1
|
McCulloch K. In preprints: new spiralian model system unlocks potential for understanding eye evolution and regeneration. Development 2024; 151:dev203163. [PMID: 39016531 DOI: 10.1242/dev.203163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Affiliation(s)
- Kyle McCulloch
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN 55108, USA
| |
Collapse
|
2
|
Banerjee SJ, Curtiss J. Dachshund and C-terminal Binding Protein bind directly during Drosophila eye development. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.001106. [PMID: 38528987 PMCID: PMC10961645 DOI: 10.17912/micropub.biology.001106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/01/2024] [Accepted: 03/07/2024] [Indexed: 03/27/2024]
Abstract
The transcription factor Dachshund (Dac) and the transcriptional co-regulator C-terminal Binding Protein (CtBP) were identified as the retinal determination factors during Drosophila eye development . A previous study established that Dac and CtBP interact genetically during eye development. Co-immunoprecipitation assays suggested that both molecules interact in the Drosophila larval eye-antennal disc. Our present study shows that Dac and CtBP bind each other directly, as determined by GST pull-down assays. Thus, our results demonstrate the molecular mechanism of Dac and CtBP interaction and suggest the direct binding of these two transcription regulators in the cells of the eye disc promotes the Drosophila eye specification.
Collapse
Affiliation(s)
| | - Jennifer Curtiss
- Biology, New Mexico State University, Las Cruces, New Mexico, United States
| |
Collapse
|
3
|
Zhang T, Xue Y, Su S, Altouma V, Ho K, Martindale JL, Lee SK, Shen W, Park A, Zhang Y, De S, Gorospe M, Wang W. RNA-binding protein Nocte regulates Drosophila development by promoting translation reinitiation on mRNAs with long upstream open reading frames. Nucleic Acids Res 2024; 52:885-905. [PMID: 38000373 PMCID: PMC10810208 DOI: 10.1093/nar/gkad1122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 10/18/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
RNA-binding proteins (RBPs) with intrinsically disordered regions (IDRs) are linked to multiple human disorders, but their mechanisms of action remain unclear. Here, we report that one such protein, Nocte, is essential for Drosophila eye development by regulating a critical gene expression cascade at translational level. Knockout of nocte in flies leads to lethality, and its eye-specific depletion impairs eye size and morphology. Nocte preferentially enhances translation of mRNAs with long upstream open reading frames (uORFs). One of the key Nocte targets, glass mRNA, encodes a transcription factor critical for differentiation of photoreceptor neurons and accessory cells, and re-expression of Glass largely rescued the eye defects caused by Nocte depletion. Mechanistically, Nocte counteracts long uORF-mediated translational suppression by promoting translation reinitiation downstream of the uORF. Nocte interacts with translation factors eIF3 and Rack1 through its BAT2 domain, and a Nocte mutant lacking this domain fails to promote translation of glass mRNA. Notably, de novo mutations of human orthologs of Nocte have been detected in schizophrenia patients. Our data suggest that Nocte family of proteins can promote translation reinitiation to overcome long uORFs-mediated translational suppression, and disruption of this function can lead to developmental defects and neurological disorders.
Collapse
Affiliation(s)
- Tianyi Zhang
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Yutong Xue
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Shuaikun Su
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Valerie Altouma
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Katherine Ho
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Jennifer L Martindale
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Seung-Kyu Lee
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Weiping Shen
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Aaron Park
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Yongqing Zhang
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Supriyo De
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Weidong Wang
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| |
Collapse
|
4
|
Brown HE, Weasner BP, Weasner BM, Kumar JP. Polycomb safeguards imaginal disc specification through control of the Vestigial-Scalloped complex. Development 2023; 150:dev201872. [PMID: 37702007 PMCID: PMC10560572 DOI: 10.1242/dev.201872] [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: 04/18/2023] [Accepted: 09/04/2023] [Indexed: 09/14/2023]
Abstract
A fundamental goal of developmental biology is to understand how cell and tissue fates are specified. The imaginal discs of Drosophila are excellent model systems for addressing this paradigm as their fate can be redirected when discs regenerate after injury or when key selector genes are misregulated. Here, we show that when Polycomb expression is reduced, the wing selector gene vestigial is ectopically activated. This leads to the inappropriate formation of the Vestigial-Scalloped complex, which forces the eye to transform into a wing. We further demonstrate that disrupting this complex does not simply block wing formation or restore eye development. Instead, immunohistochemistry and high-throughput genomic analysis show that the eye-antennal disc unexpectedly undergoes hyperplastic growth with multiple domains being organized into other imaginal discs and tissues. These findings provide insight into the complex developmental landscape that tissues must navigate before adopting their final fate.
Collapse
Affiliation(s)
- Haley E. Brown
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | | | - Bonnie M. Weasner
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Justin P. Kumar
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| |
Collapse
|
5
|
Brown HE, Weasner BP, Weasner BM, Kumar JP. Polycomb safeguards imaginal disc specification through control of the Vestigial-Scalloped complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.11.536444. [PMID: 37090526 PMCID: PMC10120697 DOI: 10.1101/2023.04.11.536444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
A fundamental goal of developmental biology is to understand how cell and tissue fates are specified. The imaginal discs of Drosophila are excellent model systems for addressing this paradigm as their fate can be redirected when discs regenerate after injury or when key selector genes are mis-regulated. Here, we show that when Polycomb expression is reduced, the wing selector gene vestigial is ectopically activated. This leads to the inappropriate formation of the Vestigial-Scalloped complex which forces the eye to transform into a wing. We further demonstrate that disrupting this complex does not simply block wing formation or restore eye development. Instead, immunohistochemistry and high throughput genomic analysis show that the eye-antennal disc unexpectedly undergoes hyperplastic growth with multiple domains being organized into other imaginal discs and tissues. These findings provide insight into the complex developmental landscape that tissues must navigate before adopting their final fate. Summary Statement Here we describe a novel mechanism by which Pc promotes an eye fate during normal development and how the eye is reprogrammed into a wing in its absence.
Collapse
Affiliation(s)
- Haley E. Brown
- Department of Biology, Indiana University, Bloomington, IN 47405 USA
| | | | - Bonnie M. Weasner
- Department of Biology, Indiana University, Bloomington, IN 47405 USA
| | - Justin P. Kumar
- Department of Biology, Indiana University, Bloomington, IN 47405 USA
| |
Collapse
|
6
|
Zhu S, Li W, Zhang H, Yan Y, Mei Q, Wu K. Retinal determination gene networks: from biological functions to therapeutic strategies. Biomark Res 2023; 11:18. [PMID: 36750914 PMCID: PMC9906957 DOI: 10.1186/s40364-023-00459-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 01/28/2023] [Indexed: 02/09/2023] Open
Abstract
The retinal determinant gene network (RDGN), originally discovered as a critical determinator in Drosophila eye specification, has become an important regulatory network in tumorigenesis and progression, as well as organogenesis. This network is not only associated with malignant biological behaviors of tumors, such as proliferation, and invasion, but also regulates the development of multiple mammalian organs. Three members of this conservative network have been extensively investigated, including DACH, SIX, and EYA. Dysregulated RDGN signaling is associated with the initiation and progression of tumors. In recent years, it has been found that the members of this network can be used as prognostic markers for cancer patients. Moreover, they are considered to be potential therapeutic targets for cancer. Here, we summarize the research progress of RDGN members from biological functions to signaling transduction, especially emphasizing their effects on tumors. Additionally, we discuss the roles of RDGN members in the development of organs and tissue as well as their correlations with the pathogenesis of chronic kidney disease and coronary heart disease. By summarizing the roles of RDGN members in human diseases, we hope to promote future investigations into RDGN and provide potential therapeutic strategies for patients.
Collapse
Affiliation(s)
- Shuangli Zhu
- grid.412793.a0000 0004 1799 5032Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 China
| | - Wanling Li
- grid.412793.a0000 0004 1799 5032Department of Geriatrics, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 China ,grid.470966.aCancer Center, Shanxi Bethune Hospital, Shanxi Academy of Medical Science, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, 030032 China
| | - Hao Zhang
- grid.412793.a0000 0004 1799 5032Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 China
| | - Yuheng Yan
- grid.412793.a0000 0004 1799 5032Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 China
| | - Qi Mei
- Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China. .,Cancer Center, Shanxi Bethune Hospital, Shanxi Academy of Medical Science, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, 030032, China.
| | - Kongming Wu
- Cancer Center, Shanxi Bethune Hospital, Shanxi Academy of Medical Science, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, 030032, China. .,Cancer Center, Tongji hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| |
Collapse
|
7
|
Paganos P, Ullrich-Lüter E, Caccavale F, Zakrzewski A, Voronov D, Fournon-Berodia I, Cocurullo M, Lüter C, Arnone MI. A New Model Organism to Investigate Extraocular Photoreception: Opsin and Retinal Gene Expression in the Sea Urchin Paracentrotus lividus. Cells 2022; 11:2636. [PMID: 36078045 PMCID: PMC9454927 DOI: 10.3390/cells11172636] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/17/2022] [Accepted: 08/18/2022] [Indexed: 11/16/2022] Open
Abstract
Molecular research on the evolution of extraocular photoreception has drawn attention to photosensitive animals lacking proper eye organs. Outside of vertebrates, little is known about this type of sensory system in any other deuterostome. In this study, we investigate such an extraocular photoreceptor cell (PRC) system in developmental stages of the sea urchin Paracentrotus lividus. We provide a general overview of the cell type families present at the mature rudiment stage using single-cell transcriptomics, while emphasizing the PRCs complexity. We show that three neuronal and one muscle-like PRC type families express retinal genes prior to metamorphosis. Two of the three neuronal PRC type families express a rhabdomeric opsin as well as an echinoderm-specific opsin (echinopsin), and their genetic wiring includes sea urchin orthologs of key retinal genes such as hlf, pp2ab56e, barh, otx, ac/sc, brn3, six1/2, pax6, six3, neuroD, irxA, isl and ato. Using qPCR, in situ hybridization, and immunohistochemical analysis, we found that the expressed retinal gene composition becomes more complex from mature rudiment to juvenile stage. The majority of retinal genes are expressed dominantly in the animals' podia, and in addition to the genes already expressed in the mature rudiment, the juvenile podia express a ciliary opsin, another echinopsin, and two Go-opsins. The expression of a core of vertebrate retinal gene orthologs indicates that sea urchins have an evolutionarily conserved gene regulatory toolkit that controls photoreceptor specification and function, and that their podia are photosensory organs.
Collapse
Affiliation(s)
- Periklis Paganos
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 80121 Naples, Italy
| | - Esther Ullrich-Lüter
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, 10115 Berlin, Germany
| | - Filomena Caccavale
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 80121 Naples, Italy
| | - Anne Zakrzewski
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, 10115 Berlin, Germany
| | - Danila Voronov
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 80121 Naples, Italy
| | - Inés Fournon-Berodia
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 80121 Naples, Italy
| | - Maria Cocurullo
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 80121 Naples, Italy
| | - Carsten Lüter
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, 10115 Berlin, Germany
| | - Maria Ina Arnone
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 80121 Naples, Italy
| |
Collapse
|
8
|
Regulation of Eye Determination and Regionalization in the Spider Parasteatoda tepidariorum. Cells 2022; 11:cells11040631. [PMID: 35203282 PMCID: PMC8870698 DOI: 10.3390/cells11040631] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/28/2022] [Accepted: 02/04/2022] [Indexed: 11/17/2022] Open
Abstract
Animal visual systems are enormously diverse, but their development appears to be controlled by a set of conserved retinal determination genes (RDGs). Spiders are particular masters of visual system innovation, and offer an excellent opportunity to study the evolution of animal eyes. Several RDGs have been identified in spider eye primordia, but their interactions and regulation remain unclear. From our knowledge of RDG network regulation in Drosophila melanogaster, we hypothesize that orthologs of Pax6, eyegone, Wnt genes, hh, dpp, and atonal could play important roles in controlling eye development in spiders. We analyzed the expression of these genes in developing embryos of the spider Parasteatodatepidariorum, both independently and in relation to the eye primordia, marked using probes for the RDG sine oculis. Our results support conserved roles for Wnt genes in restricting the size and position of the eye field, as well as for atonal initiating photoreceptor differentiation. However, we found no strong evidence for an upstream role of Pax6 in eye development, despite its label as a master regulator of animal eye development; nor do eyg, hh or dpp compensate for the absence of Pax6. Conversely, our results indicate that hh may work with Wnt signaling to restrict eye growth, a role similar to that of Sonichedgehog (Shh) in vertebrates.
Collapse
|
9
|
Nyberg KG, Carthew RW. CRISPR-/Cas9-Mediated Precise and Efficient Genome Editing in Drosophila. Methods Mol Biol 2022; 2540:135-156. [PMID: 35980576 PMCID: PMC10027364 DOI: 10.1007/978-1-0716-2541-5_6] [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: 06/15/2023]
Abstract
The CRISPR/Cas9 system provides the means to make precise and purposeful modifications to the genome via homology-directed repair (HDR). In Drosophila, a wide variety of tools provide flexibility to achieve these ends. Here, we detail a method to generate precise genome edits via HDR that is efficient and broadly applicable to any Drosophila stock or species. sgRNAs are first tested for their cleavage efficiency by injecting embryos with Cas9/sgRNA ribonucleoproteins using commercially available Cas9 protein. Using an empirically validated sgRNA, HDR is performed using a donor repair plasmid that carries two transformation markers. A fluorescent eye marker that can be seamlessly removed using PiggyBac transposase marks integration of the repair sequence. A counter-selection marker that produces small rough eyes via RNAi against eyes absent is used to screen against imprecise HDR events. Altogether, the enhancements implemented in this method expand the ease and scope of achieving precise CRISPR/Cas9 genome edits in Drosophila.
Collapse
Affiliation(s)
- Kevin G Nyberg
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Richard W Carthew
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.
- NSF Simons Center for Quantitative Biology, Northwestern University, Evanston, IL, USA.
| |
Collapse
|
10
|
Almasoudi SH, Schlosser G. Eya1 protein distribution during embryonic development of Xenopus laevis. Gene Expr Patterns 2021; 42:119213. [PMID: 34536585 DOI: 10.1016/j.gep.2021.119213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/10/2021] [Accepted: 09/10/2021] [Indexed: 11/24/2022]
Abstract
Eya1 and other Eya proteins are important regulators of progenitor proliferation, cell differentiation and morphogenesis in all three germ layers. At present, most of our knowledge of Eya1 distribution is based on in situ hybridization for Eya1 mRNA. However, to begin to dissect the mechanisms underlying Eya1 functions, we need a better understanding of the spatiotemporal distribution of Eya1 proteins during embryonic development, their subcellular localization and their levels of expression in various tissues. Here we report the localization of Eya1 protein throughout embryonic development from neural plate stages to tadpole stages of Xenopus laevis using a specific antibody for Xenopus Eya1. Our study confirms the expression of Eya1 protein in cranial placodes, placodally derived sensory primordia (olfactory epithelium, otic vesicle, lateral line primordia) and cranial ganglia, as well as in somites, secondary heart field and pharyngeal endoderm. In addition, we report here a novel expression of Eya1 proteins in scattered epidermal cells in Xenopus. Our findings also reveal that, while being predominantly expressed in nuclei in most expression domains, Eya1 protein is also localized to the cytoplasm, in particular in the early preplacodal ectoderm, some placode-derived ganglia and a subset of epidermal cells. While some cytoplasmic roles of Eya1 have been previously described in other contexts, the functions of cytoplasmic Eya1 in the preplacodal ectoderm, cranial ganglia and epidermal cells remain to be investigated.
Collapse
Affiliation(s)
| | - Gerhard Schlosser
- School of Natural Sciences, National University of Galway, Galway, Ireland.
| |
Collapse
|
11
|
The Eyes Absent proteins in development and in developmental disorders. Biochem Soc Trans 2021; 49:1397-1408. [PMID: 34196366 PMCID: PMC8286820 DOI: 10.1042/bst20201302] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/06/2021] [Accepted: 06/07/2021] [Indexed: 11/23/2022]
Abstract
The Eyes Absent (EYA) transactivator-phosphatase proteins are important contributors to cell-fate determination processes and to the development of multiple organs. The transcriptional regulatory activity as well as the protein tyrosine phosphatase activities of the EYA proteins can independently contribute to proliferation, differentiation, morphogenesis and tissue homeostasis in different contexts. Aberrant EYA levels or activity are associated with numerous syndromic and non-syndromic developmental disorders, as well as cancers. Commensurate with the multiplicity of biochemical activities carried out by the EYA proteins, they impact upon a range of cellular signaling pathways. Here, we provide a broad overview of the roles played by EYA proteins in development, and highlight the molecular signaling pathways known to be linked with EYA-associated organ development and developmental disorders.
Collapse
|
12
|
Aase-Remedios ME, Ferrier DEK. Improved Understanding of the Role of Gene and Genome Duplications in Chordate Evolution With New Genome and Transcriptome Sequences. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.703163] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Comparative approaches to understanding chordate genomes have uncovered a significant role for gene duplications, including whole genome duplications (WGDs), giving rise to and expanding gene families. In developmental biology, gene families created and expanded by both tandem and WGDs are paramount. These genes, often involved in transcription and signalling, are candidates for underpinning major evolutionary transitions because they are particularly prone to retention and subfunctionalisation, neofunctionalisation, or specialisation following duplication. Under the subfunctionalisation model, duplication lays the foundation for the diversification of paralogues, especially in the context of gene regulation. Tandemly duplicated paralogues reside in the same regulatory environment, which may constrain them and result in a gene cluster with closely linked but subtly different expression patterns and functions. Ohnologues (WGD paralogues) often diversify by partitioning their expression domains between retained paralogues, amidst the many changes in the genome during rediploidisation, including chromosomal rearrangements and extensive gene losses. The patterns of these retentions and losses are still not fully understood, nor is the full extent of the impact of gene duplication on chordate evolution. The growing number of sequencing projects, genomic resources, transcriptomics, and improvements to genome assemblies for diverse chordates from non-model and under-sampled lineages like the coelacanth, as well as key lineages, such as amphioxus and lamprey, has allowed more informative comparisons within developmental gene families as well as revealing the extent of conserved synteny across whole genomes. This influx of data provides the tools necessary for phylogenetically informed comparative genomics, which will bring us closer to understanding the evolution of chordate body plan diversity and the changes underpinning the origin and diversification of vertebrates.
Collapse
|
13
|
Gene Regulation and Cellular Metabolism: An Essential Partnership. Trends Genet 2021; 37:389-400. [PMID: 33092903 PMCID: PMC7969386 DOI: 10.1016/j.tig.2020.09.018] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/18/2020] [Accepted: 09/25/2020] [Indexed: 01/09/2023]
Abstract
It is recognized that cell metabolism is tightly connected to other cellular processes such as regulation of gene expression. Metabolic pathways not only provide the precursor molecules necessary for gene expression, but they also provide ATP, the primary fuel driving gene expression. However, metabolic conditions are highly variable since nutrient uptake is not a uniform process. Thus, cells must continually calibrate gene expression to their changing metabolite and energy budgets. This review discusses recent advances in understanding the molecular and biophysical mechanisms that connect metabolism and gene regulation as cells navigate their growth, proliferation, and differentiation. Particular focus is given to these mechanisms in the context of organismal development.
Collapse
|
14
|
Lyu J, Mu X. Genetic control of retinal ganglion cell genesis. Cell Mol Life Sci 2021; 78:4417-4433. [PMID: 33782712 DOI: 10.1007/s00018-021-03814-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 02/27/2021] [Accepted: 03/18/2021] [Indexed: 12/18/2022]
Abstract
Retinal ganglion cells (RGCs) are the only projection neurons in the neural retina. They receive and integrate visual signals from upstream retinal neurons in the visual circuitry and transmit them to the brain. The function of RGCs is performed by the approximately 40 RGC types projecting to various central brain targets. RGCs are the first cell type to form during retinogenesis. The specification and differentiation of the RGC lineage is a stepwise process; a hierarchical gene regulatory network controlling the RGC lineage has been identified and continues to be elaborated. Recent studies with single-cell transcriptomics have led to unprecedented new insights into their types and developmental trajectory. In this review, we summarize our current understanding of the functions and relationships of the many regulators of the specification and differentiation of the RGC lineage. We emphasize the roles of these key transcription factors and pathways in different developmental steps, including the transition from retinal progenitor cells (RPCs) to RGCs, RGC differentiation, generation of diverse RGC types, and central projection of the RGC axons. We discuss critical issues that remain to be addressed for a comprehensive understanding of these different aspects of RGC genesis and emerging technologies, including single-cell techniques, novel genetic tools and resources, and high-throughput genome editing and screening assays, which can be leveraged in future studies.
Collapse
Affiliation(s)
- Jianyi Lyu
- Department of Ophthalmology/Ross Eye Institute, State University of New York At Buffalo, Buffalo, NY, 14203, USA
- School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
| | - Xiuqian Mu
- Department of Ophthalmology/Ross Eye Institute, State University of New York At Buffalo, Buffalo, NY, 14203, USA.
| |
Collapse
|
15
|
Tare M, Chimata AV, Gogia N, Narwal S, Deshpande P, Singh A. An E3 ubiquitin ligase, cullin-4 regulates retinal differentiation in Drosophila eye. Genesis 2020; 58:e23395. [PMID: 32990387 PMCID: PMC9277906 DOI: 10.1002/dvg.23395] [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: 07/30/2020] [Accepted: 08/26/2020] [Indexed: 11/12/2022]
Abstract
During organogenesis, cell proliferation is followed by the differentiation of specific cell types to form an organ. Any aberration in differentiation can result in developmental defects, which can result in a partial to a near-complete loss of an organ. We employ the Drosophila eye model to understand the genetic and molecular mechanisms involved in the process of differentiation. In a forward genetic screen, we identified, cullin-4 (cul-4), which encodes an E3 ubiquitin ligase, to play an important role in retinal differentiation. During development, cul-4 is known to be involved in protein degradation, regulation of genomic stability, and regulation of cell cycle. Previously, we have reported that cul-4 regulates cell death during eye development by downregulating Wingless (Wg)/Wnt signaling pathway. We found that loss-of-function of cul-4 results in a reduced eye phenotype, which can be due to onset of cell death. However, we found that loss-of-function of cul-4 also affects retinal development by downregulating retinal determination (RD) gene expression. Early markers of retinal differentiation are dysregulated in cul-4 loss of function conditions, indicating that cul-4 is necessary for differentiation. Furthermore, loss-of-function of cul-4 ectopically induces expression of negative regulators of eye development like Wg and Homothorax (Hth). During eye development, Wg is known to block the progression of a synchronous wave of differentiation referred to as Morphogenetic furrow (MF). In cul-4 loss-of-function background, expression of dpp-lacZ, a MF marker, is significantly downregulated. Our data suggest a new role of cul-4 in retinal differentiation. These studies may have significant bearings on our understanding of early eye development.
Collapse
Affiliation(s)
- Meghana Tare
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Pilani, Rajasthan, India
| | | | - Neha Gogia
- Department of Biology, University of Dayton, 300 College Park Drive, Dayton, OH, USA
| | - Sonia Narwal
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Pilani, Rajasthan, India
| | - Prajakta Deshpande
- Department of Biology, University of Dayton, 300 College Park Drive, Dayton, OH, USA
| | - Amit Singh
- Department of Biology, University of Dayton, 300 College Park Drive, Dayton, OH, USA
- Premedical Program, University of Dayton, 300 College Park Drive, Dayton, OH, USA
- Center for Tissue Regeneration & Engineering (TREND), University of Dayton, 300 College Park Drive, Dayton, OH, USA
- The Integrative Science and Engineering Center, University of Dayton, Dayton, OH, USA
- Center for Genomic Advocacy (TCGA), Indiana State University, Terre Haute, IN, USA
| |
Collapse
|
16
|
Raj A, Chimata AV, Singh A. Motif 1 Binding Protein suppresses wingless to promote eye fate in Drosophila. Sci Rep 2020; 10:17221. [PMID: 33057115 PMCID: PMC7560846 DOI: 10.1038/s41598-020-73891-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 08/31/2020] [Indexed: 01/19/2023] Open
Abstract
The phenomenon of RNA polymerase II (Pol II) pausing at transcription start site (TSS) is one of the key rate-limiting steps in regulating genome-wide gene expression. In Drosophila embryo, Pol II pausing is known to regulate the developmental control genes expression, however, the functional implication of Pol II pausing during later developmental time windows remains largely unknown. A highly conserved zinc finger transcription factor, Motif 1 Binding Protein (M1BP), is known to orchestrate promoter-proximal pausing. We found a new role of M1BP in regulating Drosophila eye development. Downregulation of M1BP function suppresses eye fate resulting in a reduced eye or a "no-eye" phenotype. The eye suppression function of M1BP has no domain constraint in the developing eye. Downregulation of M1BP results in more than two-fold induction of wingless (wg) gene expression along with robust induction of Homothorax (Hth), a negative regulator of eye fate. The loss-of-eye phenotype of M1BP downregulation is dependent on Wg upregulation as downregulation of both M1BP and wg, by using wgRNAi, shows a significant rescue of a reduced eye or a "no-eye" phenotype, which is accompanied by normalizing of wg and hth expression levels in the eye imaginal disc. Ectopic induction of Wg is known to trigger developmental cell death. We found that upregulation of wg as a result of downregulation of M1BP also induces apoptotic cell death, which can be significantly restored by blocking caspase-mediated cell death. Our data strongly imply that transcriptional regulation of wg by Pol II pausing factor M1BP may be one of the important regulatory mechanism(s) during Drosophila eye development.
Collapse
Affiliation(s)
- Akanksha Raj
- Department of Biology, University of Dayton, Dayton, OH, 45469, USA
| | | | - Amit Singh
- Department of Biology, University of Dayton, Dayton, OH, 45469, USA. .,Premedical Program, University of Dayton, Dayton, OH, USA. .,Center for Tissue Regeneration and Engineering (TREND), University of Dayton, Dayton, OH, USA. .,Integrative Science and Engineering (ISE), University of Dayton, Dayton, OH, USA. .,Center for Genomic Advocacy (TCGA), Indiana State University, Terre Haute, IN, USA.
| |
Collapse
|
17
|
Nyberg KG, Nguyen JQ, Kwon YJ, Blythe S, Beitel GJ, Carthew R. A pipeline for precise and efficient genome editing by sgRNA-Cas9 RNPs in Drosophila. Fly (Austin) 2020; 14:34-48. [PMID: 33016195 PMCID: PMC7746241 DOI: 10.1080/19336934.2020.1832416] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/25/2020] [Accepted: 09/29/2020] [Indexed: 12/26/2022] Open
Abstract
Genome editing via homology-directed repair (HDR) has made possible precise and deliberate modifications to gene sequences. CRISPR/Cas9-mediated HDR is the simplest means to carry this out. However, technical challenges remain to improve efficiency and broaden applicability to any genetic background of Drosophila melanogaster as well as to other Drosophila species. To address these issues, we developed a two-stage marker-assisted strategy in which embryos are injected with RNPs and pre-screened using T7EI. Using sgRNA in complex with recombinant Cas9 protein, we assayed each sgRNA for genome-cutting efficiency. We then conducted HDR using sgRNAs that efficiently cut target genes and the application of a transformation marker that generates RNAi against eyes absent. This allows for screening based on eye morphology rather than colour. These new tools can be used to make a single change or a series of allelic substitutions in a region of interest, or to create additional genetic tools such as balancer chromosomes.
Collapse
Affiliation(s)
- Kevin G. Nyberg
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Joseph Q. Nguyen
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Yong-Jae Kwon
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Shelby Blythe
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Greg J. Beitel
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Richard Carthew
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL, USA
| |
Collapse
|
18
|
Fritsch C, Bernardo-Garcia FJ, Humberg TH, Mishra AK, Miellet S, Almeida S, Frochaux MV, Deplancke B, Huber A, Sprecher SG. Multilevel regulation of the glass locus during Drosophila eye development. PLoS Genet 2019; 15:e1008269. [PMID: 31299050 PMCID: PMC6655844 DOI: 10.1371/journal.pgen.1008269] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 07/24/2019] [Accepted: 06/23/2019] [Indexed: 12/28/2022] Open
Abstract
Development of eye tissue is initiated by a conserved set of transcription factors termed retinal determination network (RDN). In the fruit fly Drosophila melanogaster, the zinc-finger transcription factor Glass acts directly downstream of the RDN to control identity of photoreceptor as well as non-photoreceptor cells. Tight control of spatial and temporal gene expression is a critical feature during development, cell-fate determination as well as maintenance of differentiated tissues. The molecular mechanisms that control expression of glass, however, remain largely unknown. We here identify complex regulatory mechanisms controlling expression of the glass locus. All information to recapitulate glass expression are contained in a compact 5.2 kb cis-acting genomic element by combining different cell-type specific and general enhancers with repressor elements. Moreover, the immature RNA of the locus contains an alternative small open reading frame (smORF) upstream of the actual glass translation start, resulting in a small peptide instead of the three possible Glass protein isoforms. CRISPR/Cas9-based mutagenesis shows that the smORF is not required for the formation of functioning photoreceptors, but is able to attenuate effects of glass misexpression. Furthermore, editing the genome to generate glass loci eliminating either one or two isoforms shows that only one of the three proteins is critical for formation of functioning photoreceptors, while removing the two other isoforms did not cause defects in developmental or photoreceptor function. Our results show that eye development and function is largely unaffected by targeted manipulations of critical features of the glass transcript, suggesting a strong selection pressure to allow the formation of a functioning eye.
Collapse
Affiliation(s)
- Cornelia Fritsch
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - F. Javier Bernardo-Garcia
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, United States of America
| | | | | | - Sara Miellet
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, Australia
| | - Silvia Almeida
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | | | - Bart Deplancke
- Laboratory of Systems Biology, IBI, SV, EPFL, Lausanne, Switzerland
| | - Armin Huber
- Institute of Physiology, University of Hohenheim, Hohenheim, Germany
| | - Simon G. Sprecher
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| |
Collapse
|
19
|
Sánchez-Aragón M, Cantisán-Gómez J, Luque CM, Brás-Pereira C, Lopes CS, Lemos MC, Casares F. A Toggle-Switch and a Feed-Forward Loop Engage in the Control of the Drosophila Retinal Determination Gene Network. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
|
20
|
Contreras EG, Sierralta J, Oliva C. Novel Strategies for the Generation of Neuronal Diversity: Lessons From the Fly Visual System. Front Mol Neurosci 2019; 12:140. [PMID: 31213980 PMCID: PMC6554424 DOI: 10.3389/fnmol.2019.00140] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 05/13/2019] [Indexed: 12/17/2022] Open
Abstract
Among all organs of an adult animal, the central nervous system stands out because of its vast complexity and morphological diversity. During early development, the entire central nervous system develops from an apparently homogenous group of progenitors that differentiate into all neural cell types. Therefore, understanding the molecular and genetic mechanisms that give rise to the cellular and anatomical diversity of the brain is a key goal of the developmental neurobiology field. With this aim in mind, the development of the central nervous system of model organisms has been extensively studied. From more than a century, the mechanisms of neurogenesis have been studied in the fruit fly Drosophila melanogaster. The visual system comprises one of the major structures of the Drosophila brain. The visual information is collected by the eye-retina photoreceptors and then processed by the four optic lobe ganglia: the lamina, medulla, lobula and lobula plate. The molecular mechanisms that originate neuronal diversity in the optic lobe have been unveiled in the past decade. In this article, we describe the early development and differentiation of the lobula plate ganglion, from the formation of the optic placode and the inner proliferation center to the specification of motion detection neurons. We focused specifically on how the precise combination of signaling pathways and cell-specific transcription factors patterns the pool of neural stem cells that generates the different neurons of the motion detection system.
Collapse
Affiliation(s)
- Esteban G Contreras
- Department of Neuroscience and Biomedical Neuroscience Institute, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Jimena Sierralta
- Department of Neuroscience and Biomedical Neuroscience Institute, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Carlos Oliva
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| |
Collapse
|
21
|
Liu Z, Mar KB, Hanners NW, Perelman SS, Kanchwala M, Xing C, Schoggins JW, Alto NM. A NIK-SIX signalling axis controls inflammation by targeted silencing of non-canonical NF-κB. Nature 2019; 568:249-253. [PMID: 30894749 PMCID: PMC6812682 DOI: 10.1038/s41586-019-1041-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 02/18/2019] [Indexed: 12/31/2022]
Abstract
The non-canonical NF-κB signalling cascade is essential for lymphoid organogenesis, B cell maturation, osteoclast differentiation, and inflammation in mammals1,2; dysfunction of this system is associated with human diseases, including immunological disorders and cancer3-6. Although expression of NF-κB-inducing kinase (NIK, also known as MAP3K14) is the rate-limiting step in non-canonical NF-κB pathway activation2,7, the mechanisms by which transcriptional responses are regulated remain largely unknown. Here we show that the sine oculis homeobox (SIX) homologue family transcription factors SIX1 and SIX2 are integral components of the non-canonical NF-κB signalling cascade. The developmentally silenced SIX proteins are reactivated in differentiated macrophages by NIK-mediated suppression of the ubiquitin proteasome pathway. Consequently, SIX1 and SIX2 target a subset of inflammatory gene promoters and directly inhibit the trans-activation function of the transcription factors RELA and RELB in a negative feedback circuit. In support of a physiologically pivotal role for SIX proteins in host immunity, a human SIX1 transgene suppressed inflammation and promoted the recovery of mice from endotoxic shock. In addition, SIX1 and SIX2 protected RAS/P53-driven non-small-cell lung carcinomas from inflammatory cell death induced by SMAC-mimetic chemotherapeutic agents (small-molecule activators of the non-canonical NF-κB pathway). Our findings identify a NIK-SIX signalling axis that fine-tunes inflammatory gene expression programs under both physiological and pathological conditions.
Collapse
Affiliation(s)
- Zixu Liu
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Katrina B Mar
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Natasha W Hanners
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sofya S Perelman
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Mohammed Kanchwala
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Chao Xing
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - John W Schoggins
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Neal M Alto
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| |
Collapse
|
22
|
Bernardo-Garcia FJ, Syed M, Jékely G, Sprecher SG. Glass confers rhabdomeric photoreceptor identity in Drosophila, but not across all metazoans. EvoDevo 2019; 10:4. [PMID: 30873275 PMCID: PMC6399963 DOI: 10.1186/s13227-019-0117-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 02/15/2019] [Indexed: 12/14/2022] Open
Abstract
Across metazoans, visual systems employ different types of photoreceptor neurons (PRs) to detect light. These include rhabdomeric PRs, which exist in distantly related phyla and possess an evolutionarily conserved phototransduction cascade. While the development of rhabdomeric PRs has been thoroughly studied in the fruit fly Drosophila melanogaster, we still know very little about how they form in other species. To investigate this question, we tested whether the transcription factor Glass, which is crucial for instructing rhabdomeric PR formation in Drosophila, may play a similar role in other metazoans. Glass homologues exist throughout the animal kingdom, indicating that this protein evolved prior to the metazoan radiation. Interestingly, our work indicates that glass is not expressed in rhabdomeric photoreceptors in the planarian Schmidtea mediterranea nor in the annelid Platynereis dumerilii. Combined with a comparative analysis of the Glass DNA-binding domain, our data suggest that the fate of rhabdomeric PRs is controlled by Glass-dependent and Glass-independent mechanisms in different animal clades.
Collapse
Affiliation(s)
- F Javier Bernardo-Garcia
- 1Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland.,2Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158 USA
| | - Maryam Syed
- 1Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
| | - Gáspár Jékely
- 3Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD UK
| | - Simon G Sprecher
- 1Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
| |
Collapse
|
23
|
Ventura T, Stewart MJ, Chandler JC, Rotgans B, Elizur A, Hewitt AW. Molecular aspects of eye development and regeneration in the Australian redclaw crayfish, Cherax quadricarinatus. AQUACULTURE AND FISHERIES 2019. [DOI: 10.1016/j.aaf.2018.04.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
24
|
Mishra AK, Bernardo-Garcia FJ, Fritsch C, Humberg TH, Egger B, Sprecher SG. Patterning mechanisms diversify neuroepithelial domains in the Drosophila optic placode. PLoS Genet 2018; 14:e1007353. [PMID: 29677185 PMCID: PMC5937791 DOI: 10.1371/journal.pgen.1007353] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 05/07/2018] [Accepted: 04/04/2018] [Indexed: 12/31/2022] Open
Abstract
The central nervous system develops from monolayered neuroepithelial sheets. In a first step patterning mechanisms subdivide the seemingly uniform epithelia into domains allowing an increase of neuronal diversity in a tightly controlled spatial and temporal manner. In Drosophila, neuroepithelial patterning of the embryonic optic placode gives rise to the larval eye primordium, consisting of two photoreceptor (PR) precursor types (primary and secondary), as well as the optic lobe primordium, which during larval and pupal stages develops into the prominent optic ganglia. Here, we characterize a genetic network that regulates the balance between larval eye and optic lobe precursors, as well as between primary and secondary PR precursors. In a first step the proneural factor Atonal (Ato) specifies larval eye precursors, while the orphan nuclear receptor Tailless (Tll) is crucial for the specification of optic lobe precursors. The Hedgehog and Notch signaling pathways act upstream of Ato and Tll to coordinate neural precursor specification in a timely manner. The correct spatial placement of the boundary between Ato and Tll in turn is required to control the precise number of primary and secondary PR precursors. In a second step, Notch signaling also controls a binary cell fate decision, thus, acts at the top of a cascade of transcription factor interactions to define PR subtype identity. Our model serves as an example of how combinatorial action of cell extrinsic and cell intrinsic factors control neural tissue patterning.
Collapse
Affiliation(s)
| | | | - Cornelia Fritsch
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | | | - Boris Egger
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Simon G. Sprecher
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- * E-mail:
| |
Collapse
|
25
|
Steinmetz EL, Dewald DN, Walldorf U. Homeodomain-interacting protein kinase phosphorylates the Drosophila Paired box protein 6 (Pax6) homologues Twin of eyeless and Eyeless. INSECT MOLECULAR BIOLOGY 2018; 27:198-211. [PMID: 29205612 DOI: 10.1111/imb.12363] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Homeodomain-interacting protein kinase (Hipk), the Drosophila homologue of mammalian HIPK2, plays several important roles in regulating differentiation, proliferation, apoptosis, and stress responses and acts as a mediator for signals of diverse pathways, such as Notch or Wingless signalling. The Paired box protein 6 (Pax6) has two Drosophila homologues, Twin of eyeless (Toy) and Eyeless (Ey). Both stand atop the retinal determination gene network (RDGN), which is essential for proper eye development in Drosophila. Here, we set Hipk and the master regulators Toy and Ey in an enzyme-substrate relationship. Furthermore, we prove a physical interaction between Toy and Hipk in vivo using bimolecular fluorescence complementation. Using in vitro kinase assays with different truncated Toy constructs and mutational analyses, we mapped four Hipk phosphorylation sites of Toy, one in the paired domain (Ser121 ) and three in the C-terminal transactivation domain of Toy (Thr395 , Ser410 and Thr452 ). The interaction and phosphorylation of the master regulator Toy by Hipk may be important for precise tuning of signalling within the RDGN and therefore for Drosophila eye development.
Collapse
Affiliation(s)
- E L Steinmetz
- Developmental Biology, Saarland University, Homburg, Germany
| | - D N Dewald
- Developmental Biology, Saarland University, Homburg, Germany
| | - U Walldorf
- Developmental Biology, Saarland University, Homburg, Germany
| |
Collapse
|
26
|
Endlich N, Kliewe F, Kindt F, Schmidt K, Kotb AM, Artelt N, Lindenmeyer MT, Cohen CD, Döring F, Kuss AW, Amann K, Moeller MJ, Kabgani N, Blumenthal A, Endlich K. The transcription factor Dach1 is essential for podocyte function. J Cell Mol Med 2018; 22:2656-2669. [PMID: 29498212 PMCID: PMC5908116 DOI: 10.1111/jcmm.13544] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 12/24/2017] [Indexed: 12/27/2022] Open
Abstract
Dedifferentiation and loss of podocytes are the major cause of chronic kidney disease. Dach1, a transcription factor that is essential for cell fate, was found in genome‐wide association studies to be associated with the glomerular filtration rate. We found that podocytes express high levels of Dach1 in vivo and to a much lower extent in vitro. Parietal epithelial cells (PECs) that are still under debate to be a type of progenitor cell for podocytes expressed Dach1 only at low levels. The transfection of PECs with a plasmid encoding for Dach1 induced the expression of synaptopodin, a podocyte‐specific protein, demonstrated by immunocytochemistry and Western blot. Furthermore, synaptopodin was located along actin fibres in a punctate pattern in Dach1‐expressing PECs comparable with differentiated podocytes. Moreover, dedifferentiating podocytes of isolated glomeruli showed a significant reduction in the expression of Dach1 together with synaptopodin after 9 days in cell culture. To study the role of Dach1 in vivo, we used the zebrafish larva as an animal model. Knockdown of the zebrafish ortholog Dachd by morpholino injection into fertilized eggs resulted in a severe renal phenotype. The glomeruli of the zebrafish larvae showed morphological changes of the glomerulus accompanied by down‐regulation of nephrin and leakage of the filtration barrier. Interestingly, glomeruli of biopsies from patients suffering from diabetic nephropathy showed also a significant reduction of Dach1 and synaptopodin in contrast to control biopsies. Taken together, Dach1 is a transcription factor that is important for podocyte differentiation and proper kidney function.
Collapse
Affiliation(s)
- Nicole Endlich
- Department of Anatomy and Cell Biology, University Medicine Greifswald, Greifswald, Germany
| | - Felix Kliewe
- Department of Anatomy and Cell Biology, University Medicine Greifswald, Greifswald, Germany
| | - Frances Kindt
- Department of Anatomy and Cell Biology, University Medicine Greifswald, Greifswald, Germany
| | - Katharina Schmidt
- Department of Anatomy and Cell Biology, University Medicine Greifswald, Greifswald, Germany
| | - Ahmed M Kotb
- Department of Anatomy and Cell Biology, University Medicine Greifswald, Greifswald, Germany.,Department of Anatomy and Histology, Faculty of Veterinary Medicine, Assiut University, Assiut, Egypt
| | - Nadine Artelt
- Department of Anatomy and Cell Biology, University Medicine Greifswald, Greifswald, Germany
| | - Maja T Lindenmeyer
- Nephrological Center, Medical Clinic and Policlinic IV, University of Munich, Munich, Germany
| | - Clemens D Cohen
- Nephrological Center, Medical Clinic and Policlinic IV, University of Munich, Munich, Germany
| | - Franziska Döring
- Department of Anatomy and Cell Biology, University Medicine Greifswald, Greifswald, Germany
| | - Andreas W Kuss
- Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Kerstin Amann
- Department of Nephropathology, Institute of Pathology, University Hospital Erlangen, Erlangen, Germany
| | - Marcus J Moeller
- Department of Internal Medicine II, Nephrology and Clinical Immunology, RWTH Aachen University Hospital, Aachen, Germany
| | - Nazanin Kabgani
- Department of Internal Medicine II, Nephrology and Clinical Immunology, RWTH Aachen University Hospital, Aachen, Germany
| | - Antje Blumenthal
- Department of Anatomy and Cell Biology, University Medicine Greifswald, Greifswald, Germany
| | - Karlhans Endlich
- Department of Anatomy and Cell Biology, University Medicine Greifswald, Greifswald, Germany
| |
Collapse
|
27
|
Byrne M, Koop D, Morris VB, Chui J, Wray GA, Cisternas P. Expression of genes and proteins of the pax-six-eya-dach network in the metamorphic sea urchin: Insights into development of the enigmatic echinoderm body plan and sensory structures. Dev Dyn 2017; 247:239-249. [PMID: 28850769 DOI: 10.1002/dvdy.24584] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 07/25/2017] [Accepted: 07/31/2017] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND Photoreception-associated genes of the Pax-Six-Eya-Dach network (PSEDN) are deployed for many roles in addition to photoreception development. In this first study of PSEDN genes during development of the pentameral body in sea urchins, we investigated their spatial expression in Heliocidaris erythrogramma. RESULTS Expression of PSEDN genes in the hydrocoele of early (Dach, Eya, Six1/2) and/or late (Pax6, Six3/6) larvae, and the five hydrocoele lobes, the first morphological expression of pentamery, supports a role in body plan development. Pax6, Six1/2, and Six3/6 were localized to the primary and/or secondary podia and putative sensory/neuronal cells. Six1/2 and Six3/6 were expressed in the neuropil region in the terminal disc of the podia. Dach was localized to spines. Sequential up-regulation of gene expression as new podia and spines formed was evident. Rhabdomeric opsin and pax6 protein were localized to cells in the primary podia and spines. CONCLUSIONS Our results support roles for PSEDN genes in development of the pentameral body plan, contributing to our understanding of how the most unusual body plan in the Bilateria may have evolved. Development of sensory cells within the Pax-Six expression field is consistent with the role of these genes in sensory cell development in diverse species. Developmental Dynamics 247:239-249, 2018. © 2017 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Maria Byrne
- School of Medical Sciences, The University of Sydney, NSW, Australia.,School of Life and Environmental Sciences, The University of Sydney, NSW, Australia
| | - Demian Koop
- School of Medical Sciences, The University of Sydney, NSW, Australia
| | - Valerie B Morris
- School of Life and Environmental Sciences, The University of Sydney, NSW, Australia
| | - Juanita Chui
- School of Medical Sciences, The University of Sydney, NSW, Australia
| | - Gregory A Wray
- Department of Biology and Center for Genomic and Computational Biology, Duke University, Durham, North Carolina
| | - Paula Cisternas
- School of Medical Sciences, The University of Sydney, NSW, Australia
| |
Collapse
|
28
|
Six1 and Eya1 both promote and arrest neuronal differentiation by activating multiple Notch pathway genes. Dev Biol 2017; 431:152-167. [PMID: 28947179 DOI: 10.1016/j.ydbio.2017.09.027] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 09/19/2017] [Accepted: 09/19/2017] [Indexed: 12/12/2022]
Abstract
The transcription factor Six1 and its cofactor Eya1 are important regulators of neurogenesis in cranial placodes, activating genes promoting both a progenitor state, such as hes8, and neuronal differentiation, such as neurog1. Here, we use gain and loss of function studies in Xenopus laevis to elucidate how these genes function during placodal neurogenesis. We first establish that hes8 is activated by Notch signaling and represses neurog1 and neuronal differentiation, indicating that it mediates lateral inhibition. Using hes8 knockdown we demonstrate that hes8 is essential for limiting neuronal differentiation during normal placode development. We next show that Six1 and Eya1 cell autonomously activate both hes8 and neurog1 in a dose-dependent fashion, with increasing upregulation at higher doses, while neuronal differentiation is increasingly repressed. However, high doses of Six1 and Eya1 upregulate neurog1 only transiently, whereas low doses of Six1 and Eya1 ultimately promote both neurog1 expression and neuronal differentiation. Finally, we show that Six1 and Eya1 can activate hes8 and arrest neuronal differentiation even when Notch signaling is blocked. Our findings indicate that Six1 and Eya1 can both promote and arrest neuronal differentiation by activating the Notch pathway genes neurog1 and hes8, respectively, revealing a novel mechanism of Six1/Eya1 action during placodal neurogenesis.
Collapse
|
29
|
Apitz H, Salecker I. Retinal determination genes coordinate neuroepithelial specification and neurogenesis modes in the Drosophila optic lobe. Development 2017; 143:2431-42. [PMID: 27381228 PMCID: PMC4958324 DOI: 10.1242/dev.135004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 05/18/2016] [Indexed: 12/15/2022]
Abstract
Differences in neuroepithelial patterning and neurogenesis modes contribute to area-specific diversifications of neural circuits. In the Drosophila visual system, two neuroepithelia, the outer (OPC) and inner (IPC) proliferation centers, generate neuron subtypes for four ganglia in several ways. Whereas neuroepithelial cells in the medial OPC directly convert into neuroblasts, in an IPC subdomain they generate migratory progenitors by epithelial-mesenchymal transition that mature into neuroblasts in a second proliferative zone. The molecular mechanisms that regulate the identity of these neuroepithelia, including their neurogenesis modes, remain poorly understood. Analysis of Polycomblike revealed that loss of Polycomb group-mediated repression of the Hox gene Abdominal-B (Abd-B) caused the transformation of OPC to IPC neuroepithelial identity. This suggests that the neuroepithelial default state is IPC-like, whereas OPC identity is derived. Ectopic Abd-B blocks expression of the highly conserved retinal determination gene network members Eyes absent (Eya), Sine oculis (So) and Homothorax (Hth). These factors are essential for OPC specification and neurogenesis control. Finally, eya and so are also sufficient to confer OPC-like identity, and, in parallel with hth, the OPC-specific neurogenesis mode on the IPC. Summary: Polycomb-mediated repression of the Abd-B Hox gene controls expression of retinal determination genes and hence identity of the Drosophila optic lobe neuroepithelia.
Collapse
Affiliation(s)
- Holger Apitz
- The Francis Crick Institute, Mill Hill Laboratory, London NW7 1AA, UK
| | - Iris Salecker
- The Francis Crick Institute, Mill Hill Laboratory, London NW7 1AA, UK
| |
Collapse
|
30
|
Noncanonical Decapentaplegic Signaling Activates Matrix Metalloproteinase 1 To Restrict Hedgehog Activity and Limit Ectopic Eye Differentiation in Drosophila. Genetics 2017; 207:197-213. [PMID: 28696218 DOI: 10.1534/genetics.117.201053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 06/29/2017] [Indexed: 12/25/2022] Open
Abstract
One of the pertinent issues associated with cellular plasticity is to understand how the delicate balance between the determined state of cells and the extent to which they can transdetermine is maintained. Employing the well-established model of generating ectopic eyes in developing wing discs of Drosophila by ectopic eyeless expression, we provide evidence for the genetic basis of this mechanism. By both loss-of-function and gain-of-function genetic analyses, we demonstrate that Matrix metalloproteinase 1 (Mmp1) plays an important role in regulating the extent of ectopic ommatidial differentiation. Transcriptional activation of ectopic Mmp1 by the morphogen Decapentaplegic (Dpp) is not triggered by its canonical signaling pathway which involves Mad. Rather, Dpp activates an alternate cascade involving dTak1 and JNK, to induce ectopic Mmp1 expression. Mutational analyses reveal that Mmp1 negatively regulates ectopic eye differentiation by restricting the rate of proliferation and the levels of expression of retinal-determining genes dachshund and eyes absent This is primarily achieved by restricting the range of Hedgehog (Hh) signaling. Importantly, the increase in proliferation and upregulation of target retinal-determining genes, as observed upon attenuating Mmp1 activity, gets significantly rescued when ectopic eyes are generated in wing discs of hh heterozygous mutants. In conjunction with the previously established instructive and permissive roles of Dpp in facilitating ectopic eye differentiation in wing discs, the outcome of this study sheds light on a mechanism by which Dpp plays a dual role in modulating the delicate balance between the determined state of cells and the extent they can transdetermine.
Collapse
|
31
|
Ling X, Huang Q, Xu Y, Jin Y, Feng Y, Shi W, Ye X, Lin Y, Hou L, Lin X. The deubiquitinating enzyme Usp5 regulates Notch and RTK signaling duringDrosophilaeye development. FEBS Lett 2017; 591:875-888. [PMID: 28140449 DOI: 10.1002/1873-3468.12580] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 01/24/2017] [Accepted: 01/25/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Xuemei Ling
- School of Optometry and Ophthalmology and Eye Hospital; Wenzhou Medical University; Zhejiang China
| | - Qinzhu Huang
- Taizhou Hospital of Zhejiang Province; Wenzhou Medical University; Linhai Zhejiang China
| | - Yanqin Xu
- School of Optometry and Ophthalmology and Eye Hospital; Wenzhou Medical University; Zhejiang China
| | - Yuxiao Jin
- School of Optometry and Ophthalmology and Eye Hospital; Wenzhou Medical University; Zhejiang China
| | - Ying Feng
- School of Optometry and Ophthalmology and Eye Hospital; Wenzhou Medical University; Zhejiang China
| | - Weijie Shi
- School of Optometry and Ophthalmology and Eye Hospital; Wenzhou Medical University; Zhejiang China
| | - Xiaolei Ye
- School of Optometry and Ophthalmology and Eye Hospital; Wenzhou Medical University; Zhejiang China
| | - Yi Lin
- School of Optometry and Ophthalmology and Eye Hospital; Wenzhou Medical University; Zhejiang China
| | - Ling Hou
- School of Optometry and Ophthalmology and Eye Hospital; Wenzhou Medical University; Zhejiang China
| | - Xinhua Lin
- School of Optometry and Ophthalmology and Eye Hospital; Wenzhou Medical University; Zhejiang China
| |
Collapse
|
32
|
Bernardo-Garcia FJ, Humberg TH, Fritsch C, Sprecher SG. Successive requirement of Glass and Hazy for photoreceptor specification and maintenance in Drosophila. Fly (Austin) 2016; 11:112-120. [PMID: 27723419 PMCID: PMC5406162 DOI: 10.1080/19336934.2016.1244591] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Development of the insect compound eye requires a highly controlled interplay between transcription factors. However, the genetic mechanisms that link early eye field specification to photoreceptor terminal differentiation and fate maintenance remain largely unknown. Here, we decipher the function of 2 transcription factors, Glass and Hazy, which play a central role during photoreceptor development. The regulatory interactions between Glass and Hazy suggest that they function together in a coherent feed-forward loop in all types of Drosophila photoreceptors. While the glass mutant eye lacks the expression of virtually all photoreceptor genes, young hazy mutants correctly express most phototransduction genes. Interestingly, the expression of these genes is drastically reduced in old hazy mutants. This age-dependent loss of the phototransduction cascade correlates with a loss of phototaxis in old hazy mutant flies. We conclude that Glass can either directly or indirectly initiate the expression of most phototransduction proteins in a Hazy-independent manner, and that Hazy is mainly required for the maintenance of functional photoreceptors in adult flies.
Collapse
Affiliation(s)
| | | | - Cornelia Fritsch
- a Department of Biology , University of Fribourg , Fribourg , Switzerland
| | - Simon G Sprecher
- a Department of Biology , University of Fribourg , Fribourg , Switzerland
| |
Collapse
|
33
|
The morphogen Decapentaplegic employs a two-tier mechanism to activate target retinal determining genes during ectopic eye formation in Drosophila. Sci Rep 2016; 6:27270. [PMID: 27270790 PMCID: PMC4895176 DOI: 10.1038/srep27270] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 05/13/2016] [Indexed: 11/18/2022] Open
Abstract
Understanding the role of morphogen in activating its target genes, otherwise epigenetically repressed, during change in cell fate specification is a very fascinating yet relatively unexplored domain. Our in vivo loss-of-function genetic analyses reveal that specifically during ectopic eye formation, the morphogen Decapentaplegic (Dpp), in conjunction with the canonical signaling responsible for transcriptional activation of retinal determining (RD) genes, triggers another signaling cascade. Involving dTak1 and JNK, this pathway down-regulates the expression of polycomb group of genes to do away with their repressive role on RD genes. Upon genetic inactivation of members of this newly identified pathway, the canonical Dpp signaling fails to trigger RD gene expression beyond a threshold, critical for ectopic photoreceptor differentiation. Moreover, the drop in ectopic RD gene expression and subsequent reduction in ectopic photoreceptor differentiation resulting from inactivation of dTak1 can be rescued by down-regulating the expression of polycomb group of genes. Our results unravel an otherwise unknown role of morphogen in coordinating simultaneous transcriptional activation and de-repression of target genes implicating its importance in cellular plasticity.
Collapse
|
34
|
Retinal Axon Guidance Requires Integration of Eya and the Jak/Stat Pathway into Phosphotyrosine-Based Signaling Circuitries in Drosophila. Genetics 2016; 203:1283-95. [PMID: 27194748 DOI: 10.1534/genetics.115.185918] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 05/10/2016] [Indexed: 12/15/2022] Open
Abstract
The transcriptional coactivator and phosphatase eyes absent (Eya) is dynamically compartmentalized between the nucleus and cytoplasm. Although the nuclear transcriptional circuits within which Eya operates have been extensively characterized, understanding of its cytoplasmic functions and interactions remains limited. Our previous work showed that phosphorylation of Drosophila Eya by the Abelson tyrosine kinase can recruit Eya to the cytoplasm and that eya-abelson interactions are required for photoreceptor axons to project to correct layers in the brain. Based on these observations, we postulated that photoreceptor axon targeting might provide a suitable context for identifying the cytoplasmic signaling cascades with which Eya interacts. Using a dose-sensitive eya misexpression background, we performed an RNA interference-based genetic screen to identify suppressors. Included among the top 10 hits were nonreceptor tyrosine kinases and multiple members of the Jak/Stat signaling network (hop, Stat92E, Socs36E, and Socs44A), a pathway not previously implicated in axon targeting. Individual loss-of-function phenotypes combined with analysis of axonal projections in Stat92E null clones confirmed the importance of photoreceptor autonomous Jak/Stat signaling. Experiments in cultured cells detected cytoplasmic complexes between Eya and Hop, Socs36E and Socs44A; the latter interaction required both the Src homology 2 motif in Socs44A and tyrosine phosphorylated Eya, suggesting direct binding and validating the premise of the screen. Taken together, our data provide new insight into the cytoplasmic phosphotyrosine signaling networks that operate during photoreceptor axon guidance and suggest specific points of interaction with Eya.
Collapse
|
35
|
Evolution of mammalian sound localization circuits: A developmental perspective. Prog Neurobiol 2016; 141:1-24. [PMID: 27032475 DOI: 10.1016/j.pneurobio.2016.02.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 02/27/2016] [Accepted: 02/27/2016] [Indexed: 01/06/2023]
Abstract
Localization of sound sources is a central aspect of auditory processing. A unique feature of mammals is the smooth, tonotopically organized extension of the hearing range to high frequencies (HF) above 10kHz, which likely induced positive selection for novel mechanisms of sound localization. How this change in the auditory periphery is accompanied by changes in the central auditory system is unresolved. I will argue that the major VGlut2(+) excitatory projection neurons of sound localization circuits (dorsal cochlear nucleus (DCN), lateral and medial superior olive (LSO and MSO)) represent serial homologs with modifications, thus being paramorphs. This assumption is based on common embryonic origin from an Atoh1(+)/Wnt1(+) cell lineage in the rhombic lip of r5, same cell birth, a fusiform cell morphology, shared genetic components such as Lhx2 and Lhx9 transcription factors, and similar projection patterns. Such a parsimonious evolutionary mechanism likely accelerated the emergence of neurons for sound localization in all three dimensions. Genetic analyses indicate that auditory nuclei in fish, birds, and mammals receive contributions from the same progenitor lineages. Anatomical and physiological differences and the independent evolution of tympanic ears in vertebrate groups, however, argue for convergent evolution of sound localization circuits in tetrapods (amphibians, reptiles, birds, and mammals). These disparate findings are discussed in the context of the genetic architecture of the developing hindbrain, which facilitates convergent evolution. Yet, it will be critical to decipher the gene regulatory networks underlying development of auditory neurons across vertebrates to explore the possibility of homologous neuronal populations.
Collapse
|
36
|
Mao CA, Agca C, Mocko-Strand JA, Wang J, Ullrich-Lüter E, Pan P, Wang SW, Arnone MI, Frishman LJ, Klein WH. Substituting mouse transcription factor Pou4f2 with a sea urchin orthologue restores retinal ganglion cell development. Proc Biol Sci 2016; 283:20152978. [PMID: 26962139 PMCID: PMC4810862 DOI: 10.1098/rspb.2015.2978] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Accepted: 02/10/2016] [Indexed: 12/11/2022] Open
Abstract
Pou domain transcription factor Pou4f2 is essential for the development of retinal ganglion cells (RGCs) in the vertebrate retina. A distant orthologue of Pou4f2 exists in the genome of the sea urchin (class Echinoidea) Strongylocentrotus purpuratus (SpPou4f1/2), yet the photosensory structure of sea urchins is strikingly different from that of the mammalian retina. Sea urchins have no obvious eyes, but have photoreceptors clustered around their tube feet disc. The mechanisms that are associated with the development and function of photoreception in sea urchins are largely unexplored. As an initial approach to better understand the sea urchin photosensory structure and relate it to the mammalian retina, we asked whether SpPou4f1/2 could support RGC development in the absence of Pou4f2. To answer this question, we replaced genomic Pou4f2 with an SpPou4f1/2 cDNA. In Pou4f2-null mice, retinas expressing SpPou4f1/2 were outwardly identical to those of wild-type mice. SpPou4f1/2 retinas exhibited dark-adapted electroretinogram scotopic threshold responses, indicating functionally active RGCs. During retinal development, SpPou4f1/2 activated RGC-specific genes and in S. purpuratus, SpPou4f2 was expressed in photoreceptor cells of tube feet in a pattern distinct from Opsin4 and Pax6. Our results suggest that SpPou4f1/2 and Pou4f2 share conserved components of a gene network for photosensory development and they maintain their conserved intrinsic functions despite vast morphological differences in mouse and sea urchin photosensory structures.
Collapse
Affiliation(s)
- Chai-An Mao
- Department of Systems Biology, Unit 0950, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Cavit Agca
- Department of Systems Biology, Unit 0950, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Jing Wang
- College of Optometry, University of Houston, Houston, TX 77204, USA
| | | | - Ping Pan
- Department of Systems Biology, Unit 0950, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Steven W Wang
- Department of Systems Biology, Unit 0950, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Maria Ina Arnone
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples 80121, Italy
| | - Laura J Frishman
- College of Optometry, University of Houston, Houston, TX 77204, USA
| | - William H Klein
- Department of Systems Biology, Unit 0950, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| |
Collapse
|
37
|
Bernardo-Garcia FJ, Fritsch C, Sprecher SG. The transcription factor Glass links eye field specification with photoreceptor differentiation in Drosophila. Development 2016; 143:1413-23. [PMID: 26952983 DOI: 10.1242/dev.128801] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 02/22/2016] [Indexed: 12/12/2022]
Abstract
Eye development requires an evolutionarily conserved group of transcription factors, termed the retinal determination network (RDN). However, little is known about the molecular mechanism by which the RDN instructs cells to differentiate into photoreceptors. We show that photoreceptor cell identity in Drosophila is critically regulated by the transcription factor Glass, which is primarily expressed in photoreceptors and whose role in this process was previously unknown. Glass is both required and sufficient for the expression of phototransduction proteins. Our results demonstrate that the RDN member Sine oculis directly activates glass expression, and that Glass activates the expression of the transcription factors Hazy and Otd. We identified hazy as a direct target of Glass. Induced expression of Hazy in the retina partially rescues the glass mutant phenotype. Together, our results provide a transcriptional link between eye field specification and photoreceptor differentiation in Drosophila, placing Glass at a central position in this developmental process.
Collapse
Affiliation(s)
| | - Cornelia Fritsch
- Department of Biology, University of Fribourg, Fribourg 1700, Switzerland
| | - Simon G Sprecher
- Department of Biology, University of Fribourg, Fribourg 1700, Switzerland
| |
Collapse
|
38
|
Berndt AJE, Tang JCY, Ridyard MS, Lian T, Keatings K, Allan DW. Gene Regulatory Mechanisms Underlying the Spatial and Temporal Regulation of Target-Dependent Gene Expression in Drosophila Neurons. PLoS Genet 2015; 11:e1005754. [PMID: 26713626 PMCID: PMC4694770 DOI: 10.1371/journal.pgen.1005754] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 11/30/2015] [Indexed: 11/18/2022] Open
Abstract
Neuronal differentiation often requires target-derived signals from the cells they innervate. These signals typically activate neural subtype-specific genes, but the gene regulatory mechanisms remain largely unknown. Highly restricted expression of the FMRFa neuropeptide in Drosophila Tv4 neurons requires target-derived BMP signaling and a transcription factor code that includes Apterous. Using integrase transgenesis of enhancer reporters, we functionally dissected the Tv4-enhancer of FMRFa within its native cellular context. We identified two essential but discrete cis-elements, a BMP-response element (BMP-RE) that binds BMP-activated pMad, and a homeodomain-response element (HD-RE) that binds Apterous. These cis-elements have low activity and must be combined for Tv4-enhancer activity. Such combinatorial activity is often a mechanism for restricting expression to the intersection of cis-element spatiotemporal activities. However, concatemers of the HD-RE and BMP-RE cis-elements were found to independently generate the same spatiotemporal expression as the Tv4-enhancer. Thus, the Tv4-enhancer atypically combines two low-activity cis-elements that confer the same output from distinct inputs. The activation of target-dependent genes is assumed to 'wait' for target contact. We tested this directly, and unexpectedly found that premature BMP activity could not induce early FMRFa expression; also, we show that the BMP-insensitive HD-RE cis-element is activated at the time of target contact. This led us to uncover a role for the nuclear receptor, seven up (svp), as a repressor of FMRFa induction prior to target contact. Svp is normally downregulated immediately prior to target contact, and we found that maintaining Svp expression prevents cis-element activation, whereas reducing svp gene dosage prematurely activates cis-element activity. We conclude that the target-dependent FMRFa gene is repressed prior to target contact, and that target-derived BMP signaling directly activates FMRFa gene expression through an atypical gene regulatory mechanism.
Collapse
Affiliation(s)
- Anthony J. E. Berndt
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jonathan C. Y. Tang
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States America
| | - Marc S. Ridyard
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Tianshun Lian
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kathleen Keatings
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Douglas W. Allan
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
| |
Collapse
|
39
|
Abstract
Eyes absent (Eya), a protein conserved from plants to humans and best characterized as a transcriptional coactivator, is also the prototype for a novel class of eukaryotic aspartyl protein tyrosine phosphatases. This minireview discusses recent breakthroughs in elucidating the substrates and cellular events regulated by Eya's tyrosine phosphatase function and highlights some of the complexities, new questions, and surprises that have emerged from efforts to understand how Eya's unusual multifunctionality influences developmental regulation and signaling.
Collapse
|
40
|
Sajuthi A, Carrillo-Zazueta B, Hu B, Wang A, Brodnansky L, Mayberry J, Rivera AS. Sexually dimorphic gene expression in the lateral eyes of Euphilomedes carcharodonta (Ostracoda, Pancrustacea). EvoDevo 2015; 6:34. [PMID: 26561519 PMCID: PMC4641368 DOI: 10.1186/s13227-015-0026-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 09/22/2015] [Indexed: 12/29/2022] Open
Abstract
Background The evolution and development of sexual dimorphism illuminates a central question in biology: How do similar genomes produce different phenotypes? In an XX/XO system especially the state of a sexually dimorphic trait is determined by differences in gene expression, as there are no additional genetic loci in either sex. Here, we examine the XX/XO ostracod crustacean species Euphilomedes carcharodonta. This species exhibits radical sexual dimorphism of their lateral eyes, females have only a tiny simple lateral eye while males have elaborate ommatidial eyes. Results We find that males express three of nine eye-development gene homologs at significantly higher levels during juvenile eye development, compared to females. We also find that most eye-development genes examined are pleiotropic, with high expression levels during embryonic development as well as during juvenile eye development. Later, in adults, we find that phototransduction genes are expressed at higher levels in males than in females, as we might expect when comparing ommatidial to simple eyes. Conclusions We show here that expression changes of a handful of developmental genes may underlie the radical difference in a dimorphic character. This work gives an important point of comparison for studying eye evolution and development in the Pancrustacea. Electronic supplementary material The online version of this article (doi:10.1186/s13227-015-0026-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Andrea Sajuthi
- Department of Biological Sciences, University of the Pacific, Stockton, CA USA ; Stritch School of Medicine, Loyola University, Chicago, IL USA
| | - Brenna Carrillo-Zazueta
- Department of Biological Sciences, University of the Pacific, Stockton, CA USA ; Dugoni School of Dentistry, University of the Pacific, San Francisco, CA USA
| | - Briana Hu
- Department of Biological Sciences, University of the Pacific, Stockton, CA USA
| | - Anita Wang
- Department of Biological Sciences, University of the Pacific, Stockton, CA USA ; Thomas J. Long School of Pharmacy and Health Sciences, University of the Pacific, Stockton, CA USA
| | - Logan Brodnansky
- Department of Biological Sciences, University of the Pacific, Stockton, CA USA ; Thomas J. Long School of Pharmacy and Health Sciences, University of the Pacific, Stockton, CA USA
| | - John Mayberry
- Department of Biological Sciences, University of the Pacific, Stockton, CA USA
| | - Ajna S Rivera
- Department of Biological Sciences, University of the Pacific, Stockton, CA USA
| |
Collapse
|
41
|
Martik ML, McClay DR. Deployment of a retinal determination gene network drives directed cell migration in the sea urchin embryo. eLife 2015; 4. [PMID: 26402456 PMCID: PMC4621380 DOI: 10.7554/elife.08827] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 09/23/2015] [Indexed: 12/29/2022] Open
Abstract
Gene regulatory networks (GRNs) provide a systems-level orchestration of an organism's genome encoded anatomy. As biological networks are revealed, they continue to answer many questions including knowledge of how GRNs control morphogenetic movements and how GRNs evolve. The migration of the small micromeres to the coelomic pouches in the sea urchin embryo provides an exceptional model for understanding the genomic regulatory control of morphogenesis. An assay using the robust homing potential of these cells reveals a ‘coherent feed-forward’ transcriptional subcircuit composed of Pax6, Six3, Six1/2, Eya, and Dach1 that is responsible for the directed homing mechanism of these multipotent progenitors. The linkages of that circuit are strikingly similar to a circuit involved in retinal specification in Drosophila suggesting that systems-level tasks can be highly conserved even though the tasks drive unrelated processes in different animals. DOI:http://dx.doi.org/10.7554/eLife.08827.001 Within an animal embryo, groups of cells tend to move, or migrate, between different areas before they form into tissues and organs. These cell migrations are regulated by hundreds of genes, which must be expressed at the right time and in the right place. Cells use proteins called transcription factors to regulate the expression of genes. These proteins work together in circuit board-like networks called gene regulatory networks in order to drive different aspects of development, including cell migration. The sea urchin is a useful model organism to study how animals develop. This is because these marine animals express many of the same genes as humans, but they can be easily manipulated and studied in the laboratory. In a developing sea urchin embryo, cells called the small micromeres move towards one end of animal and get incorporated into a pocket-like structure known as the coelomic pouch. From this pouch, these cells mature and eventually contribute to the adult germ cells (the precursors to the sperm and eggs). Martik and McClay have now analyzed how small micromeres make their way to their final location in the coelomic pouch. Micromeres were labeled with a dye that fluoresces green so that they could be tracked under a microscope. This revealed that, like other moving cells, micromeres actively change their shape as they migrate. Furthermore, when micromeres were experimentally moved to abnormal locations in the sea urchin embryo, they were still able to actively home in on the coelomic pouch no matter their starting location. Martik and McClay then identified five transcription factors expressed in the coelomic pouch in the sea urchin that are involved in this homing activity. Reducing the expression of any of these transcription factors was enough to hinder the ability of the micromeres to find their way to the coelomic pouch. Further experiments and analysis then revealed that these five transcription factors work together in a sub-circuit, which is in turn embedded in a larger gene regulatory network. This sub-circuit that drives cell migration is unexpectedly similar to another circuit in the fruit fly Drosophila. Intriguingly, the sub-circuit in the fly controls eye development, which is unrelated to cell homing and migration. These observations raise the possibility that this circuit has been conserved as a unit over millions of years of evolution and redeployed in new networks under completely different circumstances. The data also suggest the possibility that additional conserved sub-circuits will be identified as more systems are analyzed in detail. DOI:http://dx.doi.org/10.7554/eLife.08827.002
Collapse
Affiliation(s)
- Megan L Martik
- University Program in Genetics and Genomics, Duke University, Durham, United States
| | - David R McClay
- Department of Biology, Duke University, Durham, United States
| |
Collapse
|
42
|
Allan DW, Thor S. Transcriptional selectors, masters, and combinatorial codes: regulatory principles of neural subtype specification. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2015; 4:505-28. [PMID: 25855098 PMCID: PMC4672696 DOI: 10.1002/wdev.191] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 03/04/2015] [Accepted: 03/04/2015] [Indexed: 01/08/2023]
Abstract
The broad range of tissue and cellular diversity of animals is generated to a large extent by the hierarchical deployment of sequence-specific transcription factors and co-factors (collectively referred to as TF's herein) during development. Our understanding of these developmental processes has been facilitated by the recognition that the activities of many TF's can be meaningfully described by a few functional categories that usefully convey a sense for how the TF's function, and also provides a sense for the regulatory organization of the developmental processes in which they participate. Here, we draw on examples from studies in Caenorhabditis elegans, Drosophila melanogaster, and vertebrates to discuss how the terms spatial selector, temporal selector, tissue/cell type selector, terminal selector and combinatorial code may be usefully applied to categorize the activities of TF's at critical steps of nervous system construction. While we believe that these functional categories are useful for understanding the organizational principles by which TF's direct nervous system construction, we however caution against the assumption that a TF's function can be solely or fully defined by any single functional category. Indeed, most TF's play diverse roles within different functional categories, and their roles can blur the lines we draw between these categories. Regardless, it is our belief that the concepts discussed here are helpful in clarifying the regulatory complexities of nervous system development, and hope they prove useful when interpreting mutant phenotypes, designing future experiments, and programming specific neuronal cell types for use in therapies. WIREs Dev Biol 2015, 4:505–528. doi: 10.1002/wdev.191 For further resources related to this article, please visit the WIREs website.
Collapse
Affiliation(s)
- Douglas W Allan
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Stefan Thor
- Department of Clinical and Experimental Medicine, Linkoping University, Linkoping, Sweden
| |
Collapse
|
43
|
Tsai YC, Grimm S, Chao JL, Wang SC, Hofmeyer K, Shen J, Eichinger F, Michalopoulou T, Yao CK, Chang CH, Lin SH, Sun YH, Pflugfelder GO. Optomotor-blind negatively regulates Drosophila eye development by blocking Jak/STAT signaling. PLoS One 2015; 10:e0120236. [PMID: 25781970 PMCID: PMC4363906 DOI: 10.1371/journal.pone.0120236] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 01/27/2015] [Indexed: 12/23/2022] Open
Abstract
Organ formation requires a delicate balance of positive and negative regulators. In Drosophila eye development, wingless (wg) is expressed at the lateral margins of the eye disc and serves to block retinal development. The T-box gene optomotor-blind (omb) is expressed in a similar pattern and is regulated by Wg. Omb mediates part of Wg activity in blocking eye development. Omb exerts its function primarily by blocking cell proliferation. These effects occur predominantly in the ventral margin. Our results suggest that the primary effect of Omb is the blocking of Jak/STAT signaling by repressing transcription of upd which encodes the Jak receptor ligand Unpaired.
Collapse
Affiliation(s)
- Yu-Chen Tsai
- Institute of Genetics, National Yang-Ming University, Taipei; Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Republic of China
- Department of Life Science and Life Science Center, Tunghai University, Taichung, Taiwan, Republic of China
| | - Stefan Grimm
- Theodor-Boveri-Institut, Biozentrum, Lehrstuhl für Genetik und Neurobiologie, Universität Würzburg, Am Hubland, Würzburg, Germany
| | - Ju-Lan Chao
- Institute of Genetics, National Yang-Ming University, Taipei; Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Republic of China
| | - Shih-Chin Wang
- Department of Life Science and Life Science Center, Tunghai University, Taichung, Taiwan, Republic of China
| | - Kerstin Hofmeyer
- Theodor-Boveri-Institut, Biozentrum, Lehrstuhl für Genetik und Neurobiologie, Universität Würzburg, Am Hubland, Würzburg, Germany
| | - Jie Shen
- Institut für Genetik, Universität Mainz, Mainz, Germany
- Department of Entomology, China Agricultural University, Beijing, China
| | | | | | - Chi-Kuang Yao
- Institute of Genetics, National Yang-Ming University, Taipei; Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Republic of China
| | - Chih-Hsuan Chang
- Department of Life Science and Life Science Center, Tunghai University, Taichung, Taiwan, Republic of China
| | - Shih-Han Lin
- Department of Life Science and Life Science Center, Tunghai University, Taichung, Taiwan, Republic of China
| | - Y. Henry Sun
- Institute of Genetics, National Yang-Ming University, Taipei; Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Republic of China
- * E-mail: (YHS); (GOP)
| | - Gert O. Pflugfelder
- Theodor-Boveri-Institut, Biozentrum, Lehrstuhl für Genetik und Neurobiologie, Universität Würzburg, Am Hubland, Würzburg, Germany
- Institut für Genetik, Universität Mainz, Mainz, Germany
- * E-mail: (YHS); (GOP)
| |
Collapse
|
44
|
Chen K, Wu K, Jiao X, Wang L, Ju X, Wang M, Di Sante G, Xu S, Wang Q, Li K, Sun X, Xu C, Li Z, Casimiro MC, Ertel A, Addya S, McCue PA, Lisanti MP, Wang C, Davis RJ, Mardon G, Pestell RG. The endogenous cell-fate factor dachshund restrains prostate epithelial cell migration via repression of cytokine secretion via a cxcl signaling module. Cancer Res 2015; 75:1992-2004. [PMID: 25769723 DOI: 10.1158/0008-5472.can-14-0611] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 02/24/2015] [Indexed: 01/01/2023]
Abstract
Prostate cancer is the second leading form of cancer-related death in men. In a subset of prostate cancer patients, increased chemokine signaling IL8 and IL6 correlates with castrate-resistant prostate cancer (CRPC). IL8 and IL6 are produced by prostate epithelial cells and promote prostate cancer cell invasion; however, the mechanisms restraining prostate epithelial cell cytokine secretion are poorly understood. Herein, the cell-fate determinant factor DACH1 inhibited CRPC tumor growth in mice. Using Dach1(fl/fl)/Probasin-Cre bitransgenic mice, we show IL8 and IL6 secretion was altered by approximately 1,000-fold by endogenous Dach1. Endogenous Dach1 is shown to serve as a key endogenous restraint to prostate epithelial cell growth and restrains migration via CXCL signaling. DACH1 inhibited expression, transcription, and secretion of the CXCL genes (IL8 and IL6) by binding to their promoter regulatory regions in chromatin. DACH1 is thus a newly defined determinant of benign and malignant prostate epithelium cellular growth, migration, and cytokine abundance in vivo.
Collapse
Affiliation(s)
- Ke Chen
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania. Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Kongming Wu
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania. Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania. Tongji Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, China.
| | - Xuanmao Jiao
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania. Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Liping Wang
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania. Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Xiaoming Ju
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania. Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Min Wang
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania. Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Gabriele Di Sante
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania. Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Shaohua Xu
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania. Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Qiong Wang
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania. Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Kevin Li
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania. Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Xin Sun
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania. Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Congwen Xu
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania. Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Zhiping Li
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania. Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Mathew C Casimiro
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania. Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Adam Ertel
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Sankar Addya
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Peter A McCue
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Michael P Lisanti
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Chenguang Wang
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania. Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | | | - Graeme Mardon
- Departments of Pathology and Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Richard G Pestell
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania. Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania. Kazan Federal University, Kazan, Republic of Tatarstan, Russian Federation.
| |
Collapse
|
45
|
Speiser DI, Pankey MS, Zaharoff AK, Battelle BA, Bracken-Grissom HD, Breinholt JW, Bybee SM, Cronin TW, Garm A, Lindgren AR, Patel NH, Porter ML, Protas ME, Rivera AS, Serb JM, Zigler KS, Crandall KA, Oakley TH. Using phylogenetically-informed annotation (PIA) to search for light-interacting genes in transcriptomes from non-model organisms. BMC Bioinformatics 2014; 15:350. [PMID: 25407802 PMCID: PMC4255452 DOI: 10.1186/s12859-014-0350-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 10/09/2014] [Indexed: 11/10/2022] Open
Abstract
Background Tools for high throughput sequencing and de novo assembly make the analysis of transcriptomes (i.e. the suite of genes expressed in a tissue) feasible for almost any organism. Yet a challenge for biologists is that it can be difficult to assign identities to gene sequences, especially from non-model organisms. Phylogenetic analyses are one useful method for assigning identities to these sequences, but such methods tend to be time-consuming because of the need to re-calculate trees for every gene of interest and each time a new data set is analyzed. In response, we employed existing tools for phylogenetic analysis to produce a computationally efficient, tree-based approach for annotating transcriptomes or new genomes that we term Phylogenetically-Informed Annotation (PIA), which places uncharacterized genes into pre-calculated phylogenies of gene families. Results We generated maximum likelihood trees for 109 genes from a Light Interaction Toolkit (LIT), a collection of genes that underlie the function or development of light-interacting structures in metazoans. To do so, we searched protein sequences predicted from 29 fully-sequenced genomes and built trees using tools for phylogenetic analysis in the Osiris package of Galaxy (an open-source workflow management system). Next, to rapidly annotate transcriptomes from organisms that lack sequenced genomes, we repurposed a maximum likelihood-based Evolutionary Placement Algorithm (implemented in RAxML) to place sequences of potential LIT genes on to our pre-calculated gene trees. Finally, we implemented PIA in Galaxy and used it to search for LIT genes in 28 newly-sequenced transcriptomes from the light-interacting tissues of a range of cephalopod mollusks, arthropods, and cubozoan cnidarians. Our new trees for LIT genes are available on the Bitbucket public repository (http://bitbucket.org/osiris_phylogenetics/pia/) and we demonstrate PIA on a publicly-accessible web server (http://galaxy-dev.cnsi.ucsb.edu/pia/). Conclusions Our new trees for LIT genes will be a valuable resource for researchers studying the evolution of eyes or other light-interacting structures. We also introduce PIA, a high throughput method for using phylogenetic relationships to identify LIT genes in transcriptomes from non-model organisms. With simple modifications, our methods may be used to search for different sets of genes or to annotate data sets from taxa outside of Metazoa. Electronic supplementary material The online version of this article (doi:10.1186/s12859-014-0350-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Daniel I Speiser
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, USA. .,Department of Biological Sciences, University of South Carolina, Columbia, SC, USA.
| | - M Sabrina Pankey
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, USA.
| | - Alexander K Zaharoff
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, USA.
| | - Barbara A Battelle
- The Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA.
| | - Heather D Bracken-Grissom
- Department of Biological Sciences, Florida International University-Biscayne Bay Campus, North Miami, FL, USA.
| | - Jesse W Breinholt
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA.
| | - Seth M Bybee
- Department of Biology, Brigham Young University, Provo, UT, USA.
| | - Thomas W Cronin
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA.
| | - Anders Garm
- Department of Biology, Marine Biological Section, University of Copenhagen, Copenhagen, Denmark.
| | - Annie R Lindgren
- Department of Biology, Portland State University, Portland, OR, USA.
| | - Nipam H Patel
- Department of Molecular and Cell Biology & Department of Integrative Biology, University of California, Berkeley, CA, USA.
| | - Megan L Porter
- Department of Biology, University of South Dakota, Vermillion, SD, USA.
| | - Meredith E Protas
- Department of Natural Sciences and Mathematics, Dominican University of California, San Rafael, CA, USA.
| | - Ajna S Rivera
- Department of Biology, University of the Pacific, Stockton, CA, USA.
| | - Jeanne M Serb
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA.
| | - Kirk S Zigler
- Department of Biology, Sewanee: The University of the South, Sewanee, TN, USA.
| | - Keith A Crandall
- Computational Biology Institute, George Washington University, Ashburn, VA, USA. .,Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.
| | - Todd H Oakley
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, USA.
| |
Collapse
|
46
|
The homeodomain of Eyeless regulates cell growth and antagonizes the paired domain-dependent retinal differentiation function. Protein Cell 2014; 6:68-78. [PMID: 25234589 PMCID: PMC4286722 DOI: 10.1007/s13238-014-0101-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 08/12/2014] [Indexed: 12/23/2022] Open
Abstract
Pax6 and its Drosophila homolog Eyeless (Ey) play essential roles during eye development. Ey/Pax6 contains two distinct DNA binding domains, a Paired domain (PD) and a Homeodomain (HD). While Ey/Pax6 PD is required for the expression of key regulators of retinal development, relatively little is known about the HD-dependent Ey function. In this study, we used the UAS/GAL4 system to determine the functions of different Ey domains on cell growth and on retinal development. We showed that Ey can promote cell growth, which requires the HD but not the PD. In contrast, the ability of Ey to activate Ato expression and induce ectopic eye formation requires the PD but not the HD. Interestingly, deletion of the HD enhanced Ey-dependent ectopic eye induction while overexpression of the HD only Ey forms antagonizes ectopic eye induction. These studies revealed a novel function of Ey HD on cell growth and a novel antagonistic effect of Ey HD on Ey PD-dependent eye induction. We further show the third helix of the Ey HD can directly interact with the RED subdomain in Ey PD and that deletion of the HD increased the binding of Ey PD to its target. These results suggest that the direct interaction between the HD and the PD potentially mediates their antagonistic effects. Since different Ey splicing forms are expressed in overlapping regions during normal development, we speculate that the expression ratios of the different Ey splice forms potentially contribute to the regulation of growth and differentiation of these tissues.
Collapse
|
47
|
Gold KS, Brand AH. Optix defines a neuroepithelial compartment in the optic lobe of the Drosophila brain. Neural Dev 2014; 9:18. [PMID: 25074684 PMCID: PMC4127074 DOI: 10.1186/1749-8104-9-18] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 06/25/2014] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND During early brain development, the organisation of neural progenitors into a neuroepithelial sheet maintains tissue integrity during growth. Neuroepithelial cohesion and patterning is essential for orderly proliferation and neural fate specification. Neuroepithelia are regionalised by the expression of transcription factors and signalling molecules, resulting in the formation of distinct developmental, and ultimately functional, domains. RESULTS We have discovered that the Six3/6 family orthologue Optix is an essential regulator of neuroepithelial maintenance and patterning in the Drosophila brain. Six3 and Six6 are required for mammalian eye and forebrain development, and mutations in humans are associated with severe eye and brain malformation. In Drosophila, Optix is expressed in a sharply defined region of the larval optic lobe, and its expression is reciprocal to that of the transcription factor Vsx1. Optix gain- and loss-of-function affects neuroepithelial adhesion, integrity and polarity. We find restricted cell lineage boundaries that correspond to transcription factor expression domains. CONCLUSION We propose that the optic lobe is compartmentalised by expression of Optix and Vsx1. Our findings provide insight into the spatial patterning of a complex region of the brain, and suggest an evolutionarily conserved principle of visual system development.
Collapse
Affiliation(s)
| | - Andrea H Brand
- The Gurdon Institute and Department of Physiology, Development & Neuroscience, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK.
| |
Collapse
|
48
|
Fortunato SA, Leininger S, Adamska M. Evolution of the Pax-Six-Eya-Dach network: the calcisponge case study. EvoDevo 2014; 5:23. [PMID: 25002963 PMCID: PMC4083861 DOI: 10.1186/2041-9139-5-23] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 05/15/2014] [Indexed: 12/21/2022] Open
Abstract
Background The Pax-Six-Eya-Dach network (PSEDN) is involved in a variety of developmental processes, including well documented roles in determination of sensory organs and morphogenesis in bilaterian animals. Expression of PSEDN components in cnidarians is consistent with function in sensory organ development. Recent work in demosponges demonstrated the presence of single homologs of Pax and Six genes, and their possible involvement in morphogenesis, but the absence of the remaining network components. Calcisponges are evolutionarily distant from demosponges, and the developmental toolkits of these two lineages differ significantly. We used an emerging model system, Sycon ciliatum, to identify components of the PSEDN and study their expression during embryonic and postembryonic development. Results We identified two Pax, three Six and one Eya genes in calcisponges, a situation strikingly different than in the previously studied demosponges. One of the calcisponge Pax genes can be identified as PaxB, while the second Pax gene has no clear affiliation. The three calcisponge Six genes could not be confidently classified within any known family of Six genes. Expression analysis in adult S. ciliatum demonstrated that representatives of Pax, Six and Eya are expressed in patterns consistent with roles in morphogenesis of the choanocyte chambers. Distinct paralogues of Pax and Six genes were expressed early in the development of the putative larval sensory cells, the cruciform cells. While lack of known photo pigments in calcisponge genomes precludes formal assignment of function to the cruciform cells, we also show that they express additional eumetazoan genes involved in specification of sensory and neuronal cells: Elav and Msi. Conclusions Our results indicate that the role of a Pax-Six-Eya network in morphogenesis likely predates the animal divergence. In addition, Pax and Six, as well as Elav and Msi are expressed during differentiation of cruciform cells, which are good candidates for being sensory cells of the calcaronean sponge larvae.
Collapse
Affiliation(s)
- Sofia Av Fortunato
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgt. 55, Bergen 5008, Norway ; Department of Biology, University of Bergen, Thormøhlensgt. 55, Bergen 5008, Norway
| | - Sven Leininger
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgt. 55, Bergen 5008, Norway ; Current address: Institute of Marine Research, Nordnesgaten 50, Bergen 5005, Norway
| | - Maja Adamska
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgt. 55, Bergen 5008, Norway
| |
Collapse
|
49
|
Piñeiro C, Lopes CS, Casares F. A conserved transcriptional network regulates lamina development in the Drosophila visual system. Development 2014; 141:2838-47. [PMID: 24924198 DOI: 10.1242/dev.108670] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The visual system of insects is a multilayered structure composed externally by the compound eye and internally by the three ganglia of the optic lobe: lamina, medulla and the lobula complex. The differentiation of lamina neurons depends heavily on Hedgehog (Hh) signaling, which is delivered by the incoming photoreceptor axons, and occurs in a wave-like fashion. Despite the primary role of lamina neurons in visual perception, it is still unclear how these neurons are specified from neuroepithelial (NE) progenitors. Here we show that a homothorax (hth)-eyes absent (eya)-sine oculis (so)-dachshund (dac) gene regulatory cassette is involved in this specification. Lamina neurons differentiate from NE progenitors that express hth, eya and so. One of the first events in the differentiation of lamina neurons is the upregulation of dac expression in response to Hh signaling. We show that this dac upregulation, which marks the transition from NE progenitors into lamina precursors, also requires Eya/So, the expression of which is locked in by mutual feedback. dac expression is crucial for lamina differentiation because it ensures repression of hth, a negative regulator of single-minded, and thus dac allows further lamina neuron differentiation. Therefore, the specification of lamina neurons is controlled by coupling the cell-autonomous hth-eya-so-dac regulatory cassette to Hh signaling.
Collapse
Affiliation(s)
- Cristina Piñeiro
- CABD (Andalusian Centre for Developmental Biology), CSIC-UPO-JA, Seville 41013, Spain
| | - Carla S Lopes
- CABD (Andalusian Centre for Developmental Biology), CSIC-UPO-JA, Seville 41013, Spain
| | - Fernando Casares
- CABD (Andalusian Centre for Developmental Biology), CSIC-UPO-JA, Seville 41013, Spain
| |
Collapse
|
50
|
Rivera A, Winters I, Rued A, Ding S, Posfai D, Cieniewicz B, Cameron K, Gentile L, Hill A. The evolution and function of the Pax/Six regulatory network in sponges. Evol Dev 2013; 15:186-96. [PMID: 23607302 DOI: 10.1111/ede.12032] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Examining the origins of highly conserved gene regulatory networks (GRNs) will inform our understanding of the evolution of animal body plans. Sponges are believed to be the most ancient extant metazoan lineage, and as such, hold clues about the evolution of genetic programs deployed in animal development. We used the emerging freshwater sponge model, Ephydatia muelleri, to study the evolutionary origins of the Pax/Six/Eya/Dac (PSED) GRN. Orthologs to Pax and Six family members are present in E. muelleri and are expressed in endothelial cells lining the canal system as well as cells in the choanoderm. Knockdown of EmPaxB and EmSix1/2 by RNAi resulted in defects to the canal systems. We further show that PaxB may be in a regulatory relationship with Six1/2 in E. muelleri, thus demonstrating that a component of the PSED network was present early in metazoan evolution.
Collapse
Affiliation(s)
- A Rivera
- University of Richmond, Richmond, VA 23173, USA
| | | | | | | | | | | | | | | | | |
Collapse
|