Profiling Novel Alternative Splicing within Multiple Tissues Provides Useful Insights into Porcine Genome Annotation.

Wen Feng,Pengju Zhao,Jianfeng Liu,Zhengzheng Hu,Xianrui Zheng

doi:10.3390/genes11121405

Abstract

Alternative splicing (AS) is a process during gene expression that results in a single gene coding for different protein variants. AS contributes to transcriptome and proteome diversity. In order to characterize AS in pigs, genome-wide transcripts and AS events were detected using RNA sequencing of 34 different tissues in Duroc pigs. In total, 138,403 AS events and 29,270 expressed genes were identified. An alternative donor site was the most common AS form and accounted for 44% of the total AS events. The percentage of the other three AS forms (exon skipping, alternative acceptor site, and intron retention) was approximately 19%. The results showed that the most common AS events involving alternative donor sites could produce different transcripts or proteins that affect the biological processes. The expression of genes with tissue-specific AS events showed that gene functions were consistent with tissue functions. AS increased proteome diversity and resulted in novel proteins that gained or lost important functional domains. In summary, these findings extend porcine genome annotation and highlight roles that AS could play in determining tissue identity.

Highlights

Alternative splicing (AS) is a regulated process that generates multiple transcripts from a single gene
A total of 1495 million high-quality reads (376.7 Gb, 135-fold genome coverage) were aligned to the porcine reference genome (Sus scrofa 11.1), and 1223 million mapped fragments (310.1 Gb, 110.8-fold genome coverage) with an average alignment rate of 88.29% were recovered (Table S1). These mapped reads were assembled and quantified as candidate transcripts using Stringtie software. This step produced a total of 2,486,239 transcripts from 29,270 genes across all tissues; of these, 60,578 transcripts (23,887 loci) were annotated in the pig Ensemble database, and 144,134 transcripts from 2424 non-coding genes, as well as 15,385 coding genes, were considered as potential AS
The percentage of the other three AS forms was approximately 19%. These results suggest that AS events involving different alternative splicing types can produce different transcripts or proteins that affect biological processes

Summary

Introduction

Alternative splicing (AS) is a regulated process that generates multiple transcripts from a single gene. It plays an important role in expanding protein diversity. AS affects 95% of multi-exonic genes in humans, and occurs in high proportions in other animals [1,2,3]. Many alternatively spliced isoforms play important roles in the biological timing and development of tissues [7,8,9,10]. It is becoming clear that a large number of AS events contributes to the acquisition of adult tissue functions and identity in human tissue development [11].

Methods

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Discussion

Conclusion