101
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Hibbins MS, Hahn MW. The effects of introgression across thousands of quantitative traits revealed by gene expression in wild tomatoes. PLoS Genet 2021; 17:e1009892. [PMID: 34748547 PMCID: PMC8601620 DOI: 10.1371/journal.pgen.1009892] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 11/18/2021] [Accepted: 10/18/2021] [Indexed: 01/13/2023] Open
Abstract
It is now understood that introgression can serve as powerful evolutionary force, providing genetic variation that can shape the course of trait evolution. Introgression also induces a shared evolutionary history that is not captured by the species phylogeny, potentially complicating evolutionary analyses that use a species tree. Such analyses are often carried out on gene expression data across species, where the measurement of thousands of trait values allows for powerful inferences while controlling for shared phylogeny. Here, we present a Brownian motion model for quantitative trait evolution under the multispecies network coalescent framework, demonstrating that introgression can generate apparently convergent patterns of evolution when averaged across thousands of quantitative traits. We test our theoretical predictions using whole-transcriptome expression data from ovules in the wild tomato genus Solanum. Examining two sub-clades that both have evidence for post-speciation introgression, but that differ substantially in its magnitude, we find patterns of evolution that are consistent with histories of introgression in both the sign and magnitude of ovule gene expression. Additionally, in the sub-clade with a higher rate of introgression, we observe a correlation between local gene tree topology and expression similarity, implicating a role for introgressed cis-regulatory variation in generating these broad-scale patterns. Our results reveal a general role for introgression in shaping patterns of variation across many thousands of quantitative traits, and provide a framework for testing for these effects using simple model-informed predictions. It is now known from studying large genetic datasets that species often hybridize and cross with each other over many generations – a phenomenon known as introgression. Introgression introduces new genetic variation into a population, and this variation can cause traits to be shared among the introgressing species. When researchers study the evolution of trait variation among species, this source of trait sharing is rarely accounted for. Here, we present a statistical model of the effects of introgression on trait variation. This model predicts that, when averaged across many thousands of traits, introgressing species are consistently more similar than expected from standard approaches. Researchers studying gene expression often consider the expression of many thousands of genes, making this a case where the expected effects of introgression are likely to manifest. We tested our model prediction using ovule gene expression data from the wild tomato genus Solanum, in two groups of species with evidence of historical introgression. We found that patterns of expression similarity in both groups are consistent with their histories of introgression and the predictions from our model. Our results highlight the importance of accounting for introgression as a source of trait variation among species.
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Affiliation(s)
- Mark S. Hibbins
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
- * E-mail:
| | - Matthew W. Hahn
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
- Department of Computer Science, Indiana University, Bloomington, Indiana, United States of America
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102
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Ding Y, Li Y, Zhao Z, Cliff Zhang Q, Liu F. The chromatin-remodeling enzyme Smarca5 regulates erythrocyte aggregation via Keap1-Nrf2 signaling. eLife 2021; 10:72557. [PMID: 34698638 PMCID: PMC8594921 DOI: 10.7554/elife.72557] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/23/2021] [Indexed: 12/30/2022] Open
Abstract
Although thrombosis has been extensively studied using various animal models, our understanding of the underlying mechanism remains elusive. Here, using zebrafish model, we demonstrated that smarca5-deficient red blood cells (RBCs) formed blood clots in the caudal vein plexus. We further used the anti-thrombosis drugs to treat smarca5zko1049a embryos and found that a thrombin inhibitor, argatroban, partially prevented blood clot formation in smarca5zko1049a. To explore the regulatory mechanism of smarca5 in RBC homeostasis, we profiled the chromatin accessibility landscape and transcriptome features in RBCs from smarca5zko1049a and their siblings and found that both the chromatin accessibility at the keap1a promoter and expression of keap1a were decreased. Keap1 is a suppressor protein of Nrf2, which is a major regulator of oxidative responses. We further identified that the expression of hmox1a, a downstream target of Keap1-Nrf2 signaling pathway, was markedly increased upon smarca5 deletion. Importantly, overexpression of keap1a or knockdown of hmox1a partially rescued the blood clot formation, suggesting that the disrupted Keap1-Nrf2 signaling is responsible for the RBC aggregation in smarca5 mutants. Together, our study using zebrafish smarca5 mutants characterizes a novel role for smarca5 in RBC aggregation, which may provide a new venous thrombosis animal model to support drug screening and pre-clinical therapeutic assessments to treat thrombosis.
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Affiliation(s)
- Yanyan Ding
- The Max-Planck Center for Tissue Stem Cell Research and Regenerative Medicine, Bioland Laboratory, Guangzhou, China.,State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yuzhe Li
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China.,Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Ziqian Zhao
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Qiangfeng Cliff Zhang
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China.,Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Feng Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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103
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Affiliation(s)
- Daniel G Bichet
- From the Departments of Medicine, Pharmacology, and Physiology, Université de Montréal, and Nephrology Service, Hôpital du Sacré-Cœur de Montréal - both in Montreal
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104
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Patel V, Matange N. Adaptation and compensation in a bacterial gene regulatory network evolving under antibiotic selection. eLife 2021; 10:70931. [PMID: 34591012 PMCID: PMC8483737 DOI: 10.7554/elife.70931] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 09/22/2021] [Indexed: 12/28/2022] Open
Abstract
Gene regulatory networks allow organisms to generate coordinated responses to environmental challenges. In bacteria, regulatory networks are re-wired and re-purposed during evolution, though the relationship between selection pressures and evolutionary change is poorly understood. In this study, we discover that the early evolutionary response of Escherichia coli to the antibiotic trimethoprim involves derepression of PhoPQ signaling, an Mg2+-sensitive two-component system, by inactivation of the MgrB feedback-regulatory protein. We report that derepression of PhoPQ confers trimethoprim-tolerance to E. coli by hitherto unrecognized transcriptional upregulation of dihydrofolate reductase (DHFR), target of trimethoprim. As a result, mutations in mgrB precede and facilitate the evolution of drug resistance. Using laboratory evolution, genome sequencing, and mutation re-construction, we show that populations of E. coli challenged with trimethoprim are faced with the evolutionary ‘choice’ of transitioning from tolerant to resistant by mutations in DHFR, or compensating for the fitness costs of PhoPQ derepression by inactivating the RpoS sigma factor, itself a PhoPQ-target. Outcomes at this evolutionary branch-point are determined by the strength of antibiotic selection, such that high pressures favor resistance, while low pressures favor cost compensation. Our results relate evolutionary changes in bacterial gene regulatory networks to strength of selection and provide mechanistic evidence to substantiate this link.
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Affiliation(s)
- Vishwa Patel
- Dr. Vikram Sarabhai Institute of Cell and Molecular Biology, The Maharaja Sayajirao University of Baroda, Vadodara, India.,Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Nishad Matange
- Indian Institute of Science Education and Research (IISER), Pune, India
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105
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Salisbury SJ, Delgado ML, Dalziel AC. Alternative splicing: An overlooked mechanism contributing to local adaptation? Mol Ecol 2021; 30:4951-4954. [PMID: 34533856 DOI: 10.1111/mec.16177] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 09/02/2021] [Indexed: 11/27/2022]
Abstract
Identifying the molecular mechanisms contributing to phenotypic variation in natural populations is a major goal of molecular ecology. However, the multiple regulatory steps between genotype and phenotype mean that many potential mechanisms can lead to trait divergence. To date, the role of transcriptional regulation in local adaptation has received much focus, as we can readily measure mRNA quantity and have a reasonable grasp of how variation in the expression of many protein-coding genes can influence phenotype. Thus, studying the evolution of protein-coding gene mRNA abundance in candidate tissues has led to successes in detecting the molecular mechanisms underlying local adaptation (reviewed by Hill et al., 2021). However, the contribution of differential splicing of precursor mRNA (pre-mRNA) to adaptive differentiation, as well as the loci controlling this variation, remains largely unexplored in wild populations. In their "From the Cover'" article in this issue of Molecular Ecology, Jacobs and Elmer (2021) reanalyse muscle RNA sequencing (RNA-seq) data to quantify the relative contributions of variation in mRNA quantity (differentially expressed "DE" genes) and splice variant identity (differentially spliced "DS" genes) to parallel divergence of wild "benthic" and "pelagic" ecotypes of a salmonid fish, the Arctic charr (Salvelinus alpinus). They found little overlap in the identity and biological functions of DE and DS genes, suggesting that these two regulatory mechanisms act on different cellular traits to complementarily alter organismal phenotype. Furthermore, many DE and DS genes could be mapped to cis-acting QTL, arguing that some of this regulatory divergence is genetically based. DE and DS genes were also more likely to be "hub genes" than their nondivergent counterparts, hinting that this regulatory variation may have a variety of phenotypic effects. The comparison of three independently evolved pairs of benthic and pelagic charr uncovered greater than expected parallelism in both expression and splicing between ecotypes across different lakes, supporting a role for these molecular phenotypes in adaptive divergence. Overall, the findings of Jacobs and Elmer (2021) highlight the importance of alternative splicing as a potential mechanism underlying local adaptation and provide a framework for others hoping to make the most of their RNA-seq data.
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Affiliation(s)
| | | | - Anne C Dalziel
- Department of Biology, Saint Mary's University, Halifax, Nova Scotia, Canada
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106
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Duveau F, Vande Zande P, Metzger BP, Diaz CJ, Walker EA, Tryban S, Siddiq MA, Yang B, Wittkopp PJ. Mutational sources of trans-regulatory variation affecting gene expression in Saccharomyces cerevisiae. eLife 2021; 10:67806. [PMID: 34463616 PMCID: PMC8456550 DOI: 10.7554/elife.67806] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 08/03/2021] [Indexed: 12/15/2022] Open
Abstract
Heritable variation in a gene’s expression arises from mutations impacting cis- and trans-acting components of its regulatory network. Here, we investigate how trans-regulatory mutations are distributed within the genome and within a gene regulatory network by identifying and characterizing 69 mutations with trans-regulatory effects on expression of the same focal gene in Saccharomyces cerevisiae. Relative to 1766 mutations without effects on expression of this focal gene, we found that these trans-regulatory mutations were enriched in coding sequences of transcription factors previously predicted to regulate expression of the focal gene. However, over 90% of the trans-regulatory mutations identified mapped to other types of genes involved in diverse biological processes including chromatin state, metabolism, and signal transduction. These data show how genetic changes in diverse types of genes can impact a gene’s expression in trans, revealing properties of trans-regulatory mutations that provide the raw material for trans-regulatory variation segregating within natural populations.
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Affiliation(s)
- Fabien Duveau
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, United States.,Laboratory of Biology and Modeling of the Cell, Ecole Normale Supérieure de Lyon, CNRS, Université Claude Bernard Lyon, Université de Lyon, Lyon, France
| | - Petra Vande Zande
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, United States
| | - Brian Ph Metzger
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, United States
| | - Crisandra J Diaz
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, United States
| | - Elizabeth A Walker
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, United States
| | - Stephen Tryban
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, United States
| | - Mohammad A Siddiq
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, United States
| | - Bing Yang
- Department of Molecular, Cellular, and Developmental 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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107
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Abstract
Saccharomyces cerevisiae rewires its transcriptional output to survive stressful environments, such as nitrogen scarcity under fermentative conditions. Although divergence in nitrogen metabolism among natural yeast populations has been reported, the impact of regulatory genetic variants modulating gene expression and nitrogen consumption remains to be investigated. Here, we employed an F1 hybrid from two contrasting S. cerevisiae strains, providing a controlled genetic environment to map cis factors involved in the divergence of gene expression regulation in response to nitrogen scarcity. We used a dual approach to obtain genome-wide allele-specific profiles of chromatin accessibility, transcription factor binding, and gene expression through ATAC-seq (assay for transposase accessible chromatin) and RNA-seq (transcriptome sequencing). We observed large variability in allele-specific expression and accessibility between the two genetic backgrounds, with a third of these differences specific to a deficient nitrogen environment. Furthermore, we discovered events of allelic bias in gene expression correlating with allelic bias in transcription factor binding solely under nitrogen scarcity, where the majority of these transcription factors orchestrates the nitrogen catabolite repression regulatory pathway and demonstrates a cis × environment-specific response. Our approach allowed us to find cis variants modulating gene expression, chromatin accessibility, and allelic differences in transcription factor binding in response to low nitrogen culture conditions. IMPORTANCE Historically, coding variants were prioritized when searching for causal mechanisms driving adaptation of natural populations to stressful environments. However, the recent focus on noncoding variants demonstrated their ubiquitous role in adaptation. Here, we performed genome-wide regulatory variation profiles between two divergent yeast strains when facing nitrogen nutritional stress. The open chromatin availability of several regulatory regions changes in response to nitrogen scarcity. Importantly, we describe regulatory events that deviate between strains. Our results demonstrate a widespread variation in gene expression regulation between naturally occurring populations in response to stressful environments.
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108
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Shih CH, Fay J. Cis-regulatory variants affect gene expression dynamics in yeast. eLife 2021; 10:e68469. [PMID: 34369376 PMCID: PMC8367379 DOI: 10.7554/elife.68469] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 08/06/2021] [Indexed: 12/14/2022] Open
Abstract
Evolution of cis-regulatory sequences depends on how they affect gene expression and motivates both the identification and prediction of cis-regulatory variants responsible for expression differences within and between species. While much progress has been made in relating cis-regulatory variants to expression levels, the timing of gene activation and repression may also be important to the evolution of cis-regulatory sequences. We investigated allele-specific expression (ASE) dynamics within and between Saccharomyces species during the diauxic shift and found appreciable cis-acting variation in gene expression dynamics. Within-species ASE is associated with intergenic variants, and ASE dynamics are more strongly associated with insertions and deletions than ASE levels. To refine these associations, we used a high-throughput reporter assay to test promoter regions and individual variants. Within the subset of regions that recapitulated endogenous expression, we identified and characterized cis-regulatory variants that affect expression dynamics. Between species, chimeric promoter regions generate novel patterns and indicate constraints on the evolution of gene expression dynamics. We conclude that changes in cis-regulatory sequences can tune gene expression dynamics and that the interplay between expression dynamics and other aspects of expression is relevant to the evolution of cis-regulatory sequences.
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Affiliation(s)
- Ching-Hua Shih
- Department of Biology, University of RochesterRochesterUnited States
| | - Justin Fay
- Department of Biology, University of RochesterRochesterUnited States
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109
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Glaser-Schmitt A, Wittmann MJ, Ramnarine TJS, Parsch J. Sexual antagonism, temporally fluctuating selection, and variable dominance affect a regulatory polymorphism in Drosophila melanogaster. Mol Biol Evol 2021; 38:4891-4907. [PMID: 34289067 PMCID: PMC8557461 DOI: 10.1093/molbev/msab215] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Understanding how genetic variation is maintained within species is a major goal of evolutionary genetics that can shed light on the preservation of biodiversity. Here, we examined the maintenance of a regulatory single-nucleotide polymorphism (SNP) of the X-linked Drosophila melanogaster gene fezzik. The derived variant at this site is at intermediate frequency in many worldwide populations but absent in populations from the ancestral species range in sub-Saharan Africa. We collected and genotyped wild-caught individuals from a single European population biannually over a period of 5 years, which revealed an overall difference in allele frequency between the sexes and a consistent change in allele frequency across seasons in females but not in males. Modeling based on the observed allele and genotype frequencies suggested that both sexually antagonistic and temporally fluctuating selection may help maintain variation at this site. The derived variant is predicted to be female-beneficial and mostly recessive; however, there was uncertainty surrounding our dominance estimates and long-term modeling projections suggest that it is more likely to be dominant. By examining gene expression phenotypes, we found that phenotypic dominance was variable and dependent upon developmental stage and genetic background, suggesting that dominance may be variable at this locus. We further determined that fezzik expression and genotype are associated with starvation resistance in a sex-dependent manner, suggesting a potential phenotypic target of selection. By characterizing the mechanisms of selection acting on this SNP, our results improve our understanding of how selection maintains genetic and phenotypic variation in natural populations.
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Affiliation(s)
- Amanda Glaser-Schmitt
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | | | - Timothy J S Ramnarine
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - John Parsch
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
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110
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Surm JM, Moran Y. Transposons Increase Transcriptional Complexity: The Good Parasite? Trends Genet 2021; 37:606-607. [PMID: 33858672 DOI: 10.1016/j.tig.2021.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 10/21/2022]
Abstract
A recent study by Cosby et al. sheds light on the role of transposons in the adaptive evolution of their hosts. These genetic elements were thought to be largely deleterious. However, when coupled with alternative splicing, there appears to be an exponential increase in the diversity of proteins encoded, which display novel functions and are conserved by natural selection.
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Affiliation(s)
- Joachim M Surm
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel.
| | - Yehu Moran
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel.
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111
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Lupo O, Krieger G, Jonas F, Barkai N. Accumulation of cis- and trans-regulatory variations is associated with phenotypic divergence of a complex trait between yeast species. G3-GENES GENOMES GENETICS 2021; 11:6121923. [PMID: 33609368 PMCID: PMC8022985 DOI: 10.1093/g3journal/jkab016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 01/07/2021] [Indexed: 11/15/2022]
Abstract
Gene regulatory variations accumulate during evolution and alter gene expression. While the importance of expression variation in phenotypic evolution is well established, the molecular basis remains largely unknown. Here, we examine two closely related yeast species, Saccharomyces cerevisiae and Saccharomyces paradoxus, which show phenotypical differences in morphology and cell cycle progression when grown in the same environment. By profiling the cell cycle transcriptome and binding of key transcription factors (TFs) in the two species and their hybrid, we show that changes in expression levels and dynamics of oscillating genes are dominated by upstream trans-variations. We find that multiple cell cycle regulators show both cis- and trans-regulatory variations, which alters their expression in favor of the different cell cycle phenotypes. Moreover, we show that variations in the cell cycle TFs, Fkh1, and Fkh2 affect both the expression of target genes, and the binding specificity of an interacting TF, Ace2. Our study reveals how multiple variations accumulate and propagate through the gene regulatory network, alter TFs binding, contributing to phenotypic changes in cell cycle progression.
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Affiliation(s)
- Offir Lupo
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Gat Krieger
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.,Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Felix Jonas
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Naama Barkai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
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