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Sun Y, Wang HY, Liu B, Yue B, Liu Q, Liu Y, Rosa IF, Doretto LB, Han S, Lin L, Gong X, Shao C. CRISPR/dCas9-Mediated DNA Methylation Editing on emx2 in Chinese Tongue Sole ( Cynoglossus semilaevis) Testis Cells. Int J Mol Sci 2024; 25:7637. [PMID: 39062879 PMCID: PMC11277268 DOI: 10.3390/ijms25147637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 07/03/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024] Open
Abstract
DNA methylation is a key epigenetic mechanism orchestrating gene expression networks in many biological processes. Nonetheless, studying the role of specific gene methylation events in fish faces challenges. In this study, we validate the regulation of DNA methylation on empty spiracles homeobox 2 (emx2) expression with decitabine treatment in Chinese tongue sole testis cells. We used the emx2 gene as the target gene and developed a new DNA methylation editing system by fusing dnmt3a with catalytic dead Cas9 (dCas9) and demonstrated its ability for sequence-specific DNA methylation editing. Results revealed that utilizing dCas9-dnmt3a to target emx2 promoter region led to increased DNA methylation levels and decreased emx2 expression in Chinese tongue sole testis cells. More importantly, the DNA methylation editing significantly suppressed the expression of MYC proto-oncogene, bHLH transcription factor (myc), one target gene of emx2. Furthermore, we assessed the off-target effects of dCas9-dnmt3a and confirmed no significant impact on the predicted off-target gene expression. Taken together, we developed the first DNA methylation editing system in marine species and demonstrated its effective editing ability in Chinese tongue sole cells. This provides a new strategy for both epigenetic research and molecular breeding of marine species.
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Affiliation(s)
- Yanxu Sun
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China; (Y.S.); (B.Y.); (X.G.)
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (H.-Y.W.); (B.L.); (Q.L.); (Y.L.); (L.B.D.); (S.H.); (L.L.)
| | - Hong-Yan Wang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (H.-Y.W.); (B.L.); (Q.L.); (Y.L.); (L.B.D.); (S.H.); (L.L.)
| | - Binghua Liu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (H.-Y.W.); (B.L.); (Q.L.); (Y.L.); (L.B.D.); (S.H.); (L.L.)
| | - Bowen Yue
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China; (Y.S.); (B.Y.); (X.G.)
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (H.-Y.W.); (B.L.); (Q.L.); (Y.L.); (L.B.D.); (S.H.); (L.L.)
| | - Qian Liu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (H.-Y.W.); (B.L.); (Q.L.); (Y.L.); (L.B.D.); (S.H.); (L.L.)
| | - Yuyan Liu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (H.-Y.W.); (B.L.); (Q.L.); (Y.L.); (L.B.D.); (S.H.); (L.L.)
| | - Ivana F. Rosa
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 01049-010, Brazil;
| | - Lucas B. Doretto
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (H.-Y.W.); (B.L.); (Q.L.); (Y.L.); (L.B.D.); (S.H.); (L.L.)
| | - Shenglei Han
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (H.-Y.W.); (B.L.); (Q.L.); (Y.L.); (L.B.D.); (S.H.); (L.L.)
| | - Lei Lin
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (H.-Y.W.); (B.L.); (Q.L.); (Y.L.); (L.B.D.); (S.H.); (L.L.)
| | - Xiaoling Gong
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China; (Y.S.); (B.Y.); (X.G.)
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai 201306, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
| | - Changwei Shao
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (H.-Y.W.); (B.L.); (Q.L.); (Y.L.); (L.B.D.); (S.H.); (L.L.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao 266237, China
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Fang X, Ye H, Zhang S, Guo L, Xu Y, Zhang D, Nie Q. Investigation of potential genetic factors for growth traits in yellow-feather broilers using weighted single-step genome-wide association study. Poult Sci 2023; 102:103034. [PMID: 37657249 PMCID: PMC10480639 DOI: 10.1016/j.psj.2023.103034] [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: 05/26/2023] [Revised: 08/04/2023] [Accepted: 08/11/2023] [Indexed: 09/03/2023] Open
Abstract
Yellow-feather broilers take a large portion of poultry industry in China due to its meat characteristics. Improving the growth traits of yellow-feathered broilers will have great significance for the Chinese poultry market. The current study was designed to investigate the potential genetic factors using the weighted single-step genome-wide association study (wssGWAS) method, which takes consideration of more factors including pedigree, sex, environment and has more accuracy than traditional GWAS. The yellow-feather dwarf chickens from Wens Nanfang Poultry Breeding Co. Ltd. were revolved to recode 9 growth traits: Average daily gain (ADG), body weight (BW) at 45 d, 49 d, 56 d, 63 d, 70 d, 77 d, 84 d, 91 d for analysis. For the results, the region 4.63 to 5.03 Mb on chromosome 15, which was the QTL overlapped in BW45, BW49, BW56, BW63, BW84, might be the crucial genetic region for growth traits. Seven GO terms and 3 KEGG pathways, GO:0005200, GO:0005882, GO:0045111, GO:0099513, GO:0099081, GO:0099512, GO:0099080, KEGG:gga04020, KEGG:gga04540, KEGG:gga04210, were detected to relevant with growth traits. The genes enriched in these biological processes (NRAS, TUBB1, ADORA2B, NTRK3, NGF, TNNC2, F-KER, LOC429492, LOC431325, LOC431324, LOC396480) might have the function in growth of yellow-feather broilers.
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Affiliation(s)
- Xiang Fang
- State Key Laboratory of Livestock and Poultry Breeding, & Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, & Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China
| | - Haoqiang Ye
- State Key Laboratory of Livestock and Poultry Breeding, & Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, & Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China
| | - Siyu Zhang
- State Key Laboratory of Livestock and Poultry Breeding, & Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, & Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China
| | - Lijin Guo
- State Key Laboratory of Livestock and Poultry Breeding, & Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, & Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China; Henry Fok School of Biology and Agriculture, Shaoguan University, Shaoguan 512005, China
| | - Yibin Xu
- State Key Laboratory of Livestock and Poultry Breeding, & Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, & Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China
| | - Dexiang Zhang
- State Key Laboratory of Livestock and Poultry Breeding, & Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, & Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China
| | - Qinghua Nie
- State Key Laboratory of Livestock and Poultry Breeding, & Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, & Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China; Henry Fok School of Biology and Agriculture, Shaoguan University, Shaoguan 512005, China.
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Keenan SR, Currie PD. The Developmental Phases of Zebrafish Myogenesis. J Dev Biol 2019; 7:E12. [PMID: 31159511 PMCID: PMC6632013 DOI: 10.3390/jdb7020012] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 05/16/2019] [Accepted: 05/31/2019] [Indexed: 01/11/2023] Open
Abstract
The development and growth of vertebrate axial muscle have been studied for decades at both the descriptive and molecular level. The zebrafish has provided an attractive model system for investigating both muscle patterning and growth due to its simple axial musculature with spatially separated fibre types, which contrasts to complex muscle groups often deployed in amniotes. In recent years, new findings have reshaped previous concepts that define how final teleost muscle form is established and maintained. Here, we summarise recent findings in zebrafish embryonic myogenesis with a focus on fibre type specification, followed by an examination of the molecular mechanisms that control muscle growth with emphasis on the role of the dermomyotome-like external cell layer. We also consider these data sets in a comparative context to gain insight into the evolution of axial myogenic patterning systems within the vertebrate lineage.
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Affiliation(s)
- Samuel R Keenan
- Australian Regenerative Medicine Institute, Monash University, Victoria 3800, Australia.
| | - Peter D Currie
- Australian Regenerative Medicine Institute, Monash University, Victoria 3800, Australia.
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