Deciphering Transcriptome and Complex Alternative Splicing Transcripts in Mammary Gland Tissues from Cows Naturally Infected with Staphylococcus aureus Mastitis.
Deciphering Transcriptome and Complex Alternative Splicing Transcripts in Mammary Gland Tissues from Cows Naturally Infected with Staphylococcus aureus Mastitis.
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破译自然感染金黄色葡萄球菌乳腺炎的奶牛乳腺组织中的转录组和复杂的选择性剪接转录本。
DOI：
10.1371/journal.pone.0159719
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发表时间：
2016
期刊：
影响因子：
3.7
通讯作者：
Huang JM
中科院分区：
文献类型：
--
作者：
Wang XG;Ju ZH;Hou MH;Jiang Q;Yang CH;Zhang Y;Sun Y;Li RL;Wang CF;Zhong JF;Huang JM
选择性剪接（alternative splicing，AS）增加了哺乳动物蛋白质组的复杂性，在疾病（包括感染性疾病）中起着重要作用。这些转录物序列之间的差异AS模式的健康（HS 3A）和乳腺炎（HS 8A）奶牛自然感染金黄色葡萄球菌进行了比较，以了解乳腺炎的抗性和易感性的分子机制。在本研究中，使用Illumina配对末端RNA测序方法，在HS 3A和HS 8A乳腺组织中发现了1352个差异表达基因（DEG），其变化高于两倍。基因本体和KEGG途径分析显示，精氨酸-细胞因子受体相互作用途径是最显著富集的途径。基于牛UMD 3.1序列的拼接和检索，在两个文库中分别鉴定了约16 k个注释的unigenes。在外显子跳跃、内含子保留、5′剪接和3 ′剪接中，分别有52.62%和51.24%的注释单基因发生了选择性剪接。此外，1,317个AS unigenes是HS 3A特异性的，而1,093个AS unigenes是HS 8A特异性的。一些免疫相关基因，如ITGB 6，MYD 88，ADA，ACKR 1和TNFRSF 1B，以及它们与乳腺炎的潜在关系。在第2、4、6、7、10、13、14、17和20号染色体上，分别有3.66%（HS 3A）和5.4%（HS 8A）的新转录本含有已知的与临床型乳腺炎相关的数量性状位点。健康乳腺和乳腺炎乳腺中的许多DEG参与免疫、防御和炎症反应。这些DEG具有多样性和特异性的剪接模式和事件，可以赋予奶牛潜在的复杂的抗乳腺炎遗传抗性。
Alternative splicing (AS) contributes to the complexity of the mammalian proteome and plays an important role in diseases, including infectious diseases. The differential AS patterns of these transcript sequences between the healthy (HS3A) and mastitic (HS8A) cows naturally infected by Staphylococcus aureus were compared to understand the molecular mechanisms underlying mastitis resistance and susceptibility. In this study, using the Illumina paired-end RNA sequencing method, 1352 differentially expressed genes (DEGs) with higher than twofold changes were found in the HS3A and HS8A mammary gland tissues. Gene ontology and KEGG pathway analyses revealed that the cytokine–cytokine receptor interaction pathway is the most significantly enriched pathway. Approximately 16k annotated unigenes were respectively identified in two libraries, based on the bovine Bos taurus UMD3.1 sequence assembly and search. A total of 52.62% and 51.24% annotated unigenes were alternatively spliced in term of exon skipping, intron retention, alternative 5′ splicing and alternative 3ʹ splicing. Additionally, 1,317 AS unigenes were HS3A-specific, whereas 1,093 AS unigenes were HS8A-specific. Some immune-related genes, such as ITGB6, MYD88, ADA, ACKR1, and TNFRSF1B, and their potential relationships with mastitis were highlighted. From Chromosome 2, 4, 6, 7, 10, 13, 14, 17, and 20, 3.66% (HS3A) and 5.4% (HS8A) novel transcripts, which harbor known quantitative trait locus associated with clinical mastitis, were identified. Many DEGs in the healthy and mastitic mammary glands are involved in immune, defense, and inflammation responses. These DEGs, which exhibit diverse and specific splicing patterns and events, can endow dairy cattle with the potential complex genetic resistance against mastitis.