Liu, L.; Wang, W.; Liu, W.; Li, X.; Yi, G.; Adetula, A.A.; Huang, H.; Tang, Z. Comprehensive Atlas of Alternative Splicing Reveals NSRP1 Promoting Adipogenesis through CCDC18. Int. J. Mol. Sci.2024, 25, 2874.
Liu, L.; Wang, W.; Liu, W.; Li, X.; Yi, G.; Adetula, A.A.; Huang, H.; Tang, Z. Comprehensive Atlas of Alternative Splicing Reveals NSRP1 Promoting Adipogenesis through CCDC18. Int. J. Mol. Sci. 2024, 25, 2874.
Liu, L.; Wang, W.; Liu, W.; Li, X.; Yi, G.; Adetula, A.A.; Huang, H.; Tang, Z. Comprehensive Atlas of Alternative Splicing Reveals NSRP1 Promoting Adipogenesis through CCDC18. Int. J. Mol. Sci.2024, 25, 2874.
Liu, L.; Wang, W.; Liu, W.; Li, X.; Yi, G.; Adetula, A.A.; Huang, H.; Tang, Z. Comprehensive Atlas of Alternative Splicing Reveals NSRP1 Promoting Adipogenesis through CCDC18. Int. J. Mol. Sci. 2024, 25, 2874.
Abstract
Alternative splicing (AS) plays a crucial role in regulating gene expression, function and diversity. However, limited reports exist on identification and comparation of AS in Eastern and Western pigs. Here, we analyzed 243 transcriptome data from eight tissues, integrating information on transcription factors (TFs), selection signals, splicing factors (SFs), and QTLs to comprehensively study alternative splicing events (ASEs) in pigs. Five ASE types were identified, with Mutually Exclusive Exon (MXE) and Skipped Exon (SE) ASEs being the most prevalent. A significant portion of genes with ASEs (ASGs) showed conservation across all eight tissues (63.21% - 76.13% per tissue). Differentially alternative splicing genes (DASGs) and differentially expressed genes (DEGs) exhibited tissue specificity, with blood and adipose tissues having more DASGs. Functional enrichment analysis revealed coDASG_DEGs in adipose were enriched in pathways associated with adipose deposition and immune inflammation, while coDASG_DEGs in blood were enriched in pathways related to immune inflammation and metabolism. Adipose deposition in Eastern pigs might be linked to down-regulation of immune-inflammation-related pathways and reduced insulin resistance. The TFs, selection signals, and SFs appeared to regulate ASEs. Notably, ARID4A (TF), NSRP1 (SF), ANKRD12, IFT74, KIAA2026, CCDC18, NEXN, PPIG, and ROCK1 genes in adipose tissue showed potential regulatory effects on adipose-deposition traits. And NSRP1 could promote adipogenesis by regulating alternative splicing and expression of CCDC18. Conducting an in-depth investigation into AS, this study has successfully identified key marker genes essential for pig genetic breeding and the enhancement of meat quality, which will play important roles in promoting the diversity of pork quality and meeting market demand.
Keywords
pigs; alternative splicing; NSRP1; CCDC18; adipose deposition
Subject
Biology and Life Sciences, Endocrinology and Metabolism
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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