1
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Vaknin I, Willinger O, Mandl J, Heuberger H, Ben-Ami D, Zeng Y, Goldberg S, Orenstein Y, Amit R. A universal system for boosting gene expression in eukaryotic cell-lines. Nat Commun 2024; 15:2394. [PMID: 38493141 PMCID: PMC10944472 DOI: 10.1038/s41467-024-46573-5] [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] [Received: 07/27/2023] [Accepted: 03/04/2024] [Indexed: 03/18/2024] Open
Abstract
We demonstrate a transcriptional regulatory design algorithm that can boost expression in yeast and mammalian cell lines. The system consists of a simplified transcriptional architecture composed of a minimal core promoter and a synthetic upstream regulatory region (sURS) composed of up to three motifs selected from a list of 41 motifs conserved in the eukaryotic lineage. The sURS system was first characterized using an oligo-library containing 189,990 variants. We validate the resultant expression model using a set of 43 unseen sURS designs. The validation sURS experiments indicate that a generic set of grammar rules for boosting and attenuation may exist in yeast cells. Finally, we demonstrate that this generic set of grammar rules functions similarly in mammalian CHO-K1 and HeLa cells. Consequently, our work provides a design algorithm for boosting the expression of promoters used for expressing industrially relevant proteins in yeast and mammalian cell lines.
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Affiliation(s)
- Inbal Vaknin
- Department of Biotechnology and Food Engineering, Technion, Haifa, Israel
| | - Or Willinger
- Department of Biotechnology and Food Engineering, Technion, Haifa, Israel
| | - Jonathan Mandl
- Department of Computer Science, Bar-Ilan University, Ramat Gan, Israel
| | - Hadar Heuberger
- School of Electrical and Computer Engineering, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Dan Ben-Ami
- School of Electrical and Computer Engineering, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Yi Zeng
- Department of Biotechnology and Food Engineering, Technion, Haifa, Israel
| | - Sarah Goldberg
- Department of Biotechnology and Food Engineering, Technion, Haifa, Israel
| | - Yaron Orenstein
- Department of Computer Science, Bar-Ilan University, Ramat Gan, Israel
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Roee Amit
- Department of Biotechnology and Food Engineering, Technion, Haifa, Israel.
- The Russell Berrie Nanotechnology Institute, Technion, Haifa, Israel.
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2
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Chen Q, Sasikala-Appukuttan AK, Husain Z, Shrivastava A, Spain M, Sendler ED, Daines B, Fischer S, Chen R, Cook TA, Friedrich M. Global Gene Expression Analysis Reveals Complex Cuticle Organization of the Tribolium Compound Eye. Genome Biol Evol 2023; 15:evac181. [PMID: 36575057 PMCID: PMC9866248 DOI: 10.1093/gbe/evac181] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/08/2022] [Accepted: 12/17/2022] [Indexed: 12/29/2022] Open
Abstract
The red flour beetle Tribolium castaneum is a resource-rich model for genomic and developmental studies. To extend previous studies on Tribolium eye development, we produced transcriptomes for normal-eyed and eye-depleted heads of pupae and adults to identify differentially transcript-enriched (DE) genes in the visual system. Unexpectedly, cuticle-related genes were the largest functional class in the pupal compound eye DE gene population, indicating differential enrichment in three distinct cuticle components: clear lens facet cuticle, highly melanized cuticle of the ocular diaphragm, which surrounds the Tribolium compound eye for internal fortification, and newly identified facet margins of the tanned cuticle, possibly enhancing external fortification. Phylogenetic, linkage, and high-throughput gene knockdown data suggest that most cuticle proteins (CPs) expressed in the Tribolium compound eye stem from the deployment of ancient CP genes. Consistent with this, TcasCPR15, which we identified as the major lens CP gene in Tribolium, is a beetle-specific but pleiotropic paralog of the ancient CPR RR-2 CP gene family. The less abundant yet most likely even more lens-specific TcasCP63 is a member of a sprawling family of noncanonical CP genes, documenting a role of local gene family expansions in the emergence of the Tribolium compound eye CP repertoire. Comparisons with Drosophila and the mosquito Anopheles gambiae reveal a steady turnover of lens-enriched CP genes during insect evolution.
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Affiliation(s)
- Qing Chen
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
| | | | - Zahabiya Husain
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
| | - Anura Shrivastava
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
| | - Marla Spain
- Center of Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Edward D Sendler
- Center of Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Bryce Daines
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Stefan Fischer
- Evolutionary Biology of Invertebrates, Institute of Evolution and Ecology, University of Tübingen, Germany
| | - Rui Chen
- Evolutionary Biology of Invertebrates, Institute of Evolution and Ecology, University of Tübingen, Germany
| | - Tiffany A Cook
- Center of Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, USA
- Department of Ophthalmological, Visual, and Anatomical Sciences, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
- Department of Ophthalmological, Visual, and Anatomical Sciences, Wayne State University School of Medicine, Detroit, Michigan, USA
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3
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Friedrich M. Coming into clear sight at last: Ancestral and derived events during chelicerate visual system development. Bioessays 2022; 44:e2200163. [DOI: 10.1002/bies.202200163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Markus Friedrich
- Department of Biological Sciences Wayne State University Detroit Michigan USA
- Department of Ophthalmological, Visual, and Anatomical Sciences, Wayne State University School of Medicine Detroit Michigan USA
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4
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van Heyningen V. A Journey Through Genetics to Biology. Annu Rev Genomics Hum Genet 2022; 23:1-27. [PMID: 35567277 DOI: 10.1146/annurev-genom-010622-095109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Although my engagement with human genetics emerged gradually, and sometimes serendipitously, it has held me spellbound for decades. Without my teachers, students, postdocs, colleagues, and collaborators, I would not be writing this review of my scientific adventures. Early gene and disease mapping was a satisfying puzzle-solving exercise, but building biological insight was my main goal. The project trajectory was hugely influenced by the evolutionarily conserved nature of the implicated genes and by the pace of progress in genetic technologies. The rich detail of clinical observations, particularly in eye disease, makes humans an excellent model, especially when complemented by the use of multiple other animal species for experimental validation. The contributions of collaborators and rivals also influenced our approach. We are very fortunate to work in this era of unprecedented progress in genetics and genomics. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Veronica van Heyningen
- UCL Institute of Ophthalmology, University College London, London, United Kingdom.,MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom;
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5
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Paris M, Wolff C, Patel NH, Averof M. The crustacean model Parhyale hawaiensis. Curr Top Dev Biol 2022; 147:199-230. [PMID: 35337450 DOI: 10.1016/bs.ctdb.2022.02.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Arthropods are the most abundant and diverse animals on earth. Among them, pancrustaceans are an ancient and morphologically diverse group, comprising a wide range of aquatic and semi-aquatic crustaceans as well as the insects, which emerged from crustacean ancestors to colonize most terrestrial habitats. Within insects, Drosophila stands out as one of the most powerful animal models, making major contributions to our understanding of development, physiology and behavior. Given these attributes, crustaceans provide a fertile ground for exploring biological diversity through comparative studies. However, beyond insects, few crustaceans are developed sufficiently as experimental models to enable such studies. The marine amphipod Parhyale hawaiensis is currently the best established crustacean system, offering year-round accessibility to developmental stages, transgenic tools, genomic resources, and established genetics and imaging approaches. The Parhyale research community is small but diverse, investigating the evolution of development, regeneration, aspects of sensory biology, chronobiology, bioprocessing and ecotoxicology.
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Affiliation(s)
- Mathilde Paris
- Institut de Génomique Fonctionnelle de Lyon, École Normale Supérieure de Lyon, Lyon, France; Centre National de la Recherche Scientifique (CNRS), France
| | - Carsten Wolff
- Marine Biological Laboratory, Woods Hole, MA, United States
| | - Nipam H Patel
- Marine Biological Laboratory, Woods Hole, MA, United States; Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, United States.
| | - Michalis Averof
- Institut de Génomique Fonctionnelle de Lyon, École Normale Supérieure de Lyon, Lyon, France; Centre National de la Recherche Scientifique (CNRS), France.
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6
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Charlton-Perkins MA, Friedrich M, Cook TA. Semper's cells in the insect compound eye: Insights into ocular form and function. Dev Biol 2021; 479:126-138. [PMID: 34343526 PMCID: PMC8410683 DOI: 10.1016/j.ydbio.2021.07.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 07/26/2021] [Accepted: 07/28/2021] [Indexed: 11/28/2022]
Abstract
The arthropod compound eye represents one of two major eye types in the animal kingdom and has served as an essential experimental paradigm for defining fundamental mechanisms underlying sensory organ formation, function, and maintenance. One of the most distinguishing features of the compound eye is the highly regular array of lens facets that define individual eye (ommatidial) units. These lens facets are produced by a deeply conserved quartet of cuticle-secreting cells, called Semper cells (SCs). Also widely known as cone cells, SCs were originally identified for their secretion of the dioptric system, i.e. the corneal lens and underlying crystalline cones. Additionally, SCs are now known to execute a diversity of patterning and glial functions in compound eye development and maintenance. Here, we present an integrated account of our current knowledge of SC multifunctionality in the Drosophila compound eye, highlighting emerging gene regulatory modules that may drive the diverse roles for these cells. Drawing comparisons with other deeply conserved retinal glia in the vertebrate single lens eye, this discussion speaks to glial cell origins and opens new avenues for understanding sensory system support programs.
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Affiliation(s)
- Mark A Charlton-Perkins
- Department of Paediatrics, Wellcome-MRC Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, United Kingdom
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI, 48202, USA; Department of Ophthalmological, Visual, and Anatomical Sciences, Wayne State University, School of Medicine, 540 East Canfield Avenue, Detroit, MI, 48201, USA
| | - Tiffany A Cook
- Department of Ophthalmological, Visual, and Anatomical Sciences, Wayne State University, School of Medicine, 540 East Canfield Avenue, Detroit, MI, 48201, USA; Center of Molecular Medicine and Genetics, Wayne State University School of Medicine, 540 East Canfield Avenue, Detroit, MI, 48201, USA.
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7
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Gaspar P, Almudi I, Nunes MDS, McGregor AP. Human eye conditions: insights from the fly eye. Hum Genet 2018; 138:973-991. [PMID: 30386938 DOI: 10.1007/s00439-018-1948-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 10/20/2018] [Indexed: 12/22/2022]
Abstract
The fruit fly Drosophila melanogaster has served as an excellent model to study and understand the genetics of many human diseases from cancer to neurodegeneration. Studying the regulation of growth, determination and differentiation of the compound eyes of this fly, in particular, have provided key insights into a wide range of diseases. Here we review the regulation of the development of fly eyes in light of shared aspects with human eye development. We also show how understanding conserved regulatory pathways in eye development together with the application of tools for genetic screening and functional analyses makes Drosophila a powerful model to diagnose and characterize the genetics underlying many human eye conditions, such as aniridia and retinitis pigmentosa. This further emphasizes the importance and vast potential of basic research to underpin applied research including identifying and treating the genetic basis of human diseases.
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Affiliation(s)
- Pedro Gaspar
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Isabel Almudi
- Centro Andaluz de Biología del Desarrollo, CSIC/ Universidad Pablo de Olavide, Carretera de Utrera Km1, 41013, Sevilla, Spain
| | - Maria D S Nunes
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Alistair P McGregor
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK.
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8
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Stahl AL, Baucom RS, Cook TA, Buschbeck EK. A Complex Lens for a Complex Eye. Integr Comp Biol 2018; 57:1071-1081. [PMID: 28992245 DOI: 10.1093/icb/icx116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
A key innovation for high resolution eyes is a sophisticated lens that precisely focuses light onto photoreceptors. The eyes of holometabolous larvae range from very simple eyes that merely detect light to eyes that are capable of high spatial resolution. Particularly interesting are the bifocal lenses of Thermonectus marmoratus larvae, which differentially focus light on spectrally-distinct retinas. While functional aspects of insect lenses have been relatively well studied, little work has explored their molecular makeup, especially in regard to more complex eye types. To investigate this question, we took a transcriptomic and proteomic approach to identify the major proteins contributing to the principal bifocal lenses of T. marmoratus larvae. Mass spectrometry revealed 10 major lens proteins. Six of these share sequence homology with cuticular proteins, a large class of proteins that are also major components of corneal lenses from adult compound eyes of Drosophila melanogaster and Anopheles gambiae. Two proteins were identified as house-keeping genes and the final two lack any sequence homologies to known genes. Overall the composition seems to follow a pattern of co-opting transparent and optically dense proteins, similar to what has been described for other animal lenses. To identify cells responsible for the secretion of specific lens proteins, we performed in situ hybridization studies and found some expression differences between distal and proximal corneagenous cells. Since the distal cells likely give rise to the periphery and the proximal cells to the center of the lens, our findings highlight a possible mechanism for establishing structural differences that are in line with the bifocal nature of these lenses. A better understanding of lens composition provides insights into the evolution of proper focusing, which is an important step in the transition between low-resolution and high-resolution eyes.
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Affiliation(s)
- Aaron L Stahl
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Regina S Baucom
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Tiffany A Cook
- Wayne State University School of Medicine, Center of Molecular Medicine and Genomics, Detroit, MI 48201, USA
| | - Elke K Buschbeck
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
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9
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Functional non-coding polymorphism in an EPHA2 promoter PAX2 binding site modifies expression and alters the MAPK and AKT pathways. Sci Rep 2017; 7:9992. [PMID: 28855599 PMCID: PMC5577203 DOI: 10.1038/s41598-017-10117-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 08/04/2017] [Indexed: 01/11/2023] Open
Abstract
To identify possible genetic variants influencing expression of EPHA2 (Ephrin-receptor Type-A2), a tyrosine kinase receptor that has been shown to be important for lens development and to contribute to both congenital and age related cataract when mutated, the extended promoter region of EPHA2 was screened for variants. SNP rs6603883 lies in a PAX2 binding site in the EPHA2 promoter region. The C (minor) allele decreased EPHA2 transcriptional activity relative to the T allele by reducing the binding affinity of PAX2. Knockdown of PAX2 in human lens epithelial (HLE) cells decreased endogenous expression of EPHA2. Whole RNA sequencing showed that extracellular matrix (ECM), MAPK-AKT signaling pathways and cytoskeleton related genes were dysregulated in EPHA2 knockdown HLE cells. Taken together, these results indicate a functional non-coding SNP in EPHA2 promoter affects PAX2 binding and reduces EPHA2 expression. They further suggest that decreasing EPHA2 levels alters MAPK, AKT signaling pathways and ECM and cytoskeletal genes in lens cells that could contribute to cataract. These results demonstrate a direct role for PAX2 in EPHA2 expression and help delineate the role of EPHA2 in development and homeostasis required for lens transparency.
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10
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Stahl AL, Charlton-Perkins M, Buschbeck EK, Cook TA. The cuticular nature of corneal lenses in Drosophila melanogaster. Dev Genes Evol 2017; 227:271-278. [PMID: 28477155 DOI: 10.1007/s00427-017-0582-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 04/24/2017] [Indexed: 01/10/2023]
Abstract
The dioptric visual system relies on precisely focusing lenses that project light onto a neural retina. While the proteins that constitute the lenses of many vertebrates are relatively well characterized, less is known about the proteins that constitute invertebrate lenses, especially the lens facets in insect compound eyes. To address this question, we used mass spectrophotometry to define the major proteins that comprise the corneal lenses from the adult Drosophila melanogaster compound eye. This led to the identification of four cuticular proteins: two previously identified lens proteins, drosocrystallin and retinin, and two newly identified proteins, Cpr66D and Cpr72Ec. To determine which ommatidial cells contribute each of these proteins to the lens, we conducted in situ hybridization at 50% pupal development, a key age for lens secretion. Our results confirm previous reports that drosocrystallin and retinin are expressed in the two primary corneagenous cells-cone cells and primary pigment cells. Cpr72Ec and Cpr66D, on the other hand, are more highly expressed in higher order interommatidial pigment cells. These data suggest that the complementary expression of cuticular proteins give rise to the center vs periphery of the corneal lens facet, possibly facilitating a refractive gradient that is known to reduce spherical aberration. Moreover, these studies provide a framework for future studies aimed at understanding the cuticular basis of corneal lens function in holometabolous insect eyes.
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Affiliation(s)
- Aaron L Stahl
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Mark Charlton-Perkins
- Division of Developmental Biology and Department of Pediatric Ophthalmology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.,Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3DY, UK
| | - Elke K Buschbeck
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA.
| | - Tiffany A Cook
- Center of Molecular Medicine and Genomics, Wayne State University School of Medicine, Detroit, MI, 48201, USA.
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11
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Moulton MJ, Letsou A. Modeling congenital disease and inborn errors of development in Drosophila melanogaster. Dis Model Mech 2016; 9:253-69. [PMID: 26935104 PMCID: PMC4826979 DOI: 10.1242/dmm.023564] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Fly models that faithfully recapitulate various aspects of human disease and human health-related biology are being used for research into disease diagnosis and prevention. Established and new genetic strategies in Drosophila have yielded numerous substantial successes in modeling congenital disorders or inborn errors of human development, as well as neurodegenerative disease and cancer. Moreover, although our ability to generate sequence datasets continues to outpace our ability to analyze these datasets, the development of high-throughput analysis platforms in Drosophila has provided access through the bottleneck in the identification of disease gene candidates. In this Review, we describe both the traditional and newer methods that are facilitating the incorporation of Drosophila into the human disease discovery process, with a focus on the models that have enhanced our understanding of human developmental disorders and congenital disease. Enviable features of the Drosophila experimental system, which make it particularly useful in facilitating the much anticipated move from genotype to phenotype (understanding and predicting phenotypes directly from the primary DNA sequence), include its genetic tractability, the low cost for high-throughput discovery, and a genome and underlying biology that are highly evolutionarily conserved. In embracing the fly in the human disease-gene discovery process, we can expect to speed up and reduce the cost of this process, allowing experimental scales that are not feasible and/or would be too costly in higher eukaryotes.
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Affiliation(s)
- Matthew J Moulton
- Department of Human Genetics, University of Utah, 15 North 2030 East, Room 5100, Salt Lake City, UT 84112-5330, USA
| | - Anthea Letsou
- Department of Human Genetics, University of Utah, 15 North 2030 East, Room 5100, Salt Lake City, UT 84112-5330, USA
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12
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Alwes F, Enjolras C, Averof M. Live imaging reveals the progenitors and cell dynamics of limb regeneration. eLife 2016; 5. [PMID: 27776632 PMCID: PMC5079749 DOI: 10.7554/elife.19766] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 09/07/2016] [Indexed: 01/23/2023] Open
Abstract
Regeneration is a complex and dynamic process, mobilizing diverse cell types and remodelling tissues over long time periods. Tracking cell fate and behaviour during regeneration in active adult animals is especially challenging. Here, we establish continuous live imaging of leg regeneration at single-cell resolution in the crustacean Parhyale hawaiensis. By live recordings encompassing the first 4-5 days after amputation, we capture the cellular events that contribute to wound closure and morphogenesis of regenerating legs with unprecedented resolution and temporal detail. Using these recordings we are able to track cell lineages, to generate fate maps of the blastema and to identify the progenitors of regenerated epidermis. We find that there are no specialized stem cells for the epidermis. Most epidermal cells in the distal part of the leg stump proliferate, acquire new positional values and contribute to new segments in the regenerating leg.
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Affiliation(s)
- Frederike Alwes
- Institut de Génomique Fonctionnelle de Lyon (IGFL), École Normale Supérieure de Lyon, Lyon, France.,Centre National de la Recherche Scientifique (CNRS), , France
| | - Camille Enjolras
- Institut de Génomique Fonctionnelle de Lyon (IGFL), École Normale Supérieure de Lyon, Lyon, France.,Centre National de la Recherche Scientifique (CNRS), , France
| | - Michalis Averof
- Institut de Génomique Fonctionnelle de Lyon (IGFL), École Normale Supérieure de Lyon, Lyon, France.,Centre National de la Recherche Scientifique (CNRS), , France
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13
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Gordon KL, Arthur RK, Ruvinsky I. Phylum-Level Conservation of Regulatory Information in Nematodes despite Extensive Non-coding Sequence Divergence. PLoS Genet 2015; 11:e1005268. [PMID: 26020930 PMCID: PMC4447282 DOI: 10.1371/journal.pgen.1005268] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 05/09/2015] [Indexed: 11/28/2022] Open
Abstract
Gene regulatory information guides development and shapes the course of evolution. To test conservation of gene regulation within the phylum Nematoda, we compared the functions of putative cis-regulatory sequences of four sets of orthologs (unc-47, unc-25, mec-3 and elt-2) from distantly-related nematode species. These species, Caenorhabditis elegans, its congeneric C. briggsae, and three parasitic species Meloidogyne hapla, Brugia malayi, and Trichinella spiralis, represent four of the five major clades in the phylum Nematoda. Despite the great phylogenetic distances sampled and the extensive sequence divergence of nematode genomes, all but one of the regulatory elements we tested are able to drive at least a subset of the expected gene expression patterns. We show that functionally conserved cis-regulatory elements have no more extended sequence similarity to their C. elegans orthologs than would be expected by chance, but they do harbor motifs that are important for proper expression of the C. elegans genes. These motifs are too short to be distinguished from the background level of sequence similarity, and while identical in sequence they are not conserved in orientation or position. Functional tests reveal that some of these motifs contribute to proper expression. Our results suggest that conserved regulatory circuitry can persist despite considerable turnover within cis elements. To explore the phylogenetic limits of conservation of cis-regulatory elements, we used transgenesis to test the functions of enhancers of four genes from several species spanning the phylum Nematoda. While we found a striking degree of functional conservation among the examined cis elements, their DNA sequences lacked apparent conservation with the C. elegans orthologs. In fact, sequence similarity between C. elegans and the distantly related nematodes was no greater than would be expected by chance. Short motifs, similar to known regulatory sequences in C. elegans, can be detected in most of the cis elements. When tested, some of these sites appear to mediate regulatory function. However, they seem to have originated through motif turnover, rather than to have been preserved from a common ancestor. Our results suggest that gene regulatory networks are broadly conserved in the phylum Nematoda, but this conservation persists despite substantial reorganization of regulatory elements and could not be detected using naïve comparisons of sequence similarity.
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Affiliation(s)
- Kacy L. Gordon
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, Illinois, United States of America
- * E-mail: (KLG); (IR)
| | - Robert K. Arthur
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, United States of America
| | - Ilya Ruvinsky
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, Illinois, United States of America
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, United States of America
- * E-mail: (KLG); (IR)
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14
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Narasimhan K, Pillay S, Huang YH, Jayabal S, Udayasuryan B, Veerapandian V, Kolatkar P, Cojocaru V, Pervushin K, Jauch R. DNA-mediated cooperativity facilitates the co-selection of cryptic enhancer sequences by SOX2 and PAX6 transcription factors. Nucleic Acids Res 2015; 43:1513-28. [PMID: 25578969 PMCID: PMC4330359 DOI: 10.1093/nar/gku1390] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Sox2 and Pax6 are transcription factors that direct cell fate decision during neurogenesis, yet the mechanism behind how they cooperate on enhancer DNA elements and regulate gene expression is unclear. By systematically interrogating Sox2 and Pax6 interaction on minimal enhancer elements, we found that cooperative DNA recognition relies on combinatorial nucleotide switches and precisely spaced, but cryptic composite DNA motifs. Surprisingly, all tested Sox and Pax paralogs have the capacity to cooperate on such enhancer elements. NMR and molecular modeling reveal very few direct protein-protein interactions between Sox2 and Pax6, suggesting that cooperative binding is mediated by allosteric interactions propagating through DNA structure. Furthermore, we detected and validated several novel sites in the human genome targeted cooperatively by Sox2 and Pax6. Collectively, we demonstrate that Sox-Pax partnerships have the potential to substantially alter DNA target specificities and likely enable the pleiotropic and context-specific action of these cell-lineage specifiers.
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Affiliation(s)
- Kamesh Narasimhan
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Shubhadra Pillay
- Genome Regulation Laboratory, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences,190 Kai Yuan Avenue, Science Park, Guangzhou 510530, China
| | - Yong-Heng Huang
- Laboratory for Structural Biochemistry, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Sriram Jayabal
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada Integrated Program in Neuroscience, McGill University, Montreal, Quebec H3G 0B1, Canada
| | - Barath Udayasuryan
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Veeramohan Veerapandian
- Laboratory for Structural Biochemistry, Genome Institute of Singapore, Singapore 138672, Singapore University of Chinese Academy of Sciences, No. 19A Yuquanlu, Beijing 100049, China
| | - Prasanna Kolatkar
- Qatar Biomedical Research Institute, Qatar Foundation, PO Box 5825, Doha, Qatar
| | - Vlad Cojocaru
- Computational Structural Biology Laboratory, Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, Münster 48149, Germany
| | - Konstantin Pervushin
- Genome Regulation Laboratory, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences,190 Kai Yuan Avenue, Science Park, Guangzhou 510530, China
| | - Ralf Jauch
- Laboratory for Structural Biochemistry, Genome Institute of Singapore, Singapore 138672, Singapore
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15
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Vassalli QA, Anishchenko E, Caputi L, Sordino P, D'Aniello S, Locascio A. Regulatory elements retained during chordate evolution: Coming across tunicates. Genesis 2014; 53:66-81. [DOI: 10.1002/dvg.22838] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 11/06/2014] [Accepted: 11/11/2014] [Indexed: 12/22/2022]
Affiliation(s)
- Quirino Attilio Vassalli
- Cellular and Developmental Biology Laboratory; Stazione Zoologica Anton Dohrn; Villa Comunale Naples Italy
| | - Evgeniya Anishchenko
- Cellular and Developmental Biology Laboratory; Stazione Zoologica Anton Dohrn; Villa Comunale Naples Italy
| | - Luigi Caputi
- Cellular and Developmental Biology Laboratory; Stazione Zoologica Anton Dohrn; Villa Comunale Naples Italy
| | - Paolo Sordino
- Cellular and Developmental Biology Laboratory; Stazione Zoologica Anton Dohrn; Villa Comunale Naples Italy
- CNR ISAFOM, Institute for Agricultural and Forest Systems in the Mediterranean, Unitá organizzativa di supporto; Catania Italy
| | - Salvatore D'Aniello
- Cellular and Developmental Biology Laboratory; Stazione Zoologica Anton Dohrn; Villa Comunale Naples Italy
| | - Annamaria Locascio
- Cellular and Developmental Biology Laboratory; Stazione Zoologica Anton Dohrn; Villa Comunale Naples Italy
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16
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Weingarten-Gabbay S, Segal E. The grammar of transcriptional regulation. Hum Genet 2014; 133:701-11. [PMID: 24390306 DOI: 10.1007/s00439-013-1413-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 12/24/2013] [Indexed: 12/22/2022]
Abstract
Eukaryotes employ combinatorial strategies to generate a variety of expression patterns from a relatively small set of regulatory DNA elements. As in any other language, deciphering the mapping between DNA and expression requires an understanding of the set of rules that govern basic principles in transcriptional regulation, the functional elements involved, and the ways in which they combine to orchestrate a transcriptional output. Here, we review the current understanding of various grammatical rules, including the effect on expression of the number of transcription factor binding sites, their location, orientation, affinity and activity; co-association with different factors; and intrinsic nucleosome organization. We review different methods that are used to study the grammar of transcription regulation, highlight gaps in current understanding, and discuss how recent technological advances may be utilized to bridge them.
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Affiliation(s)
- Shira Weingarten-Gabbay
- Department of Computer Science, Applied Mathematics and Department of Molecular Cell Biology, Weizmann Institute of Science, 76100, Rehovot, Israel,
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17
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Konstantinides N, Averof M. A Common Cellular Basis for Muscle Regeneration in Arthropods and Vertebrates. Science 2014; 343:788-91. [DOI: 10.1126/science.1243529] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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18
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Shen SP, Aleksic J, Russell S. Identifying targets of the Sox domain protein Dichaete in the Drosophila CNS via targeted expression of dominant negative proteins. BMC DEVELOPMENTAL BIOLOGY 2013; 13:1. [PMID: 23289785 PMCID: PMC3541953 DOI: 10.1186/1471-213x-13-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 01/03/2013] [Indexed: 11/10/2022]
Abstract
BACKGROUND Group B Sox domain transcription factors play important roles in metazoan central nervous system development. They are, however, difficult to study as mutations often have pleiotropic effects and other Sox family members can mask phenotypes due to functional compensation. In Drosophila melanogaster, the Sox gene Dichaete is dynamically expressed in the embryonic CNS, where it is known to have functional roles in neuroblasts and the ventral midline. In this study, we use inducible dominant negative proteins in combination with ChIP, immunohistochemistry and genome-wide expression profiling to further dissect the role of Dichaete in these two tissues. RESULTS We generated two dominant negative Dichaete constructs, one lacking a DNA binding domain and the other fused to the Engrailed transcriptional repressor domain. We expressed these tissue-specifically in the midline and in neuroblasts using the UAS/GAL4 system, validating their use at the phenotypic level and with known target genes. Using ChIP and immunohistochemistry, we identified two new likely direct Dichaete target genes, commisureless in the midline and asense in the neuroectoderm. We performed genome-wide expression profiling in stage 8-9 embryos, identifying almost a thousand potential tissue-specific Dichaete targets, with half of these genes showing evidence of Dichaete binding in vivo. These include a number of genes with known roles in CNS development, including several components of the Notch, Wnt and EGFR signalling pathways. CONCLUSIONS As well as identifying commisureless as a target, our data indicate that Dichaete helps establish its expression during early midline development but has less effect on its established later expression, highlighting Dichaete action on tissue specific enhancers. An analysis of the broader range of candidate Dichaete targets indicates that Dichaete plays diverse roles in CNS development, with the 500 or so Dichaete-bound putative targets including a number of transcription factors, signalling pathway components and terminal differentiation genes. In the early neurectoderm we implicate Dichaete in the lateral inhibition pathway and show that Dichaete acts to repress the proneural gene asense. Our analysis also reveals that dominant negatives cause off-target effects, highlighting the need to use other experimental data for validating findings from dominant negative studies.
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Affiliation(s)
- Shih Pei Shen
- Department of Genetics, University of Cambridge, Cambridge, UK
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19
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Gehring WJ. The evolution of vision. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2012; 3:1-40. [DOI: 10.1002/wdev.96] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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20
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Abstract
Charles Darwin has proposed the theory that evolution of live organisms is based on random variation and natural selection. Jacques Monod in his classic book Chance and Necessity, published 40 years ago, presented his thesis “that the biosphere does not contain a predictable class of objects or events, but constitutes a particular occurrence, compatible indeed with the first principles, but not deducible from those principals and therefore, essentially unpredictable.” Recent discoveries in eye evolution are in agreement with both of these theses. They confirm Darwin's assumption of a simple eye prototype and lend strong support for the notion of a monophyletic origin of the various eye types. Considering the complexity of the underlying gene regulatory networks the unpredictability is obvious. The evolution of the Hox gene cluster and the specification of the body plan starting from an evolutionary prototype segment is discussed. In the course of evolution, a series of similar prototypic segments gradually undergoes cephalization anteriorly and caudalization posteriorly through diversification of the Hox genes.
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Affiliation(s)
- Walter J Gehring
- Department of Growth and Development, Biozentrum University of Basel, Switzerland.
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21
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The lens in focus: a comparison of lens development in Drosophila and vertebrates. Mol Genet Genomics 2011; 286:189-213. [PMID: 21877135 DOI: 10.1007/s00438-011-0643-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Accepted: 08/04/2011] [Indexed: 12/24/2022]
Abstract
The evolution of the eye has been a major subject of study dating back centuries. The advent of molecular genetics offered the surprising finding that morphologically distinct eyes rely on conserved regulatory gene networks for their formation. While many of these advances often stemmed from studies of the compound eye of the fruit fly, Drosophila melanogaster, and later translated to discoveries in vertebrate systems, studies on vertebrate lens development far outnumber those in Drosophila. This may be largely historical, since Spemann and Mangold's paradigm of tissue induction was discovered in the amphibian lens. Recent studies on lens development in Drosophila have begun to define molecular commonalities with the vertebrate lens. Here, we provide an overview of Drosophila lens development, discussing intrinsic and extrinsic factors controlling lens cell specification and differentiation. We then summarize key morphological and molecular events in vertebrate lens development, emphasizing regulatory factors and networks strongly associated with both systems. Finally, we provide a comparative analysis that highlights areas of research that would help further clarify the degree of conservation between the formation of dioptric systems in invertebrates and vertebrates.
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22
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Dziedzic K, Heaphy J, Prescott H, Kavaler J. The transcription factor D-Pax2 regulates crystallin production during eye development in Drosophila melanogaster. Dev Dyn 2010; 238:2530-9. [PMID: 19718746 DOI: 10.1002/dvdy.22082] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
The generation of a functioning Drosophila eye requires the coordinated differentiation of multiple cell types and the morphogenesis of eye-specific structures. Here we show that D-Pax2 plays a significant role in lens development through regulation of the Crystallin gene and because Crystallin is also expressed in D-Pax2(+) cells in the external sensory organs. Loss of D-Pax2 function leads to loss of Crystallin expression in both eyes and bristles. A 2.3 kilobase (kb) upstream region of the Crystallin gene can drive GFP expression in the eye and is dependent on D-Pax2. In addition, D-Pax2 binds to an evolutionarily conserved site in this region that, by itself, is sufficient to drive GFP expression in the eye. However, mutation of this site does not greatly affect the regulatory region's function. The data indicate that D-Pax2 acts to promote lens development by controlling the production of the major protein component of the lens. Whether this control is direct or indirect remains unresolved.
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23
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Charlton-Perkins M, Cook TA. Building a fly eye: terminal differentiation events of the retina, corneal lens, and pigmented epithelia. Curr Top Dev Biol 2010; 93:129-73. [PMID: 20959165 DOI: 10.1016/b978-0-12-385044-7.00005-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In the past, vast differences in ocular structure, development, and physiology throughout the animal kingdom led to the widely accepted notion that eyes are polyphyletic, that is, they have independently arisen multiple times during evolution. Despite the dissimilarity between vertebrate and invertebrate eyes, it is becoming increasingly evident that the development of the eye in both groups shares more similarity at the genetic level than was previously assumed, forcing a reexamination of eye evolution. Understanding the molecular underpinnings of cell type specification during Drosophila eye development has been a focus of research for many labs over the past 25 years, and many of these findings are nicely reviewed in Chapters 1 and 4. A somewhat less explored area of research, however, considers how these cells, once specified, develop into functional ocular structures. This review aims to summarize the current knowledge related to the terminal differentiation events of the retina, corneal lens, and pigmented epithelia in the fly eye. In addition, we discuss emerging evidence that the different functional components of the fly eye share developmental pathways and functions with the vertebrate eye.
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Affiliation(s)
- Mark Charlton-Perkins
- Department of Pediatric Ophthalmology, Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA
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24
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Unravelling cis-regulatory elements in the genome of the smallest photosynthetic eukaryote: phylogenetic footprinting in Ostreococcus. J Mol Evol 2009; 69:249-59. [PMID: 19693423 DOI: 10.1007/s00239-009-9271-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2009] [Revised: 07/17/2009] [Accepted: 07/27/2009] [Indexed: 10/20/2022]
Abstract
We used a phylogenetic footprinting approach, adapted to high levels of divergence, to estimate the level of constraint in intergenic regions of the extremely gene dense Ostreococcus algae genomes (Chlorophyta, Prasinophyceae). We first benchmarked our method against the Saccharomyces sensu stricto genome data and found that the proportion of conserved non-coding sites was consistent with those obtained with methods using calibration by the neutral substitution rate. We then applied our method to the complete genomes of Ostreococcus tauri and O. lucimarinus, which are the most divergent species from the same genus sequenced so far. We found that 77% of intergenic regions in Ostreococcus still contain some phylogenetic footprints, as compared to 88% for Saccharomyces, corresponding to an average rate of constraint on intergenic region of 17% and 30%, respectively. A comparison with some known functional cis-regulatory elements enabled us to investigate whether some transcriptional regulatory pathways were conserved throughout the green lineage. Strikingly, the size of the phylogenetic footprints depends on gene orientation of neighboring genes, and appears to be genus-specific. In Ostreococcus, 5' intergenic regions contain four times more conserved sites than 3' intergenic regions, whereas in yeast a higher frequency of constrained sites in intergenic regions between genes on the same DNA strand suggests a higher frequency of bidirectional regulatory elements. The phylogenetic footprinting approach can be used despite high levels of divergence in the ultrasmall Ostreococcus algae, to decipher structure of constrained regulatory motifs, and identify putative regulatory pathways conserved within the green lineage.
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25
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Nanda S, DeFalco TJ, Loh SHY, Phochanukul N, Camara N, Van Doren M, Russell S. Sox100B, a Drosophila group E Sox-domain gene, is required for somatic testis differentiation. Sex Dev 2009; 3:26-37. [PMID: 19339815 DOI: 10.1159/000200079] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2008] [Accepted: 11/26/2008] [Indexed: 11/19/2022] Open
Abstract
Sex determination mechanisms are thought to evolve rapidly and show little conservation among different animal species. For example, the critical gene on the Y chromosome, SRY, that determines sex in most mammals, is not found in other animals. However, a related Sox domain transcription factor, SOX9, is also required for testis development in mammals and exhibits male-specific gonad expression in other vertebrate species. Previously, we found that the Drosophila orthologue of SOX9, Sox100B, is expressed male-specifically during gonad development. We now investigate the function of Sox100B and find, strikingly, that Sox100B is essential for testis development in Drosophila. In Sox100B mutants, the adult testis is severely reduced and fails to interact with other parts of the reproductive tract, which are themselves unaffected. While a testis initially forms in Sox100B mutants, it fails to undergo proper morphogenesis during pupal stages, likely due to defects in the pigment cells. In contrast, no substantive defects are observed in ovary development in Sox100B mutant females. Thus, as is observed in mammals, a Sox9 homolog is essential for sex-specific gonad development in Drosophila, suggesting that the molecular mechanisms regulating sexually dimorphic gonad development may be more conserved than previously suspected.
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Affiliation(s)
- S Nanda
- Department of Genetics, University of Cambridge, Cambridge, UK
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26
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Abstract
My group has long studied transcriptional gene regulation involved in cell differentiation, employing lens cell differentiation as a model. In this article, our progress over the last quarter of a century in deciphering the principles involved in developmental gene regulation is described, outlining concurrent advancement in relevant branches of developmental biology.
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Affiliation(s)
- Hisato Kondoh
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan.
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27
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Chassaing N, Gilbert-Dussardier B, Nicot F, Fermeaux V, Encha-Razavi F, Fiorenza M, Toutain A, Calvas P. Germinal mosaicism and familial recurrence of a SOX2 mutation with highly variable phenotypic expression extending from AEG syndrome to absence of ocular involvement. Am J Med Genet A 2007; 143A:289-91. [PMID: 17219395 DOI: 10.1002/ajmg.a.31524] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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28
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Vavouri T, Walter K, Gilks WR, Lehner B, Elgar G. Parallel evolution of conserved non-coding elements that target a common set of developmental regulatory genes from worms to humans. Genome Biol 2007; 8:R15. [PMID: 17274809 PMCID: PMC1852409 DOI: 10.1186/gb-2007-8-2-r15] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2006] [Revised: 10/20/2006] [Accepted: 02/02/2007] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND The human genome contains thousands of non-coding sequences that are often more conserved between vertebrate species than protein-coding exons. These highly conserved non-coding elements (CNEs) are associated with genes that coordinate development, and have been proposed to act as transcriptional enhancers. Despite their extreme sequence conservation in vertebrates, sequences homologous to CNEs have not been identified in invertebrates. RESULTS Here we report that nematode genomes contain an alternative set of CNEs that share sequence characteristics, but not identity, with their vertebrate counterparts. CNEs thus represent a very unusual class of sequences that are extremely conserved within specific animal lineages yet are highly divergent between lineages. Nematode CNEs are also associated with developmental regulatory genes, and include well-characterized enhancers and transcription factor binding sites, supporting the proposed function of CNEs as cis-regulatory elements. Most remarkably, 40 of 156 human CNE-associated genes with invertebrate orthologs are also associated with CNEs in both worms and flies. CONCLUSION A core set of genes that regulate development is associated with CNEs across three animal groups (worms, flies and vertebrates). We propose that these CNEs reflect the parallel evolution of alternative enhancers for a common set of developmental regulatory genes in different animal groups. This 're-wiring' of gene regulatory networks containing key developmental coordinators was probably a driving force during the evolution of animal body plans. CNEs may, therefore, represent the genomic traces of these 'hard-wired' core gene regulatory networks that specify the development of each alternative animal body plan.
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Affiliation(s)
- Tanya Vavouri
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- School of Biological and Chemical Sciences, Queen Mary, University of London, London E1 4NS, UK
| | - Klaudia Walter
- MRC Biostatistics Unit, Institute of Public Health, Cambridge CB2 2SR, UK
| | - Walter R Gilks
- Department of Statistics, University of Leeds, Leeds LS2 9JT, UK
| | - Ben Lehner
- EMBL/CRG Systems Biology Unit, Centre for Genomic Regulation (CRG), UPF, C/Dr. Aiguader 88, Barcelona 08003, Spain
| | - Greg Elgar
- School of Biological and Chemical Sciences, Queen Mary, University of London, London E1 4NS, UK
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29
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Girard F, Joly W, Savare J, Bonneaud N, Ferraz C, Maschat F. Chromatin immunoprecipitation reveals a novel role for the Drosophila SoxNeuro transcription factor in axonal patterning. Dev Biol 2006; 299:530-42. [PMID: 16979619 DOI: 10.1016/j.ydbio.2006.08.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2005] [Revised: 07/31/2006] [Accepted: 08/06/2006] [Indexed: 02/07/2023]
Abstract
In all metazoans, the expression of group B HMG domain Sox transcription factors is associated with the earliest stages of CNS development. In Drosophila, SoxNeuro (SoxN) is involved in dorso-ventral patterning of the neuroectoderm, and in the formation and segregation of neuroblasts. In this report, we show that SoxN expression persists in a subset of neurons and glial cells of the ventral nerve cord at embryonic stages 15/16. In an attempt to address SoxN function in late stages of CNS development, we have used a chromatin immunoprecipitation approach to isolate genomic regions bound in vivo by SoxN. We identified several genes involved in the regulation of axon scaffolding as potential direct target genes of SoxN, including beat1a, semaphorin2a, fasciclin2, longitudinal lacking and tailup/islet. We present genetic evidence for a direct involvement of SoxN in axonal patterning. Indeed, overexpressing a transcriptionally hyperactive mutated SoxN protein in neurons results in specific defects in axon scaffolding, which are also observed in transheterozygous combinations of SoxN null mutation and mutations in its target genes.
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Affiliation(s)
- Franck Girard
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique UPR1142, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France.
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30
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Bermingham-McDonogh O, Oesterle EC, Stone JS, Hume CR, Huynh HM, Hayashi T. Expression of Prox1 during mouse cochlear development. J Comp Neurol 2006; 496:172-86. [PMID: 16538679 PMCID: PMC2572724 DOI: 10.1002/cne.20944] [Citation(s) in RCA: 132] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We carried out an analysis of the expression of Prox1, a homeo-domain transcription factor, during mouse inner ear development with particular emphasis on the auditory system. Prox1 is expressed in the otocyst beginning at embryonic day (E)11, in the developing vestibular sensory patches. Expression is down regulated in maturing (myosin VIIA immunoreactive) vestibular hair cells and subsequently in the underlying support cell layer by E16.5. In the auditory sensory epithelium, Prox1 is initially expressed at embryonic day 14.5 in a narrow stripe of cells at the base of the cochlea. This stripe encompasses the full thickness of the sensory epithelium, including developing hair cells and support cells. Over the next several days the stripe of expression extends to the apex, and as the sensory epithelium differentiates Prox1 becomes restricted to a subset of support cells. Double labeling for Prox1 and cell-type-specific markers revealed that the outer hair cells transiently express Prox1. After E18, Prox1 protein is no longer detectable in hair cells, but it continues to be expressed in support cells for the rest of embryogenesis and into the second postnatal week. During this time, Prox1 is not expressed in all support cell types in the organ of Corti, but is restricted to developing Deiters' and pillar cells. The expression is maintained in these cells into the second week of postnatal life, at which time Prox1 is dynamically down regulated. These studies form a baseline from which we can analyze the role of Prox1 in vertebrate sensory development.
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Affiliation(s)
- Olivia Bermingham-McDonogh
- Virginia Merrill Bloedel Hearing Research Center and Department of Otolaryngology, University of Washington School of Medicine, Seattle, Washington 98195, USA.
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31
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Hou HH, Kuo MYP, Luo YW, Chang BE. Recapitulation of human betaB1-crystallin promoter activity in transgenic zebrafish. Dev Dyn 2006; 235:435-43. [PMID: 16331646 DOI: 10.1002/dvdy.20652] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Development of the eye is morphologically similar among vertebrates, indicating that the underlying mechanism regulating the process may have been highly conserved during evolution. Herein we analyzed the promoter of the human betaB1-crytallin gene in zebrafish by transgenic experiments. To delineate the evolutionarily conserved regulatory elements, we performed serial deletion assays in the promoter region. The results demonstrated that the -90/+61-bp upstream proximal promoter region is sufficient to confer lens-tissue specificity to the human betaB1-crystallin gene in transgenic zebrafish. Through phylogenetic sequence comparisons and an electrophoretic mobility shift assay (EMSA), a highly conserved cis-element of a six-base pair sequence TG(A/C)TGA, the consensus sequence for the Maf protein binding site, within the proximal promoter region was revealed. Further, a site-mutational assay showed that this element is crucial for promoter activity. These data suggest that the fundamental transcriptional regulatory mechanism of the betaB1-crystallin gene has been well conserved between humans and zebrafish, and plausibly among all vertebrates, during evolution.
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Affiliation(s)
- Hsin-Han Hou
- Graduate Institute of Oral Biology, College of Medicine, National Taiwan University, Taipei, Taiwan, Republic of China
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32
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Savare J, Bonneaud N, Girard F. SUMO represses transcriptional activity of the Drosophila SoxNeuro and human Sox3 central nervous system-specific transcription factors. Mol Biol Cell 2005; 16:2660-9. [PMID: 15788563 PMCID: PMC1142414 DOI: 10.1091/mbc.e04-12-1062] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Sry high mobility group (HMG) box (Sox) transcription factors are involved in the development of central nervous system (CNS) in all metazoans. Little is known on the molecular mechanisms that regulate their transcriptional activity. Covalent posttranslational modification by small ubiquitin-like modifier (SUMO) regulates several nuclear events, including the transcriptional activity of transcription factors. Here, we demonstrate that SoxNeuro, an HMG box-containing transcription factor involved in neuroblast formation in Drosophila, is a substrate for SUMO modification. SUMOylation assays in HeLa cells and Drosophila S2 cells reveal that lysine 439 is the major SUMO acceptor site. The sequence in SoxNeuro targeted for SUMOylation, IKSE, is part of a small inhibitory domain, able to repress in cis the activity of two adjacent transcriptional activation domains. Our data show that SUMO modification represses SoxNeuro transcriptional activity in transfected cells. Overexpression in Drosophila embryos of a SoxN form that cannot be targeted for SUMOylation strongly impairs the development of the CNS, suggesting that SUMO modification of SoxN is crucial for regulating its activity in vivo. Finally, we present evidence that SUMO modification of group B1 Sox factors was conserved during evolution, because Sox3, the human counterpart of SoxN, is also negatively regulated through SUMO modification.
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Affiliation(s)
- Jean Savare
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique Unité Propre de Recherche 1142, 34396 Montpellier, France
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