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Minhas R, Paterek A, Łapiński M, Bazała M, Korzh V, Winata CL. A novel conserved enhancer at zebrafish zic3 and zic6 loci drives neural expression. Dev Dyn 2019; 248:837-849. [PMID: 31194899 PMCID: PMC6771876 DOI: 10.1002/dvdy.69] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 05/28/2019] [Accepted: 06/07/2019] [Indexed: 01/15/2023] Open
Abstract
Background Identifying enhancers and deciphering their putative roles represent a major step to better understand the mechanism of metazoan gene regulation, development, and the role of regulatory elements in disease. Comparative genomics and transgenic assays have been used with some success to identify critical regions that are involved in regulating the spatiotemporal expression of genes during embryogenesis. Results We identified two novel tetrapod‐teleost conserved noncoding elements within the vicinity of the zic3 and zic6 loci in the zebrafish genome and demonstrated their ability to drive tissue‐specific expression in a transgenic zebrafish assay. The syntenic analysis and robust green fluorescent expression in the developing habenula in the stable transgenic line were correlated with known sites of endogenous zic3 and zic6 expression. Conclusion This transgenic line that expresses green fluorescent protein in the habenula is a valuable resource for studying a specific population of cells in the zebrafish central nervous system. Our observations indicate that a genomic sequence that is conserved between humans and zebrafish acts as an enhancer that likely controls zic3 and zic6 expression. Identified a novel enhancer near zebrafish zic3/zic6 locus. The novel enhancer drives tissue‐specific expression in the habenula. Zebrafish transgenic line generated in this study can be a useful resource for studying development of habenula.
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Affiliation(s)
- Rashid Minhas
- International Institute of Molecular and Cell Biology, Warsaw, Poland.,Randall Centre of Cell and Molecular Biophysics, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Aleksandra Paterek
- International Institute of Molecular and Cell Biology, Warsaw, Poland.,Department of Clinical Physiology, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Maciej Łapiński
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Michał Bazała
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Vladimir Korzh
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Cecilia L Winata
- International Institute of Molecular and Cell Biology, Warsaw, Poland.,Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
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Jia ZL, He S, Jiang SY, Zhang BH, Duan SJ, Shi JY, Huang N, Zhu WC, Shi B. Rs12941170 at SOX9 gene associated with orofacial clefts in Chinese. Arch Oral Biol 2016; 76:14-19. [PMID: 28068523 DOI: 10.1016/j.archoralbio.2016.12.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 10/20/2016] [Accepted: 12/27/2016] [Indexed: 02/05/2023]
Abstract
OBJECTIVE Non-syndromic orofacial cleftings (NSOCs) are considered as complex trait, which results from genetic and/or environmental modifiers. Current findings could only explain small portion of the NSOCs. SOX9 gene plays an important role during craniofacial development in animal models and the Pierre Robin sequence (PRS). However, its role in non-syndromic clefts remains unknown. DESIGN In this study, we selected eight SNPs in and around SOX9 gene to make maximum coverage, and genotyped them by using RFLP-PCR and ligase detection reaction (LDR) methods to test its associations among 151 NSOCs (53 NSCLP, 52 NSCLO and 46 NSCPO) from Western Han Chinese population. RESULTS Allelic TDT results showed that G allele at rs12941170 of SOX9 was under-transmitted among NSOCs (p=0.00014, OR=0.55 and 95%CI: 0.40-0.75), which could indicate that the G allele is protective against NSOCs; parent-of-origin effect analysis showed that G allele at rs12941170 was maternally under-transmitted (p=0.002), while there was no statistically difference between the maternal and paternal transmission of it. To test if the adjacent SNPs travel together from parents to the affected individual, we carried out the sliding window haplotype analysis, it is interesting to find that the haplotypes carrying the G allele at rs12941170 also was under-transmitted for NSOCs, NSCL/P, NSCLP and NSCPO (lowest p=0.00033). CONCLUSIONS This study suggested that G allele at rs12941170 was protective, which could decrease the risk for NSOCs from Western Han Chinese population, and it will provide new reference for future research and genetic counseling in NSOCs.
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Affiliation(s)
- Zhong-Lin Jia
- State Key Laboratory of Oral Disease, West China hospital of Stomatology, Sichuan University, Chengdu, PR China
| | - Sha He
- State Key Laboratory of Oral Disease, West China hospital of Stomatology, Sichuan University, Chengdu, PR China; Department of Cleft Lip and Palate Surgery, West China College of Stomatology, Sichuan University, Chengdu, PR China; Department of Stomatology, The third People's hospital of Chengdu, Chengdu, PR China
| | - Shu-Yuan Jiang
- State Key Laboratory of Oral Disease, West China hospital of Stomatology, Sichuan University, Chengdu, PR China; Department of Cleft Lip and Palate Surgery, West China College of Stomatology, Sichuan University, Chengdu, PR China
| | - Bi-He Zhang
- State Key Laboratory of Oral Disease, West China hospital of Stomatology, Sichuan University, Chengdu, PR China; Department of Cleft Lip and Palate Surgery, West China College of Stomatology, Sichuan University, Chengdu, PR China
| | - Shi-Jun Duan
- State Key Laboratory of Oral Disease, West China hospital of Stomatology, Sichuan University, Chengdu, PR China; Department of Cleft Lip and Palate Surgery, West China College of Stomatology, Sichuan University, Chengdu, PR China
| | - Jia-Yu Shi
- Division of Growth and Development and Section of Orthodontics, School of Dentistry, University of California, Los Angeles, CA 90095, United States
| | - Ning Huang
- State Key Laboratory of Oral Disease, West China hospital of Stomatology, Sichuan University, Chengdu, PR China; Department of Cleft Lip and Palate Surgery, West China College of Stomatology, Sichuan University, Chengdu, PR China
| | - Wen-Chao Zhu
- State Key Laboratory of Oral Disease, West China hospital of Stomatology, Sichuan University, Chengdu, PR China; Department of Cleft Lip and Palate Surgery, West China College of Stomatology, Sichuan University, Chengdu, PR China
| | - Bing Shi
- State Key Laboratory of Oral Disease, West China hospital of Stomatology, Sichuan University, Chengdu, PR China; Department of Cleft Lip and Palate Surgery, West China College of Stomatology, Sichuan University, Chengdu, PR China.
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