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Wang W, Li W, Liu W, Wang Z, Xie B, Yang X, Tang Z. Exploring Multi-Tissue Alternative Splicing and Skeletal Muscle Metabolism Regulation in Obese- and Lean-Type Pigs. Genes (Basel) 2024; 15:196. [PMID: 38397185 PMCID: PMC10888101 DOI: 10.3390/genes15020196] [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: 01/08/2024] [Revised: 01/26/2024] [Accepted: 01/28/2024] [Indexed: 02/25/2024] Open
Abstract
Alternative splicing (AS) is a crucial mechanism in post-transcriptional regulation, contributing significantly to the diversity of the transcriptome and proteome. In this study, we performed a comprehensive AS profile in nine tissues obtained from Duroc (lean-type) and Luchuan (obese-type) pigs. Notably, 94,990 AS events from 14,393 genes were identified. Among these AS events, it was observed that 80% belonged to the skipped exon (SE) type. Functional enrichment analysis showed that genes with more than ten AS events were closely associated with tissue-specific functions. Additionally, the analysis of overlap between differentially alternative splicing genes (DSGs) and differentially expressed genes (DEGs) revealed the highest number of overlapped genes in the heart and skeletal muscle. The novelty of our study is that it identified and validated three genes (PYGM, MAPK11 and CAMK2B) in the glucagon signaling pathway, and their alternative splicing differences were highly significant across two pig breeds. In conclusion, our study offers novel insights into the molecular regulation of diverse tissue physiologies and the phenotypic differences between obese- and lean-type pigs, which are helpful for pig breeding.
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Affiliation(s)
- Wei Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China;
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan 528226, China; (W.L.); (W.L.); (Z.W.)
| | - Wangchang Li
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan 528226, China; (W.L.); (W.L.); (Z.W.)
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science & Technology, Guangxi University, Nanning 530004, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Weiwei Liu
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan 528226, China; (W.L.); (W.L.); (Z.W.)
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science & Technology, Guangxi University, Nanning 530004, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Zishuai Wang
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan 528226, China; (W.L.); (W.L.); (Z.W.)
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Bingkun Xie
- Animal Husbandry Research Institute, Guangxi Vocational University of Agriculture, Nanning 530001, China;
| | - Xiaogan Yang
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science & Technology, Guangxi University, Nanning 530004, China
| | - Zhonglin Tang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China;
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan 528226, China; (W.L.); (W.L.); (Z.W.)
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science & Technology, Guangxi University, Nanning 530004, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Animal Husbandry Research Institute, Guangxi Vocational University of Agriculture, Nanning 530001, China;
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Hao W, Yang Z, Sun Y, Li J, Zhang D, Liu D, Yang X. Characterization of Alternative Splicing Events in Porcine Skeletal Muscles with Different Intramuscular Fat Contents. Biomolecules 2022; 12:biom12020154. [PMID: 35204660 PMCID: PMC8961525 DOI: 10.3390/biom12020154] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/11/2022] [Accepted: 01/14/2022] [Indexed: 02/06/2023] Open
Abstract
Meat quality is one of the most important economic traits in pig breeding and production. Intramuscular fat (IMF) is a major factor that improves meat quality. To better understand the alternative splicing (AS) events underlying meat quality, long-read isoform sequencing (Iso-seq) was used to identify differential (D)AS events between the longissimus thoracis (LT) and semitendinosus (ST), which differ in IMF content, together with short-read RNA-seq. Through Iso-seq analysis, we identified a total of 56,789 novel transcripts covering protein-coding genes, lncRNA, and fusion transcripts that were not previously annotated in pigs. We also identified 456,965 AS events, among which 3930 were DAS events, corresponding to 2364 unique genes. Through integrative analysis of Iso-seq and RNA-seq, we identified 1174 differentially expressed genes (DEGs), among which 122 were DAS genes, i.e., DE-DAS genes. There are 12 overlapped pathways between the top 20 DEGs and DE-DAS genes, as revealed by KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis, indicating that DE-DAS genes play important roles in the differential phenotype of LT and ST. Further analysis showed that upregulated DE-DAS genes are more important than downregulated ones in IMF deposition. Fatty acid degradation and the PPAR (peroxisome proliferator-activated receptor) signaling pathway were found to be the most important pathways regulating the differential fat deposition of the two muscles. The results update the existing porcine genome annotations and provide data for the in-depth exploration of the mechanisms underlying meat quality and IMF deposition.
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Affiliation(s)
- Wanjun Hao
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China; (W.H.); (Z.Y.); (Y.S.); (J.L.)
| | - Zewei Yang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China; (W.H.); (Z.Y.); (Y.S.); (J.L.)
| | - Yuanlu Sun
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China; (W.H.); (Z.Y.); (Y.S.); (J.L.)
| | - Jiaxin Li
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China; (W.H.); (Z.Y.); (Y.S.); (J.L.)
| | - Dongjie Zhang
- Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China;
| | - Di Liu
- Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China;
- Correspondence: (D.L.); (X.Y.); Tel.: +86-451-8667-7458 (D.L.); +86-451-5519-1738 (X.Y.)
| | - Xiuqin Yang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China; (W.H.); (Z.Y.); (Y.S.); (J.L.)
- Correspondence: (D.L.); (X.Y.); Tel.: +86-451-8667-7458 (D.L.); +86-451-5519-1738 (X.Y.)
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Vancheri C, Morini E, Prandi FR, Alkhoury E, Celotto R, Romeo F, Novelli G, Amati F. Two RECK Splice Variants (Long and Short) Are Differentially Expressed in Patients with Stable and Unstable Coronary Artery Disease: A Pilot Study. Genes (Basel) 2021; 12:genes12060939. [PMID: 34205376 PMCID: PMC8234100 DOI: 10.3390/genes12060939] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/10/2021] [Accepted: 06/15/2021] [Indexed: 12/12/2022] Open
Abstract
Primary prevention is crucial for coronary heart disease (CAD) and the identification of new reliable biomarkers might help risk stratification or predict adverse coronary events. Alternative splicing (AS) is a less investigated genetic factors implicated in CAD etiology. We performed an RNA-seq study on PBMCs from CAD patients and control subjects (CTR) and observed 113 differentially regulated AS events (24 up and 89 downregulated) in 86 genes. The RECK (Reversion-inducing-cysteine-rich protein with Kazal motifs) gene was further analyzed in a larger case study (24 CTR subjects, 72 CAD and 32 AMI patients) for its Splicing-Index FC (FC = −2.64; p = 0.0217), the AS event involving an exon (exon 18), and its role in vascular inflammation and remodeling. We observed a significant downregulation of Long RECK splice variant (containing exon 18) in PBMCs of AMI compared to CTR subjects (FC = −3.3; p < 0.005). Interestingly, the Short RECK splice variant (lacking exon 18) was under-expressed in AMI compared to both CTR (FC = −4.5; p < 0.0001) and CAD patients (FC = −4.2; p < 0.0001). A ROC curve, constructed combining Long and Short RECK expression data, shows an AUC = 0.81 (p < 0.001) to distinguish AMI from stable CAD patients. A significant negative correlation between Long RECK and triglycerides in CTR group and a positive correlation in the AMI group was found. The combined evaluation of Long and Short RECK expression levels is a potential genomic biomarker for the discrimination of AMI from CAD patients. Our results underline the relevance of deeper studies on the expression of these two splice variants to elucidate their functional role in CAD development and progression.
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Affiliation(s)
- Chiara Vancheri
- Genetics Unit, Department of Biomedicine and Prevention, University of Rome “Tor Vergata”, 00133 Rome, Italy; (C.V.); (E.M.); (G.N.)
| | - Elena Morini
- Genetics Unit, Department of Biomedicine and Prevention, University of Rome “Tor Vergata”, 00133 Rome, Italy; (C.V.); (E.M.); (G.N.)
| | - Francesca Romana Prandi
- Unit of Cardiology, University Hospital “Tor Vergata”, 00133 Rome, Italy; (F.R.P.); (E.A.); (R.C.); (F.R.)
| | - Elie Alkhoury
- Unit of Cardiology, University Hospital “Tor Vergata”, 00133 Rome, Italy; (F.R.P.); (E.A.); (R.C.); (F.R.)
| | - Roberto Celotto
- Unit of Cardiology, University Hospital “Tor Vergata”, 00133 Rome, Italy; (F.R.P.); (E.A.); (R.C.); (F.R.)
| | - Francesco Romeo
- Unit of Cardiology, University Hospital “Tor Vergata”, 00133 Rome, Italy; (F.R.P.); (E.A.); (R.C.); (F.R.)
- Unicamillus International Medical University, 00131 Rome, Italy
| | - Giuseppe Novelli
- Genetics Unit, Department of Biomedicine and Prevention, University of Rome “Tor Vergata”, 00133 Rome, Italy; (C.V.); (E.M.); (G.N.)
- Medical Genetics Laboratories, Tor Vergata University Hospital, PTV, 00133 Rome, Italy
- Neuromed IRCCS Institute, 86077 Pozzilli, Italy
- School of Medicine, Reno University of Nevada, Reno, NV 1664, USA
| | - Francesca Amati
- Genetics Unit, Department of Biomedicine and Prevention, University of Rome “Tor Vergata”, 00133 Rome, Italy; (C.V.); (E.M.); (G.N.)
- Department for the Promotion of Human Science and Quality of Life, University San Raffaele, 00166 Rome, Italy
- Correspondence:
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