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Ostalé CM, Prado AD, Martín M, Esteban N, López-Varea A, de Celis JF. A function of spalt major as a sequence-specific DNA binding transcription factor mediates repression of knirps in the Drosophila wing imaginal disc. Dev Biol 2024; 510:40-49. [PMID: 38493946 DOI: 10.1016/j.ydbio.2024.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 01/30/2024] [Accepted: 03/14/2024] [Indexed: 03/19/2024]
Abstract
The Spalt transcriptional regulators participate in a variety of cell fate decisions during multicellular development. Vertebrate Spalt proteins have been mostly associated to the organization of heterochromatic regions, but they also contribute regulatory functions through binding to A/T rich motives present in their target genes. The developmental processes in which the Drosophila spalt genes participate are well known through genetic analysis, but the mechanism by which the Spalt proteins regulate transcription are still unknown. Furthermore, despite the prominent changes in gene expression associated to mutations in the spalt genes, the specific DNA sequences they bind are unknow. Here, we analyze a DNA fragment present in the regulatory region of the knirps gene. Spalt proteins are candidate repressors of knirps expression during the formation of the venation pattern in the wing disc, and we identified a minimal conserved 30bp sequence that binds to Spalt major both in vivo and in vitro. This sequence mediates transcriptional repression in the central region of the wing blade, constituting the first confirmed case of a direct regulatory interaction between Spalt major and its target DNA in Drosophila. Interestingly, we also find similar sequences in a set of eight novel candidate Spalt target genes, pointing to a common mechanism of transcriptional repression mediated by Spalt proteins.
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Affiliation(s)
- Cristina M Ostalé
- Centro de Biología Molecular "Severo Ochoa", CSIC and Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Alicia Del Prado
- Centro de Biología Molecular "Severo Ochoa", CSIC and Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Mercedes Martín
- Centro de Biología Molecular "Severo Ochoa", CSIC and Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Nuria Esteban
- Centro de Biología Molecular "Severo Ochoa", CSIC and Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Ana López-Varea
- Centro de Biología Molecular "Severo Ochoa", CSIC and Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Jose F de Celis
- Centro de Biología Molecular "Severo Ochoa", CSIC and Universidad Autónoma de Madrid, Madrid, 28049, Spain.
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Gu R, Zhang S, Saha SK, Ji Y, Reynolds K, McMahon M, Sun B, Islam M, Trainor PA, Chen Y, Xu Y, Chai Y, Burkart-Waco D, Zhou CJ. Single-cell transcriptomic signatures and gene regulatory networks modulated by Wls in mammalian midline facial formation and clefts. Development 2022; 149:dev200533. [PMID: 35781558 PMCID: PMC9382898 DOI: 10.1242/dev.200533] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 06/21/2022] [Indexed: 07/24/2023]
Abstract
Formation of highly unique and complex facial structures is controlled by genetic programs that are responsible for the precise coordination of three-dimensional tissue morphogenesis. However, the underlying mechanisms governing these processes remain poorly understood. We combined mouse genetic and genomic approaches to define the mechanisms underlying normal and defective midfacial morphogenesis. Conditional inactivation of the Wnt secretion protein Wls in Pax3-expressing lineage cells disrupted frontonasal primordial patterning, cell survival and directional outgrowth, resulting in altered facial structures, including midfacial hypoplasia and midline facial clefts. Single-cell RNA sequencing revealed unique transcriptomic atlases of mesenchymal subpopulations in the midfacial primordia, which are disrupted in the conditional Wls mutants. Differentially expressed genes and cis-regulatory sequence analyses uncovered that Wls modulates and integrates a core gene regulatory network, consisting of key midfacial regulatory transcription factors (including Msx1, Pax3 and Pax7) and their downstream targets (including Wnt, Shh, Tgfβ and retinoic acid signaling components), in a mesenchymal subpopulation of the medial nasal prominences that is responsible for midline facial formation and fusion. These results reveal fundamental mechanisms underlying mammalian midfacial morphogenesis and related defects at single-cell resolution.
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Affiliation(s)
- Ran Gu
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA
- Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children and UC Davis School of Medicine, Sacramento, CA 95817, USA
| | - Shuwen Zhang
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA
- Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children and UC Davis School of Medicine, Sacramento, CA 95817, USA
| | - Subbroto Kumar Saha
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA
- Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children and UC Davis School of Medicine, Sacramento, CA 95817, USA
| | - Yu Ji
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA
- Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children and UC Davis School of Medicine, Sacramento, CA 95817, USA
| | - Kurt Reynolds
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA
- Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children and UC Davis School of Medicine, Sacramento, CA 95817, USA
| | - Moira McMahon
- Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children and UC Davis School of Medicine, Sacramento, CA 95817, USA
| | - Bo Sun
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA
- Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children and UC Davis School of Medicine, Sacramento, CA 95817, USA
| | - Mohammad Islam
- Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children and UC Davis School of Medicine, Sacramento, CA 95817, USA
| | - Paul A. Trainor
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - YiPing Chen
- Department of Cell and Molecular Biology, Tulane University, New Orleans, LA 70118, USA
| | - Ying Xu
- Can-SU Genomic Resource Center, Medical College of Soochow University, Suzhou 215006, China
| | - Yang Chai
- Center for Craniofacial Molecular Biology, Ostrow School of Dentistry, University of Southern California, Los Angeles, CA 90033, USA
| | - Diana Burkart-Waco
- DNA Technologies and Expression Analysis Core, Genome Center, University of California, Davis, California 95616, USA
| | - Chengji J. Zhou
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA
- Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children and UC Davis School of Medicine, Sacramento, CA 95817, USA
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Wester JVWC, Lima CAC, Machado MCR, Zampar PV, Tavares SS, Monesi N. Characterization of a novel Drosophila melanogaster cis-regulatory module that drives gene expression to the larval tracheal system and adult thoracic musculature. Genesis 2018; 56:e23222. [PMID: 30096221 DOI: 10.1002/dvg.23222] [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: 05/23/2018] [Revised: 06/10/2018] [Accepted: 06/11/2018] [Indexed: 11/05/2022]
Abstract
In a previous bioinformatics analysis we identified 10 conserved Drosophila melanogaster sequences that reside upstream from protein coding genes (CGs). Here we characterize one of these genomic regions, which constitutes a Drosophila melanogaster cis-regulatory module (CRM) that we denominate TT-CRM. The TT-CRM is 646 bp long and is located in one of the introns of CG32239 and resides about 3,500 bp upstream of CG13711 and about 620 bp upstream of CG12493. Analysis of 646 bp-lacZ lines revealed that TT-CRM drives gene expression not only to the larval, prepupal, and pupal tracheal system but also to the adult dorsal longitudinal muscles. The patterns of mRNA expression of the transgene and of the CGs that lie in the vicinity of TT-CRM were investigated both in dissected trachea and in adult thoraces. Through RT-qPCR we observed that in the tracheal system the pattern of expression of 646 bp-lacZ is similar to the pattern of expression of CG32239 and CG13711, whereas in the thoracic muscles 646 bp-lacZ expression accompanies the expression of CG12493. Together, these results suggest new functions for two previously characterized D. melanogaster genes and also contribute to the initial characterization of a novel CRM that drives a dynamic pattern of expression throughout development.
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Affiliation(s)
- Jorge Victor Wilfredo Cachay Wester
- Programa de Pós-Graduação em Biologia Celular e Molecular, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Carlos Antonio Couto Lima
- Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Maiaro Cabral Rosa Machado
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Patrícia Vieira Zampar
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Simone Sakagute Tavares
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Nadia Monesi
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
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Martín M, Ostalé CM, de Celis JF. Patterning of the Drosophila L2 vein is driven by regulatory interactions between region-specific transcription factors expressed in response to Dpp signalling. Development 2017; 144:3168-3176. [PMID: 28760811 DOI: 10.1242/dev.143461] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 07/25/2017] [Indexed: 01/31/2023]
Abstract
Pattern formation relies on the generation of transcriptional landscapes regulated by signalling pathways. A paradigm of epithelial patterning is the distribution of vein territories in the Drosophila wing disc. In this tissue, Decapentaplegic signalling regulates its target genes at different distances from the source of the ligand. The transformation of signalling into coherent territories of gene expression requires regulatory cross-interactions between these target genes. Here, we analyse the mechanisms generating the domain of knirps expression in the presumptive L2 vein of the wing imaginal disc. We find that knirps is regulated by four Decapentaplegic target genes encoding the transcription factors aristaless, spalt major, spalt-related and optix The expression of optix is activated by Dpp and repressed by the Spalt proteins, becoming restricted to the most anterior region of the wing blade. In turn, the expression of knirps is activated by Aristaless and repressed by Optix and the Spalt proteins. In this manner, the expression of knirps becomes restricted to those cells where Spalt levels are sufficient to repress optix, but not sufficient to repress knirps.
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Affiliation(s)
- Mercedes Martín
- Centro de Biología Molecular 'Severo Ochoa', CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Cristina M Ostalé
- Centro de Biología Molecular 'Severo Ochoa', CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Jose F de Celis
- Centro de Biología Molecular 'Severo Ochoa', CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
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