鸡胸腺组织中免疫相关circRNA鉴定

doi:10.16431/j.cnki.1671-7236.2022.06.002

摘要/Abstract

摘要： 【目的】筛选鸡胸腺中免疫相关的环状RNA （circular RNA，circRNA），研究circRNA在鸡免疫调节中的作用。【方法】采用高通量测序平台Illumina PE150对黄羽肉鸡和山地乌骨鸡的胸腺组织进行转录组测序，用生物信息学分析软件find_circ和CIRI识别circRNA分子，鉴别其基本结构特征。通过差异显著性分析筛选差异表达circRNA，再经过GO功能和KEGG通路富集分析筛选出免疫相关circRNA，用IRESfinder和PFAM软件进行circRNA编码潜能预测，并用实时荧光定量PCR进行验证。【结果】 circRNA在鸡胸腺中有丰富的表达，共识别到8 015个circRNAs，其中115个circRNAs在胸腺组织中的表达量呈显著差异（log₂|FoldChange|>1，P<0.05），在黄羽肉鸡中上调表达基因54个，下调表达基因61个（以山地乌骨鸡为对照）。GO功能富集结果显示有104个GO条目与免疫相关，涉及23个差异表达cricRNAs，占比高达20%（23/115）。KEGG通路分析结果显示，差异表达circRNA来源基因集中在细胞因子-细胞因子受体相互作用、RIG-Ⅰ样受体信号通路、Toll样受体信号通路等7个免疫相关通路中，共涉及7个差异表达circRNAs。有5个circRNAs在GO功能和KEGG通路富集分析中重复出现：circ_0002478（IL-1R1）、circ_0003208（MAPK11）、circ_0001674（STX8）、circ_0005105（RIPK2）和circ_0003590（BRAF），推测它们可能在免疫系统调节中扮演着重要角色。实时荧光定量PCR结果显示，5个circRNAs在2个鸡品种胸腺组织中的表达差异与测序结果一致，circ_0002478（IL-1R1）不仅在两品种间差异极显著（P<0.01），而且具有编码多肽潜能，它可能以多种方式参与免疫调节。【结论】鸡胸腺组织中有丰富的circRNA，在与免疫相关的circRNA中circ_0002478（IL-1R1）可能通过多种方式参与免疫调节，可作为鸡免疫力研究的重点关注靶点。

关键词: 鸡; 胸腺; circRNA; 免疫调节; 免疫

Abstract: 【Objective】 This study was aimed to identify immune-related circRNA of thymus in chickens, and investigate the role of circRNA in immune regulation of chickens.【Method】 The transcriptome of thymus in Yellow-feather broilers and mountain Black-bone chickens was sequenced by high-throughput sequencing platform Illumina PE150.Bioinformatics software find_circ and CIRI were used to identify circRNA molecules and analysis their basic structural characteristics.Difference significant analysis was performed to screen differenttially expressed circRNA, GO function and KEGG pathway enrichment analysis conducted to reveal the immune-related circRNAs, and the potential translation ability were predicted by IRESfinder and PFAM softwares, and it was verified by Real-time quantitative PCR.【Result】 There was abundant expression of circRNA in thymus of chickens.A total of 8 015 circRNAs were identified, and 115 circRNAs were significant differentially expressed in thymus of chickens (log₂|FoldChange|>1, P<0.05), 54 circRNAs upregulated and 61 circRNAs downregulated in Yellow-feather broilers(mountain Black-bone chickens was used as control).The GO function enrichment showed that there were 104 GO terms related to immune, involved 23 differential expression circRNAs, up to 20%(23/115).KEGG pathway analysis showed that there were 7 immune related pathways, including cytokine-cytokine receptor interaction, RIG-Ⅰ-like receptor signal pathway and Toll-like receptor signal pathway, which covered 7 differentially expressed circRNAs.5 circRNAs came out of GO function and KEGG pathway enrichment analysis were identical:circ_0002478(IL-1R1), circ_0003208(MAPK11), circ_0001674(STX8), circ_0005105(RIPK2) and circ_0003590(BRAF), which might play an important role in the regulation of immune system.Real-time quantitative PCR results showed that 5 circRNAs difference expression trend in thymus of two chicken breeds were consistent with the sequencing.circ_0002478(IL-1R1) not only had extremely significant difference between the two varieties (P<0.01), but also had the potential to encode peptides, it might participate in immune regulation in many ways.【Conclusion】 circRNA was rich in thymus of chickens, the immune-related circRNA circ_0002478(IL-1R1) might affect immune regulation in many ways, and could be a key target gene in immunity research of chickens.

Key words: chickens; thymus; circRNA; immune regulation; immune

中图分类号:

S831

刘锐, 李江凌, 杜华锐, 杨朝武, 陈家磊, 赵素君, 王秋实. 鸡胸腺组织中免疫相关circRNA鉴定[J]. 中国畜牧兽医, 2022, 49(6): 2022-2032.

LIU Rui, LI Jiangling, DU Huarui, YANG Chaowu, CHEN Jialei, ZHAO Sujun, WANG Qiushi. Identification of Immune-Related circRNA of Thymus in Chickens[J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(6): 2022-2032.

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