1
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Zhang X, Bell JT. Detecting genetic effects on phenotype variability to capture gene-by-environment interactions: a systematic method comparison. G3 (BETHESDA, MD.) 2024; 14:jkae022. [PMID: 38289865 PMCID: PMC10989912 DOI: 10.1093/g3journal/jkae022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/16/2024] [Accepted: 01/19/2024] [Indexed: 02/01/2024]
Abstract
Genetically associated phenotypic variability has been widely observed across organisms and traits, including in humans. Both gene-gene and gene-environment interactions can lead to an increase in genetically associated phenotypic variability. Therefore, detecting the underlying genetic variants, or variance Quantitative Trait Loci (vQTLs), can provide novel insights into complex traits. Established approaches to detect vQTLs apply different methodologies from variance-only approaches to mean-variance joint tests, but a comprehensive comparison of these methods is lacking. Here, we review available methods to detect vQTLs in humans, carry out a simulation study to assess their performance under different biological scenarios of gene-environment interactions, and apply the optimal approaches for vQTL identification to gene expression data. Overall, with a minor allele frequency (MAF) of less than 0.2, the squared residual value linear model (SVLM) and the deviation regression model (DRM) are optimal when the data follow normal and non-normal distributions, respectively. In addition, the Brown-Forsythe (BF) test is one of the optimal methods when the MAF is 0.2 or larger, irrespective of phenotype distribution. Additionally, a larger sample size and more balanced sample distribution in different exposure categories increase the power of BF, SVLM, and DRM. Our results highlight vQTL detection methods that perform optimally under realistic simulation settings and show that their relative performance depends on the phenotype distribution, allele frequency, sample size, and the type of exposure in the interaction model underlying the vQTL.
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Affiliation(s)
- Xiaopu Zhang
- Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas’ Hospital, Westminster Bridge Road, London SE1 7EH, UK
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas’ Hospital, Westminster Bridge Road, London SE1 7EH, UK
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2
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Kovuri P, Yadav A, Sinha H. Role of genetic architecture in phenotypic plasticity. Trends Genet 2023; 39:703-714. [PMID: 37173192 DOI: 10.1016/j.tig.2023.04.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 04/06/2023] [Accepted: 04/11/2023] [Indexed: 05/15/2023]
Abstract
Phenotypic plasticity, the ability of an organism to display different phenotypes across environments, is widespread in nature. Plasticity aids survival in novel environments. Herein, we review studies from yeast that allow us to start uncovering the genetic architecture of phenotypic plasticity. Genetic variants and their interactions impact the phenotype in different environments, and distinct environments modulate the impact of genetic variants and their interactions on the phenotype. Because of this, certain hidden genetic variation is expressed in specific genetic and environmental backgrounds. A better understanding of the genetic mechanisms of phenotypic plasticity will help to determine short- and long-term responses to selection and how wide variation in disease manifestation occurs in human populations.
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Affiliation(s)
- Purnima Kovuri
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, IIT Madras, Chennai, India; Centre for Integrative Biology and Systems mEdicine (IBSE), IIT Madras, Chennai, India; Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), IIT Madras, Chennai, India
| | - Anupama Yadav
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Himanshu Sinha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, IIT Madras, Chennai, India; Centre for Integrative Biology and Systems mEdicine (IBSE), IIT Madras, Chennai, India; Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), IIT Madras, Chennai, India.
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3
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Lutz S, Van Dyke K, Feraru MA, Albert FW. Multiple epistatic DNA variants in a single gene affect gene expression in trans. Genetics 2022; 220:iyab208. [PMID: 34791209 PMCID: PMC8733636 DOI: 10.1093/genetics/iyab208] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 11/09/2021] [Indexed: 01/08/2023] Open
Abstract
DNA variants that alter gene expression in trans are important sources of phenotypic variation. Nevertheless, the identity of trans-acting variants remains poorly understood. Single causal variants in several genes have been reported to affect the expression of numerous distant genes in trans. Whether these simple molecular architectures are representative of trans-acting variation is unknown. Here, we studied the large RAS signaling regulator gene IRA2, which contains variants with extensive trans-acting effects on gene expression in the yeast Saccharomyces cerevisiae. We used systematic CRISPR-based genome engineering and a sensitive phenotyping strategy to dissect causal variants to the nucleotide level. In contrast to the simple molecular architectures known so far, IRA2 contained at least seven causal nonsynonymous variants. The effects of these variants were modulated by nonadditive, epistatic interactions. Two variants at the 5'-end affected gene expression and growth only when combined with a third variant that also had no effect in isolation. Our findings indicate that the molecular basis of trans-acting genetic variation may be considerably more complex than previously appreciated.
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Affiliation(s)
- Sheila Lutz
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Krisna Van Dyke
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Matthew A Feraru
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Frank W Albert
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
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4
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Palme J, Wang J, Springer M. Variation in the modality of a yeast signaling pathway is mediated by a single regulator. eLife 2021; 10:69974. [PMID: 34369878 PMCID: PMC8373380 DOI: 10.7554/elife.69974] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 07/10/2021] [Indexed: 11/13/2022] Open
Abstract
Bimodal gene expression by genetically identical cells is a pervasive feature of signaling networks and has been suggested to allow organisms to hedge their ‘bets’ in uncertain conditions. In the galactose-utilization (GAL) pathway of Saccharomyces cerevisiae, gene induction is unimodal or bimodal depending on natural genetic variation and pre-induction conditions. Here, we find that this variation in modality arises from regulation of two features of the pathway response: the fraction of cells that show induction and their level of expression. GAL3, the galactose sensor, controls the fraction of induced cells, and titrating its expression is sufficient to control modality; moreover, all the observed differences in modality between different pre-induction conditions and among natural isolates can be explained by changes in GAL3’s regulation and activity. The ability to switch modality by tuning the activity of a single protein may allow rapid adaptation of bet hedging to maximize fitness in complex environments.
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Affiliation(s)
- Julius Palme
- Department of Systems Biology, Harvard Medical School, Boston, United States
| | - Jue Wang
- Department of Chemical Engineering, University of Washington, Seattle, United States
| | - Michael Springer
- Department of Systems Biology, Harvard Medical School, Boston, United States
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5
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Triqueneaux G, Burny C, Symmons O, Janczarski S, Gruffat H, Yvert G. Cell-to-cell expression dispersion of B-cell surface proteins is linked to genetic variants in humans. Commun Biol 2020; 3:346. [PMID: 32620900 PMCID: PMC7335051 DOI: 10.1038/s42003-020-1075-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 06/12/2020] [Indexed: 01/02/2023] Open
Abstract
Variability in gene expression across a population of homogeneous cells is known to influence various biological processes. In model organisms, natural genetic variants were found that modify expression dispersion (variability at a fixed mean) but very few studies have detected such effects in humans. Here, we analyzed single-cell expression of four proteins (CD23, CD55, CD63 and CD86) across cell lines derived from individuals of the Yoruba population. Using data from over 30 million cells, we found substantial inter-individual variation of dispersion. We demonstrate, via de novo cell line generation and subcloning experiments, that this variation exceeds the variation associated with cellular immortalization. We detected a genetic association between the expression dispersion of CD63 and the rs971 SNP. Our results show that human DNA variants can have inherently-probabilistic effects on gene expression. Such subtle genetic effects may participate to phenotypic variation and disease outcome. Triqueneaux, Burny, Symmons et al. show association between gene expression noise and genotypes, using single-cell expression of four proteins across human-derived lymphoblastoid cell lines. This study suggests that very subtle regulatory effects of human DNA variants may contribute to phenotypic variation and disease outcome.
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Affiliation(s)
- Gérard Triqueneaux
- Laboratory of Biology and Modeling of the Cell, Univ Lyon, Ecole Normale Superieure de Lyon, CNRS UMR5239, Universite Claude Bernard Lyon 1, 69007, Lyon, France
| | - Claire Burny
- Laboratory of Biology and Modeling of the Cell, Univ Lyon, Ecole Normale Superieure de Lyon, CNRS UMR5239, Universite Claude Bernard Lyon 1, 69007, Lyon, France.,Institut für Populationsgenetik, Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Vienna, Austria
| | - Orsolya Symmons
- Laboratory of Biology and Modeling of the Cell, Univ Lyon, Ecole Normale Superieure de Lyon, CNRS UMR5239, Universite Claude Bernard Lyon 1, 69007, Lyon, France.,Max Planck Institute for Biology of Ageing, Cologne, 50931, Germany
| | - Stéphane Janczarski
- Laboratory of Biology and Modeling of the Cell, Univ Lyon, Ecole Normale Superieure de Lyon, CNRS UMR5239, Universite Claude Bernard Lyon 1, 69007, Lyon, France
| | - Henri Gruffat
- CIRI-Centre International de Recherche en Infectiologie, Universite Claude Bernard Lyon 1, Univ Lyon, Inserm U1111, CNRS UMR5308, Ecole Normale Superieure de Lyon, 69007, Lyon, France
| | - Gaël Yvert
- Laboratory of Biology and Modeling of the Cell, Univ Lyon, Ecole Normale Superieure de Lyon, CNRS UMR5239, Universite Claude Bernard Lyon 1, 69007, Lyon, France.
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6
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DNA variants affecting the expression of numerous genes in trans have diverse mechanisms of action and evolutionary histories. PLoS Genet 2019; 15:e1008375. [PMID: 31738765 PMCID: PMC6886874 DOI: 10.1371/journal.pgen.1008375] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 12/02/2019] [Accepted: 10/28/2019] [Indexed: 12/13/2022] Open
Abstract
DNA variants that alter gene expression contribute to variation in many phenotypic traits. In particular, trans-acting variants, which are often located on different chromosomes from the genes they affect, are an important source of heritable gene expression variation. However, our knowledge about the identity and mechanism of causal trans-acting variants remains limited. Here, we developed a fine-mapping strategy called CRISPR-Swap and dissected three expression quantitative trait locus (eQTL) hotspots known to alter the expression of numerous genes in trans in the yeast Saccharomyces cerevisiae. Causal variants were identified by engineering recombinant alleles and quantifying the effects of these alleles on the expression of a green fluorescent protein-tagged gene affected by the given locus in trans. We validated the effect of each variant on the expression of multiple genes by RNA-sequencing. The three variants differed in their molecular mechanism, the type of genes they reside in, and their distribution in natural populations. While a missense leucine-to-serine variant at position 63 in the transcription factor Oaf1 (L63S) was almost exclusively present in the reference laboratory strain, the two other variants were frequent among S. cerevisiae isolates. A causal missense variant in the glucose receptor Rgt2 (V539I) occurred at a poorly conserved amino acid residue and its effect was strongly dependent on the concentration of glucose in the culture medium. A noncoding variant in the conserved fatty acid regulated (FAR) element of the OLE1 promoter influenced the expression of the fatty acid desaturase Ole1 in cis and, by modulating the level of this essential enzyme, other genes in trans. The OAF1 and OLE1 variants showed a non-additive genetic interaction, and affected cellular lipid metabolism. These results demonstrate that the molecular basis of trans-regulatory variation is diverse, highlighting the challenges in predicting which natural genetic variants affect gene expression. Differences in the DNA sequence of individual genomes contribute to differences in many traits, such as appearance, physiology, and the risk for common diseases. An important group of these DNA variants influences how individual genes across the genome are turned on or off. In this paper, we describe a strategy for identifying such “trans-acting” variants in different strains of baker’s yeast. We used this strategy to reveal three single DNA base changes that each influences the expression of dozens of genes. These three DNA variants were very different from each other. Two of them changed the protein sequence, one in a transcription factor and the other in a sugar sensor. The third changed the expression of an enzyme, a change that in turn caused other genes to alter their expression. One variant existed in only a few yeast isolates, while the other two existed in many isolates collected from around the world. This diversity of DNA variants that influence the expression of many other genes illustrates how difficult it is to predict which DNA variants in an individual’s genome will have effects on the organism.
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7
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Duveau F, Hodgins-Davis A, Metzger BP, Yang B, Tryban S, Walker EA, Lybrook T, Wittkopp PJ. Fitness effects of altering gene expression noise in Saccharomyces cerevisiae. eLife 2018; 7:37272. [PMID: 30124429 PMCID: PMC6133559 DOI: 10.7554/elife.37272] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 08/17/2018] [Indexed: 01/22/2023] Open
Abstract
Gene expression noise is an evolvable property of biological systems that describes differences in expression among genetically identical cells in the same environment. Prior work has shown that expression noise is heritable and can be shaped by selection, but the impact of variation in expression noise on organismal fitness has proven difficult to measure. Here, we quantify the fitness effects of altering expression noise for the TDH3 gene in Saccharomyces cerevisiae. We show that increases in expression noise can be deleterious or beneficial depending on the difference between the average expression level of a genotype and the expression level maximizing fitness. We also show that a simple model relating single-cell expression levels to population growth produces patterns consistent with our empirical data. We use this model to explore a broad range of average expression levels and expression noise, providing additional insight into the fitness effects of variation in expression noise.
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Affiliation(s)
- Fabien Duveau
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, United States.,Laboratoire Matière et Systèmes Complexes, CNRS UMR 7057, Université Paris Diderot, Paris, France
| | - Andrea Hodgins-Davis
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, United States
| | - Brian Ph Metzger
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, United States.,Department of Ecology and Evolution, University of Chicago, Chicago, United States
| | - Bing Yang
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, United States
| | - Stephen Tryban
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, United States
| | - Elizabeth A Walker
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, United States
| | - Tricia Lybrook
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, United States
| | - Patricia J Wittkopp
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, United States.,Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, United States
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8
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Albert FW, Bloom JS, Siegel J, Day L, Kruglyak L. Genetics of trans-regulatory variation in gene expression. eLife 2018; 7:e35471. [PMID: 30014850 PMCID: PMC6072440 DOI: 10.7554/elife.35471] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 06/30/2018] [Indexed: 12/02/2022] Open
Abstract
Heritable variation in gene expression forms a crucial bridge between genomic variation and the biology of many traits. However, most expression quantitative trait loci (eQTLs) remain unidentified. We mapped eQTLs by transcriptome sequencing in 1012 yeast segregants. The resulting eQTLs accounted for over 70% of the heritability of mRNA levels, allowing comprehensive dissection of regulatory variation. Most genes had multiple eQTLs. Most expression variation arose from trans-acting eQTLs distant from their target genes. Nearly all trans-eQTLs clustered at 102 hotspot locations, some of which influenced the expression of thousands of genes. Fine-mapped hotspot regions were enriched for transcription factor genes. While most genes had a local eQTL, most of these had no detectable effects on the expression of other genes in trans. Hundreds of non-additive genetic interactions accounted for small fractions of expression variation. These results reveal the complexity of genetic influences on transcriptome variation in unprecedented depth and detail.
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Affiliation(s)
- Frank Wolfgang Albert
- Department of Genetics, Cell Biology and DevelopmentUniversity of MinnesotaMinneapolisUnited States
| | - Joshua S Bloom
- Department of Human GeneticsUniversity of California, Los AngelesLos AngelesUnited States
- Department of Biological ChemistryUniversity of California, Los AngelesLos AngelesUnited States
- Howard Hughes Medical InstituteLos AngelesUnited States
| | - Jake Siegel
- Department of Human GeneticsUniversity of California, Los AngelesLos AngelesUnited States
- Department of Biological ChemistryUniversity of California, Los AngelesLos AngelesUnited States
- Howard Hughes Medical InstituteLos AngelesUnited States
| | - Laura Day
- Department of Human GeneticsUniversity of California, Los AngelesLos AngelesUnited States
- Department of Biological ChemistryUniversity of California, Los AngelesLos AngelesUnited States
- Howard Hughes Medical InstituteLos AngelesUnited States
| | - Leonid Kruglyak
- Department of Human GeneticsUniversity of California, Los AngelesLos AngelesUnited States
- Department of Biological ChemistryUniversity of California, Los AngelesLos AngelesUnited States
- Howard Hughes Medical InstituteLos AngelesUnited States
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9
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Conley D, Johnson R, Domingue B, Dawes C, Boardman J, Siegal M. A sibling method for identifying vQTLs. PLoS One 2018; 13:e0194541. [PMID: 29617452 PMCID: PMC5884517 DOI: 10.1371/journal.pone.0194541] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 03/05/2018] [Indexed: 12/11/2022] Open
Abstract
The propensity of a trait to vary within a population may have evolutionary, ecological, or clinical significance. In the present study we deploy sibling models to offer a novel and unbiased way to ascertain loci associated with the extent to which phenotypes vary (variance-controlling quantitative trait loci, or vQTLs). Previous methods for vQTL-mapping either exclude genetically related individuals or treat genetic relatedness among individuals as a complicating factor addressed by adjusting estimates for non-independence in phenotypes. The present method uses genetic relatedness as a tool to obtain unbiased estimates of variance effects rather than as a nuisance. The family-based approach, which utilizes random variation between siblings in minor allele counts at a locus, also allows controls for parental genotype, mean effects, and non-linear (dominance) effects that may spuriously appear to generate variation. Simulations show that the approach performs equally well as two existing methods (squared Z-score and DGLM) in controlling type I error rates when there is no unobserved confounding, and performs significantly better than these methods in the presence of small degrees of confounding. Using height and BMI as empirical applications, we investigate SNPs that alter within-family variation in height and BMI, as well as pathways that appear to be enriched. One significant SNP for BMI variability, in the MAST4 gene, replicated. Pathway analysis revealed one gene set, encoding members of several signaling pathways related to gap junction function, which appears significantly enriched for associations with within-family height variation in both datasets (while not enriched in analysis of mean levels). We recommend approximating laboratory random assignment of genotype using family data and more careful attention to the possible conflation of mean and variance effects.
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Affiliation(s)
- Dalton Conley
- Department of Sociology, Princeton University, Princeton, NJ, United States of America
| | - Rebecca Johnson
- Department of Sociology, Princeton University, Princeton, NJ, United States of America
| | - Ben Domingue
- Graduate School of Education, Stanford University, Stanford, CA, United States of America
| | - Christopher Dawes
- Wilff Family Department of Politics, New York University, New York City, NY, United States of America
| | - Jason Boardman
- Institute for Behavioral Sciences, University of Colorado, Boulder, Boulder, CO, United States of America
| | - Mark Siegal
- Center for Genomics and Systems Biology, New York University, New York University, New York City, NY, United States of America
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10
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Yang E, Wang G, Yang J, Zhou B, Tian Y, Cai JJ. Epistasis and destabilizing mutations shape gene expression variability in humans via distinct modes of action. Hum Mol Genet 2018; 25:4911-4919. [PMID: 28171656 DOI: 10.1093/hmg/ddw314] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 08/19/2016] [Accepted: 09/12/2016] [Indexed: 11/14/2022] Open
Abstract
Increasing evidence shows that phenotypic variance is genetically determined, but the underlying mechanisms of genetic control over the variance remain obscure. Here, we conducted variance-association mapping analyses to identify expression variability QTLs (evQTLs), i.e. genomic loci associated with gene expression variance, in humans. We discovered that common genetic variants may contribute to increasing gene expression variance via two distinct modes of action—epistasis and destabilization. Specifically, epistasis explains a quarter of the identified evQTLs, of which the formation is attributed to the presence of ‘third-party’ eQTLs that influence the gene expression mean in a fraction, rather than the entire set, of sampled individuals. On the other hand, the destabilization model explains the other three-quarters of evQTLs, caused by mutations that disrupt the stability of the transcription process of genes. To show the destabilizing effect, we measured discordant gene expression between monozygotic twins, and estimated the stability of gene expression in single samples using repetitive qRT-PCR assays. The mutations that cause destabilizing evQTLs were found to be associated with more pronounced expression discordance between twin pairs and less stable gene expression in single samples. Together, our results suggest that common genetic variants work either interactively or independently to shape the variability of gene expression in humans. Our findings contribute to the understanding of the mechanisms of genetic control over phenotypic variance and may have implications for the development of variance-centred analytic methods for quantitative trait mapping.
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Affiliation(s)
- Ence Yang
- Department of Veterinary Integrative Biosciences.,Institute for Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Gang Wang
- Department of Veterinary Integrative Biosciences
| | - Jizhou Yang
- Department of Veterinary Integrative Biosciences
| | - Beiyan Zhou
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX, USA.,Department of Immunology, University of Connecticut Health Center, Farmington, CT, USA
| | - Yanan Tian
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX, USA
| | - James J Cai
- Department of Veterinary Integrative Biosciences.,Interdisciplinary Program of Genetics, Texas A&M University, College Station, TX, USA
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11
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Richard M, Chuffart F, Duplus-Bottin H, Pouyet F, Spichty M, Fulcrand E, Entrevan M, Barthelaix A, Springer M, Jost D, Yvert G. Assigning function to natural allelic variation via dynamic modeling of gene network induction. Mol Syst Biol 2018; 14:e7803. [PMID: 29335276 PMCID: PMC5787706 DOI: 10.15252/msb.20177803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
More and more natural DNA variants are being linked to physiological traits. Yet, understanding what differences they make on molecular regulations remains challenging. Important properties of gene regulatory networks can be captured by computational models. If model parameters can be “personalized” according to the genotype, their variation may then reveal how DNA variants operate in the network. Here, we combined experiments and computations to visualize natural alleles of the yeast GAL3 gene in a space of model parameters describing the galactose response network. Alleles altering the activation of Gal3p by galactose were discriminated from those affecting its activity (production/degradation or efficiency of the activated protein). The approach allowed us to correctly predict that a non‐synonymous SNP would change the binding affinity of Gal3p with the Gal80p transcriptional repressor. Our results illustrate how personalizing gene regulatory models can be used for the mechanistic interpretation of genetic variants.
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Affiliation(s)
- Magali Richard
- Laboratoire de Biologie et de Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, Université Lyon 1 Université de Lyon, Lyon, France .,Univ. Grenoble Alpes, CNRS CHU Grenoble Alpes Grenoble INP TIMC-IMAG, Grenoble, France
| | - Florent Chuffart
- Laboratoire de Biologie et de Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, Université Lyon 1 Université de Lyon, Lyon, France
| | - Hélène Duplus-Bottin
- Laboratoire de Biologie et de Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, Université Lyon 1 Université de Lyon, Lyon, France
| | - Fanny Pouyet
- Laboratoire de Biologie et de Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, Université Lyon 1 Université de Lyon, Lyon, France
| | - Martin Spichty
- Laboratoire de Biologie et de Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, Université Lyon 1 Université de Lyon, Lyon, France
| | - Etienne Fulcrand
- Laboratoire de Biologie et de Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, Université Lyon 1 Université de Lyon, Lyon, France
| | - Marianne Entrevan
- Laboratoire de Biologie et de Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, Université Lyon 1 Université de Lyon, Lyon, France
| | - Audrey Barthelaix
- Laboratoire de Biologie et de Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, Université Lyon 1 Université de Lyon, Lyon, France
| | - Michael Springer
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Daniel Jost
- Univ. Grenoble Alpes, CNRS CHU Grenoble Alpes Grenoble INP TIMC-IMAG, Grenoble, France
| | - Gaël Yvert
- Laboratoire de Biologie et de Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, Université Lyon 1 Université de Lyon, Lyon, France
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12
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Katsanos D, Koneru SL, Mestek Boukhibar L, Gritti N, Ghose R, Appleford PJ, Doitsidou M, Woollard A, van Zon JS, Poole RJ, Barkoulas M. Stochastic loss and gain of symmetric divisions in the C. elegans epidermis perturbs robustness of stem cell number. PLoS Biol 2017; 15:e2002429. [PMID: 29108019 PMCID: PMC5690688 DOI: 10.1371/journal.pbio.2002429] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 11/16/2017] [Accepted: 10/20/2017] [Indexed: 11/19/2022] Open
Abstract
Biological systems are subject to inherent stochasticity. Nevertheless, development is remarkably robust, ensuring the consistency of key phenotypic traits such as correct cell numbers in a certain tissue. It is currently unclear which genes modulate phenotypic variability, what their relationship is to core components of developmental gene networks, and what is the developmental basis of variable phenotypes. Here, we start addressing these questions using the robust number of Caenorhabditis elegans epidermal stem cells, known as seam cells, as a readout. We employ genetics, cell lineage tracing, and single molecule imaging to show that mutations in lin-22, a Hes-related basic helix-loop-helix (bHLH) transcription factor, increase seam cell number variability. We show that the increase in phenotypic variability is due to stochastic conversion of normally symmetric cell divisions to asymmetric and vice versa during development, which affect the terminal seam cell number in opposing directions. We demonstrate that LIN-22 acts within the epidermal gene network to antagonise the Wnt signalling pathway. However, lin-22 mutants exhibit cell-to-cell variability in Wnt pathway activation, which correlates with and may drive phenotypic variability. Our study demonstrates the feasibility to study phenotypic trait variance in tractable model organisms using unbiased mutagenesis screens.
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Affiliation(s)
- Dimitris Katsanos
- Department of Life Sciences, Imperial College, London, United Kingdom
| | - Sneha L. Koneru
- Department of Life Sciences, Imperial College, London, United Kingdom
| | | | - Nicola Gritti
- Institute for Atomic and Molecular Physics (AMOLF), Amsterdam, The Netherlands
| | - Ritobrata Ghose
- Department of Life Sciences, Imperial College, London, United Kingdom
| | - Peter J. Appleford
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Maria Doitsidou
- Centre for Integrative Physiology, University of Edinburgh, Edinburgh, United Kingdom
| | - Alison Woollard
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Jeroen S. van Zon
- Institute for Atomic and Molecular Physics (AMOLF), Amsterdam, The Netherlands
| | - Richard J. Poole
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
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13
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Pelechano V. From transcriptional complexity to cellular phenotypes: Lessons from yeast. Yeast 2017; 34:475-482. [PMID: 28866863 DOI: 10.1002/yea.3277] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 08/16/2017] [Accepted: 08/17/2017] [Indexed: 12/12/2022] Open
Abstract
Pervasive transcription has been reported in many eukaryotic organisms, revealing a highly interleaved transcriptome organization that involves thousands of coding and non-coding RNAs. However, to date, the biological impact of transcriptome complexity is still poorly understood. Here I will review how subtle variations of the transcriptome can lead to divergent cellular phenotypes by fine-tuning both its coding potential and regulation. I will discuss strategies that can be used to link molecular variations with divergent biological outcomes. Finally, I will explore the implication of transcriptional complexity for our understanding of gene expression in the context of cell-to-cell phenotypic variability. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, P-Box 1031, 171 21, Solna, Sweden
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14
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Huang CW, Walker ME, Fedrizzi B, Gardner RC, Jiranek V. Yeast genes involved in regulating cysteine uptake affect production of hydrogen sulfide from cysteine during fermentation. FEMS Yeast Res 2017; 17:3934655. [PMID: 28810701 DOI: 10.1093/femsyr/fox046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 07/04/2017] [Indexed: 11/13/2022] Open
Abstract
An early burst of hydrogen sulfide (H2S) produced by Saccharomyces cerevisiae during fermentation could increase varietal thiols and therefore enhance desirable tropical aromas in varieties such as Sauvignon Blanc. Here we attempted to identify genes affecting H2S formation from cysteine by screening yeast deletion libraries via a colony colour assay on media resembling grape juice. Both Δlst4 and Δlst7 formed lighter coloured colonies and produced significantly less H2S than the wild type on high concentrations of cysteine, likely because they are unable to take up cysteine efficiently. We then examined the nine known cysteine permeases and found that deletion of AGP1, GNP1 and MUP1 led to reduced production of H2S from cysteine. We further showed that deleting genes involved in the SPS-sensing pathway such as STP1 and DAL81 also reduced H2S from cysteine. Together, this study indirectly confirms that Agp1p, Gnp1p and Mup1p are the major cysteine permeases and that they are regulated by the SPS-sensing and target of rapamycin pathways under the grape juice-like, cysteine-supplemented, fermentation conditions. The findings highlight that cysteine transportation could be a limiting factor for yeast to generate H2S from cysteine, and therefore selecting wine yeasts without defects in cysteine uptake could maximise thiol production potential.
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Affiliation(s)
- Chien-Wei Huang
- Department of Wine and Food Science, University of Adelaide, Adelaide, SA 5064, Australia
| | - Michelle E Walker
- Department of Wine and Food Science, University of Adelaide, Adelaide, SA 5064, Australia
| | - Bruno Fedrizzi
- Wine Science Programme, School of Chemical Sciences, University of Auckland, Auckland 1142, New Zealand
| | - Richard C Gardner
- Wine Science Programme, School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand
| | - Vladimir Jiranek
- Department of Wine and Food Science, University of Adelaide, Adelaide, SA 5064, Australia
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15
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Maxwell CS, Magwene PM. The quick and the dead: microbial demography at the yeast thermal limit. Mol Ecol 2017; 26:1631-1640. [DOI: 10.1111/mec.13955] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 10/25/2016] [Accepted: 11/21/2016] [Indexed: 12/27/2022]
Affiliation(s)
- Colin S. Maxwell
- Department of Biology Duke University Box 90338 Durham NC 27708 USA
| | - Paul M. Magwene
- Department of Biology Duke University Box 90338 Durham NC 27708 USA
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16
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Batch effects and the effective design of single-cell gene expression studies. Sci Rep 2017; 7:39921. [PMID: 28045081 PMCID: PMC5206706 DOI: 10.1038/srep39921] [Citation(s) in RCA: 192] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 11/29/2016] [Indexed: 01/20/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) can be used to characterize variation in gene expression levels at high resolution. However, the sources of experimental noise in scRNA-seq are not yet well understood. We investigated the technical variation associated with sample processing using the single-cell Fluidigm C1 platform. To do so, we processed three C1 replicates from three human induced pluripotent stem cell (iPSC) lines. We added unique molecular identifiers (UMIs) to all samples, to account for amplification bias. We found that the major source of variation in the gene expression data was driven by genotype, but we also observed substantial variation between the technical replicates. We observed that the conversion of reads to molecules using the UMIs was impacted by both biological and technical variation, indicating that UMI counts are not an unbiased estimator of gene expression levels. Based on our results, we suggest a framework for effective scRNA-seq studies.
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17
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Thompson DA, Cubillos FA. Natural gene expression variation studies in yeast. Yeast 2016; 34:3-17. [PMID: 27668700 DOI: 10.1002/yea.3210] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 09/16/2016] [Accepted: 09/18/2016] [Indexed: 11/06/2022] Open
Abstract
The rise of sequence information across different yeast species and strains is driving an increasing number of studies in the emerging field of genomics to associate polymorphic variants, mRNA abundance and phenotypic differences between individuals. Here, we gathered evidence from recent studies covering several layers that define the genotype-phenotype gap, such as mRNA abundance, allele-specific expression and translation efficiency to demonstrate how genetic variants co-evolve and define an individual's genome. Moreover, we exposed several antecedents where inter- and intra-specific studies led to opposite conclusions, probably owing to genetic divergence. Future studies in this area will benefit from the access to a massive array of well-annotated genomes and new sequencing technologies, which will allow the fine breakdown of the complex layers that delineate the genotype-phenotype map. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
| | - Francisco A Cubillos
- Centro de Estudios en Ciencia y Tecnología de Alimentos, Universidad de Santiago de Chile, Santiago, Chile.,Millennium Nucleus for Fungal Integrative and Synthetic Biology.,Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
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18
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Exploiting Single-Cell Quantitative Data to Map Genetic Variants Having Probabilistic Effects. PLoS Genet 2016; 12:e1006213. [PMID: 27479122 PMCID: PMC4968810 DOI: 10.1371/journal.pgen.1006213] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 07/02/2016] [Indexed: 01/11/2023] Open
Abstract
Despite the recent progress in sequencing technologies, genome-wide association studies (GWAS) remain limited by a statistical-power issue: many polymorphisms contribute little to common trait variation and therefore escape detection. The small contribution sometimes corresponds to incomplete penetrance, which may result from probabilistic effects on molecular regulations. In such cases, genetic mapping may benefit from the wealth of data produced by single-cell technologies. We present here the development of a novel genetic mapping method that allows to scan genomes for single-cell Probabilistic Trait Loci that modify the statistical properties of cellular-level quantitative traits. Phenotypic values are acquired on thousands of individual cells, and genetic association is obtained from a multivariate analysis of a matrix of Kantorovich distances. No prior assumption is required on the mode of action of the genetic loci involved and, by exploiting all single-cell values, the method can reveal non-deterministic effects. Using both simulations and yeast experimental datasets, we show that it can detect linkages that are missed by classical genetic mapping. A probabilistic effect of a single SNP on cell shape was detected and validated. The method also detected a novel locus associated with elevated gene expression noise of the yeast galactose regulon. Our results illustrate how single-cell technologies can be exploited to improve the genetic dissection of certain common traits. The method is available as an open source R package called ptlmapper.
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19
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Liu J, François JM, Capp JP. Use of noise in gene expression as an experimental parameter to test phenotypic effects. Yeast 2016; 33:209-16. [DOI: 10.1002/yea.3152] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 01/12/2016] [Accepted: 01/14/2016] [Indexed: 01/12/2023] Open
Affiliation(s)
- Jian Liu
- INSA/Université Fédérale Toulouse Midi-Pyrénées; Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés; UMR CNRS 5504 UMR INRA 792 Toulouse France
| | - Jean-Marie François
- INSA/Université Fédérale Toulouse Midi-Pyrénées; Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés; UMR CNRS 5504 UMR INRA 792 Toulouse France
| | - Jean-Pascal Capp
- INSA/Université Fédérale Toulouse Midi-Pyrénées; Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés; UMR CNRS 5504 UMR INRA 792 Toulouse France
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20
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Mestek Boukhibar L, Barkoulas M. The developmental genetics of biological robustness. ANNALS OF BOTANY 2016; 117:699-707. [PMID: 26292993 PMCID: PMC4845795 DOI: 10.1093/aob/mcv128] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 05/07/2015] [Accepted: 06/29/2015] [Indexed: 05/10/2023]
Abstract
BACKGROUND Living organisms are continuously confronted with perturbations, such as environmental changes that include fluctuations in temperature and nutrient availability, or genetic changes such as mutations. While some developmental systems are affected by such challenges and display variation in phenotypic traits, others continue consistently to produce invariable phenotypes despite perturbation. This ability of a living system to maintain an invariable phenotype in the face of perturbations is termed developmental robustness. Biological robustness is a phenomenon observed across phyla, and studying its mechanisms is central to deciphering the genotype-phenotype relationship. Recent work in yeast, animals and plants has shown that robustness is genetically controlled and has started to reveal the underlying mechinisms behind it. SCOPE AND CONCLUSIONS Studying biological robustness involves focusing on an important property of developmental traits, which is the phenotypic distribution within a population. This is often neglected because the vast majority of developmental biology studies instead focus on population aggregates, such as trait averages. By drawing on findings in animals and yeast, this Viewpoint considers how studies on plant developmental robustness may benefit from strict definitions of what is the developmental system of choice and what is the relevant perturbation, and also from clear distinctions between gene effects on the trait mean and the trait variance. Recent advances in quantitative developmental biology and high-throughput phenotyping now allow the design of targeted genetic screens to identify genes that amplify or restrict developmental trait variance and to study how variation propagates across different phenotypic levels in biological systems. The molecular characterization of more quantitative trait loci affecting trait variance will provide further insights into the evolution of genes modulating developmental robustness. The study of robustness mechanisms in closely related species will address whether mechanisms of robustness are evolutionarily conserved.
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Affiliation(s)
- Lamia Mestek Boukhibar
- Imperial College London, Department of Life Sciences, Sir Alexander Fleming Building, South Kensington Campus, London SW7 2AZ, UK
| | - Michalis Barkoulas
- Imperial College London, Department of Life Sciences, Sir Alexander Fleming Building, South Kensington Campus, London SW7 2AZ, UK
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21
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22
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23
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Liu J, Martin-Yken H, Bigey F, Dequin S, François JM, Capp JP. Natural yeast promoter variants reveal epistasis in the generation of transcriptional-mediated noise and its potential benefit in stressful conditions. Genome Biol Evol 2015; 7:969-84. [PMID: 25762217 PMCID: PMC4419794 DOI: 10.1093/gbe/evv047] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The increase in phenotypic variability through gene expression noise is proposed to be an evolutionary strategy in selective environments. Differences in promoter-mediated noise between Saccharomyces cerevisiae strains could have been selected for thanks to the benefit conferred by gene expression heterogeneity in the stressful conditions, for instance, those experienced by industrial strains. Here, we used a genome-wide approach to identify promoters conferring high noise levels in the industrial wine strain EC1118. Many promoters of genes related to environmental factors were identified, some of them containing genetic variations compared with their counterpart in the laboratory strain S288c. Each variant of eight promoters has been fused to yeast-Enhanced Green Fluorescent Protein and integrated in the genome of both strains. Some industrial variants conferred higher expression associated, as expected, with lower noise, but other variants either increased or decreased expression without modifying variability, so that they might exhibit different levels of transcriptional-mediated noise at equal mean. At different induction conditions giving similar expression for both variants of the CUP1 promoter, we indeed observed higher noise with the industrial variant. Nevertheless, this difference was only observed in the industrial strain, revealing epistasis in the generation of promoter-mediated noise. Moreover, the increased expression variability conferred by this natural yeast promoter variant provided a clear benefit in the face of an environmental stress. Thus, modulation of gene expression noise by a combination of promoter modifications and trans-influences might be a possible adaptation mechanism in yeast.
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Affiliation(s)
- Jian Liu
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, UMR CNRS 5504, UMR INRA 792, INSA/Université de Toulouse, France
| | - Hélène Martin-Yken
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, UMR CNRS 5504, UMR INRA 792, INSA/Université de Toulouse, France
| | - Frédéric Bigey
- INRA, UMR 1083 Sciences Pour l'Œnologie, Montpellier, France
| | - Sylvie Dequin
- INRA, UMR 1083 Sciences Pour l'Œnologie, Montpellier, France
| | - Jean-Marie François
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, UMR CNRS 5504, UMR INRA 792, INSA/Université de Toulouse, France
| | - Jean-Pascal Capp
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, UMR CNRS 5504, UMR INRA 792, INSA/Université de Toulouse, France
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24
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Abstract
Part of molecular and phenotypic differences between individual cells, between body parts, or between individuals can result from biological noise. This source of variation is becoming more and more apparent thanks to the recent advances in dynamic imaging and single-cell analysis. Some of these studies showed that the link between genotype and phenotype is not strictly deterministic. Mutations can change various statistical properties of a biochemical reaction, and thereby the probability of a trait outcome. The fact that they can modulate phenotypic noise brings up an intriguing question: how may selection act on these mutations? In this review, we approach this question by first covering the evidence that biological noise is under genetic control and therefore a substrate for evolution. We then sequentially inspect the possibilities of negative, neutral, and positive selection for mutations increasing biological noise. Finally, we hypothesize on the specific case of H2A.Z, which was shown to both buffer phenotypic noise and modulate transcriptional efficiency.
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Affiliation(s)
- Magali Richard
- Laboratoire de Biologie Moléculaire de la Cellule, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique - Université de Lyon Lyon, France
| | - Gaël Yvert
- Laboratoire de Biologie Moléculaire de la Cellule, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique - Université de Lyon Lyon, France
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25
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Romagnoli G, Knijnenburg TA, Liti G, Louis EJ, Pronk JT, Daran JM. Deletion of theSaccharomyces cerevisiae ARO8gene, encoding an aromatic amino acid transaminase, enhances phenylethanol production from glucose. Yeast 2014; 32:29-45. [DOI: 10.1002/yea.3015] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 03/18/2014] [Accepted: 04/04/2014] [Indexed: 11/11/2022] Open
Affiliation(s)
- Gabriele Romagnoli
- Department of Biotechnology; Delft University of Technology; Delft The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation; Delft The Netherlands
| | | | - Gianni Liti
- Centre for Genetics and Genomics, Queens Medical Centre; University of Nottingham; UK
- Institute for Research on Cancer and Ageing; CNRS UMR 7284-INSERM U 1081- UNS NICE; Nice France
| | - Edward J. Louis
- Centre for Genetics and Genomics, Queens Medical Centre; University of Nottingham; UK
- Centre for Genetic Architecture of Complex Traits, Department of Genetics; University of Leicester; UK
| | - Jack T. Pronk
- Department of Biotechnology; Delft University of Technology; Delft The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation; Delft The Netherlands
- Platform Green Synthetic Biology; Delft The Netherlands
| | - Jean-Marc Daran
- Department of Biotechnology; Delft University of Technology; Delft The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation; Delft The Netherlands
- Platform Green Synthetic Biology; Delft The Netherlands
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26
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Simons AM. Playing smart vs. playing safe: the joint expression of phenotypic plasticity and potential bet hedging across and within thermal environments. J Evol Biol 2014; 27:1047-56. [DOI: 10.1111/jeb.12378] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 03/17/2014] [Accepted: 03/18/2014] [Indexed: 11/28/2022]
Affiliation(s)
- A. M. Simons
- Department of Biology; Carleton University; Ottawa ON Canada
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27
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Pancaldi V. Biological noise to get a sense of direction: an analogy between chemotaxis and stress response. Front Genet 2014; 5:52. [PMID: 24659996 PMCID: PMC3952082 DOI: 10.3389/fgene.2014.00052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Accepted: 02/21/2014] [Indexed: 11/13/2022] Open
Affiliation(s)
- Vera Pancaldi
- Structural Computational Biology, Spanish National Cancer Research Centre (CNIO) Madrid, Spain
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28
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Papakostas S, Vasemägi A, Himberg M, Primmer CR. Proteome variance differences within populations of European whitefish (Coregonus lavaretus) originating from contrasting salinity environments. J Proteomics 2014; 105:144-50. [PMID: 24406297 DOI: 10.1016/j.jprot.2013.12.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 12/22/2013] [Indexed: 01/09/2023]
Abstract
UNLABELLED Variation in gene expression is an important component of the phenotypic differences observed in nature. Gene expression variance across biological groups and environmental conditions has been studied extensively and has revealed specific genes and molecular mechanisms of interest. However, little is known regarding the importance of within-population gene expression variation to environmental adaptation. To address this issue, we quantified the proteomes of individuals of European whitefish (Coregonus lavaretus) from populations that have previously been shown to have adapted during early development to freshwater and brackishwater salinity environments. Using MS-based label-free proteomics, we studied 955 proteins in eight hatch-stage fish embryos from each population that had been reared in either freshwater or brackishwater salinity conditions. By comparing the levels of within-population protein expression variance over individuals and per protein between populations, we found that fish embryos from the population less affected by salinity level had also markedly higher levels of expression variance. Gene Ontologies and molecular pathways associated with osmoregulation showed the most significant difference of within-population proteome variance between populations. Several new candidate genes for salinity adaptation were identified, emphasising the added value of combining assessments of within-population gene expression variation with standard gene expression analysis practices for better understanding the mechanisms of environmental adaptation. BIOLOGICAL SIGNIFICANCE We demonstrate the benefits of studying within-population gene expression variance together with more typical methods of gene expression profiling. Proteome variance differences within European whitefish populations originating from different salinity environments allowed us to identify several new candidate genes for salinity adaptation in teleost fish and generate many further hypotheses to be tested. This article is part of a Special Issue entitled: Proteomics of non-model organisms.
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Affiliation(s)
- Spiros Papakostas
- Division of Genetics and Physiology, Department of Biology, University of Turku, 20014, Turku, Finland
| | - Anti Vasemägi
- Division of Genetics and Physiology, Department of Biology, University of Turku, 20014, Turku, Finland; Department of Aquaculture, Institute of Veterinary Medicine and Animal Science, Estonian University of Life Sciences, 51014 Tartu, Estonia
| | - Mikael Himberg
- Laboratory of Aquatic Pathobiology, Åbo Academy University, 20520, Turku, Finland
| | - Craig R Primmer
- Division of Genetics and Physiology, Department of Biology, University of Turku, 20014, Turku, Finland.
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29
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Yvert G. 'Particle genetics': treating every cell as unique. Trends Genet 2013; 30:49-56. [PMID: 24315431 DOI: 10.1016/j.tig.2013.11.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 11/06/2013] [Accepted: 11/13/2013] [Indexed: 12/18/2022]
Abstract
Genotype-phenotype relations are usually inferred from a deterministic point of view. For example, quantitative trait loci (QTL), which describe regions of the genome associated with a particular phenotype, are based on a mean trait difference between genotype categories. However, living systems comprise huge numbers of cells (the 'particles' of biology). Each cell can exhibit substantial phenotypic individuality, which can have dramatic consequences at the organismal level. Now, with technology capable of interrogating individual cells, it is time to consider how genotypes shape the probability laws of single cell traits. The possibility of mapping single cell probabilistic trait loci (PTL), which link genomic regions to probabilities of cellular traits, is a promising step in this direction. This approach requires thinking about phenotypes in probabilistic terms, a concept that statistical physicists have been applying to particles for a century. Here, I describe PTL and discuss their potential to enlarge our understanding of genotype-phenotype relations.
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Affiliation(s)
- Gaël Yvert
- Laboratoire de Biologie Moléculaire de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, Université de Lyon, Lyon, France.
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