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Goes CP, Botezelli VS, De La Cruz SM, Cruz MC, Azambuja AP, Simoes-Costa M, Yan CYI. ASCL1 promotes Scrt2 expression in the neural tube. Front Cell Dev Biol 2024; 12:1324584. [PMID: 38655067 PMCID: PMC11036302 DOI: 10.3389/fcell.2024.1324584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 03/05/2024] [Indexed: 04/26/2024] Open
Abstract
ASCL1 is a transcription factor that directs neural progenitors towards lineage differentiation. Although many of the molecular mechanisms underlying its action have been described, several of its targets remain unidentified. We identified in the chick genome a putative enhancer (cE1) upstream of the transcription factor Scratch2 (Scrt2) locus with a predicted heterodimerization motif for ASCL1 and POU3F2. In this study, we investigated the role of ASCL1 and this enhancer in regulating the expression of the Scrt2 in the embryonic spinal cord. We confirmed that cE1 region interacted with the Scrt2 promoter. cE1 was sufficient to mediate ASCL1-driven expression in the neural tube through the heterodimerization sites. Moreover, Scrt2 expression was inhibited when we removed cE1 from the genome. These findings strongly indicate that ASCL1 regulates Scrt2 transcription in the neural tube through cE1.
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Affiliation(s)
- Carolina Purcell Goes
- Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, Brazil
| | - Vitória Samartin Botezelli
- Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, Brazil
| | - Shirley Mirna De La Cruz
- Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, Brazil
- Facultad de Ciencias de la Salud, Universidad Científica del Sur, Lima, Peru
| | - Mário Costa Cruz
- Core Research Facilities (CEFAP), Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, Brazil
| | - Ana Paula Azambuja
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States
- Department of Systems Biology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Marcos Simoes-Costa
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States
- Department of Systems Biology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Chao Yun Irene Yan
- Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, Brazil
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Goes CP, Kanno TY, Yan CYI. In Embryo Gene Reporter Assays for Evaluation of Cis-Regulatory Regions. Methods Mol Biol 2023; 2599:227-239. [PMID: 36427153 DOI: 10.1007/978-1-0716-2847-8_16] [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: 06/16/2023]
Abstract
Gene expression reporter assays measure the relevance of cis-regulatory elements and DNA-binding proteins in modulating transcriptional activity. Commonly, they are performed in cell lines. However, regulation of transcriptional activity during development is complex and dynamic, and not many cell lines reproduce the embryonic conditions. Thus, conclusions derived from cell line data provide limited information about embryonic development. On the other hand, one of the major hurdles for embryonic assays is delivering reporter plasmids in a tissue-specific manner. In this sense, the chick embryo is a good model system to perform these assays. Electroporation of chick embryos provides temporal and spatially controlled plasmid delivery. Further, it is a well-established, easy, and an economical procedure. Here, we describe in detail how to measure in the chick neural tube (1) enhancer activity with GFP, (2) enhancer activity with luciferase, and (3) 3'UTR activity with luciferase.
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Affiliation(s)
- Carolina Purcell Goes
- Department of Cell and Developmental Biology, Biomedical Sciences Institute, Universidade de São Paulo, São Paulo, Brazil
| | - Tatiane Y Kanno
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - C Y Irene Yan
- Department of Cell and Developmental Biology, Biomedical Sciences Institute, Universidade de São Paulo, São Paulo, Brazil.
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Liu Y, Zhou Z, He X, Tao L, Jiang Y, Lan R, Hong Q, Chu M. Integrated analyses of miRNA-mRNA expression profiles of ovaries reveal the crucial interaction networks that regulate the prolificacy of goats in the follicular phase. BMC Genomics 2021; 22:812. [PMID: 34763659 PMCID: PMC8582148 DOI: 10.1186/s12864-021-08156-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 11/08/2021] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Litter size is an important index of mammalian prolificacy and is determined by the ovulation rate. The ovary is a crucial organ for mammalian reproduction and is associated with follicular development, maturation and ovulation. However, prolificacy is influenced by multiple factors, and its molecular regulation in the follicular phase remains unclear. METHODS Ten female goats with no significant differences in age and weight were randomly selected and divided into either the high-yielding group (n = 5, HF) or the low-yielding group (n = 5, LF). Ovarian tissues were collected from goats in the follicular phase and used to construct mRNA and miRNA sequencing libraries to analyze transcriptomic variation between high- and low-yield Yunshang black goats. Furthermore, integrated analysis of the differentially expressed (DE) miRNA-mRNA pairs was performed based on their correlation. The STRING database was used to construct a PPI network of the DEGs. RT-qPCR was used to validate the results of the predicted miRNA-mRNA pairs. Luciferase analysis and CCK-8 assay were used to detect the function of the miRNA-mRNA pairs and the proliferation of goat granulosa cells (GCs). RESULTS A total of 43,779 known transcripts, 23,067 novel transcripts, 424 known miRNAs and 656 novel miRNAs were identified by RNA-seq in the ovaries from both groups. Through correlation analysis of the miRNA and mRNA expression profiles, 263 negatively correlated miRNA-mRNA pairs were identified in the LF vs. HF comparison. Annotation analysis of the DE miRNA-mRNA pairs identified targets related to biological processes such as "estrogen receptor binding (GO:0030331)", "oogenesis (GO:0048477)", "ovulation cycle process (GO:0022602)" and "ovarian follicle development (GO:0001541)". Subsequently, five KEGG pathways (oocyte meiosis, progesterone-mediated oocyte maturation, GnRH signaling pathway, Notch signaling pathway and TGF-β signaling pathway) were identified in the interaction network related to follicular development, and a PPI network was also constructed. In the network, we found that CDK12, FAM91A1, PGS1, SERTM1, SPAG5, SYNE1, TMEM14A, WNT4, and CAMK2G were the key nodes, all of which were targets of the DE miRNAs. The PPI analysis showed that there was a clear interaction among the CAMK2G, SERTM1, TMEM14A, CDK12, SYNE1 and WNT4 genes. In addition, dual luciferase reporter and CCK-8 assays confirmed that miR-1271-3p suppressed the proliferation of GCs by inhibiting the expression of TXLNA. CONCLUSIONS These results increase the understanding of the molecular mechanisms underlying goat prolificacy. These results also provide a basis for studying interactions between genes and miRNAs, as well as the functions of the pathways in ovarian tissues involved in goat prolificacy in the follicular phase.
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Affiliation(s)
- Yufang Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Rd, Beijing, 100193, China.,College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, 056021, China
| | - Zuyang Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Rd, Beijing, 100193, China.,College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, 056021, China
| | - Xiaoyun He
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Rd, Beijing, 100193, China
| | - Lin Tao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Rd, Beijing, 100193, China
| | - Yanting Jiang
- Yunnan Animal Science and Veterinary Institute, Kunming, 650224, China
| | - Rong Lan
- Yunnan Animal Science and Veterinary Institute, Kunming, 650224, China
| | - Qionghua Hong
- Yunnan Animal Science and Veterinary Institute, Kunming, 650224, China.
| | - Mingxing Chu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Rd, Beijing, 100193, China.
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