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Gui Y, Zhang Y, Zhang Q, Chen X, Wang F, Wu F, Gui Y, Li Q. The functional verification and analysis of Fugu promoter of cardiac gene tnni1a in zebrafish. Cells Dev 2022; 171:203801. [PMID: 35787465 DOI: 10.1016/j.cdev.2022.203801] [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: 01/19/2022] [Revised: 05/09/2022] [Accepted: 06/28/2022] [Indexed: 01/25/2023]
Abstract
Troponin I type 1b (Tnni1b) is thought to be a novel isoform that is expressed only in the zebrafish heart. Knocking down of tnni1b can lead to cardiac defects in zebrafish. Although both the zebrafish tnni1b and human troponin I1 (TNNI1) genes are thought to be closely associated with fatal cardiac development, the regulatory molecular mechanisms of these genes are poorly understood. Analyzing the functionally conserved sequence, especially in the noncoding regulatory region involved in gene expression, clarified these mechanisms. In this study, we isolated a 3 kb fragment upstream of Fugu tnni1a that can regulate green fluorescence protein (GFP) expression in a heart-specific manner, similar to the pattern of zebrafish homologue expression. Three evolutionarily conserved regions (ECRs) in the 5'-flanking sequence of Fugu tnni1a were identified by sequence alignment. Deletion analysis led to the identification of ECR2 as a core sequence that affects the heart-specific expression function of the Fugu tnni1a promoter. Interestingly, both the Fugu tnni1a promoter and ECR2 sequence were functionally conserved in zebrafish, although they shared no sequence similarity. Together, the findings of our study provided further evidence for the important role of tnni1a homologous in cardiac development and demonstrated that two functionally conserved sequences in the zebrafish and Fugu genomes may be ECRs, despite their lack of similarity.
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Affiliation(s)
- Yiting Gui
- Translational Medical Center for Development and Disease, Shanghai Key Laboratory of Birth Defect Prevention and Control, NHC Key Laboratory of Neonatal Diseases, Institute of Pediatrics, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China; Cardiovascular Center, NHC Key Laboratory of Neonatal Diseases, Fudan University, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Yawen Zhang
- Translational Medical Center for Development and Disease, Shanghai Key Laboratory of Birth Defect Prevention and Control, NHC Key Laboratory of Neonatal Diseases, Institute of Pediatrics, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China; Cardiovascular Center, NHC Key Laboratory of Neonatal Diseases, Fudan University, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Qi Zhang
- Translational Medical Center for Development and Disease, Shanghai Key Laboratory of Birth Defect Prevention and Control, NHC Key Laboratory of Neonatal Diseases, Institute of Pediatrics, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Xudong Chen
- Translational Medical Center for Development and Disease, Shanghai Key Laboratory of Birth Defect Prevention and Control, NHC Key Laboratory of Neonatal Diseases, Institute of Pediatrics, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Feng Wang
- Translational Medical Center for Development and Disease, Shanghai Key Laboratory of Birth Defect Prevention and Control, NHC Key Laboratory of Neonatal Diseases, Institute of Pediatrics, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China; Cardiovascular Center, NHC Key Laboratory of Neonatal Diseases, Fudan University, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Fang Wu
- Department of Neonatology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201600, China
| | - Yonghao Gui
- Cardiovascular Center, NHC Key Laboratory of Neonatal Diseases, Fudan University, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China.
| | - Qiang Li
- Translational Medical Center for Development and Disease, Shanghai Key Laboratory of Birth Defect Prevention and Control, NHC Key Laboratory of Neonatal Diseases, Institute of Pediatrics, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China.
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Association of variants in FABP4, FASN, SCD, SREBP1 and TCAP genes with intramuscular fat, carcass traits and body size in Chinese Qinchuan cattle. Meat Sci 2022; 192:108882. [PMID: 35714427 DOI: 10.1016/j.meatsci.2022.108882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 06/04/2022] [Accepted: 06/05/2022] [Indexed: 12/17/2022]
Abstract
This study aimed to genotype the variants in FABP4, FASN, SCD, SREBP1 and TCAP genes, and to analyze their associations with intramuscular fat (IMF) content, carcass traits and body size in Chinese Qinchuan cattle (QC). The association studies showed that the FABP4 c.220A > G polymorphism was significantly associated with ultrasound longissimus muscle depth (ULMD) and IMF, the FASN g.16024A > G polymorphism was significantly associated with ULMD and some body size traits, the SREBP1 84 bp indel was significantly associated with back fat thickness, ULMD and some body size traits. The frequencies of well-characterized A allele in FABP4 c.220A > G in Korean cattle (KOR) and Japanese Black cattle (JB), T allele in SCD g.8586C > T in KOR, SS genotype in SREBP1 84 bp indel in KOR and JB, DELDEL genotype in TCAP g.592-597CTGCAGinsdel in KOR were significantly higher than in Chinese cattle breeds. Thus, the associated four polymorphisms were expected to be genetic selection markers for meat quality, carcass traits and body size of QC.
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Liu J, Shi L, Li Y, Chen L, Garrick D, Wang L, Zhao F. Estimates of genomic inbreeding and identification of candidate regions that differ between Chinese indigenous sheep breeds. J Anim Sci Biotechnol 2021; 12:95. [PMID: 34348773 PMCID: PMC8340518 DOI: 10.1186/s40104-021-00608-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 06/01/2021] [Indexed: 11/10/2022] Open
Abstract
Background A run of homozygosity (ROH) is a consecutive tract of homozygous genotypes in an individual that indicates it has inherited the same ancestral haplotype from both parents. Genomic inbreeding can be quantified based on ROH. Genomic regions enriched with ROH may be indicative of selection sweeps and are known as ROH islands. We carried out ROH analyses in five Chinese indigenous sheep breeds; Altay sheep (n = 50 individuals), Large-tailed Han sheep (n = 50), Hulun Buir sheep (n = 150), Short-tailed grassland sheep (n = 150), and Tibetan sheep (n = 50), using genotypes from an Ovine Infinium HD SNP BeadChip. Results A total of 18,288 ROH were identified. The average number of ROH per individual across the five sheep breeds ranged from 39 (Hulun Buir sheep) to 78 (Large-tailed Han sheep) and the average length of ROH ranged from 0.929 Mb (Hulun Buir sheep) to 2.544 Mb (Large-tailed Han sheep). The effective population size (Ne) of Altay sheep, Large-tailed Han sheep, Hulun Buir sheep, Short-tailed grassland sheep and Tibetan sheep were estimated to be 81, 78, 253, 238 and 70 five generations ago. The highest ROH-based inbreeding estimate (FROH) was 0.0808 in Large-tailed Han sheep, whereas the lowest FROH was 0.0148 in Hulun Buir sheep. Furthermore, the highest proportion of long ROH fragments (> 5 Mb) was observed in the Large-tailed Han sheep breed which indicated recent inbreeding. In total, 49 ROH islands (the top 0.1% of the SNPs most commonly observed in ROH) were identified in the five sheep breeds. Three ROH islands were common to all the five sheep breeds, and were located on OAR2: 12.2–12.3 Mb, OAR12: 78.4–79.1 Mb and OAR13: 53.0–53.6 Mb. Three breed-specific ROH islands were observed in Altay sheep (OAR15: 3.4–3.8 Mb), Large-tailed Han sheep (ORA17: 53.5–53.8 Mb) and Tibetan sheep (ORA5:19.8–20.2 Mb). Collectively, the ROH islands harbored 78 unique genes, including 19 genes that have been documented as having associations with tail types, adaptation, growth, body size, reproduction or immune response. Conclusion Different ROH patterns were observed in five Chinese indigenous sheep breeds, which reflected their different population histories. Large-tailed Han sheep had the highest genomic inbreeding coefficients and the highest proportion of long ROH fragments indicating recent inbreeding. Candidate genes in ROH islands could be used to illustrate the genetic characteristics of these five sheep breeds. Our findings contribute to the understanding of genetic diversity and population demography, and help design and implement breeding and conservation strategies for Chinese sheep. Supplementary Information The online version contains supplementary material available at 10.1186/s40104-021-00608-9.
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Affiliation(s)
- Jiaxin Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Liangyu Shi
- Key Laboratory of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yang Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Liang Chen
- The Affiliated High School of Peking University, Beijing, 100192, China
| | - Dorian Garrick
- A.L. Rae Centre of Genetics and Breeding, Massey University, Hamilton, 3240, New Zealand
| | - Lixian Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Fuping Zhao
- Key Laboratory of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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Yan X, Wang J, Li H, Gao L, Geng J, Ma Z, Liu J, Zhang J, Xie P, Chen L. Combined transcriptome and proteome analyses reveal differences in the longissimus dorsi muscle between Kazakh cattle and Xinjiang brown cattle. Anim Biosci 2021; 34:1439-1450. [PMID: 33677919 PMCID: PMC8495333 DOI: 10.5713/ab.20.0751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 01/29/2021] [Indexed: 01/09/2023] Open
Abstract
Objective With the rapid development of proteomics sequencing and RNA sequencing technology, multi-omics analysis has become a current research hotspot. Our previous study indicated that Xinjiang brown cattle have better meat quality than Kazakh cattle. In this study, Xinjiang brown cattle and Kazakh cattle were used as the research objects. Methods Proteome sequencing and RNA sequencing technology were used to analyze the proteome and transcriptome of the longissimus dorsi muscle of the two breeds of adult steers (n = 3). Results In this project, 22,677 transcripts and 1,874 proteins were identified through quantitative analysis of the transcriptome and proteome. By comparing the identified transcriptome and proteome, we found that 1,737 genes were identified at both the transcriptome and proteome levels. The results of the study revealed 12 differentially expressed genes and proteins: troponin I1, crystallin alpha B, cysteine, and glycine rich protein 3, phosphotriesterase-related, myosin-binding protein H, glutathione s-transferase mu 3, myosin light chain 3, nidogen 2, dihydropyrimidinase like 2, glutamate-oxaloacetic transaminase 1, receptor accessory protein 5, and aspartoacylase. We performed functional enrichment of these differentially expressed genes and proteins. The Kyoto encyclopedia of genes and genomes results showed that these differentially expressed genes and proteins are enriched in the fatty acid degradation and histidine metabolism signaling pathways. We performed parallel reaction monitoring (PRM) verification of the differentially expressed proteins, and the PRM results were consistent with the sequencing results. Conclusion Our study provided and identified the differentially expressed genes and proteins. In addition, identifying functional genes and proteins with important breeding value will provide genetic resources and technical support for the breeding and industrialization of new genetically modified beef cattle breeds.
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Affiliation(s)
- XiangMin Yan
- Institute of Animal Husbandry, Xinjiang Academy of Animal Husbandry, Urumqi 830057, China
| | - Jia Wang
- College of Geographic Science, Shanxi Normal University, Linfen 041000, China
| | - Hongbo Li
- Institute of Animal Husbandry, Xinjiang Academy of Animal Husbandry, Urumqi 830057, China
| | - Liang Gao
- Yili Vocational and Technical College, Yili, 835000, China
| | - Juan Geng
- Xinjiang Animal Husbandry General Station, Urumqi 830057, China
| | - Zhen Ma
- Institute of Animal Husbandry, Xinjiang Academy of Animal Husbandry, Urumqi 830057, China
| | - Jianming Liu
- Yili Animal Husbandry General Station, Yili 835000, China
| | - Jinshan Zhang
- Institute of Animal Husbandry, Xinjiang Academy of Animal Husbandry, Urumqi 830057, China
| | - Penggui Xie
- Yili Vocational and Technical College, Yili, 835000, China
| | - Lei Chen
- College of Animal Science and Technology, Shihezi University, Shihezi 832000, China
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Wang S, Raza SHA, Mei C, Zhu K, Garcia M, Schreurs NM, Liang C, Yang X, Zan L. Transcriptome profiling reveals differential expression of genes potentially involved in muscle and adipose tissue development of cattle. ELECTRON J BIOTECHN 2020. [DOI: 10.1016/j.ejbt.2020.09.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
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