Characterization of Alternative Splicing Events in Porcine Skeletal Muscles with Different Intramuscular Fat Contents

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.

Comprehensive analysis of pre-mRNA alternative splicing regulated by m6A methylation in pig oxidative and glycolytic skeletal muscles

“…2 C) (Additional file 5 : Table S4) were identified. Notably, a very small fraction of DASGs was differentially expressed, consistent with the previous reports [ 33 – 35 ]. This suggested that the dynamic AS change in genes has potential to affect muscle heterogeneity in addition to gene dysregulation.…”

Alternative Splicing Isoforms of Porcine CREB Are Differentially Involved in Transcriptional Transactivation

“…A total of six libraries were prepared from the experimental and control groups, each with three replicates. The libraries were prepared and sequenced on a NovaSeq 6000 sequence analyzer (Illumina, San Diego, CA, USA) by the Frasergen company (Wuhan, China), as described previously [ 33 ].…”

“…The transcript assembly and quantification in fragments per kilobase million (FPKM) were performed with Cufflinks (v2.2.1) [ 36 ]. The threshold for expression was set at FPKM > 0.1 in at least one sample, as used previously [ 33 ]. The gene expression levels were compared between groups with DESeq2 (v1.22.2) [ 37 ], and DEGs were identified according to the criteria of absolute Log2-foldchange > 1 and p < 0.05.…”

Transcriptomic Analysis Reveals mRNA and Alternative Splicing Events in Ovine Skeletal Muscle Satellite Cells during Proliferation and Differentiation

“…The AS events of precursor messenger RNA (pre-mRNA) occur due to the involvement of five small nuclear ribonucleoprotein (snRNP) complexes in the removal of introns [ 21 ]. In general, AS events display five patterns: exon skipping (ES), intron retention (IR), mutually exclusive exons (MEE), alternative acceptor site (AAS), and alternative donor site (ADS) [ 22 ]. Previous studies have indicated that the AS is associated with the regulation of proliferation [ 23 ], differentiation [ 24 , 25 ], and apoptosis [ 26 ] of the cell.…”