1
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Wu S, Tong X, Peng C, Luo J, Zhang C, Lu K, Li C, Ding X, Duan X, Lu Y, Hu H, Tan D, Dai F. The BTB-ZF gene Bm-mamo regulates pigmentation in silkworm caterpillars. eLife 2024; 12:RP90795. [PMID: 38587455 PMCID: PMC11001300 DOI: 10.7554/elife.90795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2024] Open
Abstract
The color pattern of insects is one of the most diverse adaptive evolutionary phenotypes. However, the molecular regulation of this color pattern is not fully understood. In this study, we found that the transcription factor Bm-mamo is responsible for black dilute (bd) allele mutations in the silkworm. Bm-mamo belongs to the BTB zinc finger family and is orthologous to mamo in Drosophila melanogaster. This gene has a conserved function in gamete production in Drosophila and silkworms and has evolved a pleiotropic function in the regulation of color patterns in caterpillars. Using RNAi and clustered regularly interspaced short palindromic repeats (CRISPR) technology, we showed that Bm-mamo is a repressor of dark melanin patterns in the larval epidermis. Using in vitro binding assays and gene expression profiling in wild-type and mutant larvae, we also showed that Bm-mamo likely regulates the expression of related pigment synthesis and cuticular protein genes in a coordinated manner to mediate its role in color pattern formation. This mechanism is consistent with the dual role of this transcription factor in regulating both the structure and shape of the cuticle and the pigments that are embedded within it. This study provides new insight into the regulation of color patterns as well as into the construction of more complex epidermal features in some insects.
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Affiliation(s)
- Songyuan Wu
- State Key Laboratory of Resource Insects, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Sericulture, Textile and Biomass Sciences, Southwest UniversityChongqingChina
| | - Xiaoling Tong
- State Key Laboratory of Resource Insects, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Sericulture, Textile and Biomass Sciences, Southwest UniversityChongqingChina
| | - Chenxing Peng
- State Key Laboratory of Resource Insects, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Sericulture, Textile and Biomass Sciences, Southwest UniversityChongqingChina
| | - Jiangwen Luo
- State Key Laboratory of Resource Insects, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Sericulture, Textile and Biomass Sciences, Southwest UniversityChongqingChina
| | - Chenghao Zhang
- State Key Laboratory of Resource Insects, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Sericulture, Textile and Biomass Sciences, Southwest UniversityChongqingChina
| | - Kunpeng Lu
- State Key Laboratory of Resource Insects, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Sericulture, Textile and Biomass Sciences, Southwest UniversityChongqingChina
| | - Chunlin Li
- State Key Laboratory of Resource Insects, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Sericulture, Textile and Biomass Sciences, Southwest UniversityChongqingChina
| | - Xin Ding
- State Key Laboratory of Resource Insects, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Sericulture, Textile and Biomass Sciences, Southwest UniversityChongqingChina
| | - Xiaohui Duan
- State Key Laboratory of Resource Insects, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Sericulture, Textile and Biomass Sciences, Southwest UniversityChongqingChina
| | - Yaru Lu
- State Key Laboratory of Resource Insects, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Sericulture, Textile and Biomass Sciences, Southwest UniversityChongqingChina
| | - Hai Hu
- State Key Laboratory of Resource Insects, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Sericulture, Textile and Biomass Sciences, Southwest UniversityChongqingChina
| | - Duan Tan
- State Key Laboratory of Resource Insects, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Sericulture, Textile and Biomass Sciences, Southwest UniversityChongqingChina
| | - Fangyin Dai
- State Key Laboratory of Resource Insects, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Sericulture, Textile and Biomass Sciences, Southwest UniversityChongqingChina
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2
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Bachem K, Li X, Ceolin S, Mühling B, Hörl D, Harz H, Leonhardt H, Arnoult L, Weber S, Matarlo B, Prud’homme B, Gompel N. Regulatory evolution tuning pigmentation intensity quantitatively in Drosophila. SCIENCE ADVANCES 2024; 10:eadl2616. [PMID: 38266088 PMCID: PMC10807792 DOI: 10.1126/sciadv.adl2616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 12/21/2023] [Indexed: 01/26/2024]
Abstract
Quantitative variation in attributes such as color, texture, or stiffness dominates morphological diversification. It results from combinations of alleles at many Mendelian loci. Here, we identify an additional source of quantitative variation among species, continuous evolution in a gene regulatory region. Specifically, we examined the modulation of wing pigmentation in a group of fly species and showed that inter-species variation correlated with the quantitative expression of the pigmentation gene yellow. This variation results from an enhancer of yellow determining darkness through species-specific activity. We mapped the divergent activities between two sister species and found the changes to be broadly distributed along the enhancer. Our results demonstrate that enhancers can act as dials fueling quantitative morphological diversification by modulating trait properties.
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Affiliation(s)
- Katharina Bachem
- Department of Evolutionary Ecology, Ludwig-Maximilians Universität München, München 82152, Germany
| | - Xinyi Li
- Department of Evolutionary Ecology, Ludwig-Maximilians Universität München, München 82152, Germany
| | - Stefano Ceolin
- Department of Evolutionary Ecology, Ludwig-Maximilians Universität München, München 82152, Germany
| | - Bettina Mühling
- Department of Evolutionary Ecology, Ludwig-Maximilians Universität München, München 82152, Germany
| | - David Hörl
- Human Biology and Bioimaging, Ludwig-Maximilians Universität München, München 82152, Germany
| | - Hartmann Harz
- Human Biology and Bioimaging, Ludwig-Maximilians Universität München, München 82152, Germany
| | - Heinrich Leonhardt
- Human Biology and Bioimaging, Ludwig-Maximilians Universität München, München 82152, Germany
| | - Laurent Arnoult
- Institut de Biologie du Développement de Marseille, Aix-Marseille Université, Marseille 13288, France
| | - Sabrina Weber
- Department of Evolutionary Ecology, Ludwig-Maximilians Universität München, München 82152, Germany
| | - Blair Matarlo
- Department of Evolutionary Ecology, Ludwig-Maximilians Universität München, München 82152, Germany
| | - Benjamin Prud’homme
- Institut de Biologie du Développement de Marseille, Aix-Marseille Université, Marseille 13288, France
| | - Nicolas Gompel
- Department of Evolutionary Ecology, Ludwig-Maximilians Universität München, München 82152, Germany
- Bonn Institute for Organismic Biology, University of Bonn, Bonn 53115, Germany
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3
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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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4
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Galupa R, Alvarez-Canales G, Borst NO, Fuqua T, Gandara L, Misunou N, Richter K, Alves MRP, Karumbi E, Perkins ML, Kocijan T, Rushlow CA, Crocker J. Enhancer architecture and chromatin accessibility constrain phenotypic space during Drosophila development. Dev Cell 2023; 58:51-62.e4. [PMID: 36626871 PMCID: PMC9860173 DOI: 10.1016/j.devcel.2022.12.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/18/2022] [Accepted: 12/07/2022] [Indexed: 01/11/2023]
Abstract
Developmental enhancers bind transcription factors and dictate patterns of gene expression during development. Their molecular evolution can underlie phenotypical evolution, but the contributions of the evolutionary pathways involved remain little understood. Here, using mutation libraries in Drosophila melanogaster embryos, we observed that most point mutations in developmental enhancers led to changes in gene expression levels but rarely resulted in novel expression outside of the native pattern. In contrast, random sequences, often acting as developmental enhancers, drove expression across a range of cell types; random sequences including motifs for transcription factors with pioneer activity acted as enhancers even more frequently. Our findings suggest that the phenotypic landscapes of developmental enhancers are constrained by enhancer architecture and chromatin accessibility. We propose that the evolution of existing enhancers is limited in its capacity to generate novel phenotypes, whereas the activity of de novo elements is a primary source of phenotypic novelty.
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Affiliation(s)
- Rafael Galupa
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
| | | | | | - Timothy Fuqua
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Lautaro Gandara
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Natalia Misunou
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Kerstin Richter
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | | | - Esther Karumbi
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | | | - Tin Kocijan
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | | | - Justin Crocker
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
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5
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Laiker I, Frankel N. Pleiotropic enhancers are ubiquitous regulatory elements in the human genome. Genome Biol Evol 2022; 14:6585219. [PMID: 35552697 PMCID: PMC9156028 DOI: 10.1093/gbe/evac071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/09/2022] [Indexed: 11/13/2022] Open
Abstract
Enhancers are regulatory elements of genomes that determine spatio-temporal patterns of gene expression. The human genome contains a vast number of enhancers, which largely outnumber protein-coding genes. Historically, enhancers have been regarded as highly tissue-specific. However, recent evidence has demonstrated that many enhancers are pleiotropic, with activity in multiple developmental contexts. Yet, the extent and impact of pleiotropy remain largely unexplored. In this study we analyzed active enhancers across human organs based on the analysis of both eRNA transcription (FANTOM5 consortium data sets) and chromatin architecture (ENCODE consortium data sets). We show that pleiotropic enhancers are pervasive in the human genome and that most enhancers active in a particular organ are also active in other organs. In addition, our analysis suggests that the proportion of context-specific enhancers of a given organ is explained, at least in part, by the proportion of context-specific genes in that same organ. The notion that such a high proportion of human enhancers can be pleiotropic suggests that small regions of regulatory DNA contain abundant regulatory information and that these regions evolve under important evolutionary constraints.
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Affiliation(s)
- Ian Laiker
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) y Universidad de Buenos Aires (UBA), Buenos Aires 1428, Argentina
| | - Nicolas Frankel
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) y 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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6
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Akiyama N, Sato S, Tanaka KM, Sakai T, Takahashi A. The role of the epidermis enhancer element in positive and negative transcriptional regulation of ebony in Drosophila melanogaster. G3 GENES|GENOMES|GENETICS 2022; 12:6506522. [PMID: 35100378 PMCID: PMC8895987 DOI: 10.1093/g3journal/jkac010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 01/06/2022] [Indexed: 11/15/2022]
Abstract
The spatiotemporal regulation of gene expression is essential to ensure robust phenotypic outcomes. Pigmentation patterns in Drosophila are determined by pigments biosynthesized in the developing epidermis and the cis-regulatory elements of the genes involved in this process are well-characterized. Here, we report that the known primary epidermal enhancer is dispensable for the transcriptional activation of ebony (involved in light-colored pigment synthesis) in the developing epidermis of Drosophila melanogaster. The evidence was obtained by introducing an approximately 1 kbp deletion at the primary epidermal enhancer by genome editing. The effect of the primary epidermal enhancer deletion on pigmentation and on the endogenous expression pattern of a mCherry-fused ebony allele was examined in the abdomen. The expression levels of the mCherry-fused ebony in the primary epidermal enhancer-deleted strains were slightly higher than that of the control strain, indicating that the sequences outside the primary epidermal enhancer have an ability to drive an expression of this gene in the epidermis. Interestingly, the primary epidermal enhancer deletion resulted in a derepression of this gene in the dorsal midline of the abdominal tergites, where dark pigmentation is present in the wild-type individuals. This indicated that the primary epidermal enhancer fragment contains a silencer. Furthermore, the endogenous expression pattern of ebony in the 2 additional strains with partially deleted primary epidermal enhancer revealed that the silencer resides within a 351-bp fragment in the 5' portion of the primary epidermal enhancer. These results demonstrated that deletion assays combined with reporter assays are highly effective in detecting the presence of positively and negatively regulating sequences within and outside the focal cis-regulatory elements.
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Affiliation(s)
- Noriyoshi Akiyama
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji 192-0397, Japan
| | - Shoma Sato
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji 192-0397, Japan
| | - Kentaro M Tanaka
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji 192-0397, Japan
| | - Takaomi Sakai
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji 192-0397, Japan
| | - Aya Takahashi
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji 192-0397, Japan
- Research Center for Genomics and Bioinformatics, Tokyo Metropolitan University, Hachioji 192-0397, Japan
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7
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Common Themes and Future Challenges in Understanding Gene Regulatory Network Evolution. Cells 2022; 11:cells11030510. [PMID: 35159319 PMCID: PMC8834487 DOI: 10.3390/cells11030510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/26/2022] [Accepted: 01/29/2022] [Indexed: 12/18/2022] Open
Abstract
A major driving force behind the evolution of species-specific traits and novel structures is alterations in gene regulatory networks (GRNs). Comprehending evolution therefore requires an understanding of the nature of changes in GRN structure and the responsible mechanisms. Here, we review two insect pigmentation GRNs in order to examine common themes in GRN evolution and to reveal some of the challenges associated with investigating changes in GRNs across different evolutionary distances at the molecular level. The pigmentation GRN in Drosophila melanogaster and other drosophilids is a well-defined network for which studies from closely related species illuminate the different ways co-option of regulators can occur. The pigmentation GRN for butterflies of the Heliconius species group is less fully detailed but it is emerging as a useful model for exploring important questions about redundancy and modularity in cis-regulatory systems. Both GRNs serve to highlight the ways in which redeployment of trans-acting factors can lead to GRN rewiring and network co-option. To gain insight into GRN evolution, we discuss the importance of defining GRN architecture at multiple levels both within and between species and of utilizing a range of complementary approaches.
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8
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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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9
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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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10
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Le Poul Y, Xin Y, Ling L, Mühling B, Jaenichen R, Hörl D, Bunk D, Harz H, Leonhardt H, Wang Y, Osipova E, Museridze M, Dharmadhikari D, Murphy E, Rohs R, Preibisch S, Prud'homme B, Gompel N. Regulatory encoding of quantitative variation in spatial activity of a Drosophila enhancer. SCIENCE ADVANCES 2020; 6:6/49/eabe2955. [PMID: 33268361 PMCID: PMC7821883 DOI: 10.1126/sciadv.abe2955] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 10/20/2020] [Indexed: 06/12/2023]
Abstract
Developmental enhancers control the expression of genes prefiguring morphological patterns. The activity of an enhancer varies among cells of a tissue, but collectively, expression levels in individual cells constitute a spatial pattern of gene expression. How the spatial and quantitative regulatory information is encoded in an enhancer sequence is elusive. To link spatial pattern and activity levels of an enhancer, we used systematic mutations of the yellow spot enhancer, active in developing Drosophila wings, and tested their effect in a reporter assay. Moreover, we developed an analytic framework based on the comprehensive quantification of spatial reporter activity. We show that the quantitative enhancer activity results from densely packed regulatory information along the sequence, and that a complex interplay between activators and multiple tiers of repressors carves the spatial pattern. Our results shed light on how an enhancer reads and integrates trans-regulatory landscape information to encode a spatial quantitative pattern.
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Affiliation(s)
- Yann Le Poul
- Evolutionary Ecology, Ludwig-Maximilians Universität München, Fakultät für Biologie, Biozentrum, Grosshaderner Strasse 2, 82152 Planegg-Martinsried, Germany
| | - Yaqun Xin
- Evolutionary Ecology, Ludwig-Maximilians Universität München, Fakultät für Biologie, Biozentrum, Grosshaderner Strasse 2, 82152 Planegg-Martinsried, Germany
| | - Liucong Ling
- Evolutionary Ecology, Ludwig-Maximilians Universität München, Fakultät für Biologie, Biozentrum, Grosshaderner Strasse 2, 82152 Planegg-Martinsried, Germany
| | - Bettina Mühling
- Evolutionary Ecology, Ludwig-Maximilians Universität München, Fakultät für Biologie, Biozentrum, Grosshaderner Strasse 2, 82152 Planegg-Martinsried, Germany
| | - Rita Jaenichen
- Evolutionary Ecology, Ludwig-Maximilians Universität München, Fakultät für Biologie, Biozentrum, Grosshaderner Strasse 2, 82152 Planegg-Martinsried, Germany
| | - David Hörl
- Human Biology and Bioimaging, Ludwig-Maximilians Universität München, Fakultät für Biologie, Biozentrum, Grosshaderner Strasse 2, 82152 Planegg-Martinsried, Germany
| | - David Bunk
- Human Biology and Bioimaging, Ludwig-Maximilians Universität München, Fakultät für Biologie, Biozentrum, Grosshaderner Strasse 2, 82152 Planegg-Martinsried, Germany
| | - Hartmann Harz
- Human Biology and Bioimaging, Ludwig-Maximilians Universität München, Fakultät für Biologie, Biozentrum, Grosshaderner Strasse 2, 82152 Planegg-Martinsried, Germany
| | - Heinrich Leonhardt
- Human Biology and Bioimaging, Ludwig-Maximilians Universität München, Fakultät für Biologie, Biozentrum, Grosshaderner Strasse 2, 82152 Planegg-Martinsried, Germany
| | - Yingfei Wang
- Quantitative and Computational Biology, Departments of Biological Sciences, Chemistry, Physics and Astronomy, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA
| | - Elena Osipova
- Evolutionary Ecology, Ludwig-Maximilians Universität München, Fakultät für Biologie, Biozentrum, Grosshaderner Strasse 2, 82152 Planegg-Martinsried, Germany
| | - Mariam Museridze
- Evolutionary Ecology, Ludwig-Maximilians Universität München, Fakultät für Biologie, Biozentrum, Grosshaderner Strasse 2, 82152 Planegg-Martinsried, Germany
| | - Deepak Dharmadhikari
- Evolutionary Ecology, Ludwig-Maximilians Universität München, Fakultät für Biologie, Biozentrum, Grosshaderner Strasse 2, 82152 Planegg-Martinsried, Germany
| | - Eamonn Murphy
- Evolutionary Ecology, Ludwig-Maximilians Universität München, Fakultät für Biologie, Biozentrum, Grosshaderner Strasse 2, 82152 Planegg-Martinsried, Germany
| | - Remo Rohs
- Quantitative and Computational Biology, Departments of Biological Sciences, Chemistry, Physics and Astronomy, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA
| | - Stephan Preibisch
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13092 Berlin, Germany
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Benjamin Prud'homme
- Aix-Marseille Université, CNRS, IBDM, Institut de Biologie du Développement de Marseille, Campus de Luminy Case 907, 13288 Marseille Cedex 9, France.
| | - Nicolas Gompel
- Evolutionary Ecology, Ludwig-Maximilians Universität München, Fakultät für Biologie, Biozentrum, Grosshaderner Strasse 2, 82152 Planegg-Martinsried, Germany.
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11
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Vinogradov AE, Anatskaya OV. Systemic evolutionary changes in mammalian gene expression. Biosystems 2020; 198:104256. [PMID: 32976926 DOI: 10.1016/j.biosystems.2020.104256] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 09/18/2020] [Accepted: 09/18/2020] [Indexed: 12/16/2022]
Abstract
Changes in gene expression play an important role in evolution and can be relevant to evolutionary medicine. In this work, a strong relationship was found between the statistical significance of evolutionary changes in the expression of orthologous genes in the five or six homologous mammalian tissues and the across-tissues unidirectionality of changes (i.e., they occur in the same direction in different tissues -- all upward or all downward). In the area of highly significant changes, the fraction of unidirectionally changed genes (UCG) was above 0.9 (random expectation is 0.03). This observation indicates that the most pronounced evolutionary changes in mammalian gene expression are systemic (i.e., they operate at the whole-organism level). The UCG are strongly enriched in the housekeeping genes. More specifically, in the human-chimpanzee comparison, the UCG are enriched in the pathways belonging to gene expression (translation is prominent), cell cycle control, ubiquitin-dependent protein degradation (mostly related to cell cycle control), apoptosis, and Parkinson's disease. In the human-macaque comparison, the two other neurodegenerative diseases (Alzheimer's and Huntington's) are added to the enriched pathways. The consolidation of gene expression changes at the level of pathways indicates that they are not neutral but functional. The systemic expression changes probably maintain the across-tissues balance of basic physiological processes in the course of evolution (e.g., during the movement along the fast-slow life axis). These results can be useful for understanding the variation in longevity and susceptibility to cancer and widespread neurodegenerative diseases. This approach can also guide the choice of prospective genes for studies aiming to decipher cis-regulatory code (the gene list is provided).
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Affiliation(s)
| | - Olga V Anatskaya
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russia
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