1
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Ciren D, Zebell S, Lippman ZB. Extreme restructuring of cis-regulatory regions controlling a deeply conserved plant stem cell regulator. PLoS Genet 2024; 20:e1011174. [PMID: 38437180 PMCID: PMC10911594 DOI: 10.1371/journal.pgen.1011174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 02/07/2024] [Indexed: 03/06/2024] Open
Abstract
A striking paradox is that genes with conserved protein sequence, function and expression pattern over deep time often exhibit extremely divergent cis-regulatory sequences. It remains unclear how such drastic cis-regulatory evolution across species allows preservation of gene function, and to what extent these differences influence how cis-regulatory variation arising within species impacts phenotypic change. Here, we investigated these questions using a plant stem cell regulator conserved in expression pattern and function over ~125 million years. Using in-vivo genome editing in two distantly related models, Arabidopsis thaliana (Arabidopsis) and Solanum lycopersicum (tomato), we generated over 70 deletion alleles in the upstream and downstream regions of the stem cell repressor gene CLAVATA3 (CLV3) and compared their individual and combined effects on a shared phenotype, the number of carpels that make fruits. We found that sequences upstream of tomato CLV3 are highly sensitive to even small perturbations compared to its downstream region. In contrast, Arabidopsis CLV3 function is tolerant to severe disruptions both upstream and downstream of the coding sequence. Combining upstream and downstream deletions also revealed a different regulatory outcome. Whereas phenotypic enhancement from adding downstream mutations was predominantly weak and additive in tomato, mutating both regions of Arabidopsis CLV3 caused substantial and synergistic effects, demonstrating distinct distribution and redundancy of functional cis-regulatory sequences. Our results demonstrate remarkable malleability in cis-regulatory structural organization of a deeply conserved plant stem cell regulator and suggest that major reconfiguration of cis-regulatory sequence space is a common yet cryptic evolutionary force altering genotype-to-phenotype relationships from regulatory variation in conserved genes. Finally, our findings underscore the need for lineage-specific dissection of the spatial architecture of cis-regulation to effectively engineer trait variation from conserved productivity genes in crops.
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Affiliation(s)
- Danielle Ciren
- Cold Spring Harbor Laboratory, School of Biological Sciences, Cold Spring Harbor, New York, United States of America
| | - Sophia Zebell
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Zachary B Lippman
- Cold Spring Harbor Laboratory, School of Biological Sciences, Cold Spring Harbor, New York, United States of America
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
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2
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Sabarís G, Ortíz DM, Laiker I, Mayansky I, Naik S, Cavalli G, Stern DL, Preger-Ben Noon E, Frankel N. The Density of Regulatory Information Is a Major Determinant of Evolutionary Constraint on Noncoding DNA in Drosophila. Mol Biol Evol 2024; 41:msae004. [PMID: 38364113 PMCID: PMC10871701 DOI: 10.1093/molbev/msae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 11/26/2023] [Accepted: 01/05/2024] [Indexed: 02/18/2024] Open
Abstract
Evolutionary analyses have estimated that ∼60% of nucleotides in intergenic regions of the Drosophila melanogaster genome are functionally relevant, suggesting that regulatory information may be encoded more densely in intergenic regions than has been revealed by most functional dissections of regulatory DNA. Here, we approached this issue through a functional dissection of the regulatory region of the gene shavenbaby (svb). Most of the ∼90 kb of this large regulatory region is highly conserved in the genus Drosophila, though characterized enhancers occupy a small fraction of this region. By analyzing the regulation of svb in different contexts of Drosophila development, we found that the regulatory information that drives svb expression in the abdominal pupal epidermis is organized in a different way than the elements that drive svb expression in the embryonic epidermis. While in the embryonic epidermis svb is activated by compact enhancers separated by large inactive DNA regions, svb expression in the pupal epidermis is driven by regulatory information distributed over broader regions of svb cis-regulatory DNA. In the same vein, we observed that other developmental genes also display a dense distribution of putative regulatory elements in their regulatory regions. Furthermore, we found that a large percentage of conserved noncoding DNA of the Drosophila genome is contained within regions of open chromatin. These results suggest that part of the evolutionary constraint on noncoding DNA of Drosophila is explained by the density of regulatory information, which may be greater than previously appreciated.
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Affiliation(s)
- Gonzalo Sabarís
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad de Buenos Aires (UBA), Buenos Aires 1428, Argentina
- Institute of Human Genetics, UMR 9002 CNRS-Université de Montpellier, Montpellier, France
| | - Daniela M Ortíz
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad de Buenos Aires (UBA), Buenos Aires 1428, Argentina
| | - Ian Laiker
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad de Buenos Aires (UBA), Buenos Aires 1428, Argentina
| | - Ignacio Mayansky
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad de Buenos Aires (UBA), Buenos Aires 1428, Argentina
| | - Sujay Naik
- Department of Genetics and Developmental Biology, The Rappaport Faculty of Medicine and Research Institute, Technion—Israel Institute of Technology, Haifa 3109601, Israel
| | - Giacomo Cavalli
- Institute of Human Genetics, UMR 9002 CNRS-Université de Montpellier, Montpellier, France
| | - David L Stern
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Ella Preger-Ben Noon
- Department of Genetics and Developmental Biology, The Rappaport Faculty of Medicine and Research Institute, Technion—Israel Institute of Technology, Haifa 3109601, Israel
| | - Nicolás Frankel
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad de Buenos Aires (UBA), Buenos Aires 1428, Argentina
- Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales (FCEN), Universidad de Buenos Aires (UBA), Buenos Aires 1428, Argentina
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3
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Ciren D, Zebell S, Lippman ZB. Extreme restructuring of cis -regulatory regions controlling a deeply conserved plant stem cell regulator. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.20.572550. [PMID: 38187729 PMCID: PMC10769289 DOI: 10.1101/2023.12.20.572550] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
A striking paradox is that genes with conserved protein sequence, function and expression pattern over deep time often exhibit extremely divergent cis -regulatory sequences. It remains unclear how such drastic cis -regulatory evolution across species allows preservation of gene function, and to what extent these differences influence how cis- regulatory variation arising within species impacts phenotypic change. Here, we investigated these questions using a plant stem cell regulator conserved in expression pattern and function over ∼125 million years. Using in-vivo genome editing in two distantly related models, Arabidopsis thaliana (Arabidopsis) and Solanum lycopersicum (tomato), we generated over 70 deletion alleles in the upstream and downstream regions of the stem cell repressor gene CLAVATA3 ( CLV3 ) and compared their individual and combined effects on a shared phenotype, the number of carpels that make fruits. We found that sequences upstream of tomato CLV3 are highly sensitive to even small perturbations compared to its downstream region. In contrast, Arabidopsis CLV3 function is tolerant to severe disruptions both upstream and downstream of the coding sequence. Combining upstream and downstream deletions also revealed a different regulatory outcome. Whereas phenotypic enhancement from adding downstream mutations was predominantly weak and additive in tomato, mutating both regions of Arabidopsis CLV3 caused substantial and synergistic effects, demonstrating distinct distribution and redundancy of functional cis -regulatory sequences. Our results demonstrate remarkable malleability in cis -regulatory structural organization of a deeply conserved plant stem cell regulator and suggest that major reconfiguration of cis -regulatory sequence space is a common yet cryptic evolutionary force altering genotype-to-phenotype relationships from regulatory variation in conserved genes. Finally, our findings underscore the need for lineage-specific dissection of the spatial architecture of cis -regulation to effectively engineer trait variation from conserved productivity genes in crops. Author summary We investigated the evolution of cis -regulatory elements (CREs) and their interactions in the regulation of a plant stem cell regulator gene, CLAVATA3 (CLV3) , in Arabidopsis and tomato. Despite diverging ∼125 million years ago, the function and expression of CLV3 is conserved in these species; however, cis -regulatory sequences upstream and downstream have drastically diverged, preventing identification of conserved non-coding sequences between them. We used CRISPR-Cas9 to engineer dozens of mutations within the cis -regulatory regions of Arabidopsis and tomato CLV3. In tomato, our results show that tomato CLV3 function primarily relies on interactions among CREs in the 5' non-coding region, unlike Arabidopsis CLV3 , which depends on a more balanced distribution of functional CREs between the 5' and 3' regions. Therefore, despite a high degree of functional conservation, our study demonstrates divergent regulatory strategies between two distantly related CLV3 orthologs, with substantial alterations in regulatory sequences, their spatial arrangement, and their relative effects on CLV3 regulation. These results suggest that regulatory regions are not only extremely robust to mutagenesis, but also that the sequences underlying this robustness can be lineage-specific for conserved genes, due to the complex and often redundant interactions among CREs that ensure proper gene function amidst large-scale sequence turnover.
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4
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Li XC, Fuqua T, van Breugel ME, Crocker J. Mutational scans reveal differential evolvability of Drosophila promoters and enhancers. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220054. [PMID: 37004721 PMCID: PMC10067265 DOI: 10.1098/rstb.2022.0054] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023] Open
Abstract
Rapid enhancer and slow promoter evolution have been demonstrated through comparative genomics. However, it is not clear how this information is encoded genetically and if this can be used to place evolution in a predictive context. Part of the challenge is that our understanding of the potential for regulatory evolution is biased primarily toward natural variation or limited experimental perturbations. Here, to explore the evolutionary capacity of promoter variation, we surveyed an unbiased mutation library for three promoters in Drosophila melanogaster. We found that mutations in promoters had limited to no effect on spatial patterns of gene expression. Compared to developmental enhancers, promoters are more robust to mutations and have more access to mutations that can increase gene expression, suggesting that their low activity might be a result of selection. Consistent with these observations, increasing the promoter activity at the endogenous locus of shavenbaby led to increased transcription yet limited phenotypic changes. Taken together, developmental promoters may encode robust transcriptional outputs allowing evolvability through the integration of diverse developmental enhancers. This article is part of the theme issue ‘Interdisciplinary approaches to predicting evolutionary biology’.
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Affiliation(s)
- Xueying C. Li
- European Molecular Biology Laboratory, Heidelberg, Baden-Württemberg 69117, Germany
| | - Timothy Fuqua
- European Molecular Biology Laboratory, Heidelberg, Baden-Württemberg 69117, Germany
| | | | - Justin Crocker
- European Molecular Biology Laboratory, Heidelberg, Baden-Württemberg 69117, Germany
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5
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Smith GD, Ching WH, Cornejo-Páramo P, Wong ES. Decoding enhancer complexity with machine learning and high-throughput discovery. Genome Biol 2023; 24:116. [PMID: 37173718 PMCID: PMC10176946 DOI: 10.1186/s13059-023-02955-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
Enhancers are genomic DNA elements controlling spatiotemporal gene expression. Their flexible organization and functional redundancies make deciphering their sequence-function relationships challenging. This article provides an overview of the current understanding of enhancer organization and evolution, with an emphasis on factors that influence these relationships. Technological advancements, particularly in machine learning and synthetic biology, are discussed in light of how they provide new ways to understand this complexity. Exciting opportunities lie ahead as we continue to unravel the intricacies of enhancer function.
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Affiliation(s)
- Gabrielle D Smith
- Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, NSW, Australia
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Kensington, NSW, Australia
| | - Wan Hern Ching
- Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, NSW, Australia
| | - Paola Cornejo-Páramo
- Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, NSW, Australia
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Kensington, NSW, Australia
| | - Emily S Wong
- Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, NSW, Australia.
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Kensington, NSW, Australia.
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6
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Méndez-González ID, Williams TM, Rebeiz M. Changes in locus wide repression underlie the evolution of Drosophila abdominal pigmentation. PLoS Genet 2023; 19:e1010722. [PMID: 37134121 PMCID: PMC10184908 DOI: 10.1371/journal.pgen.1010722] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 05/15/2023] [Accepted: 03/28/2023] [Indexed: 05/04/2023] Open
Abstract
Changes in gene regulation represent an important path to generate developmental differences affecting anatomical traits. Interspecific divergence in gene expression often results from changes in transcription-stimulating enhancer elements. While gene repression is crucial for precise spatiotemporal expression patterns, the relative contribution of repressive transcriptional silencers to regulatory evolution remains to be addressed. Here, we show that the Drosophila pigmentation gene ebony has mainly evolved through changes in the spatial domains of silencers patterning its abdominal expression. By precisely editing the endogenous ebony locus of D. melanogaster, we demonstrate the requirement of two redundant abdominal enhancers and three silencers that repress the redundant enhancers in a patterned manner. We observe a role for changes in these silencers in every case of ebony evolution observed to date. Our findings suggest that negative regulation by silencers likely has an under-appreciated role in gene regulatory evolution.
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Affiliation(s)
- Iván D Méndez-González
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Thomas M Williams
- Department of Biology, University of Dayton, Dayton, Ohio, United States of America
| | - Mark Rebeiz
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
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7
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Ling L, Mühling B, Jaenichen R, Gompel N. Increased chromatin accessibility promotes the evolution of a transcriptional silencer in Drosophila. SCIENCE ADVANCES 2023; 9:eade6529. [PMID: 36800429 PMCID: PMC9937571 DOI: 10.1126/sciadv.ade6529] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 01/17/2023] [Indexed: 06/18/2023]
Abstract
The loss of discrete morphological traits, the most common evolutionary transition, is typically driven by changes in developmental gene expression. Mutations accumulating in regulatory elements of these genes can disrupt DNA binding sites for transcription factors patterning their spatial expression, or delete entire enhancers. Regulatory elements, however, may be silenced through changes in chromatin accessibility or the emergence of repressive elements. Here, we show that increased chromatin accessibility at the gene yellow, combined with the gain of a repressor site, underlies the loss of a wing spot pigmentation pattern in a Drosophila species. The gain of accessibility of this repressive element is regulated by E93, a transcription factor governing the progress of metamorphosis. This convoluted evolutionary scenario contrasts with the parsimonious mutational paths generally envisioned and often documented for morphological losses. It illustrates how evolutionary changes in chromatin accessibility may directly contribute to morphological diversification.
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8
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Buffry AD, Kittelmann S, McGregor AP. Characterisation of the role and regulation of Ultrabithorax in sculpting fine-scale leg morphology. Front Cell Dev Biol 2023; 11:1119221. [PMID: 36861038 PMCID: PMC9968978 DOI: 10.3389/fcell.2023.1119221] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 01/20/2023] [Indexed: 02/16/2023] Open
Abstract
Hox genes are expressed during embryogenesis and determine the regional identity of animal bodies along the antero-posterior axis. However, they also function post-embryonically to sculpt fine-scale morphology. To better understand how Hox genes are integrated into post-embryonic gene regulatory networks, we further analysed the role and regulation of Ultrabithorax (Ubx) during leg development in Drosophila melanogaster. Ubx regulates several aspects of bristle and trichome patterning on the femurs of the second (T2) and third (T3) leg pairs. We found that repression of trichomes in the proximal posterior region of the T2 femur by Ubx is likely mediated by activation of the expression of microRNA-92a and microRNA-92b by this Hox protein. Furthermore, we identified a novel enhancer of Ubx that recapitulates the temporal and regional activity of this gene in T2 and T3 legs. We then used transcription factor (TF) binding motif analysis in regions of accessible chromatin in T2 leg cells to predict and functionally test TFs that may regulate the Ubx leg enhancer. We also tested the role of the Ubx co-factors Homothorax (Hth) and Extradenticle (Exd) in T2 and T3 femurs. We found several TFs that may act upstream or in concert with Ubx to modulate trichome patterning along the proximo-distal axis of developing femurs and that the repression of trichomes also requires Hth and Exd. Taken together our results provide insights into how Ubx is integrated into a post-embryonic gene regulatory network to determine fine-scale leg morphology.
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Affiliation(s)
- Alexandra D. Buffry
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Sebastian Kittelmann
- Centre for Functional Genomics, Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Alistair P. McGregor
- Department of Biosciences, Durham University, Durham, United Kingdom,*Correspondence: Alistair P. McGregor,
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9
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Can changes in 3D genome architecture create new regulatory landscapes that contribute to phenotypic evolution? Essays Biochem 2022; 66:745-752. [PMID: 36250960 DOI: 10.1042/ebc20220057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/20/2022] [Accepted: 09/23/2022] [Indexed: 12/13/2022]
Abstract
Animal genomes are compartmentalized into insulated regulatory units named topology-associated domains (TADs). TADs insulate gene promoters from enhancers that occupy neighboring TADs. Chromosomal rearrangements that disrupt TAD structure can generate new regulatory interactions between enhancers and promoters that were once separated into different TADs, which might lead to new gene expression patterns. On the one hand, TAD rearrangements are known to cause deleterious phenotypes, but, on the other hand, rearrangements can also create novel expression patterns that may be selected during evolution because they generate advantageous phenotypes. Here, we review recent studies that explore the effects of chromosomal rearrangements and genetic perturbations on TAD structure and gene regulation in the context of development and evolution. We discuss the possible contribution of evolutionary breakpoints (EBRs) that affect TAD structure to the evolution of gene regulation and the phenotype.
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10
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Calderon D, Blecher-Gonen R, Huang X, Secchia S, Kentro J, Daza RM, Martin B, Dulja A, Schaub C, Trapnell C, Larschan E, O'Connor-Giles KM, Furlong EEM, Shendure J. The continuum of Drosophila embryonic development at single-cell resolution. Science 2022; 377:eabn5800. [PMID: 35926038 PMCID: PMC9371440 DOI: 10.1126/science.abn5800] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Drosophila melanogaster is a powerful, long-standing model for metazoan development and gene regulation. We profiled chromatin accessibility in almost 1 million and gene expression in half a million nuclei from overlapping windows spanning the entirety of embryogenesis. Leveraging developmental asynchronicity within embryo collections, we applied deep neural networks to infer the age of each nucleus, resulting in continuous, multimodal views of molecular and cellular transitions in absolute time. We identify cell lineages; infer their developmental relationships; and link dynamic changes in enhancer usage, transcription factor (TF) expression, and the accessibility of TFs' cognate motifs. With these data, the dynamics of enhancer usage and gene expression can be explored within and across lineages at the scale of minutes, including for precise transitions like zygotic genome activation.
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Affiliation(s)
- Diego Calderon
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Ronnie Blecher-Gonen
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.,The Crown Genomics Institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Xingfan Huang
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.,Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA 98195, USA
| | - Stefano Secchia
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - James Kentro
- Molecular Biology, Cell Biology, and Biochemistry Graduate Program, Brown University, Providence, RI 02912, USA
| | - Riza M Daza
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Beth Martin
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Alessandro Dulja
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Christoph Schaub
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.,Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA.,Allen Discovery Center for Cell Lineage Tracing, Seattle, WA 98195, USA
| | - Erica Larschan
- Molecular Biology, Cell Biology, and Biochemistry Graduate Program, Brown University, Providence, RI 02912, USA
| | - Kate M O'Connor-Giles
- Department of Neuroscience and Carney Institute for Brain Science, Brown University, Providence, RI 02912, USA
| | - Eileen E M Furlong
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.,Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA.,Allen Discovery Center for Cell Lineage Tracing, Seattle, WA 98195, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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11
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Luecke D, Rice G, Kopp A. Sex-specific evolution of a Drosophila sensory system via interacting cis- and trans-regulatory changes. Evol Dev 2022; 24:37-60. [PMID: 35239254 PMCID: PMC9179014 DOI: 10.1111/ede.12398] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 01/20/2022] [Accepted: 01/25/2022] [Indexed: 12/13/2022]
Abstract
The evolution of gene expression via cis-regulatory changes is well established as a major driver of phenotypic evolution. However, relatively little is known about the influence of enhancer architecture and intergenic interactions on regulatory evolution. We address this question by examining chemosensory system evolution in Drosophila. Drosophila prolongata males show a massively increased number of chemosensory bristles compared to females and males of sibling species. This increase is driven by sex-specific transformation of ancestrally mechanosensory organs. Consistent with this phenotype, the Pox neuro transcription factor (Poxn), which specifies chemosensory bristle identity, shows expanded expression in D. prolongata males. Poxn expression is controlled by nonadditive interactions among widely dispersed enhancers. Although some D. prolongata Poxn enhancers show increased activity, the additive component of this increase is slight, suggesting that most changes in Poxn expression are due to epistatic interactions between Poxn enhancers and trans-regulatory factors. Indeed, the expansion of D. prolongata Poxn enhancer activity is only observed in cells that express doublesex (dsx), the gene that controls sexual differentiation in Drosophila and also shows increased expression in D. prolongata males due to cis-regulatory changes. Although expanded dsx expression may contribute to increased activity of D. prolongata Poxn enhancers, this interaction is not sufficient to explain the full expansion of Poxn expression, suggesting that cis-trans interactions between Poxn, dsx, and additional unknown genes are necessary to produce the derived D. prolongata phenotype. Overall, our results demonstrate the importance of epistatic gene interactions for evolution, particularly when pivotal genes have complex regulatory architecture.
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Affiliation(s)
- David Luecke
- Department of Evolution and Ecology, University of California – Davis,Current Address: Department of Integrative Biology, Michigan State University
| | - Gavin Rice
- Department of Evolution and Ecology, University of California – Davis,Current Address: Department of Biological Sciences, University of Pittsburgh
| | - Artyom Kopp
- Department of Evolution and Ecology, University of California – Davis
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12
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Ficarrotta V, Hanly JJ, Loh LS, Francescutti CM, Ren A, Tunström K, Wheat CW, Porter AH, Counterman BA, Martin A. A genetic switch for male UV iridescence in an incipient species pair of sulphur butterflies. Proc Natl Acad Sci U S A 2022; 119:e2109255118. [PMID: 35012980 PMCID: PMC8784150 DOI: 10.1073/pnas.2109255118] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 11/19/2021] [Indexed: 11/18/2022] Open
Abstract
Mating cues evolve rapidly and can contribute to species formation and maintenance. However, little is known about how sexual signals diverge and how this variation integrates with other barrier loci to shape the genomic landscape of reproductive isolation. Here, we elucidate the genetic basis of ultraviolet (UV) iridescence, a courtship signal that differentiates the males of Colias eurytheme butterflies from a sister species, allowing females to avoid costly heterospecific matings. Anthropogenic range expansion of the two incipient species established a large zone of secondary contact across the eastern United States with strong signatures of genomic admixtures spanning all autosomes. In contrast, Z chromosomes are highly differentiated between the two species, supporting a disproportionate role of sex chromosomes in speciation known as the large-X (or large-Z) effect. Within this chromosome-wide reproductive barrier, linkage mapping indicates that cis-regulatory variation of bric a brac (bab) underlies the male UV-iridescence polymorphism between the two species. Bab is expressed in all non-UV scales, and butterflies of either species or sex acquire widespread ectopic iridescence following its CRISPR knockout, demonstrating that Bab functions as a suppressor of UV-scale differentiation that potentiates mating cue divergence. These results highlight how a genetic switch can regulate a premating signal and integrate with other reproductive barriers during intermediate phases of speciation.
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Affiliation(s)
- Vincent Ficarrotta
- Department of Biological Sciences, The George Washington University, Washington, DC 20052
| | - Joseph J Hanly
- Department of Biological Sciences, The George Washington University, Washington, DC 20052
| | - Ling S Loh
- Department of Biological Sciences, The George Washington University, Washington, DC 20052
| | | | - Anna Ren
- Department of Biological Sciences, The George Washington University, Washington, DC 20052
| | - Kalle Tunström
- Department of Zoology, Stockholm University, Stockholm S-10691, Sweden
| | | | - Adam H Porter
- Department of Biology, University of Massachusetts Amherst, Amherst, MA 01003
| | | | - Arnaud Martin
- Department of Biological Sciences, The George Washington University, Washington, DC 20052;
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13
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Pu J, Wang Z, Cong H, Chin JSR, Justen J, Finet C, Yew JY, Chung H. Repression precedes independent evolutionary gains of a highly specific gene expression pattern. Cell Rep 2021; 37:109896. [PMID: 34706247 PMCID: PMC8578697 DOI: 10.1016/j.celrep.2021.109896] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 08/24/2021] [Accepted: 10/06/2021] [Indexed: 12/12/2022] Open
Abstract
Highly specific expression patterns can be caused by the overlapping activities of activator and repressor sequences in enhancers. However, few studies illuminate how these sequences evolve in the origin of new enhancers. Here, we show that expression of the bond gene in the semicircular wall epithelium (swe) of the Drosophila melanogaster male ejaculatory bulb (EB) is controlled by an enhancer consisting of an activator region that requires Abdominal-B driving expression in the entire EB and a repressor region that restricts this expression to the EB swe. Although this expression pattern is independently gained in the distantly related Scaptodrosophila lebanonensis and does not require Abdominal-B, we show that functionally similar repressor sequences are present in Scaptodrosophila and also in species that do not express bond in the EB. We suggest that during enhancer evolution, repressor sequences can precede the evolution of activator sequences and may lead to similar but independently evolved expression patterns. Pu et al. show that the independent gain of a highly specific expression pattern across distantly related species may be because of the preexistence of repressor sequences that precedes the diversification of these species. This may reflect a general mechanism underlying the evolution of highly specific enhancers.
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Affiliation(s)
- Jian Pu
- Department of Entomology, Michigan State University, East Lansing, MI 48824, USA.
| | - Zinan Wang
- Department of Entomology, Michigan State University, East Lansing, MI 48824, USA; Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI 48824, USA
| | - Haosu Cong
- Department of Entomology, Michigan State University, East Lansing, MI 48824, USA
| | - Jacqueline S R Chin
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A(∗)STAR), Brenner Centre for Molecular Medicine, Singapore 117609, Singapore
| | - Jessa Justen
- Laboratory of Cellular and Molecular Biology, University of Wisconsin, Madison, WI 53706, USA
| | - Cédric Finet
- Yale-NUS College, 16 College Avenue West, Singapore 138527, Singapore
| | - Joanne Y Yew
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, HI 96822, USA
| | - Henry Chung
- Department of Entomology, Michigan State University, East Lansing, MI 48824, USA; Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI 48824, USA.
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14
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Al Hayek S, Alsawadi A, Kambris Z, Boquete JP, Bohère J, Immarigeon C, Ronsin B, Plaza S, Lemaitre B, Payre F, Osman D. Steroid-dependent switch of OvoL/Shavenbaby controls self-renewal versus differentiation of intestinal stem cells. EMBO J 2021; 40:e104347. [PMID: 33372708 PMCID: PMC7883054 DOI: 10.15252/embj.2019104347] [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: 12/24/2019] [Revised: 11/23/2020] [Accepted: 11/24/2020] [Indexed: 12/27/2022] Open
Abstract
Adult stem cells must continuously fine-tune their behavior to regenerate damaged organs and avoid tumors. While several signaling pathways are well known to regulate somatic stem cells, the underlying mechanisms remain largely unexplored. Here, we demonstrate a cell-intrinsic role for the OvoL family transcription factor, Shavenbaby (Svb), in balancing self-renewal and differentiation of Drosophila intestinal stem cells. We find that svb is a downstream target of Wnt and EGFR pathways, mediating their activity for stem cell survival and proliferation. This requires post-translational processing of Svb into a transcriptional activator, whose upregulation induces tumor-like stem cell hyperproliferation. In contrast, the unprocessed form of Svb acts as a repressor that imposes differentiation into enterocytes, and suppresses tumors induced by altered signaling. We show that the switch between Svb repressor and activator is triggered in response to systemic steroid hormone, which is produced by ovaries. Therefore, the Svb axis allows intrinsic integration of local signaling cues and inter-organ communication to adjust stem cell proliferation versus differentiation, suggesting a broad role of OvoL/Svb in adult and cancer stem cells.
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Affiliation(s)
- Sandy Al Hayek
- Faculty of Sciences III, Lebanese University, Tripoli, Lebanon.,Azm Center for Research in Biotechnology and its Applications, LBA3B, EDST, Lebanese University, Tripoli, Lebanon.,Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Toulouse, France
| | - Ahmad Alsawadi
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Toulouse, France
| | - Zakaria Kambris
- Biology Department, Faculty of Arts and Sciences, American University of Beirut, Beirut, Lebanon
| | | | - Jérôme Bohère
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Toulouse, France
| | - Clément Immarigeon
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Toulouse, France
| | - Brice Ronsin
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Toulouse, France
| | - Serge Plaza
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Toulouse, France
| | - Bruno Lemaitre
- Global Health Institute, School of Life Sciences, Lausanne, Switzerland
| | - François Payre
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Toulouse, France
| | - Dani Osman
- Faculty of Sciences III, Lebanese University, Tripoli, Lebanon.,Azm Center for Research in Biotechnology and its Applications, LBA3B, EDST, Lebanese University, Tripoli, Lebanon
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15
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Kittelmann S, Preger-Ben Noon E, McGregor AP, Frankel N. A complex gene regulatory architecture underlies the development and evolution of cuticle morphology in Drosophila. Curr Opin Genet Dev 2021; 69:21-27. [PMID: 33529925 DOI: 10.1016/j.gde.2021.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/18/2020] [Accepted: 01/05/2021] [Indexed: 10/22/2022]
Abstract
The cuticle of insects is decorated with non-sensory hairs called trichomes. A few Drosophila species independently lost most of the dorso-lateral trichomes on first instar larvae. Genetic experiments revealed that this naked cuticle phenotype was caused by the evolution of enhancer function at the ovo/shavenbaby (ovo/svb) locus. Here we explore how this discovery catalyzed major new insights into morphological evolution in different developmental contexts, enhancer pleiotropy in gene regulation and the functionality and evolution of the Svb gene regulatory network (GRN). Taken together this highlights the importance of understanding the architecture and evolution of gene regulatory networks in detail and the great potential for further study of the Svb GRN.
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Affiliation(s)
- Sebastian Kittelmann
- Centre for Functional Genomics, Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, United Kingdom
| | - Ella Preger-Ben Noon
- Department of Genetics and Developmental Biology, The Rappaport Faculty of Medicine and Research Institute, Technion - Israel Institute of Technology, Haifa 3109601, Israel
| | - Alistair P McGregor
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, United Kingdom
| | - Nicolás Frankel
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE, CONICET-UBA), Buenos Aires 1428, Argentina; Departamento de Ecología, Genética y Evolución (FCEyN, UBA), Buenos Aires 1428, Argentina.
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16
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Tsai A, Galupa R, Crocker J. Robust and efficient gene regulation through localized nuclear microenvironments. Development 2020; 147:147/19/dev161430. [PMID: 33020073 DOI: 10.1242/dev.161430] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Developmental enhancers drive gene expression in specific cell types during animal development. They integrate signals from many different sources mediated through the binding of transcription factors, producing specific responses in gene expression. Transcription factors often bind low-affinity sequences for only short durations. How brief, low-affinity interactions drive efficient transcription and robust gene expression is a central question in developmental biology. Localized high concentrations of transcription factors have been suggested as a possible mechanism by which to use these enhancer sites effectively. Here, we discuss the evidence for such transcriptional microenvironments, mechanisms for their formation and the biological consequences of such sub-nuclear compartmentalization for developmental decisions and evolution.
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Affiliation(s)
- Albert Tsai
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Rafael Galupa
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Justin Crocker
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
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17
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Hajheidari M, Wang Y, Bhatia N, Vuolo F, Franco-Zorrilla JM, Karady M, Mentink RA, Wu A, Oluwatobi BR, Müller B, Dello Ioio R, Laurent S, Ljung K, Huijser P, Gan X, Tsiantis M. Autoregulation of RCO by Low-Affinity Binding Modulates Cytokinin Action and Shapes Leaf Diversity. Curr Biol 2019; 29:4183-4192.e6. [PMID: 31761704 DOI: 10.1016/j.cub.2019.10.040] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 10/08/2019] [Accepted: 10/21/2019] [Indexed: 11/28/2022]
Abstract
Mechanisms through which the evolution of gene regulation causes morphological diversity are largely unclear. The tremendous shape variation among plant leaves offers attractive opportunities to address this question. In cruciferous plants, the REDUCED COMPLEXITY (RCO) homeodomain protein evolved via gene duplication and acquired a novel expression domain that contributed to leaf shape diversity. However, the molecular pathways through which RCO regulates leaf growth are unknown. A key question is to identify genome-wide transcriptional targets of RCO and the DNA sequences to which RCO binds. We investigate this question using Cardamine hirsuta, which has complex leaves, and its relative Arabidopsis thaliana, which evolved simple leaves through loss of RCO. We demonstrate that RCO directly regulates genes controlling homeostasis of the hormone cytokinin to repress growth at the leaf base. Elevating cytokinin signaling in the RCO expression domain is sufficient to both transform A. thaliana simple leaves into complex ones and partially bypass the requirement for RCO in C. hirsuta complex leaf development. We also identify RCO as its own target gene. RCO directly represses its own transcription via an array of low-affinity binding sites, which evolved after RCO duplicated from its progenitor sequence. This autorepression is required to limit RCO expression. Thus, evolution of low-affinity binding sites created a negative autoregulatory loop that facilitated leaf shape evolution by defining RCO expression and fine-tuning cytokinin activity. In summary, we identify a transcriptional mechanism through which conflicts between novelty and pleiotropy are resolved during evolution and lead to morphological differences between species.
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Affiliation(s)
- Mohsen Hajheidari
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Yi Wang
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Neha Bhatia
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Francesco Vuolo
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - José Manuel Franco-Zorrilla
- Unidad de Genómica and Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas, Calle Darwin 3, 28049 Madrid, Spain
| | - Michal Karady
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83 Umeå, Sweden
| | - Remco A Mentink
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Anhui Wu
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Bello Rilwan Oluwatobi
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Bruno Müller
- Leibniz Institute of Plant Genetics and Crop Plant Research, Correnstr. 3, 06466 Seeland, Gatersleben, Germany
| | - Raffaele Dello Ioio
- Department of Biology and Biotechnology, Laboratory of Functional Genomics and Proteomics of Model Systems, Sapienza University of Rome, Via dei Sardi 70, 00185 Rome, Italy
| | - Stefan Laurent
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Karin Ljung
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83 Umeå, Sweden
| | - Peter Huijser
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Xiangchao Gan
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Miltos Tsiantis
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany.
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18
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Sabarís G, Laiker I, Preger-Ben Noon E, Frankel N. Actors with Multiple Roles: Pleiotropic Enhancers and the Paradigm of Enhancer Modularity. Trends Genet 2019; 35:423-433. [DOI: 10.1016/j.tig.2019.03.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 03/21/2019] [Indexed: 10/27/2022]
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19
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Ray S, Rosenberg MI, Chanut-Delalande H, Decaras A, Schwertner B, Toubiana W, Auman T, Schnellhammer I, Teuscher M, Valenti P, Khila A, Klingler M, Payre F. The mlpt/Ubr3/Svb module comprises an ancient developmental switch for embryonic patterning. eLife 2019; 8:e39748. [PMID: 30896406 PMCID: PMC6428570 DOI: 10.7554/elife.39748] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 03/07/2019] [Indexed: 12/30/2022] Open
Abstract
Small open reading frames (smORFs) encoding 'micropeptides' exhibit remarkable evolutionary complexity. Conserved peptides encoded by mille-pattes (mlpt)/polished rice (pri)/tarsal less (tal) are essential for embryo segmentation in Tribolium but, in Drosophila, function in terminal epidermal differentiation and patterning of adult legs. Here, we show that a molecular complex identified in Drosophila epidermal differentiation, comprising Mlpt peptides, ubiquitin-ligase Ubr3 and transcription factor Shavenbaby (Svb), represents an ancient developmental module required for early insect embryo patterning. We find that loss of segmentation function for this module in flies evolved concomitantly with restriction of Svb expression in early Drosophila embryos. Consistent with this observation, artificially restoring early Svb expression in flies causes segmentation defects that depend on mlpt function, demonstrating enduring potency of an ancestral developmental switch despite evolving embryonic patterning modes. These results highlight the evolutionary plasticity of conserved molecular complexes under the constraints of essential genetic networks. Editorial note This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).
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Affiliation(s)
- Suparna Ray
- Department of Biology, Developmental BiologyUniversity of Erlangen-NurembergErlangenGermany
| | - Miriam I Rosenberg
- Department of Ecology, Evolution and BehaviorHebrew University of JerusalemJerusalemIsrael
| | | | | | - Barbara Schwertner
- Department of Biology, Developmental BiologyUniversity of Erlangen-NurembergErlangenGermany
| | | | - Tzach Auman
- Department of Ecology, Evolution and BehaviorHebrew University of JerusalemJerusalemIsrael
| | - Irene Schnellhammer
- Department of Biology, Developmental BiologyUniversity of Erlangen-NurembergErlangenGermany
| | - Matthias Teuscher
- Department of Biology, Developmental BiologyUniversity of Erlangen-NurembergErlangenGermany
| | - Philippe Valenti
- Centre de Biologie du Développement, Université Paul Sabatier de ToulouseToulouseFrance
| | | | - Martin Klingler
- Department of Biology, Developmental BiologyUniversity of Erlangen-NurembergErlangenGermany
| | - François Payre
- Centre de Biologie du Développement, Université Paul Sabatier de ToulouseToulouseFrance
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20
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Redundant and Cryptic Enhancer Activities of the Drosophila yellow Gene. Genetics 2019; 212:343-360. [PMID: 30842209 DOI: 10.1534/genetics.119.301985] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 02/25/2019] [Indexed: 11/18/2022] Open
Abstract
Cis-regulatory sequences known as enhancers play a key role in regulating gene expression. Evolutionary changes in these DNA sequences contribute to phenotypic evolution. The Drosophila yellow gene, which is required for pigmentation, has emerged as a model system for understanding how cis-regulatory sequences evolve, providing some of the most detailed insights available into how activities of orthologous enhancers have diverged between species. Here, we examine the evolution of yellow cis-regulatory sequences on a broader scale, by comparing the distribution and function of yellow enhancer activities throughout the 5' intergenic and intronic sequences of Drosophila melanogaster, D. pseudoobscura, and D. willistoni We find that cis-regulatory sequences driving expression in a particular tissue are not as modular as previously described, but rather have many redundant and cryptic enhancer activities distributed throughout the regions surveyed. Interestingly, cryptic enhancer activities of sequences from one species often drove patterns of expression observed in other species, suggesting that the frequent evolutionary changes in yellow expression observed among Drosophila species may be facilitated by gaining and losing repression of preexisting cis-regulatory sequences.
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21
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Bohère J, Mancheno-Ferris A, Al Hayek S, Zanet J, Valenti P, Akino K, Yamabe Y, Inagaki S, Chanut-Delalande H, Plaza S, Kageyama Y, Osman D, Polesello C, Payre F. Shavenbaby and Yorkie mediate Hippo signaling to protect adult stem cells from apoptosis. Nat Commun 2018; 9:5123. [PMID: 30504772 PMCID: PMC6269459 DOI: 10.1038/s41467-018-07569-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 11/12/2018] [Indexed: 01/06/2023] Open
Abstract
To compensate for accumulating damages and cell death, adult homeostasis (e.g., body fluids and secretion) requires organ regeneration, operated by long-lived stem cells. How stem cells can survive throughout the animal life remains poorly understood. Here we show that the transcription factor Shavenbaby (Svb, OvoL in vertebrates) is expressed in renal/nephric stem cells (RNSCs) of Drosophila and required for their maintenance during adulthood. As recently shown in embryos, Svb function in adult RNSCs further needs a post-translational processing mediated by the Polished rice (Pri) smORF peptides and impairing Svb function leads to RNSC apoptosis. We show that Svb interacts both genetically and physically with Yorkie (YAP/TAZ in vertebrates), a nuclear effector of the Hippo pathway, to activate the expression of the inhibitor of apoptosis DIAP1. These data therefore identify Svb as a nuclear effector in the Hippo pathway, critical for the survival of adult somatic stem cells.
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Affiliation(s)
- Jérôme Bohère
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Bat 4R3, 118 route de Narbonne, F-31062, Toulouse, France
| | - Alexandra Mancheno-Ferris
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Bat 4R3, 118 route de Narbonne, F-31062, Toulouse, France
| | - Sandy Al Hayek
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Bat 4R3, 118 route de Narbonne, F-31062, Toulouse, France
- Faculty of Sciences III, Lebanese University, Tripoli, 1300, Lebanon
- Azm Center for Research in Biotechnology and its Applications, LBA3B, EDST, Lebanese University, Tripoli, 1300, Lebanon
| | - Jennifer Zanet
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Bat 4R3, 118 route de Narbonne, F-31062, Toulouse, France
| | - Philippe Valenti
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Bat 4R3, 118 route de Narbonne, F-31062, Toulouse, France
| | - Kohsuke Akino
- Department of Biology, Graduate School of Science, Kobe, 657-8501, Japan
| | - Yuya Yamabe
- Department of Biology, Graduate School of Science, Kobe, 657-8501, Japan
| | - Sachi Inagaki
- Biosignal Research Center, Kobe University, 1-1 Rokko-dai, Nada, Kobe, 657-8501, Japan
| | - Hélène Chanut-Delalande
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Bat 4R3, 118 route de Narbonne, F-31062, Toulouse, France
| | - Serge Plaza
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Bat 4R3, 118 route de Narbonne, F-31062, Toulouse, France
- Laboratoire de Recherche en Sciences Végétales (LSRV), CNRS, UPS, 24 chemin de Borde Rouge, Auzeville, 31326, Castanet-Tolosan, France
| | - Yuji Kageyama
- Department of Biology, Graduate School of Science, Kobe, 657-8501, Japan
- Biosignal Research Center, Kobe University, 1-1 Rokko-dai, Nada, Kobe, 657-8501, Japan
| | - Dani Osman
- Faculty of Sciences III, Lebanese University, Tripoli, 1300, Lebanon
- Azm Center for Research in Biotechnology and its Applications, LBA3B, EDST, Lebanese University, Tripoli, 1300, Lebanon
| | - Cédric Polesello
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Bat 4R3, 118 route de Narbonne, F-31062, Toulouse, France.
| | - François Payre
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Bat 4R3, 118 route de Narbonne, F-31062, Toulouse, France.
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22
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Gene regulatory network architecture in different developmental contexts influences the genetic basis of morphological evolution. PLoS Genet 2018; 14:e1007375. [PMID: 29723190 PMCID: PMC5953500 DOI: 10.1371/journal.pgen.1007375] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 05/15/2018] [Accepted: 04/23/2018] [Indexed: 01/09/2023] Open
Abstract
Convergent phenotypic evolution is often caused by recurrent changes at particular nodes in the underlying gene regulatory networks (GRNs). The genes at such evolutionary ‘hotspots’ are thought to maximally affect the phenotype with minimal pleiotropic consequences. This has led to the suggestion that if a GRN is understood in sufficient detail, the path of evolution may be predictable. The repeated evolutionary loss of larval trichomes among Drosophila species is caused by the loss of shavenbaby (svb) expression. svb is also required for development of leg trichomes, but the evolutionary gain of trichomes in the ‘naked valley’ on T2 femurs in Drosophila melanogaster is caused by reduced microRNA-92a (miR-92a) expression rather than changes in svb. We compared the expression and function of components between the larval and leg trichome GRNs to investigate why the genetic basis of trichome pattern evolution differs in these developmental contexts. We found key differences between the two networks in both the genes employed, and in the regulation and function of common genes. These differences in the GRNs reveal why mutations in svb are unlikely to contribute to leg trichome evolution and how instead miR-92a represents the key evolutionary switch in this context. Our work shows that variability in GRNs across different developmental contexts, as well as whether a morphological feature is lost versus gained, influence the nodes at which a GRN evolves to cause morphological change. Therefore, our findings have important implications for understanding the pathways and predictability of evolution. A major goal of biology is to identify the genetic causes of organismal diversity. Convergent evolution of traits is often caused by changes in the same genes–evolutionary ‘hotspots’. shavenbaby is a ‘hotspot’ for larval trichome loss in Drosophila, but microRNA-92a underlies the gain of leg trichomes. To understand this difference in the genetics of phenotypic evolution, we compared the expression and function of genes in the underlying regulatory networks. We found that the pathway of evolution is influenced by differences in gene regulatory network architecture in different developmental contexts, as well as by whether a trait is lost or gained. Therefore, hotspots in one context may not readily evolve in a different context. This has important implications for understanding the genetic basis of phenotypic change and the predictability of evolution.
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24
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Crocker J, Ilsley GR. Using synthetic biology to study gene regulatory evolution. Curr Opin Genet Dev 2017; 47:91-101. [DOI: 10.1016/j.gde.2017.09.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 09/06/2017] [Accepted: 09/11/2017] [Indexed: 12/21/2022]
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25
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Infante CR, Rasys AM, Menke DB. Appendages and gene regulatory networks: Lessons from the limbless. Genesis 2017; 56. [PMID: 29076617 DOI: 10.1002/dvg.23078] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 10/06/2017] [Accepted: 10/06/2017] [Indexed: 01/19/2023]
Abstract
Among squamate reptiles, dozens of lineages have independently evolved complete or partial limb reduction. This remarkable convergence of limbless and limb-reduced phenotypes provides multiple natural replicates of different ages to explore the evolution and development of the vertebrate limb and the gene regulatory network that controls its formation. The most successful and best known of the limb-reduced squamates are snakes, which evolved a limb-reduced body form more than 100 million years ago. Recent studies have revealed the unexpected finding that many ancient limb enhancers are conserved in the genomes of snakes. Analyses in limbed animals show that many of these limb enhancers are also active during development of the phallus, suggesting that these enhancers may have been retained in snakes due their importance in regulating transcription in the external genitalia. This hypothesis is substantiated by functional tests of snake enhancers, which demonstrate that snake enhancer elements have lost limb function while retaining genital enhancer function. The large degree of overlap in the gene regulatory networks deployed during limb and phallus development may act to constrain the divergence of shared gene network components and the evolution of appendage morphology. Future studies will reveal whether limb regulatory elements have undergone similar functional changes in other lineages of limb-reduced squamates.
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Affiliation(s)
- Carlos R Infante
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, 85721
| | - Ashley M Rasys
- Department of Cellular Biology, University of Georgia, Athens, Georgia, 30602.,Department of Genetics, University of Georgia, Athens, Georgia, 30602
| | - Douglas B Menke
- Department of Genetics, University of Georgia, Athens, Georgia, 30602
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Rebeiz M, Tsiantis M. Enhancer evolution and the origins of morphological novelty. Curr Opin Genet Dev 2017; 45:115-123. [PMID: 28527813 DOI: 10.1016/j.gde.2017.04.006] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 03/25/2017] [Accepted: 04/27/2017] [Indexed: 01/07/2023]
Abstract
A central goal of evolutionary biology is to understand the genetic origin of morphological novelties-i.e. anatomical structures unique to a taxonomic group. Elaboration of morphology during development depends on networks of regulatory genes that activate patterned gene expression through transcriptional enhancer regions. We summarize recent case studies and genome-wide investigations that have uncovered diverse mechanisms though which new enhancers arise. We also discuss how these enhancer-originating mechanisms have clarified the history of genetic networks underlying diversification of genital structures in flies, limbs and neural crest in chordates, and plant leaves. These studies have identified enhancers that were pivotal for morphological divergence and highlighted how novel genetic networks shaping form emerged from pre-existing ones.
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Affiliation(s)
- Mark Rebeiz
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15215, USA.
| | - Miltos Tsiantis
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, 50829 Köln, Germany.
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