PolyI:C刺激猪PK15细胞后病毒感染应答基因未注释转录本鉴定及其特征分析

doi:10.16431/j.cnki.1671-7236.2024.04.030

Abstract

Abstract: 【Objective】 The purpose of this study was to identify the number of unannotated transcripts,splicing types,new protein coding and molecular structure of genes response to viral infection in porcine PK15 cells after polyI:C stimulation,which would lay a foundation on the function of these unannotated transcripts for further study.【Method】 Porcine PK15 cells were divided into control group and experimental group,with 3 replicates in each group.The experimental group was added with PolyI:C at a final concentration of 20 μg/mL,and the control group was added with an equal volume (2 μL) of PBS.The two groups were stimulated at 37 ℃ and 5% CO₂ for 6 h,respectively.After then,Nanopore sequencing was performed to identify the total transcripts and differentially expressed genes of the two groups.GO function analysis was performed on the differentially expressed genes to further screen the genes response to viral infection.The total transcripts were compared with the Ensemble annotated transcript sequences,and unannotated transcripts were identified.The unannotated transcripts genes response to viral infection were compared with their corresponding Ensemble annotated transcripts,and the splicing types and encoded proteins of unannotated transcripts were analyzed.【Result】 After PolyI:C stimulation,a total of 61 505 protein-coding transcripts were identified in the two groups,of which 39 497 were annotated in the Ensemble database,and 22 008 were unannotated transcripts,accounting for 35.78% of the total.At the same time,71 differential protein-coding genes were identified in the two groups.Compared with control group,57 genes were up-regulated and 14 genes were down-regulated in experimental group.GO functional enrichment analysis showed that these differentially expressed genes were enriched into 20 biological processes,of which the first three most enriched biological processes were virus defense response,type Ⅰ interferon signaling pathway and response related to virus.Among the 24 genes response to viral infection,16 genes had unannotated transcripts.Among them,the number of unannotated transcripts of CCL5,IFI6,BST2 and MX1 genes was more than the total number of transcripts annotated by Ensemble,and most of the unannotated transcripts produced new protein sequences.Unannotated transcripts of 9 genes including IFIT3,OAS2,RSAD2,CCL5,IFI44,CD40,IFI6,BST and MX1 were differentially expressed.【Conclusion】 This study systematically identified the molecular characteristics of unannotated transcripts of genes response to viral infection in porcine PK15 cells stimulated by PolyI:C.The differentially expressed unannotated transcripts of 9 genes,including IFIT3,OAS2,RSAD2,CCL5,IFI44, CD40,IFI6,BST and MX1 might play an important biological role,which provided a basis for further analysis of the complex transcriptional regulation mechanism of host genes in antiviral response.

Key words: Nanopore sequencing; PolyI:C; viral infection; transcripts; alternative splicing

CLC Number:

S852.65

ZHAO Weimin, WANG Hong, XU Pan, CHEN Zhe, TAO Xiaoli, LI Bixia, FU Yanfeng, CHENG Jinhua. Identification and Characterization Analysis of Unannotated Transcripts of Genes Response to Viral Infection in Porcine PK15 Cells Stimulated by PolyI:C[J]. China Animal Husbandry and Veterinary Medicine, 2024, 51(4): 1622-1631.

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Identification and Characterization Analysis of Unannotated Transcripts of Genes Response to Viral Infection in Porcine PK15 Cells Stimulated by PolyI:C

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