Analysis of alternative splicing in chicken macrophages transfected with overexpression/knockdown of RIP2 gene

Abstract

Receptor-interacting protein 2 (RIP2) plays a critical role in the transduction of many signaling pathways and is associated with many diseases. Alternative splicing (AS) is an essential and ubiquitous regulatory mechanism of gene expression that contributes to distinct transcript variants and many different kinds of proteins. In this present study, we characterized genome-wide AS events in wild-type chicken macrophages (WT) and RIP2 overexpression/knockdown chicken macrophages (oeRIP2/shRIP2) by high-throughput RNA sequencing technology. A total of 1901, 2061, and 817 differentially expressed (DE) AS genes were identified in the comparison of oeRIP2 vs. WT, oeRIP2 vs. shRIP2, and shRIP2 vs. WT, respectively. These DE AS genes participated in many important KEGG pathways, including regulation of autophagy, Wnt signaling pathway, Ubiquitin mediated proteolysis, MAPK signaling pathway, and Focal adhesion, etc. In conclusion, this research provided a broad atlas of the genome-wide scale of the AS event landscape in RIP2 overexpression/knockdown and wild-type chicken macrophages. This research also provides the theoretical basis of the gene network related to RIP2.

Keywords:

• Alternative splicing
• macrophages
• RIP2
• expression
• sequencing

Acknowledgements

The authors want to thank Dr Xuming Hu for generously provide the chicken HD11 cell line.

Ethics approval and consent to participate

Not applicable

Patient consent for publication

Not applicable

Authors’ contributions

HL and HS designed the study, drafted and revised the manuscript. HL, YL and CS performed the experiments and analyzed the data. All authors read and approved the final manuscript. HS confirms the authenticity of all the raw data.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statements

The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request. The raw sequence reads were deposited into NCBI SRA database under accession no. PRJNA890141

Additional information

Funding

This research was supported by the National Natural Science Foundation of China (Grant No. 31802053), The Natural Science Foundation of Jiangsu Province (Grant No. BK20180907), the China Postdoctoral Science Foundation (2019M661950), Jiangsu Postdoctoral Science Foundation (137070510), Qing Lan project of Jiangsu Province (2022), Excellent Educational Talents Program of Talent Cultivation Plan in Yangzhou City (2020).