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Salomone J, Qin S, Fufa TD, Cain B, Farrow E, Guan B, Hufnagel RB, Nakafuku M, Lim HW, Campbell K, Gebelein B. Conserved Gsx2/Ind homeodomain monomer versus homodimer DNA binding defines regulatory outcomes in flies and mice. Genes Dev 2020; 35:157-174. [PMID: 33334823 PMCID: PMC7778271 DOI: 10.1101/gad.343053.120] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 11/19/2020] [Indexed: 12/18/2022]
Abstract
How homeodomain proteins gain sufficient specificity to control different cell fates has been a long-standing problem in developmental biology. The conserved Gsx homeodomain proteins regulate specific aspects of neural development in animals from flies to mammals, and yet they belong to a large transcription factor family that bind nearly identical DNA sequences in vitro. Here, we show that the mouse and fly Gsx factors unexpectedly gain DNA binding specificity by forming cooperative homodimers on precisely spaced and oriented DNA sites. High-resolution genomic binding assays revealed that Gsx2 binds both monomer and homodimer sites in the developing mouse ventral telencephalon. Importantly, reporter assays showed that Gsx2 mediates opposing outcomes in a DNA binding site-dependent manner: Monomer Gsx2 binding represses transcription, whereas homodimer binding stimulates gene expression. In Drosophila, the Gsx homolog, Ind, similarly represses or stimulates transcription in a site-dependent manner via an autoregulatory enhancer containing a combination of monomer and homodimer sites. Integrating these findings, we test a model showing how the homodimer to monomer site ratio and the Gsx protein levels defines gene up-regulation versus down-regulation. Altogether, these data serve as a new paradigm for how cooperative homeodomain transcription factor binding can increase target specificity and alter regulatory outcomes.
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Affiliation(s)
- Joseph Salomone
- Graduate Program in Molecular and Developmental Biology, Cincinnati Children's Hospital Research Foundation, Cincinnati, Ohio 45229, USA.,Medical-Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, Ohio 45229, USA
| | - Shenyue Qin
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio 45229, USA
| | - Temesgen D Fufa
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Brittany Cain
- Department of Biomedical Engineering, University of Cincinnati, Cincinnati, Ohio 45219, USA
| | - Edward Farrow
- Medical-Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, Ohio 45229, USA
| | - Bin Guan
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Robert B Hufnagel
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Masato Nakafuku
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio 45229, USA
| | - Hee-Woong Lim
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio 45229, USA.,Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA.,Department of Biomedical Informatics, University of Cincinnati College of Medicine, Cincinnati, Ohio 45229, USA
| | - Kenneth Campbell
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio 45229, USA
| | - Brian Gebelein
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio 45229, USA
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Roychoudhury K, Salomone J, Qin S, Cain B, Adam M, Potter SS, Nakafuku M, Gebelein B, Campbell K. Physical interactions between Gsx2 and Ascl1 balance progenitor expansion versus neurogenesis in the mouse lateral ganglionic eminence. Development 2020; 147:dev.185348. [PMID: 32122989 DOI: 10.1242/dev.185348] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 02/13/2020] [Indexed: 12/15/2022]
Abstract
The Gsx2 homeodomain transcription factor promotes neural progenitor identity in the lateral ganglionic eminence (LGE), despite upregulating the neurogenic factor Ascl1. How this balance in maturation is maintained is unclear. Here, we show that Gsx2 and Ascl1 are co-expressed in subapical progenitors that have unique transcriptional signatures in LGE ventricular zone (VZ) cells. Moreover, whereas Ascl1 misexpression promotes neurogenesis in dorsal telencephalic progenitors, the co-expression of Gsx2 with Ascl1 inhibits neurogenesis. Using luciferase assays, we found that Gsx2 reduces the ability of Ascl1 to activate gene expression in a dose-dependent and DNA binding-independent manner. Furthermore, Gsx2 physically interacts with the basic helix-loop-helix (bHLH) domain of Ascl1, and DNA-binding assays demonstrated that this interaction interferes with the ability of Ascl1 to bind DNA. Finally, we modified a proximity ligation assay for tissue sections and found that Ascl1-Gsx2 interactions are enriched within LGE VZ progenitors, whereas Ascl1-Tcf3 (E-protein) interactions predominate in the subventricular zone. Thus, Gsx2 contributes to the balance between progenitor maintenance and neurogenesis by physically interacting with Ascl1, interfering with its DNA binding and limiting neurogenesis within LGE progenitors.
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Affiliation(s)
- Kaushik Roychoudhury
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Joseph Salomone
- Graduate Program in Molecular and Developmental Biology, Cincinnati Children's Hospital Research Foundation, Cincinnati, OH 45229, USA.,Medical-Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Shenyue Qin
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Brittany Cain
- Department of Biomedical Engineering, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Mike Adam
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - S Steven Potter
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Masato Nakafuku
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Brian Gebelein
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH 45229, USA .,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Kenneth Campbell
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH 45229, USA .,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
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Maguire RJ, Isaacs HV, Pownall ME. Early transcriptional targets of MyoD link myogenesis and somitogenesis. Dev Biol 2012; 371:256-68. [PMID: 22954963 DOI: 10.1016/j.ydbio.2012.08.027] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Revised: 07/10/2012] [Accepted: 08/22/2012] [Indexed: 12/20/2022]
Abstract
In order to identify early transcriptional targets of MyoD prior to skeletal muscle differentiation, we have undertaken a transcriptomic analysis on gastrula stage Xenopus embryos in which MyoD has been knocked-down. Our validated list of genes transcriptionally regulated by MyoD includes Esr1 and Esr2, which are known targets of Notch signalling, and Tbx6, mesogenin, and FoxC1; these genes are all are known to be essential for normal somitogenesis but are expressed surprisingly early in the mesoderm. In addition we found that MyoD is required for the expression of myf5 in the early mesoderm, in contrast to the reverse relationship of these two regulators in amniote somites. These data highlight a role for MyoD in the early mesoderm in regulating a set of genes that are essential for both myogenesis and somitogenesis.
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Affiliation(s)
- Richard J Maguire
- Biology Department, University of York, Heslington, York, North Yorkshire YO10 5YW, UK
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