Abstract
Alternative splicing (AS) is an important post-transcriptional regulatory mechanism for cells to generate transcript variability and proteome diversity. No systematic investigation of AS events among different tissues in response to stressors is available for tilapia currently. In this study, AS among different tissues was identified and the cold stress-related AS events were explored in a Nile tilapia (Oreochromis niloticus) line based on 42 RNA-seq datasets using a bioinformatics pipeline. 14,796 (82.76%; SD = 2,840) of the expression genes showed AS events. The two most abundant AS types were alternative transcription start site (TSS) and terminal site (TTS) in tilapia. Testis, brain and kidney possess the most abundant AS gene number, while the blood, muscle and liver possess the least number in each tissue. Furthermore, 208 differentially alternative splicing (DAS) genes in heart and 483 DAS in brain in response to cold stress. The number of AS types for alternative exon end, exon skipping and retention of single intron increased significantly under cold stress. GO enrichment and pathway overrepresentation analysis indicated that many DAS genes, e.g., genes in circadian clock pathway, may influence expression of downstream genes under cold stress. Our study revealed that AS exists extensively in tilapia and plays an important role in cold adaption.
Highlights
Alternative splicing (AS) generates multiple functional messenger RNA (mRNA) and enables different proteins to be synthesized from one single gene (Maniatis and Tasic, 2002; Nilsen and Graveley, 2010)
To obtain an overview of AS events in tilapia genome, 30 RNA-seq datasets were downloaded from the NCBI database (Supplementary Additional File 1)
These datasets consisted of RNA-seq reads from 10 tissues, including testis, brain, kidney, eye, ovary, skin, heart, blood, muscle, and liver
Summary
Alternative splicing (AS) generates multiple functional mRNAs and enables different proteins to be synthesized from one single gene (Maniatis and Tasic, 2002; Nilsen and Graveley, 2010). This regulatory mechanism significantly expands transcript variability and proteome diversity, as well as provides additional information in eukaryotic cells (Nilsen and Graveley, 2010). AS events widely exist in eukaryotes (Sorek, 2007). Many AS events are well conserved and appear to be related to the phylogenetic distance among species (Mastrangelo et al, 2012; Jonsson et al, 2016)
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