Global Analysis of Alternative Splicing Difference in Peripheral Immune Organs between Tongcheng Pigs and Large White Pigs Artificially Infected with PRRSV In Vivo.

Yu Zhang,Wan Liang,Hang Xu,Liyao Xue,Qingqing Wu,Qingde Zhang,Bang Liu,Xiang Zhou

doi:10.1155/2020/4045204

Abstract

Alternative splicing (AS) plays a significant role in regulating gene expression at the transcriptional level in eukaryotes. Flexibility and diversity of transcriptome and proteome can be significantly increased through alternative splicing of genes. In the present study, transcriptome data of peripheral immune organs including spleen and inguinal lymph nodes (ILN) were used to identify AS difference between PRRSV-resistant Tongcheng (TC) pigs and PRRSV-susceptible Large White (LW) pigs artificially infected with porcine reproductive and respiratory syndrome virus (PRRSV) in vivo. The results showed that PRRSV infection induced global alternative splicing events (ASEs) with different modes. Among them, 373 genes and 595 genes in the spleen and ILN of TC pigs, while 458 genes and 560 genes in the spleen and ILN of LW pigs had significantly differential ASEs. Alternative splicing was subject to tissue-specific and lineage-specific regulation in response to PRRSV infection. Enriched GO terms and pathways showed that genes with differential ASEs played important roles in transcriptional regulation, immune response, metabolism, and apoptosis. Furthermore, a splicing factor associated with apoptosis, SRSF4, was significantly upregulated in LW pigs. Functional analysis on apoptosis associated genes was validated by RT-PCR and DNA sequencing. These findings revealed different response to PRRSV between PRRSV-resistant TC pigs and PRRSV-susceptible LW pigs at the level of alternative splicing, suggesting the potential relationship between AS and disease resistance to PRRSV.

Highlights

Porcine reproductive and respiratory syndrome (PRRS) has devastated the swine industries in Africa, Asia, Europe, and North America for many years
19730 and 17888 alternative splicing events (ASEs) were identified in the spleen of Large White (LW) pigs and TC pigs, which were assigned to 6991 and 6766 genes, respectively. e Venn diagram showed the four datasets had 4905 genes in common, accounting for average of 70%, while only about 5.6% ASE genes were unique in each dataset (Figure 1(a) and Table 1)
ASEs were categorized as five types including alternative 3′ splice sites (A3SS), alternative 5′ splice sites (A5SS), mutually exclusive exon (MXE), retained intron (RI), and skipped exon (SE)

Summary

Introduction

Porcine reproductive and respiratory syndrome (PRRS) has devastated the swine industries in Africa, Asia, Europe, and North America for many years. PRRS presents a major health challenge and economic burdens for the swine industry worldwide [3]. E major clinical symptoms of PRRS include severe respiratory diseases in pigs of any age and reproductive disorder in sows [1, 4]. E pathogen of PRRS is called the PRRS virus (PRRSV), which is a small positive strand RNA virus belonging to Arterivirus family. E target cells of PRRSV are monocytes and macrophages in different tissues, and the fully differentiated porcine alveolar macrophages (PAMs) are the major target cell [7, 8] Type I and type II PRRSV only share approximate 55–70% nucleotide identity and 50–80% amino acid identity of viral genes [6]. e target cells of PRRSV are monocytes and macrophages in different tissues, and the fully differentiated porcine alveolar macrophages (PAMs) are the major target cell [7, 8].

Methods

Results

Conclusion