Genome-wide analysis of differentially expressed profiles of mRNAs, lncRNAs and circRNAs in chickens during Eimeria necatrix infection
Genome-wide analysis of differentially expressed profiles of mRNAs, lncRNAs and circRNAs in chickens during Eimeria necatrix infection
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DOI：
10.1186/s13071-020-04047-9
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发表时间：
2020-04-03
影响因子：
3.2
通讯作者：
Zhao, Guang-Hui
中科院分区：
文献类型：
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作者：
Fan, Xian-Cheng;Liu, Ting-Li;Zhao, Guang-Hui
研究背景毒害艾美耳球虫（Eimeria necatrix）是鸡小肠中致病性最强的球虫，可导致易感禽类的高发病率和死亡率，给家禽生产造成严重的经济损失。necatrix并没有完全揭示。越来越多的证据表明，长链非编码RNA（lncRNA）和环状RNA（circRNA）是多种感染性疾病的关键调控因子。然而，这两种非编码RNA（ncRNA）在大肠杆菌中的表达谱和作用尚不清楚。方法采用免疫组织化学方法检测鸡小肠中段感染E.结果经过严格筛选后，共鉴定出49,183条mRNA、818条lncRNA和4153条circRNA。其中基因间型228条（27.87%），内含子型67条（8.19%），反义型166条（20.29%），正义重叠型357条（43.64%），其中571条为新发现的。预测了5种类型的推定circRNA，包括180个外显子，54个内含子，113个反义，109个基因间和3697个正义重叠circRNA。毒害艾美耳球虫感染显著改变了1543个mRNA（707个上调和836个下调）、95个lncRNA（49个上调和46个下调）和13个circRNA（9个上调和4个下调）的表达。靶点预测结果显示，38个异常表达的lncRNA可以顺式调节73个mRNA，1453个mRNA可以被87个差异调节的lncRNA反式调节。此外，还针对9种循环RNA鉴定了109种潜在的海绵状miRNA。通过对lncRNA的靶mRNA进行GO和KEGG富集分析，以及对circRNA的miRNA靶基因和源基因进行海绵化分析，确定了lncRNA和circRNA与宿主免疫防御和E.结论本研究首次在全基因组范围内对感染大肠杆菌的鸡小肠组织中的mRNA、lncRNA和circRNA进行了分析。死灵研究结果为探索鸡与艾美耳球虫相互作用机制提供了新的线索。
BackgroundEimeria necatrix, the most highly pathogenic coccidian in chicken small intestines, can cause high morbidity and mortality in susceptible birds and devastating economic losses in poultry production, but the underlying molecular mechanisms in interaction between chicken and E. necatrix are not entirely revealed. Accumulating evidence shows that the long-non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) are key regulators in various infectious diseases. However, the expression profiles and roles of these two non-coding RNAs (ncRNAs) during E. necatrix infection are still unclear.MethodsThe expression profiles of mRNAs, lncRNAs and circRNAs in mid-segments of chicken small intestines at 108 h post-infection (pi) with E. necatrix were analyzed by using the RNA-seq technique.ResultsAfter strict filtering of raw data, we putatively identified 49,183 mRNAs, 818 lncRNAs and 4153 circRNAs. The obtained lncRNAs were classified into four types, including 228 (27.87%) intergenic, 67 (8.19%) intronic, 166 (20.29%) anti-sense and 357 (43.64%) sense-overlapping lncRNAs; of these, 571 were found to be novel. Five types were also predicted for putative circRNAs, including 180 exonic, 54 intronic, 113 antisense, 109 intergenic and 3697 sense-overlapping circRNAs. Eimeria necatrix infection significantly altered the expression of 1543 mRNAs (707 upregulated and 836 downregulated), 95 lncRNAs (49 upregulated and 46 downregulated) and 13 circRNAs (9 upregulated and 4 downregulated). Target predictions revealed that 38 aberrantly expressed lncRNAs would cis-regulate 73 mRNAs, and 1453 mRNAs could be trans-regulated by 87 differentially regulated lncRNAs. Additionally, 109 potential sponging miRNAs were also identified for 9 circRNAs. GO and KEGG enrichment analysis of target mRNAs for lncRNAs, and sponging miRNA targets and source genes for circRNAs identified associations of both lncRNAs and circRNAs with host immune defense and pathogenesis during E. necatrix infection.ConclusionsTo the best of our knowledge, the present study provides the first genome-wide analysis of mRNAs, lncRNAs and circRNAs in chicken small intestines infected with E. necatrix. The obtained data will offer novel clues for exploring the interaction mechanisms between chickens and Eimeria spp.