible, even under conditions where the number of cell generations per day varied. Conclusion We propose that such a cell division independent 'off' mechanism could play a role in endogenous gene expression, potentially providing an epigenetically based timer for extended periods.
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Affiliation(s)
- Clifford L Wang
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143-0414, USA
| | - Desirée C Yang
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143-0414, USA
| | - Matthias Wabl
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143-0414, USA
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100
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Abstract
We consider a stochastic model of transcription factor (TF)-regulated gene expression. The model describes two genes, gene A and gene B, which synthesize the TFs and the target gene proteins, respectively. We show through analytic calculations that the TF fluctuations have a significant effect on the distribution of the target gene protein levels when the mean TF level falls in the highest sensitive region of the dose-response curve. We further study the effect of reducing the copy number of gene A from two to one. The enhanced TF fluctuations yield results different from those in the deterministic case. The probability that the target gene protein level exceeds a threshold value is calculated with the knowledge of the probability density functions associated with the TF and target gene protein levels. Numerical simulation results for a more detailed stochastic model are shown to be in agreement with those obtained through analytic calculations. The relevance of these results in the context of the genetic disorder haploinsufficiency is pointed out. Some experimental observations on the haploinsufficiency of the tumour suppressor gene, Nkx 3.1, are explained with the help of the stochastic model of TF-regulated gene expression.
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