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Wang Z, Wang X, Lan X, Zhu H, Qu L, Pan C. Polymorphism within the GATA binding protein 4 gene is significantly associated with goat litter size. Anim Biotechnol 2023; 34:4291-4300. [PMID: 36421983 DOI: 10.1080/10495398.2022.2147533] [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] [Indexed: 11/27/2022]
Abstract
GATA binding protein 4 (GATA4) is a typical transcription binding factor, and its main functions include regulating the proliferation, differentiation and apoptosis of ovarian granulosa cells, promoting spermatogenesis and sex differentiation, implying that this gene have possibly roles in animal reproduction. This study aims to detect five potential insertion/deletions (indels) of the GATA4 gene in 606 healthy unrelated Shaanbei white cashmere (SBWC) goats and analyze its association with the litter size. The electrophoresis and DNA sequencing identified two polymorphic indels (e.g., P4-Del-8bp and P5-Ins-9bp indel). Then T-test analysis showed that P4-Del-8bp was significantly correlated with litter size (p = 0.022) because of two different genotypes detected, e.g., insertion-deletion (ID) and deletion-deletion (DD), and the average litter size of individuals with DD genotype goats was higher than that of others. However, there was no correlation between P5-Ins-9bp and lambing of goats. Chi-square (X2) test found that the distribution of and P4-Del-8bp genotypes (X2 = 6.475, p = 0.011) was significantly different between single and multiple-lamb groups, while P5-Ins-9bp (X2 = 0.030, p = 0.862) was not. Therefore, these findings revealed that P4-Del-8bp polymorphism of goat GATA4 gene was a potential molecular marker significantly associated with litter size, which can be used for the marker-assisted selection (MAS) breeding to improve goat industry.
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Affiliation(s)
- Zhiying Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xinyu Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Haijing Zhu
- Life Science Research Center, Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, China
| | - Lei Qu
- Life Science Research Center, Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, China
| | - Chuanying Pan
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
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Imai KS. Gene regulatory networks in ascidian embryos. Genesis 2023; 61:e23570. [PMID: 37942672 DOI: 10.1002/dvg.23570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 10/22/2023] [Accepted: 10/25/2023] [Indexed: 11/10/2023]
Affiliation(s)
- Kaoru S Imai
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
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Tokuoka M, Satou Y. A digital twin reproducing gene regulatory network dynamics of early Ciona embryos indicates robust buffers in the network. PLoS Genet 2023; 19:e1010953. [PMID: 37756274 PMCID: PMC10530022 DOI: 10.1371/journal.pgen.1010953] [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: 03/17/2023] [Accepted: 09/01/2023] [Indexed: 09/29/2023] Open
Abstract
How gene regulatory networks (GRNs) encode gene expression dynamics and how GRNs evolve are not well understood, although these problems have been studied extensively. We created a digital twin that accurately reproduces expression dynamics of 13 genes that initiate expression in 32-cell ascidian embryos. We first showed that gene expression patterns can be manipulated according to predictions by this digital model. Next, to simulate GRN rewiring, we changed regulatory functions that represented their regulatory mechanisms in the digital twin, and found that in 55 of 100 cases, removal of a single regulator from a conjunctive clause of Boolean functions did not theoretically alter qualitative expression patterns of these genes. In other words, we found that more than half the regulators gave theoretically redundant temporal or spatial information to target genes. We experimentally substantiated that the expression pattern of Nodal was maintained without one of these factors, Zfpm, by changing the upstream regulatory sequence of Nodal. Such robust buffers of regulatory mechanisms may provide a basis of enabling developmental system drift, or rewiring of GRNs without changing expression patterns of downstream genes, during evolution.
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Affiliation(s)
- Miki Tokuoka
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto, Japan
| | - Yutaka Satou
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto, Japan
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Bettoni R, Hudson C, Williaume G, Sirour C, Yasuo H, de Buyl S, Dupont G. Model of neural induction in the ascidian embryo. PLoS Comput Biol 2023; 19:e1010335. [PMID: 36735746 PMCID: PMC9931142 DOI: 10.1371/journal.pcbi.1010335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 02/15/2023] [Accepted: 01/17/2023] [Indexed: 02/04/2023] Open
Abstract
How cell specification can be controlled in a reproducible manner is a fundamental question in developmental biology. In ascidians, a group of invertebrate chordates, geometry plays a key role in achieving this control. Here, we use mathematical modeling to demonstrate that geometry dictates the neural-epidermal cell fate choice in the 32-cell stage ascidian embryo by a two-step process involving first the modulation of ERK signaling and second, the expression of the neural marker gene, Otx. The model describes signal transduction by the ERK pathway that is stimulated by FGF and attenuated by ephrin, and ERK-mediated control of Otx gene expression, which involves both an activator and a repressor of ETS-family transcription factors. Considering the measured area of cell surface contacts with FGF- or ephrin-expressing cells as inputs, the solutions of the model reproduce the experimental observations about ERK activation and Otx expression in the different cells under normal and perturbed conditions. Sensitivity analyses and computations of Hill coefficients allow us to quantify the robustness of the specification mechanism controlled by cell surface area and to identify the respective role played by each signaling input. Simulations also predict in which conditions the dual control of gene expression by an activator and a repressor that are both under the control of ERK can induce a robust ON/OFF control of neural fate induction.
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Affiliation(s)
- Rossana Bettoni
- Unité de Chronobiologie Théorique, Faculté des Sciences, CP231, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, Brussels, Belgium
- Applied Physics Research Group, Vrije Universiteit Brussel, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus, Brussels, Belgium
| | - Clare Hudson
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche-sur-Mer, Sorbonne Université, CNRS, Villefranche-sur-Mer, France
- * E-mail: (CH); (GD)
| | - Géraldine Williaume
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche-sur-Mer, Sorbonne Université, CNRS, Villefranche-sur-Mer, France
| | - Cathy Sirour
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche-sur-Mer, Sorbonne Université, CNRS, Villefranche-sur-Mer, France
| | - Hitoyoshi Yasuo
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche-sur-Mer, Sorbonne Université, CNRS, Villefranche-sur-Mer, France
| | - Sophie de Buyl
- Applied Physics Research Group, Vrije Universiteit Brussel, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus, Brussels, Belgium
| | - Geneviève Dupont
- Unité de Chronobiologie Théorique, Faculté des Sciences, CP231, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus, Brussels, Belgium
- * E-mail: (CH); (GD)
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Satou Y, Tokuoka M, Oda-Ishii I, Tokuhiro S, Ishida T, Liu B, Iwamura Y. A Manually Curated Gene Model Set for an Ascidian, Ciona robusta (Ciona intestinalis Type A). Zoolog Sci 2022; 39:253-260. [DOI: 10.2108/zs210102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 01/15/2022] [Indexed: 11/17/2022]
Affiliation(s)
- Yutaka Satou
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Miki Tokuoka
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Izumi Oda-Ishii
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Sinichi Tokuhiro
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Tasuku Ishida
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Boqi Liu
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Yuri Iwamura
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
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Tokuoka M, Maeda K, Kobayashi K, Mochizuki A, Satou Y. The gene regulatory system for specifying germ layers in early embryos of the simple chordate. SCIENCE ADVANCES 2021; 7:7/24/eabf8210. [PMID: 34108211 PMCID: PMC8189585 DOI: 10.1126/sciadv.abf8210] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 04/23/2021] [Indexed: 06/12/2023]
Abstract
In animal embryos, gene regulatory networks control the dynamics of gene expression in cells and coordinate such dynamics among cells. In ascidian embryos, gene expression dynamics have been dissected at the single-cell resolution. Here, we revealed mathematical functions that represent the regulatory logics of all regulatory genes expressed at the 32-cell stage when the germ layers are largely specified. These functions collectively explain the entire mechanism by which gene expression dynamics are controlled coordinately in early embryos. We found that regulatory functions for genes expressed in each of the specific lineages contain a common core regulatory mechanism. Last, we showed that the expression of the regulatory genes became reproducible by calculation and controllable by experimental manipulations. Thus, these regulatory functions represent an architectural design for the germ layer specification of this chordate and provide a platform for simulations and experiments to understand the operating principles of gene regulatory networks.
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Affiliation(s)
- Miki Tokuoka
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Kazuki Maeda
- Faculty of Informatics, University of Fukuchiyama, 3370 Hori, Fukuchiyama, Kyoto 620-0886, Japan
| | - Kenji Kobayashi
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Atsushi Mochizuki
- Institute for Frontier Life and Medical Sciences, Kyoto University, Sakyo, Kyoto 606-8507, Japan
| | - Yutaka Satou
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan.
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Liu B, Satou Y. The genetic program to specify ectodermal cells in ascidian embryos. Dev Growth Differ 2020; 62:301-310. [PMID: 32130723 DOI: 10.1111/dgd.12660] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 02/11/2020] [Accepted: 02/21/2020] [Indexed: 12/18/2022]
Abstract
The ascidian belongs to the sister group of vertebrates and shares many features with them. The gene regulatory network (GRN) controlling gene expression in ascidian embryonic development leading to the tadpole larva has revealed evolutionarily conserved gene circuits between ascidians and vertebrates. These conserved mechanisms are indeed useful to infer the original developmental programs of the ancestral chordates. Simultaneously, these studies have revealed which gene circuits are missing in the ascidian GRN; these gene circuits may have been acquired in the vertebrate lineage. In particular, the GRN responsible for gene expression in ectodermal cells of ascidian embryos has revealed the genetic programs that regulate the regionalization of the brain, formation of palps derived from placode-like cells, and differentiation of sensory neurons derived from neural crest-like cells. We here discuss how these studies have given insights into the evolution of these traits.
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Affiliation(s)
- Boqi Liu
- Department of Zoology, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Yutaka Satou
- Department of Zoology, Graduate School of Science, Kyoto University, Kyoto, Japan
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