Identification, biogenesis and function prediction of novel circRNA during the chicken ALV-J infection

Abstract

Circular RNA (circRNA) is a new non-coding RNA with a highly conserved and stable covalently closed loop structure, and it plays an important role in a variety of biological processes and the occurrence of diseases. Based on the sequencing results, circRNA_3079 had the most significant difference between the infected group and normal group, up to about 8 times. It has attracted our attention and was selected for further verification and analysis. Though the characteristics analysis of circRNA_3079 in chicken, we found circRNA_3079 is a stable, circular transcript, which mainly exists in the cytoplasm. And it is widely expressed in various tissues of chickens, and highly expressed in lung, spleen, lymph and bursa of fabricius. Bioinformatics analysis results showed that circRNA_3079 and the predicted target genes are enriched in many pathways related to immunity or tumors, such as p53 signaling pathway, Jak−STAT signaling pathway and NOD−like receptor signaling pathway, which revealed that circRNA_3079 may indirectly regulate the ALV-J infection process through the regulation of target genes.

HIGHLIGHTS

• CircRNA_3079 is an abundant and stable circular RNA expressed in different tissues and cells in chicken.

• The circularization of circRNA_3079 does not depend on the reverse complementary repetitive sequence of the flanking sequence.

• CircRNA_3079 may indirectly regulate the ALV-J infection process.

Keywords:

• circRNA
• ALV-J
• circularization mechanism
• function prediction

Acknowledgments

We appreciate the support provided by Lihua animal husbandry Co. Ltd. (Jiangsu, China) for providing the chickens with or without spontaneous avian leukosis virus subgroup J (ALV-J) infection and Prof. Susan J. Lamont from Iowa State University from providing chicken HD11 macrophage cell line.

Ethics statement

All experimental procedures were performed in accordance with the Regulations on The Administration of Experimental Animals issued by the Ministry of Science and Technology in 2001 (Beijing, China). All animal protocols were approved and guided by the Animal Care and Use Committee of Yangzhou University.

Disclosure statement

The authors declare that they have no conflicts of interest.

Authors’ contributions

GC and TY conceived and designed the experiments. TY, LQ and MB performed the experiments. TY, and LQ analyzed the data. LW, XH, LH, and GC contributed the reagents/materials/analysis tools, and TY was a major contributor in writing the manuscript. All authors read and approved the final manuscript.

Additional information

Funding

This work was supported by the National special support plan for high-level talents-“Ten Thousand Talents Program” project, the “333 High-level Talent Training Project” in Jiangsu Province [BRA2020077], and the National Science & Technology Pillar Program of China [2015BAD03B03]. The funders had no role in study design, in the collection, analysis, and interpretation of data, in the writing of the report, or in the decision to submit the article for publication.