1
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Verd B, Monk NAM, Jaeger J. Modularity, criticality, and evolvability of a developmental gene regulatory network. eLife 2019; 8:e42832. [PMID: 31169494 PMCID: PMC6645726 DOI: 10.7554/elife.42832] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 06/05/2019] [Indexed: 01/16/2023] Open
Abstract
The existence of discrete phenotypic traits suggests that the complex regulatory processes which produce them are functionally modular. These processes are usually represented by networks. Only modular networks can be partitioned into intelligible subcircuits able to evolve relatively independently. Traditionally, functional modularity is approximated by detection of modularity in network structure. However, the correlation between structure and function is loose. Many regulatory networks exhibit modular behaviour without structural modularity. Here we partition an experimentally tractable regulatory network-the gap gene system of dipteran insects-using an alternative approach. We show that this system, although not structurally modular, is composed of dynamical modules driving different aspects of whole-network behaviour. All these subcircuits share the same regulatory structure, but differ in components and sensitivity to regulatory interactions. Some subcircuits are in a state of criticality, while others are not, which explains the observed differential evolvability of the various expression features in the system.
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Affiliation(s)
- Berta Verd
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
- Universitat Pompeu Fabra (UPF)BarcelonaSpain
- Konrad Lorenz Institute for Evolution and Cognition Research (KLI)KlosterneuburgAustria
- Department of GeneticsUniversity of CambridgeCambridgeUnited Kingdom
| | - Nicholas AM Monk
- School of Mathematics and StatisticsUniversity of SheffieldSheffieldUnited States
| | - Johannes Jaeger
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
- Universitat Pompeu Fabra (UPF)BarcelonaSpain
- Konrad Lorenz Institute for Evolution and Cognition Research (KLI)KlosterneuburgAustria
- School of Mathematics and StatisticsUniversity of SheffieldSheffieldUnited States
- Wissenschaftskolleg zu BerlinBerlinGermany
- Center for Systems Biology Dresden (CSBD)DresdenGermany
- Complexity Science Hub (CSH)ViennaAustria
- Centre de Recherches Interdisciplinaires (CRI)ParisFrance
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2
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Buffry AD, Mendes CC, McGregor AP. The Functionality and Evolution of Eukaryotic Transcriptional Enhancers. ADVANCES IN GENETICS 2016; 96:143-206. [PMID: 27968730 DOI: 10.1016/bs.adgen.2016.08.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Enhancers regulate precise spatial and temporal patterns of gene expression in eukaryotes and, moreover, evolutionary changes in these modular cis-regulatory elements may represent the predominant genetic basis for phenotypic evolution. Here, we review approaches to identify and functionally analyze enhancers and their transcription factor binding sites, including assay for transposable-accessible chromatin-sequencing (ATAC-Seq) and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9, respectively. We also explore enhancer functionality, including how transcription factor binding sites combine to regulate transcription, as well as research on shadow and super enhancers, and how enhancers can act over great distances and even in trans. Finally, we discuss recent theoretical and empirical data on how transcription factor binding sites and enhancers evolve. This includes how the function of enhancers is maintained despite the turnover of transcription factor binding sites as well as reviewing studies where mutations in enhancers have been shown to underlie morphological change.
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Affiliation(s)
- A D Buffry
- Oxford Brookes University, Oxford, United Kingdom
| | - C C Mendes
- Oxford Brookes University, Oxford, United Kingdom
| | - A P McGregor
- Oxford Brookes University, Oxford, United Kingdom
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3
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Schmidt-Ott U, Lynch JA. Emerging developmental genetic model systems in holometabolous insects. Curr Opin Genet Dev 2016; 39:116-128. [PMID: 27399647 DOI: 10.1016/j.gde.2016.06.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 05/25/2016] [Accepted: 06/08/2016] [Indexed: 01/08/2023]
Abstract
The number of insect species that are amenable to functional genetic studies is growing rapidly and provides many new research opportunities in developmental and evolutionary biology. The holometabolous insects represent a disproportionate percentage of animal diversity and are thus well positioned to provide model species for a wide variety of developmental processes. Here we discuss emerging holometabolous models, and review some recent breakthroughs. For example, flies and midges were found to use structurally unrelated long-range pattern organizers, butterflies and moths revealed extensive pattern formation during oogenesis, new imaging possibilities in the flour beetle Tribolium castaneum showed how embryos break free of their extraembryonic membranes, and the complex genetics governing interspecies difference in head shape were revealed in Nasonia wasps.
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Affiliation(s)
- Urs Schmidt-Ott
- Department of Organismal Biology and Anatomy, University of Chicago, United States.
| | - Jeremy A Lynch
- Department of Biological Sciences, University of Illinois at Chicago, United States.
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4
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Wotton KR, Jiménez-Guri E, Jaeger J. Maternal co-ordinate gene regulation and axis polarity in the scuttle fly Megaselia abdita. PLoS Genet 2015; 11:e1005042. [PMID: 25757102 PMCID: PMC4355411 DOI: 10.1371/journal.pgen.1005042] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Accepted: 01/30/2015] [Indexed: 02/01/2023] Open
Abstract
Axis specification and segment determination in dipteran insects are an excellent model system for comparative analyses of gene network evolution. Antero-posterior polarity of the embryo is established through systems of maternal morphogen gradients. In Drosophila melanogaster, the anterior system acts through opposing gradients of Bicoid (Bcd) and Caudal (Cad), while the posterior system involves Nanos (Nos) and Hunchback (Hb) protein. These systems act redundantly. Both Bcd and Hb need to be eliminated to cause a complete loss of polarity resulting in mirror-duplicated abdomens, so-called bicaudal phenotypes. In contrast, knock-down of bcd alone is sufficient to induce double abdomens in non-drosophilid cyclorrhaphan dipterans such as the hoverfly Episyrphus balteatus or the scuttle fly Megaselia abdita. We investigate conserved and divergent aspects of axis specification in the cyclorrhaphan lineage through a detailed study of the establishment and regulatory effect of maternal gradients in M. abdita. Our results show that the function of the anterior maternal system is highly conserved in this species, despite the loss of maternal cad expression. In contrast, hb does not activate gap genes in this species. The absence of this activatory role provides a precise genetic explanation for the loss of polarity upon bcd knock-down in M. abdita, and suggests a general scenario in which the posterior maternal system is increasingly replaced by the anterior one during the evolution of the cyclorrhaphan dipteran lineage. The basic head-to-tail polarity of an animal is established very early in development. In dipteran insects (flies, midges, and mosquitoes), polarity is established with the help of so-called morphogen gradients. Morphogens are regulatory proteins that are distributed as a concentration gradient, often involving diffusion from a localised source. This graded distribution then leads to the concentration-dependent activation of different target genes along the embryo’s axis. We examine this process, which differs to a surprising extent between dipteran species, in the scuttle fly Megaselia abdita, and compare our results to the model organism Drosophila melanogaster. In this way, we not only gain insights into how the mechanisms that establish polarity function differently in different species, but also how the system has evolved since these two flies shared a common ancestor. Specifically, we pin down the main difference between Drosophila and Megaselia in the altered function of the maternal Hunchback morphogen gradient, which activates target genes in the former, but not the latter species, where it has been completely replaced by the Bicoid morphogen during evolution.
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Affiliation(s)
- Karl R. Wotton
- EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- * E-mail: (KW); (JJ)
| | - Eva Jiménez-Guri
- EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Johannes Jaeger
- EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- * E-mail: (KW); (JJ)
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5
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Wotton KR, Jiménez-Guri E, Crombach A, Janssens H, Alcaine-Colet A, Lemke S, Schmidt-Ott U, Jaeger J. Quantitative system drift compensates for altered maternal inputs to the gap gene network of the scuttle fly Megaselia abdita. eLife 2015; 4:e04785. [PMID: 25560971 PMCID: PMC4337606 DOI: 10.7554/elife.04785] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 01/02/2015] [Indexed: 12/20/2022] Open
Abstract
The segmentation gene network in insects can produce equivalent phenotypic outputs despite differences in upstream regulatory inputs between species. We investigate the mechanistic basis of this phenomenon through a systems-level analysis of the gap gene network in the scuttle fly Megaselia abdita (Phoridae). It combines quantification of gene expression at high spatio-temporal resolution with systematic knock-downs by RNA interference (RNAi). Initiation and dynamics of gap gene expression differ markedly between M. abdita and Drosophila melanogaster, while the output of the system converges to equivalent patterns at the end of the blastoderm stage. Although the qualitative structure of the gap gene network is conserved, there are differences in the strength of regulatory interactions between species. We term such network rewiring 'quantitative system drift'. It provides a mechanistic explanation for the developmental hourglass model in the dipteran lineage. Quantitative system drift is likely to be a widespread mechanism for developmental evolution.
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Affiliation(s)
- Karl R Wotton
- European Molecular Biology Laboratory, CRG Systems Biology Research Unit, Centre for Genomic Regulation, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Eva Jiménez-Guri
- European Molecular Biology Laboratory, CRG Systems Biology Research Unit, Centre for Genomic Regulation, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Anton Crombach
- European Molecular Biology Laboratory, CRG Systems Biology Research Unit, Centre for Genomic Regulation, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Hilde Janssens
- European Molecular Biology Laboratory, CRG Systems Biology Research Unit, Centre for Genomic Regulation, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Anna Alcaine-Colet
- European Molecular Biology Laboratory, CRG Systems Biology Research Unit, Centre for Genomic Regulation, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- Universitat de Barcelona, Barcelona, Spain
| | - Steffen Lemke
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, United States
| | - Urs Schmidt-Ott
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, United States
| | - Johannes Jaeger
- European Molecular Biology Laboratory, CRG Systems Biology Research Unit, Centre for Genomic Regulation, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
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6
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Wessinger CA, Rausher MD. PREDICTABILITY AND IRREVERSIBILITY OF GENETIC CHANGES ASSOCIATED WITH FLOWER COLOR EVOLUTION INPENSTEMON BARBATUS. Evolution 2014; 68:1058-70. [DOI: 10.1111/evo.12340] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 12/06/2013] [Indexed: 12/27/2022]
Affiliation(s)
| | - Mark D. Rausher
- Department of Biology; Duke University; Box 90338 Durham North Carolina 27708
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7
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Coevolution within and between regulatory loci can preserve promoter function despite evolutionary rate acceleration. PLoS Genet 2012; 8:e1002961. [PMID: 23028368 PMCID: PMC3447958 DOI: 10.1371/journal.pgen.1002961] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 08/06/2012] [Indexed: 11/19/2022] Open
Abstract
Phenotypes that appear to be conserved could be maintained not only by strong purifying selection on the underlying genetic systems, but also by stabilizing selection acting via compensatory mutations with balanced effects. Such coevolution has been invoked to explain experimental results, but has rarely been the focus of study. Conserved expression driven by the unc-47 promoters of Caenorhabditis elegans and C. briggsae persists despite divergence within a cis-regulatory element and between this element and the trans-regulatory environment. Compensatory changes in cis and trans are revealed when these promoters are used to drive expression in the other species. Functional changes in the C. briggsae promoter, which has experienced accelerated sequence evolution, did not lead to alteration of gene expression in its endogenous environment. Coevolution among promoter elements suggests that complex epistatic interactions within cis-regulatory elements may facilitate their divergence. Our results offer a detailed picture of regulatory evolution in which subtle, lineage-specific, and compensatory modifications of interacting cis and trans regulators together maintain conserved gene expression patterns. Some phenotypes, including gene expression patterns, are conserved between distantly related species. However, the molecular bases of those phenotypes are not necessarily conserved. Instead, regulatory DNA sequences and the proteins with which they interact can change over time with balanced effects, preserving expression patterns and concealing regulatory divergence. Coevolution between interacting molecules makes gene regulation highly species-specific, and it can be detected when the cis-regulatory DNA of one species is used to drive expression in another species. In this way, we identified regions of the C. elegans and C. briggsae unc-47 promoters that have coevolved with the lineage-specific trans-regulatory environments of these organisms. The C. briggsae promoter experienced accelerated sequence change relative to related species. All of this evolution occurred without changing the expression pattern driven by the promoter in its endogenous environment.
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8
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Llopart A. The Rapid Evolution of X-linked Male-Biased Gene Expression and the Large-X Effect in Drosophila yakuba, D. santomea, and Their Hybrids. Mol Biol Evol 2012; 29:3873-86. [DOI: 10.1093/molbev/mss190] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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9
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Cruickshank T, Nista P. Selection and constraint on regulatory elements in Drosophila simulans. J Mol Evol 2011; 73:94-100. [DOI: 10.1007/s00239-011-9458-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Accepted: 08/19/2011] [Indexed: 10/17/2022]
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10
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Two types of cis-trans compensation in the evolution of transcriptional regulation. Proc Natl Acad Sci U S A 2011; 108:15276-81. [PMID: 21876147 DOI: 10.1073/pnas.1105814108] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Because distant species often share similar macromolecules, regulatory mutations are often considered responsible for much of their biological differences. Recently, a large portion of regulatory changes has been attributed to cis-regulatory mutations. Here, we examined an alternative possibility that the putative contribution of cis-regulatory changes was, in fact, caused by compensatory action of cis- and trans-regulatory elements. First, we show by stochastic simulations that compensatory cis-trans evolution maintains the binding affinity of a transcription factor at a constant level, thereby spuriously exaggerating the contribution of cis-regulatory mutations to gene expression divergence. This exaggeration was not observed when changes in the binding affinity were compensated by variable transcription factor concentration. Second, using reciprocal introgressions of Drosophila, we show that relative expression of heterozygous alleles from two distinct species often varied significantly between different species backgrounds, indicating the possible action of cis-trans compensation. Taken together, we propose that cis-trans hybrid incompatibilities are accumulating much faster than generally considered.
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11
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He Z, Eichel K, Ruvinsky I. Functional conservation of cis-regulatory elements of heat-shock genes over long evolutionary distances. PLoS One 2011; 6:e22677. [PMID: 21799932 PMCID: PMC3143172 DOI: 10.1371/journal.pone.0022677] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Accepted: 06/30/2011] [Indexed: 12/02/2022] Open
Abstract
Transcriptional control of gene regulation is an intricate process that requires precise orchestration of a number of molecular components. Studying its evolution can serve as a useful model for understanding how complex molecular machines evolve. One way to investigate evolution of transcriptional regulation is to test the functions of cis-elements from one species in a distant relative. Previous results suggested that few, if any, tissue-specific promoters from Drosophila are faithfully expressed in C. elegans. Here we show that, in contrast, promoters of fly and human heat-shock genes are upregulated in C. elegans upon exposure to heat. Inducibility under conditions of heat shock may represent a relatively simple “on-off” response, whereas complex expression patterns require integration of multiple signals. Our results suggest that simpler aspects of regulatory logic may be retained over longer periods of evolutionary time, while more complex ones may be diverging more rapidly.
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Affiliation(s)
- Zhengying He
- Department of Ecology and Evolution, Institute for Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, United States of America
| | - Kelsie Eichel
- Department of Ecology and Evolution, Institute for Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, United States of America
| | - Ilya Ruvinsky
- Department of Ecology and Evolution, Institute for Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, United States of America
- * E-mail:
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12
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Lavore A, Pagola L, Esponda-Behrens N, Rivera-Pomar R. The gap gene giant of Rhodnius prolixus is maternally expressed and required for proper head and abdomen formation. Dev Biol 2011; 361:147-55. [PMID: 21763688 DOI: 10.1016/j.ydbio.2011.06.038] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Revised: 06/09/2011] [Accepted: 06/11/2011] [Indexed: 01/20/2023]
Abstract
The segmentation process in insects depends on a hierarchical cascade of gene activity. The first effectors downstream of the maternal activation are the gap genes, which divide the embryo in broad fields. We discovered a sequence corresponding to the leucine-zipper domain of the orthologue of the gene giant (Rp-gt) in traces from the genome of Rhodnius prolixus, a hemipteran with intermediate germ-band development. We cloned the Rp-gt gene from a normalized cDNA library and characterized its expression and function. Bioinformatic analysis of 12.5 kbp of genomic sequence containing the Rp-gt transcriptional unit shows a cluster of bona fide regulatory binding sites, which is similar in location and structure to the predicted posterior expression domain of the Drosophila orthologue. Rp-gt is expressed in ovaries and maternally supplied in the early embryo. The maternal contribution forms a gradient of scattered patches of mRNA in the preblastoderm embryo. Zygotic Rp-gt is expressed in two domains that after germ band extension are restricted to the head and the posterior growth zone. Parental RNAi shows that Rp-gt is required for proper head and abdomen formation. The head lacks mandibulary and maxillary appendages and shows reduced clypeus-labrum, while the abdomen lacks anterior segments. We conclude that Rp-gt is a gap gene on the head and abdomen and, in addition, has a function in patterning the anterior head capsule suggesting that the function of gt in hemipterans is more similar to dipterans than expected.
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Affiliation(s)
- Andrés Lavore
- Laboratorio de Genética y Genómica Funcional, Centro Regional de Estudios Genómicos, Universidad Nacional de La Plata, Florencio Varela, Argentina
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13
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He BZ, Holloway AK, Maerkl SJ, Kreitman M. Does positive selection drive transcription factor binding site turnover? A test with Drosophila cis-regulatory modules. PLoS Genet 2011; 7:e1002053. [PMID: 21572512 PMCID: PMC3084208 DOI: 10.1371/journal.pgen.1002053] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2010] [Accepted: 03/02/2011] [Indexed: 12/04/2022] Open
Abstract
Transcription factor binding site(s) (TFBS) gain and loss (i.e., turnover) is a well-documented feature of cis-regulatory module (CRM) evolution, yet little attention has been paid to the evolutionary force(s) driving this turnover process. The predominant view, motivated by its widespread occurrence, emphasizes the importance of compensatory mutation and genetic drift. Positive selection, in contrast, although it has been invoked in specific instances of adaptive gene expression evolution, has not been considered as a general alternative to neutral compensatory evolution. In this study we evaluate the two hypotheses by analyzing patterns of single nucleotide polymorphism in the TFBS of well-characterized CRM in two closely related Drosophila species, Drosophila melanogaster and Drosophila simulans. An important feature of the analysis is classification of TFBS mutations according to the direction of their predicted effect on binding affinity, which allows gains and losses to be evaluated independently along the two phylogenetic lineages. The observed patterns of polymorphism and divergence are not compatible with neutral evolution for either class of mutations. Instead, multiple lines of evidence are consistent with contributions of positive selection to TFBS gain and loss as well as purifying selection in its maintenance. In discussion, we propose a model to reconcile the finding of selection driving TFBS turnover with constrained CRM function over long evolutionary time.
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Affiliation(s)
- Bin Z He
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, USA.
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14
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Abstract
Gap genes are involved in segment determination during the early development of the fruit fly Drosophila melanogaster as well as in other insects. This review attempts to synthesize the current knowledge of the gap gene network through a comprehensive survey of the experimental literature. I focus on genetic and molecular evidence, which provides us with an almost-complete picture of the regulatory interactions responsible for trunk gap gene expression. I discuss the regulatory mechanisms involved, and highlight the remaining ambiguities and gaps in the evidence. This is followed by a brief discussion of molecular regulatory mechanisms for transcriptional regulation, as well as precision and size-regulation provided by the system. Finally, I discuss evidence on the evolution of gap gene expression from species other than Drosophila. My survey concludes that studies of the gap gene system continue to reveal interesting and important new insights into the role of gene regulatory networks in development and evolution.
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Affiliation(s)
- Johannes Jaeger
- Centre de Regulació Genòmica, Universtitat Pompeu Fabra, Barcelona, Spain.
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15
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Zill OA, Scannell D, Teytelman L, Rine J. Co-evolution of transcriptional silencing proteins and the DNA elements specifying their assembly. PLoS Biol 2010; 8:e1000550. [PMID: 21151344 PMCID: PMC2994660 DOI: 10.1371/journal.pbio.1000550] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Accepted: 10/18/2010] [Indexed: 01/18/2023] Open
Abstract
Co-evolution of transcriptional regulatory proteins and their sites of action has been often hypothesized but rarely demonstrated. Here we provide experimental evidence of such co-evolution in yeast silent chromatin, a finding that emerged from studies of hybrids formed between two closely related Saccharomyces species. A unidirectional silencing incompatibility between S. cerevisiae and S. bayanus led to a key discovery: asymmetrical complementation of divergent orthologs of the silent chromatin component Sir4. In S. cerevisiae/S. bayanus interspecies hybrids, ChIP-Seq analysis revealed a restriction against S. cerevisiae Sir4 associating with most S. bayanus silenced regions; in contrast, S. bayanus Sir4 associated with S. cerevisiae silenced loci to an even greater degree than did S. cerevisiae's own Sir4. Functional changes in silencer sequences paralleled changes in Sir4 sequence and a reduction in Sir1 family members in S. cerevisiae. Critically, species-specific silencing of the S. bayanus HMR locus could be reconstituted in S. cerevisiae by co-transfer of the S. bayanus Sir4 and Kos3 (the ancestral relative of Sir1) proteins. As Sir1/Kos3 and Sir4 bind conserved silencer-binding proteins, but not specific DNA sequences, these rapidly evolving proteins served to interpret differences in the two species' silencers presumably involving emergent features created by the regulatory proteins that bind sequences within silencers. The results presented here, and in particular the high resolution ChIP-Seq localization of the Sir4 protein, provided unanticipated insights into the mechanism of silent chromatin assembly in yeast.
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Affiliation(s)
- Oliver A. Zill
- Department of Molecular and Cell Biology, and California Institute for Quantitative Biosciences, University of California–Berkeley, Berkeley, California, United States of America
- * E-mail: (JR); (OAZ)
| | - Devin Scannell
- Department of Molecular and Cell Biology, and California Institute for Quantitative Biosciences, University of California–Berkeley, Berkeley, California, United States of America
| | - Leonid Teytelman
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Jasper Rine
- Department of Molecular and Cell Biology, and California Institute for Quantitative Biosciences, University of California–Berkeley, Berkeley, California, United States of America
- * E-mail: (JR); (OAZ)
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16
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Hill-Burns EM, Clark AG. Functional regulatory divergence of the innate immune system in interspecific Drosophila hybrids. Mol Biol Evol 2010; 27:2596-605. [PMID: 20551040 DOI: 10.1093/molbev/msq146] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
In order to investigate divergence of immune regulation among Drosophila species, we have engaged in a study of innate immune function in F1 hybrids of Drosophila melanogaster and D. simulans. If pathways have diverged between the species such that incompatibilities have arisen between interacting components of the immune network, we expect the hybrids to display dysregulation of immune genes. We have quantified gene induction in hybrid and parental flies in response to bacterial infection. These results show that although the hybrids do not suffer widespread immune breakdown, they show significantly different regulation of many immune genes relative to the parents. We examine this divergence in terms of additivity and expression differences among genes, observing distinct patterns of dysregulation among functional groups within the pathways of the innate immune system. The functional groups most sensitive to misexpression in the hybrids are the downstream components of the network, indicative of some propagation of dysregulation throughout the immune pathways. Interestingly, this dysregulation does not appear to associate with phenotypic differences in bacterial load after infection in hybrids, possibly highlighting some robustness of function of the innate immune response to perturbations like hybridization.
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Affiliation(s)
- Erin M Hill-Burns
- Field of Genetics and Development, Department of Molecular Biology and Genetics, Cornell University.
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17
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Regulatory divergence in Drosophila melanogaster and D. simulans, a genomewide analysis of allele-specific expression. Genetics 2009; 183:547-61, 1SI-21SI. [PMID: 19667135 DOI: 10.1534/genetics.109.105957] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Species-specific regulation of gene expression contributes to the development and maintenance of reproductive isolation and to species differences in ecologically important traits. A better understanding of the evolutionary forces that shape regulatory variation and divergence can be developed by comparing expression differences among species and interspecific hybrids. Once expression differences are identified, the underlying genetics of regulatory variation or divergence can be explored. With the goal of associating cis and/or trans components of regulatory divergence with differences in gene expression, overall and allele-specific expression levels were assayed genomewide in female adult heads of Drosophila melanogaster, D. simulans, and their F1 hybrids. A greater proportion of cis differences than trans differences were identified for genes expressed in heads and, in accordance with previous studies, cis differences also explained a larger number of species differences in overall expression level. Regulatory divergence was found to be prevalent among genes associated with defense, olfaction, and among genes downstream of the Drosophila sex determination hierarchy. In addition, two genes, with critical roles in sex determination and micro RNA processing, Sxl and loqs, were identified as misexpressed in hybrid female heads, potentially contributing to hybrid incompatibility.
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18
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Mavarez J, Audet C, Bernatchez L. Major disruption of gene expression in hybrids between young sympatric anadromous and resident populations of brook charr (Salvelinus fontinalis Mitchill). J Evol Biol 2009; 22:1708-20. [PMID: 19549137 DOI: 10.1111/j.1420-9101.2009.01785.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Genome-wide analyses of the transcriptome have suggested that male-biased genes are the first targets of genomic incompatibilities (g.i.) in inter-specific hybrids. However, those studies have almost invariably focused on Drosophila species that diverged at least 0.9 Ma, and with sterile male hybrids. Here, we use microarrays to analyse patterns of gene expression in very closely related (divergence <12,000 years), sympatric, but ecologically divergent anadromous and resident populations of brook charr (Salvelinus fontinalis) and their F(1) hybrids. Our results show a dramatic breakdown of gene expression patterns in hybrids compared with their parental relatives. Several disrupted genes are related to energetic metabolism, immune response, osmoregulation and protection against oxidative stress, and none has sex-biased functions. Besides, pure individuals show no expression differences at most of the genes disrupted in hybrids, which may suggest the operation of some form of stabilizing selection. Taken together, these results both confirm the idea that perturbations of regulatory networks represent a significant source of g.i. and support the suggestion that developmental pathways can diverge through time without any manifest change in the phenotypic outcome. While the role of other evolutionary forces (e.g. genetic drift) cannot be ruled out, this study suggests that ecological selective processes may provide the initial driving force behind disruption of gene expression in inter-specific hybrids.
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Affiliation(s)
- Jesus Mavarez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
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19
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Voolstra CR, Sunagawa S, Schwarz JA, Coffroth MA, Yellowlees D, Leggat W, Medina M. Evolutionary analysis of orthologous cDNA sequences from cultured and symbiotic dinoflagellate symbionts of reef-building corals (Dinophyceae: Symbiodinium). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2008; 4:67-74. [PMID: 20403741 DOI: 10.1016/j.cbd.2008.11.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2008] [Revised: 11/13/2008] [Accepted: 11/16/2008] [Indexed: 10/21/2022]
Abstract
Dinoflagellates are ubiquitous marine and freshwater protists. The endosymbiotic relationship between dinoflagellates of the genus Symbiodinium (also known as zooxanthellae) and corals forms the basis of coral reefs. We constructed and analyzed a cDNA library from a cultured Symbiodinium species clade A (CassKB8). The majority of annotated ESTs from the Symbiodinium sp. CassKB8 library cover metabolic genes. Most of those belong to either carbohydrate or energy metabolism. In addition, components of extracellular signal transduction pathways and genes that play a role in cell-cell communication were identified. In a subsequent analysis, we determined all orthologous cDNA sequences between this library (1,484 unique sequences) and a library from a Symbiodinium species clade C (C3) (3,336 unique sequences) that was isolated directly from its symbiotic host. A set of 115 orthologs were identified between Symbiodinium sp. CassKB8 and Symbiodinium sp. C3. These orthologs were subdivided into three groups that show different characteristics and functions: conserved across eukaryotes (CE), dinoflagellate-specific (DS) and Symbiodinium-specific (SS). Orthologs conserved across eukaryotes are mainly comprised of housekeeping genes, photosynthesis-related transcripts and metabolic proteins, whereas the function for most of the dinoflagellate-specific orthologs remains unknown. A dN/dS analysis identified the highest ratio in a Symbiodinium-specific ortholog and evidence for positive selection in a dinoflagellate-specific gene. Evolution of genes and pathways in different dinoflagellates seems to be affected by different lifestyles, and a symbiotic lifestyle may affect population structure and strength of selection. This study is the first evolutionary comparative analysis of orthologs from two coral dinoflagellate symbionts.
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Affiliation(s)
- Christian R Voolstra
- School of Natural Sciences, University of California, Merced, P.O. Box 2039, Merced, CA 95344, USA
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20
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Copley RR. The animal in the genome: comparative genomics and evolution. Philos Trans R Soc Lond B Biol Sci 2008; 363:1453-61. [PMID: 18192189 PMCID: PMC2614226 DOI: 10.1098/rstb.2007.2235] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Comparisons between completely sequenced metazoan genomes have generally emphasized how similar their encoded protein content is, even when the comparison is between phyla. Given the manifest differences between phyla and, in particular, intuitive notions that some animals are more complex than others, this creates something of a paradox. Simplistic explanations have included arguments such as increased numbers of genes; greater numbers of protein products produced through alternative splicing; increased numbers of regulatory non-coding RNAs and increased complexity of the cis-regulatory code. An obvious value of complete genome sequences lies in their ability to provide us with inventories of such components. I examine progress being made in linking genome content to the pattern of animal evolution, and argue that the gap between genomic and phenotypic complexity can only be understood through the totality of interacting components.
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21
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Choi SH, Lee G, Monahan P, Park JH. Spatial regulation of Corazonin neuropeptide expression requires multiple cis-acting elements in Drosophila melanogaster. J Comp Neurol 2008; 507:1184-95. [PMID: 18181151 DOI: 10.1002/cne.21594] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Although most invertebrate neuropeptide-encoding genes display distinct expression patterns in the central nervous system (CNS), the molecular mechanisms underlying spatial regulation of the neuropeptide genes are largely unknown. Expression of the neuropeptide Corazonin (Crz) is limited to only 24 neurons in the larval CNS of Drosophila melanogaster, and these neurons have been categorized into three groups, namely, DL, DM, and vCrz. To identify cis-regulatory elements that control transcription of Crz in each neuronal group, reporter gene expression patterns driven by various 5' flanking sequences of Crz were analyzed to assess their promoter activities in the CNS. We show that the 504-bp 5' upstream sequence is the shortest promoter directing reporter activities in all Crz neurons. Further dissection of this sequence revealed two important regions responsible for group specificity: -504::-419 for DM expression and -380::-241 for DL and vCrz expression. The latter region is further subdivided into three sites (proximal, center, and distal), in which any combinations of the two are sufficient for DL expression, whereas both proximal and distal sites are required for vCrz expression. Interestingly, the TATA box does not play a role in Crz transcription in most neurons. We also show that a 434-bp 5' upstream sequence of the D. virilis Crz gene, when introduced into the D. melanogaster genome, drives reporter expression in the DL and vCrz neurons, suggesting that regulatory mechanisms for Crz expression in at least two such neuronal groups are conserved between the two species.
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Affiliation(s)
- Seung-Hoon Choi
- Laboratory of Neurogenetics, Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, USA
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22
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Gregor T, McGregor AP, Wieschaus EF. Shape and function of the Bicoid morphogen gradient in dipteran species with different sized embryos. Dev Biol 2008; 316:350-8. [PMID: 18328473 DOI: 10.1016/j.ydbio.2008.01.039] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2007] [Revised: 01/21/2008] [Accepted: 01/23/2008] [Indexed: 12/19/2022]
Abstract
The Bicoid morphogen evolved approximately 150 MYA from a Hox3 duplication and is only found in higher dipterans. A major difference between dipteran species, however, is the size of the embryo, which varies up to 5-fold. Although the expression of developmental factors scale with egg length, it remains unknown how this scaling is achieved. To test whether scaling is accounted for by the properties of Bicoid, we expressed eGFP fused to the coding region of bicoid from three dipteran species in transgenic Drosophila embryos using the Drosophila bicoid cis-regulatory and mRNA localization sequences. In such embryos, we find that Lucilia sericata and Calliphora vicina Bicoid produce gradients very similar to the endogenous Drosophila gradient and much shorter than what they would have produced in their own respective species. The common shape of the Drosophila, Lucilia and Calliphora Bicoid gradients appears to be a conserved feature of the Bicoid protein. Surprisingly, despite their similar distributions, we find that Bicoid from Lucilia and Calliphora do not rescue Drosophila bicoid mutants, suggesting that that Bicoid proteins have evolved species-specific functional amino acid differences. We also found that maternal expression and anteriorly localization of proteins other than Bcd does not necessarily give rise to a gradient; eGFP produced a uniform protein distribution. However, a shallow gradient was observed using eGFP-NLS, suggesting nuclear localization may be necessary but not sufficient for gradient formation.
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Affiliation(s)
- Thomas Gregor
- Howard Hughes Medical Institute, Princeton University, Princeton, NJ 08544, USA
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23
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Simpson P, Ayyar S. Chapter 3 Evolution of Cis‐Regulatory Sequences in Drosophila. LONG-RANGE CONTROL OF GENE EXPRESSION 2008; 61:67-106. [DOI: 10.1016/s0065-2660(07)00003-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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24
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Abstract
Arabidopsis class III homeodomain-leucine zipper (HD-Zip III) proteins play overlapping, distinct, and antagonistic roles in key aspects of development that have evolved during land plant evolution. To better understand this gene family's role in plant evolution and development as well as to address broader questions of how duplicated genes functionally diversify, we investigated the evolutionary history of this gene family. Phylogenetic analyses including homologs from diverse land plants indicate that a gene duplication event before the angiosperm--gymnosperm split gave rise to two gene lineages that diversified during angiosperm plant radiation. Heterologous expression of an HD-Zip III gene from the nonvascular plant moss within the Arabidopsis HD-zip III revoluta mutant modified but did not complement the phenotype. Comparison of the expression domains of flowering and nonflowering plant homologs indicate an ancestral role in vascular development and organ initiation but not in specifying organ polarity, a prominent role for angiosperm homologs.
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Affiliation(s)
- Michael J Prigge
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109-1048, USA
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25
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Landry CR, Hartl DL, Ranz JM. Genome clashes in hybrids: insights from gene expression. Heredity (Edinb) 2007; 99:483-93. [PMID: 17687247 DOI: 10.1038/sj.hdy.6801045] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
In interspecific hybrids, novel phenotypes often emerge from the interaction of two divergent genomes. Interactions between the two transcriptional networks are assumed to contribute to these unpredicted new phenotypes by inducing novel patterns of gene expression. Here we provide a review of the recent literature on the accumulation of regulatory incompatibilities. We review specific examples of regulatory incompatibilities reported at particular loci as well as genome-scale surveys of gene expression in interspecific hybrids. Finally, we consider and preview novel technologies that could help decipher how divergent transcriptional networks interact in hybrids between species.
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Affiliation(s)
- C R Landry
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
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26
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Marcellini S, Simpson P. Two or four bristles: functional evolution of an enhancer of scute in Drosophilidae. PLoS Biol 2007; 4:e386. [PMID: 17105353 PMCID: PMC1635746 DOI: 10.1371/journal.pbio.0040386] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2006] [Accepted: 09/14/2006] [Indexed: 12/04/2022] Open
Abstract
Changes in cis-regulatory sequences are proposed to underlie much of morphological evolution. Yet, little is known about how such modifications translate into phenotypic differences. To address this problem, we focus on the dorsocentral bristles of Drosophilidae. In Drosophila melanogaster, development of these bristles depends on a cis-regulatory element, the dorsocentral enhancer, to activate scute in a cluster of cells from which two bristles on the posterior scutum arise. A few species however, such as D. quadrilineata, bear anterior dorsocentral bristles as well as posterior ones, a derived feature. This correlates with an anterior expansion of the scute expression domain. Here, we show that the D. quadrilineata enhancer has evolved, and is now active in more anterior regions. When used to rescue scute expression in transgenic D. melanogaster, the D. quadrilineata enhancer is able to induce anterior bristles. Importantly, these properties are not displayed by homologous enhancers from control species bearing only two posterior bristles. We also provide evidence that upstream regulation of the enhancer, by the GATA transcription factor Pannier, has been evolutionarily conserved. This work illustrates how, in the context of a conserved trans-regulatory landscape, evolutionary tinkering of pre-existing enhancers can modify gene expression patterns and contribute to morphological diversification. Evolutionary change in function of the dorsocentral enhancer (DCE) of scute has resulted in altered bristle formation between two species of Drosophila.
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Affiliation(s)
- Sylvain Marcellini
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom.
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27
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Coevolution, modularity and human disease. Curr Opin Genet Dev 2006; 16:637-44. [PMID: 17005391 DOI: 10.1016/j.gde.2006.09.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2006] [Accepted: 09/15/2006] [Indexed: 01/08/2023]
Abstract
The concepts of coevolution and modularity have been studied separately for decades. Recent advances in genomics have led to the first systematic studies in each of these fields at the molecular level, resulting in several important discoveries. Both coevolution and modularity appear to be pervasive features of genomic data from all species studied to date, and their presence can be detected in many types of datasets, including genome sequences, gene expression data, and protein-protein interaction data. Moreover, the combination of these two ideas might have implications for our understanding of many aspects of biology, ranging from the general architecture of living systems to the causes of various human diseases.
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28
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Abstract
Cis-regulatory sequences direct patterns of gene expression essential for development and physiology. Evolutionary changes in these sequences contribute to phenotypic divergence. Despite their importance, cis-regulatory regions remain one of the most enigmatic features of the genome. Patterns of sequence evolution can be used to identify cis-regulatory elements, but the power of this approach depends upon the relationship between sequence and function. Comparative studies of gene regulation among Diptera reveal that divergent sequences can underlie conserved expression, and that expression differences can evolve despite largely similar sequences. This complex structure-function relationship is the primary impediment for computational identification and interpretation of cis-regulatory sequences. Biochemical characterization and in vivo assays of cis-regulatory sequences on a genomic-scale will relieve this barrier.
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Affiliation(s)
- P J Wittkopp
- Department of Ecology and Evolutionary Biology, University of Michigan, 1061 Natural Science Building, 830 North University Ave., Ann Arbor, MI 48109-1048, USA.
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29
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Haerty W, Singh RS. Gene regulation divergence is a major contributor to the evolution of Dobzhansky-Muller incompatibilities between species of Drosophila. Mol Biol Evol 2006; 23:1707-14. [PMID: 16757655 DOI: 10.1093/molbev/msl033] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The Dobzhansky-Muller model denotes incompatible gene interactions between diverging populations/species and is recognized as the basis of postzygotic reproductive isolation. Little is known about the molecular nature of such gene interactions. We have carried out comparative gene expression analyses in the testes of 3 closely related species of the Drosophila melanogaster subgroup and their hybrids (all of which are sterile). We show that in hybrids 1) a higher proportion of male-biased genes (i.e., genes with a higher level of expression in males) are underexpressed (or not expressed) compared with non-sex-biased genes, 2) the majority of the underexpressed genes appear to be under stabilizing selection by virtue of showing similar levels of expression in the parental species, and only a small proportion of genes show signs of directional selection, 3) very few of the misexpressed genes are shared between species pairs, suggesting that there may not be a "common" set of "speciation genes," and 4) expression of non-testes-specific genes is observed in the testes of interspecific hybrids, and the number of such genes is positively correlated with divergence time. These results suggest that gene regulation divergence of sex- and reproduction-related genes is a major contributor to the evolution of Dobzhansky-Muller incompatibilities between species of Drosophila.
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Affiliation(s)
- Wilfried Haerty
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
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30
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Wratten NS, McGregor AP, Shaw PJ, Dover GA. Evolutionary and functional analysis of the tailless enhancer in Musca domestica and Drosophila melanogaster. Evol Dev 2006; 8:6-15. [PMID: 16409378 DOI: 10.1111/j.1525-142x.2006.05070.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To further understand the evolutionary dynamics of the regulatory interactions underlying development, we expand on our previous analysis of hunchback and compare the structure and function of the tailless enhancer between Musca domestica and Drosophila melanogaster. Our analysis shows that although the expression patterns and functional protein domains of tll are conserved between Musca and Drosophila, the enhancer sequences are unalignable. Upon closer investigation, we find that these highly diverged enhancer sequences encode the same regulatory information necessary for Bicoid, Dorsal, and the terminal system to drive tll expression. The binding sites for these transcription factors differ in the sequence, number, spacing, and position between the Drosophila and Musca tll enhancers, and we were unable to establish homology between binding sites from each species. This implies that the Musca and Drosophila Bcd-binding sites have evolved de novo in the 100 million years since these species diverged. However, in transgenic Drosophila embryos the Musca tll enhancer is able to drive the same expression pattern as endogenous Drosophila tll. Therefore, during the rapid evolution of enhancer sequences individual binding sites are continually lost and gained, but the transcriptional output is maintained by compensatory mutations in cis and in trans.
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Affiliation(s)
- Naomi S Wratten
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
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31
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Abstract
Most of the phenotypic diversity that we perceive in the natural world is directly attributable to the peculiar structure of the eukaryotic gene, which harbors numerous embellishments relative to the situation in prokaryotes. The most profound changes include introns that must be spliced out of precursor mRNAs, transcribed but untranslated leader and trailer sequences (untranslated regions), modular regulatory elements that drive patterns of gene expression, and expansive intergenic regions that harbor additional diffuse control mechanisms. Explaining the origins of these features is difficult because they each impose an intrinsic disadvantage by increasing the genic mutation rate to defective alleles. To address these issues, a general hypothesis for the emergence of eukaryotic gene structure is provided here. Extensive information on absolute population sizes, recombination rates, and mutation rates strongly supports the view that eukaryotes have reduced genetic effective population sizes relative to prokaryotes, with especially extreme reductions being the rule in multicellular lineages. The resultant increase in the power of random genetic drift appears to be sufficient to overwhelm the weak mutational disadvantages associated with most novel aspects of the eukaryotic gene, supporting the idea that most such changes are simple outcomes of semi-neutral processes rather than direct products of natural selection. However, by establishing an essentially permanent change in the population-genetic environment permissive to the genome-wide repatterning of gene structure, the eukaryotic condition also promoted a reliable resource from which natural selection could secondarily build novel forms of organismal complexity. Under this hypothesis, arguments based on molecular, cellular, and/or physiological constraints are insufficient to explain the disparities in gene, genomic, and phenotypic complexity between prokaryotes and eukaryotes.
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Affiliation(s)
- Michael Lynch
- Department of Biology, Indiana University, Bloomington, USA.
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32
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Landry CR, Wittkopp PJ, Taubes CH, Ranz JM, Clark AG, Hartl DL. Compensatory cis-trans evolution and the dysregulation of gene expression in interspecific hybrids of Drosophila. Genetics 2005; 171:1813-22. [PMID: 16143608 PMCID: PMC1456106 DOI: 10.1534/genetics.105.047449] [Citation(s) in RCA: 162] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Hybrids between species are often characterized by novel gene-expression patterns. A recent study on allele-specific gene expression in hybrids between species of Drosophila revealed cases in which cis- and trans-regulatory elements within species had coevolved in such a way that changes in cis-regulatory elements are compensated by changes in trans-regulatory elements. We hypothesized that such coevolution should often lead to gene misexpression in the hybrid. To test this hypothesis, we estimated allele-specific expression and overall expression levels for 31 genes in D. melanogaster, D. simulans, and their F1 hybrid. We found that 13 genes with cis-trans compensatory evolution are in fact misexpressed in the hybrid. These represent candidate genes whose dysregulation might be the consequence of coevolution of cis- and trans-regulatory elements within species. Using a mathematical model for the regulation of gene expression, we explored the conditions under which cis-trans compensatory evolution can lead to misexpression in interspecific hybrids.
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Affiliation(s)
- Christian R Landry
- Department of Organismic and Evolutionary Biology, The Biological laboratories, 16 Divinity Avenue, Harvard University, Cambridge, MA 02138, USA
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33
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Palmer CA, Watts RA, Gregg RG, McCall MA, Houck LD, Highton R, Arnold SJ. Lineage-specific differences in evolutionary mode in a salamander courtship pheromone. Mol Biol Evol 2005; 22:2243-56. [PMID: 16033988 DOI: 10.1093/molbev/msi219] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Functionally equivalent genes may evolve heterogeneously across closely related taxa as a consequence of lineage-specific selective pressures. Such disparate evolutionary modes are especially prevalent in genes that encode postcopulatory reproductive proteins, presumably as a result of sexual selection. We might therefore expect genes that mediate reproduction prior to insemination to evolve in a similar manner. Plethodontid receptivity factor (PRF), a proteinaceous salamander pheromone produced by the male, increases female receptivity during courtship interactions. To test for lineage-specific differences in PRF's evolution, we intensively sampled PRF genes across the eastern Plethodon phylogeny (27 spp.; 34 populations) to compare gene diversification, rates of evolution, modes of selection, and types of amino acid substitution. Our analyses indicate that PRF evolutionary dynamics vary considerably from lineage to lineage. Underlying this heterogeneity, however, are two well-defined transitions in evolutionary mode. The first mode is representative of a typical protein profile, wherein neutral divergence and purifying selection are the dominant features. The second mode is characterized by incessant, cyclical evolution driven by positive selection. In this mode, the positively selected sites are bound by a limited assortment of acceptable amino acids that appear to evolve independently of other sites, resulting in a tremendous number of unique PRF alleles. Several of these selected sites are implicated in receptor binding. These sites are apparently involved in a molecular tango in which the male signal and female receptors coevolve within a confined molecular space. PRF's lineage-specific evolutionary dynamics, in combination with evidence of a molecular tango, highlight the molecular action of sexual selection on a chemical signal that is used during courtship.
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34
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Hersh BM, Carroll SB. Direct regulation of knot gene expression by Ultrabithorax and the evolution of cis-regulatory elements in Drosophila. Development 2005; 132:1567-77. [PMID: 15753212 DOI: 10.1242/dev.01737] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The regulation of development by Hox proteins is important in the evolution of animal morphology, but how the regulatory sequences of Hox-regulated target genes function and evolve is unclear. To understand the regulatory organization and evolution of a Hox target gene, we have identified a wing-specific cis-regulatory element controlling the knot gene, which is expressed in the developing Drosophila wing but not the haltere. This regulatory element contains a single binding site that is crucial for activation by the transcription factor Cubitus interruptus (Ci), and a cluster of binding sites for repression by the Hox protein Ultrabithorax (UBX). The negative and positive control regions are physically separable, demonstrating that UBX does not repress by competing for occupancy of Ci-binding sites. Although knot expression is conserved among Drosophilaspecies, this cluster of UBX binding sites is not. We isolated the knot wing cis-regulatory element from D. pseudoobscura,which contains a cluster of UBX-binding sites that is not homologous to the functionally defined D. melanogaster cluster. It is, however,homologous to a second D. melanogaster region containing a cluster of UBX sites that can also function as a repressor element. Thus, the knot regulatory region in D. melanogaster has two apparently functionally redundant blocks of sequences for repression by UBX, both of which are widely separated from activator sequences. This redundancy suggests that the complete evolutionary unit of regulatory control is larger than the minimal experimentally defined control element. The span of regulatory sequences upon which selection acts may, in general, be more expansive and less modular than functional studies of these elements have previously indicated.
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Affiliation(s)
- Bradley M Hersh
- University of Wisconsin-Madison, Howard Hughes Medical Institute, 1525 Linden Drive, Madison, WI 53706, USA
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35
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Abstract
In Drosophila, a Bcd protein gradient orchestrates patterning along the anteroposterior embryonic axis. However, studies of basal flies and other insects have revealed that bcd is a derived Hox3 gene found only in higher dipterans. To understand how bcd acquired its role in flies and how anteroposterior patterning mechanisms have evolved, I first review key features of bcd function in Drosophila: anterior localization and transcriptional and translation control of gene expression. I then discuss investigations of bcd in other higher dipterans that have provided insight into the evolution of regulatory interactions and the Bcd gradient. Finally, I review studies of Drosophila and other insects that address the evolution of bcd function and integration of bcd into ancestral regulatory mechanisms. I suggest further comparative studies may allow us to identify the intermediate steps in bcd evolution. This will make bcd a paradigm for the origin and evolution of genes and regulatory networks.
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Affiliation(s)
- Alistair P McGregor
- Department of Ecology and Evolutionary Biology, Princeton University, New Jersey 08540, USA.
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36
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Berman BP, Pfeiffer BD, Laverty TR, Salzberg SL, Rubin GM, Eisen MB, Celniker SE. Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura. Genome Biol 2004; 5:R61. [PMID: 15345045 PMCID: PMC522868 DOI: 10.1186/gb-2004-5-9-r61] [Citation(s) in RCA: 170] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2004] [Revised: 08/04/2004] [Accepted: 08/06/2004] [Indexed: 01/03/2023] Open
Abstract
27 predicted gene-regulatory regions in the Drosophila melanogaster genome were analyzed in vivo, confirming 15 active enhancer regions. A comparison with Drosophila pseudoobscura sequences revealed that conservation of binding-site clusters accurately discriminates functional regions from non-functional ones. Background The identification of sequences that control transcription in metazoans is a major goal of genome analysis. In a previous study, we demonstrated that searching for clusters of predicted transcription factor binding sites could discover active regulatory sequences, and identified 37 regions of the Drosophila melanogaster genome with high densities of predicted binding sites for five transcription factors involved in anterior-posterior embryonic patterning. Nine of these clusters overlapped known enhancers. Here, we report the results of in vivo functional analysis of 27 remaining clusters. Results We generated transgenic flies carrying each cluster attached to a basal promoter and reporter gene, and assayed embryos for reporter gene expression. Six clusters are enhancers of adjacent genes: giant, fushi tarazu, odd-skipped, nubbin, squeeze and pdm2; three drive expression in patterns unrelated to those of neighboring genes; the remaining 18 do not appear to have enhancer activity. We used the Drosophila pseudoobscura genome to compare patterns of evolution in and around the 15 positive and 18 false-positive predictions. Although conservation of primary sequence cannot distinguish true from false positives, conservation of binding-site clustering accurately discriminates functional binding-site clusters from those with no function. We incorporated conservation of binding-site clustering into a new genome-wide enhancer screen, and predict several hundred new regulatory sequences, including 85 adjacent to genes with embryonic patterns. Conclusions Measuring conservation of sequence features closely linked to function - such as binding-site clustering - makes better use of comparative sequence data than commonly used methods that examine only sequence identity.
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Affiliation(s)
- Benjamin P Berman
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Barret D Pfeiffer
- Berkeley Drosophila Genome Project, Genome Sciences Department, Life Sciences Division, Lawrence Orlando Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Todd R Laverty
- Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Steven L Salzberg
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20878, USA
| | - Gerald M Rubin
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- Berkeley Drosophila Genome Project, Genome Sciences Department, Life Sciences Division, Lawrence Orlando Berkeley National Laboratory, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Michael B Eisen
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- Genome Sciences Department, Genomics Division, Lawrence Orlando Berkeley National Laboratory, Berkeley, CA 94720, USA
- Center for Integrative Genomics, University of California, Berkeley, CA 94720, USA
| | - Susan E Celniker
- Berkeley Drosophila Genome Project, Genome Sciences Department, Life Sciences Division, Lawrence Orlando Berkeley National Laboratory, Berkeley, CA 94720, USA
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37
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Castillo-Davis CI, Kondrashov FA, Hartl DL, Kulathinal RJ. The functional genomic distribution of protein divergence in two animal phyla: coevolution, genomic conflict, and constraint. Genome Res 2004; 14:802-11. [PMID: 15123580 PMCID: PMC479106 DOI: 10.1101/gr.2195604] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We compare the functional spectrum of protein evolution in two separate animal lineages with respect to two hypotheses: (1) rates of divergence are distributed similarly among functional classes within both lineages, indicating that selective pressure on the proteome is largely independent of organismic-level biological requirements; and (2) rates of divergence are distributed differently among functional classes within each lineage, indicating species-specific selective regimes impact genome-wide substitutional patterns. Integrating comparative genome sequence with data from tissue-specific expressed-sequence-tag (EST) libraries and detailed database annotations, we find a functional genomic signature of rapid evolution and selective constraint shared between mammalian and nematode lineages despite their extensive morphological and ecological differences and distant common ancestry. In both phyla, we find evidence of accelerated evolution among components of molecular systems involved in coevolutionary change. In mammals, lineage-specific fast evolving genes include those involved in reproduction, immunity, and possibly, maternal-fetal conflict. Likelihood ratio tests provide evidence for positive selection in these rapidly evolving functional categories in mammals. In contrast, slowly evolving genes, in terms of amino acid or insertion/deletion (indel) change, in both phyla are involved in core molecular processes such as transcription, translation, and protein transport. Thus, strong purifying selection appears to act on the same core cellular processes in both mammalian and nematode lineages, whereas positive and/or relaxed selection acts on different biological processes in each lineage.
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Affiliation(s)
- Cristian I Castillo-Davis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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38
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Castillo-Davis CI, Hartl DL, Achaz G. cis-Regulatory and protein evolution in orthologous and duplicate genes. Genome Res 2004; 14:1530-6. [PMID: 15256508 PMCID: PMC509261 DOI: 10.1101/gr.2662504] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The relationship between protein and regulatory sequence evolution is a central question in molecular evolution. It is currently not known to what extent changes in gene expression are coupled with the evolution of protein coding sequences, or whether these changes differ among orthologs (species homologs) and paralogs (duplicate genes). Here, we develop a method to measure the extent of functionally relevant cis-regulatory sequence change in homologous genes, and validate it using microarray data and experimentally verified regulatory elements in different eukaryotic species. By comparing the genomes of Caenorhabditis elegans and C. briggsae, we found that protein and regulatory evolution is weakly coupled in orthologs but not paralogs, suggesting that selective pressure on gene expression and protein evolution is quite similar and persists for a significant amount of time following speciation but not gene duplication. Additionally, duplicates of both species exhibit a dramatic acceleration of both regulatory and protein evolution compared to orthologs, suggesting increased directional selection and/or relaxed selection on both gene expression patterns and protein function in duplicate genes.
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Affiliation(s)
- Cristian I Castillo-Davis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, 02138 USA
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39
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Ranz JM, Namgyal K, Gibson G, Hartl DL. Anomalies in the expression profile of interspecific hybrids of Drosophila melanogaster and Drosophila simulans. Genome Res 2004; 14:373-9. [PMID: 14962989 PMCID: PMC353219 DOI: 10.1101/gr.2019804] [Citation(s) in RCA: 113] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
When females of Drosophila melanogaster and males of Drosophila simulans are mated, the male progeny are inviable, whereas the female progeny display manifold malformations and are sterile. These abnormalities result from genetic incompatibilities accumulated since the time the lineages of the species diverged, and may have their origin in aberrant gene transcription. Because compensatory changes within species may obscure differences at the regulatory level in conventional comparisons of the expression profile between species, we have compared the gene-expression profile of hybrid females with those of females of the parental species in order to identify regulatory incompatibilities. In the hybrid females, we find abnormal levels of messenger RNA for a large fraction of the Drosophila transcriptome. These include a gross underexpression of genes preferentially expressed in females, accompanying gonadal atrophy. The hybrid females also show significant overexpression of male-biased genes, which we attribute to incompatibilities in the regulatory mechanisms that normally act to control the expression of these genes in females. The net result of the multiple incompatibilities is that the gene-expression profiles of the parental females are more similar to each other than either is to that of the hybrid.
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MESH Headings
- Animals
- Breeding/methods
- Crosses, Genetic
- DNA, Complementary/classification
- DNA, Complementary/genetics
- Drosophila/embryology
- Drosophila/genetics
- Drosophila melanogaster/embryology
- Drosophila melanogaster/genetics
- Embryo, Nonmammalian/abnormalities
- Embryo, Nonmammalian/chemistry
- Embryo, Nonmammalian/metabolism
- Female
- Gene Expression Profiling/methods
- Gene Expression Regulation, Developmental/genetics
- Genes, Insect/genetics
- Genes, Lethal/genetics
- Hybridization, Genetic/genetics
- Male
- Molecular Sequence Data
- Oligonucleotide Array Sequence Analysis/methods
- Sex Factors
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Affiliation(s)
- José M Ranz
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
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40
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Sackton TB, Haney RA, Rand DM. Cytonuclear coadaptation in Drosophila: disruption of cytochrome c oxidase activity in backcross genotypes. Evolution 2003; 57:2315-25. [PMID: 14628919 DOI: 10.1111/j.0014-3820.2003.tb00243.x] [Citation(s) in RCA: 124] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The cytochrome c oxidase enzyme (COX) is comprised of 10 nuclear-encoded subunits and three mitochondrial-encoded subunits in close physical association in the inner mitochondrial membrane. COX passes electrons from cytochrome c to molecular oxygen and pumps protons into the inner mitochondrial space for ATP production. Selection on nuclear-mitochondrial interactions within species should lead to coadaptation of the proteins comprising this important enzyme. Under this model, there should be relatively little disruption of COX activity when mitochondrial genomes are crossed among strains within species. A more pronounced disruption of activity is expected when the mitochondrial genome is expressed in the nuclear background of a different species. We test these hypotheses in Drosophila using hybridization and backcrossing among lines of D. simulans and D. mauritiana. Disrupted cytonuclear genotypes were constructed using backcrosses between two lines of D. simulans (siI and siII) that introduced each divergent mitochondrial DNA (mtDNA) into each nuclear background due to maternal inheritance of mtDNA. Similar crosses were used to introduce each D. simulans mtDNA into the D. mauritiana maI nuclear background. Reconstituted cytonuclear control genotypes were constructed by backcrossing the initial F1 females to males of the maternal genotype. COX enzyme activities were compared among these disrupted and reconstituted backcross genotypes within and between species. The disruption effect on COX activity was restricted to males of interspecific genotypes. These data support the coadaptation hypothesis and are consistent with predictions that the evolution of modifiers of male mitochondrial dysfunction is hindered by the maternal inheritance of mtDNA. New sequence data for nuclear encoded subunits of COX identified amino acids that may play a role in the disruption effect.
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Affiliation(s)
- Timothy B Sackton
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island 02912, USA.
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41
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Emberly E, Rajewsky N, Siggia ED. Conservation of regulatory elements between two species of Drosophila. BMC Bioinformatics 2003; 4:57. [PMID: 14629780 PMCID: PMC302112 DOI: 10.1186/1471-2105-4-57] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2003] [Accepted: 11/20/2003] [Indexed: 12/19/2022] Open
Abstract
Background One of the important goals in the post-genomic era is to determine the regulatory elements within the non-coding DNA of a given organism's genome. The identification of functional cis-regulatory modules has proven difficult since the component factor binding sites are small and the rules governing their arrangement are poorly understood. However, the genomes of suitably diverged species help to predict regulatory elements based on the generally accepted assumption that conserved blocks of genomic sequence are likely to be functional. To judge the efficacy of strategies that prefilter by sequence conservation it is important to know to what extent the converse assumption holds, namely that functional elements common to both species will fall within these conserved blocks. The recently completed sequence of a second Drosophila species provides an opportunity to test this assumption for one of the experimentally best studied regulatory networks in multicellular organisms, the body patterning of the fly embryo. Results We find that 50%–70% of known binding sites reside in conserved sequence blocks, but these percentages are not greatly enriched over what is expected by chance. Finally, a computational genome-wide search in both species for regulatory modules based on clusters of binding sites suggests that genes central to the regulatory network are consistently recovered. Conclusions Our results indicate that binding sites remain clustered for these "core modules" while not necessarily residing in conserved blocks. This is an important clue as to how regulatory information is encoded in the genome and how modules evolve.
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Affiliation(s)
- Eldon Emberly
- Center for Studies in Physics and Biology, The Rockefeller University, 1230 York Avenue, New York, NY, USA
| | - Nikolaus Rajewsky
- Department of Biology, New York University, 1009 Main Building, 100 Washington Square East, New York, NY, USA
| | - Eric D Siggia
- Center for Studies in Physics and Biology, The Rockefeller University, 1230 York Avenue, New York, NY, USA
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Zhao C, Fu D, Dave V, Ma J. A composite motif of the Drosophila morphogenetic protein bicoid critical to transcription control. J Biol Chem 2003; 278:43901-9. [PMID: 12939280 DOI: 10.1074/jbc.m302714200] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bicoid is a molecular morphogen-controlling embryonic patterning in Drosophila. It is a homeodomain-containing protein that activates specific target genes during early embryogenesis. Our recent studies have identified a domain of Bcd located outside its homeodomain and referred to as a self-inhibitory domain that can dramatically repress its own ability to activate transcription. Here we present evidence that the self-inhibitory function is evolutionarily conserved. A systematic analysis of this domain reveals a composite 10-amino acid motif with interdigitating residues that regulate Bcd activity in opposite manners. Mutations within the Bcd motif can exert their respective effects when the self-inhibitory domain is grafted to an entirely heterologous activator, but they do not affect DNA binding in vitro or subcellular localization of Bcd in cells. We further show that the self-inhibitory domain of Bcd can interact with Sin3A, a component of the histone deacetylase co-repressor complex. Our study suggests that the activity of Bcd is intricately controlled by multiple mechanisms involving the actions of co-repressor proteins.
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Affiliation(s)
- Chen Zhao
- Division of Developmental Biology, Children's Hospital Research Foundation, Cincinnati, Ohio 45229, USA
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Ruvinsky I, Ruvkun G. Functional tests of enhancer conservation between distantly related species. Development 2003; 130:5133-42. [PMID: 12944426 DOI: 10.1242/dev.00711] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Expression patterns of orthologous genes are often conserved, even between distantly related organisms, suggesting that once established, developmental programs can be stably maintained over long periods of evolutionary time. Because many orthologous transcription factors are also functionally conserved, one possible model to account for homologous gene expression patterns, is conservation of specific binding sites within cis-regulatory elements of orthologous genes. If this model is correct, a cis-regulatory element from one organism would be expected to function in a distantly related organism. To test this hypothesis, we fused the green fluorescent protein gene to neuronal and muscular enhancer elements from a variety of Drosophila melanogaster genes, and tested whether these would activate expression in the homologous cell types in Caenorhabditis elegans. Regulatory elements from several genes directed appropriate expression in homologous tissue types, suggesting conservation of regulatory sites. However, enhancers of most Drosophila genes tested were not properly recognized in C. elegans, implying that over this evolutionary distance enough changes occurred in cis-regulatory sequences and/or transcription factors to prevent proper recognition of heterospecific enhancers. Comparisons of enhancer elements of orthologous genes between C. elegans and C. briggsae revealed extensive conservation, as well as specific instances of functional divergence. Our results indicate that functional changes in cis-regulatory sequences accumulate on timescales much shorter than the divergence of arthropods and nematodes, and that mechanisms other than conservation of individual binding sites within enhancer elements are responsible for the conservation of expression patterns of homologous genes between distantly related species.
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Affiliation(s)
- Ilya Ruvinsky
- Department of Molecular Biology, Massachusetts General Hospital and Department of Genetics, Harvard Medical School, Wellman 8, Boston, MA 02114, USA
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44
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Sackton TB, Haney RA, Rand DM. CYTONUCLEAR COADAPTATION IN DROSOPHILA: DISRUPTION OF CYTOCHROME C OXIDASE ACTIVITY IN BACKCROSS GENOTYPES. Evolution 2003. [DOI: 10.1554/02-580] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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45
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Abstract
One of the main challenges in evolutionary biology is to identify the molecular changes that underlie phenotypic differences that are of evolutionary significance. Comparative studies of early development have shown that changes in the spatio-temporal use of regulatory genes, as well as changes in the specificity of regulatory proteins, are correlated with important differences in morphology between phylogenetically distant species. However, it is not known how such changes take place in natural populations, and whether they result from a single, or many small, additive events. Extending this approach to the study of development of closely related species promises to enrich this debate.
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Affiliation(s)
- Pat Simpson
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.
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