金黄色葡萄球菌型乳房炎奶牛乳腺组织的lncRNA差异表达分析

doi:10.13560/j.cnki.biotech.bull.1985.2024-0159

摘要/Abstract

摘要：

【目的】长链非编码RNA（lncRNA）可参与机体炎症反应，但其在奶牛乳房炎中的表达模式及分子调控机制仍不完全清楚。分析金黄色葡萄球菌（Staphylococcus aureus, S.aureus）型乳房炎奶牛乳腺组织中的差异表达lncRNA（DElncRNA）及其功能，为后续深入研究提供支撑。【方法】利用转录组测序（RNA-Seq）技术和生物信息学方法对健康奶牛和S. aureus诱导乳房炎的奶牛乳腺组织进行lncRNA测序、DElncRNA分析及GO和KEGG功能富集分析。【结果】在两组乳腺组织中共检测到1 012个lncRNA。相比于健康奶牛组，S. aureus诱导组筛选到75个表达上调的和114个表达下调的lncRNA。GO和KEGG富集分析结果表明，上述DElncRNA可通过免疫相关信号通路而调节奶牛乳房炎症。进一步分析发现，DElncRNA TCONS_00042123、TCONS_00068055、TCONS_00108420和TCONS_00076361可能参与MAPK、NLR、Jak-STAT和TLR信号通路，进而调节S. aureus型奶牛乳房炎的发生与发展。【结论】在S. aureus诱导炎症的奶牛乳腺组织中获得了189个DElncRNA，可能通过潜在靶基因调控S. aureus型奶牛乳房炎的发生与发展过程。

关键词: 奶牛, 乳房炎, lncRNA, 差异表达分析, 金黄色葡萄球菌

Abstract:

【Objective】Long non-coding RNA（lncRNA）is involved in inflammatory responses, however, their specific molecular regulatory mechanism in dairy mastitis remains unclear. In this study, differentially expressed lncRNA（DElncRNA）and its function in mammary tissues of cows with Staphylococcus aureus（S. aureus）-type mastitis were analysed to support subsequent in-depth studies.【Method】Transcriptome sequencing（RNA-Seq）technology and bioinformatics methods were used to carry out lncRNA sequencing, DElncRNA analysis, and GO and KEGG functional enrichment analysis of mammary tissues from healthy cows and cows with S. aureus-induced mastitis.【Result】A total of 1012 lncRNA are detected in the mammary tissues of both groups. Compared to the healthy dairy cows, total 75 lncRNA are up-regulated and 114 down-regulated in cows with S. aureus-induced mastitis. Further analysis reveals that DElncRNA TCONS_00042123, TCONS_00068055, TCONS_00108420 and TCONS_00076361 may be involved in the MAPK, NLR, Jak-STAT and TLR signaling pathways related to inflammation, regulating the occurrence and development of S.aureus-type mastitis in the dairy cows.【Conclusion】189 DElncRNA were obtained from mammary tissues of cows with S. aureus-induced inflammation, which may regulate the process of onset and progression of S. aureus-type cow mastitis through potential target genes.

Key words: dairy cow, mastitis, lncRNA, differential expression analysis, Staphylococcus aureus

周冉, 王兴平, 李彦霞, 罗仍卓么. 金黄色葡萄球菌型乳房炎奶牛乳腺组织的lncRNA差异表达分析[J]. 生物技术通报, 2024, 40(8): 320-328.

ZHOU Ran, WANG Xing-ping, LI Yan-xia, LUORENG Zhuo-ma. Analysis of LncRNA Differential Expression in Mammary Tissue of Cows with Staphylococcus aureus Mastitis[J]. Biotechnology Bulletin, 2024, 40(8): 320-328.

图/表 7

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长链非编码RNA lncRNA	引物序列 Primer sequence（5'-3'）	产物长度 Product length/bp
TCONS_00018117	F: TGCCAGGACAAGGAGAAA R: TCAGCACCTAAACCACAAGA	100
TCONS_00096253	F: GGAGCGTAAGTAGGAAGCG R: AATGGTCCTGAATAGGGGTT	92
TCONS_00013236	F: ATGGAAAAACGGACTCGG R: CGGTCTGCCTGAGTCTTG	88
TCONS_00026262	F: AATGCCAGGGCTCCAGTT R: CTCAGATGGACAGTATTCCCTTT	89
TCONS_00018115	F: GCCAGGACAAGGAGAAACA R: TCAGCACCTAAACCACAAGAC	100
TCONS_00113348	F: GGTTCTATTGGATACTGGACAT R: CCTTGCTCTGCTCTTCTTTA	100
TCONS_00120135	F: GCCTTTCATTTTCAAGAGCAT R: TGTCAAGGGAAGGGTGTCTG	90
TCONS_00044738	F: AGGGCTGTTTACCTGCTTA R: GGTGATTTCGGTTCCTCTA	93
TCONS_00032949	F: CAAGACGGCGACTTAGAAA R: ATGCCATCAAGTGGAACAA	94
TCONS_00124429	F: GTCCACCTCCACCCTACA R: ATGCTCACCGAAGTCAAAG	100
TCONS_00117470	F: TGTGCTGGACATAAATCGTG R: AGGTTCTGGGATTGTCTGC	93
TCONS_00088875	F: GATGGTGCTGCTTCAGGATG R: TGGAGGCTACGCCAGGTT	94
GAPDH^a	F: GGCATCGTGGAGGGACTTATG R: CCAGTGAGCTTCCCGTTGAG	185
RPS18^b	F: GTGGTGTTGAGGAAAGCAGACA R: TGATCACACGTTCCACCTCATC	79

长链非编码RNA lncRNA	引物序列 Primer sequence（5'-3'）	产物长度 Product length/bp
TCONS_00018117	F: TGCCAGGACAAGGAGAAA R: TCAGCACCTAAACCACAAGA	100
TCONS_00096253	F: GGAGCGTAAGTAGGAAGCG R: AATGGTCCTGAATAGGGGTT	92
TCONS_00013236	F: ATGGAAAAACGGACTCGG R: CGGTCTGCCTGAGTCTTG	88
TCONS_00026262	F: AATGCCAGGGCTCCAGTT R: CTCAGATGGACAGTATTCCCTTT	89
TCONS_00018115	F: GCCAGGACAAGGAGAAACA R: TCAGCACCTAAACCACAAGAC	100
TCONS_00113348	F: GGTTCTATTGGATACTGGACAT R: CCTTGCTCTGCTCTTCTTTA	100
TCONS_00120135	F: GCCTTTCATTTTCAAGAGCAT R: TGTCAAGGGAAGGGTGTCTG	90
TCONS_00044738	F: AGGGCTGTTTACCTGCTTA R: GGTGATTTCGGTTCCTCTA	93
TCONS_00032949	F: CAAGACGGCGACTTAGAAA R: ATGCCATCAAGTGGAACAA	94
TCONS_00124429	F: GTCCACCTCCACCCTACA R: ATGCTCACCGAAGTCAAAG	100
TCONS_00117470	F: TGTGCTGGACATAAATCGTG R: AGGTTCTGGGATTGTCTGC	93
TCONS_00088875	F: GATGGTGCTGCTTCAGGATG R: TGGAGGCTACGCCAGGTT	94
GAPDH^a	F: GGCATCGTGGAGGGACTTATG R: CCAGTGAGCTTCCCGTTGAG	185
RPS18^b	F: GTGGTGTTGAGGAAAGCAGACA R: TGATCACACGTTCCACCTCATC	79

样品 Sample	质控后的读段数 Clean reads	对比到参考基因组的读段数 Mapped reads	参考基因组上有唯一比对位置的读段数 Uniq mapped reads	参考基因组上有多个比对位置的读段数 Multiple mapped reads	GC /%	Q30 /%
M.C	128 303 002	108 631 698 （84.67%）	97 000 181 （89.29%）	11 631 517 （10.71%）	52.30	85.60
M.S	108 776 484	91 300 177 （83.93%）	84 635 626 （92.70%）	6 664 551 （7.30%）	50.84	85.16

样品 Sample	质控后的读段数 Clean reads	对比到参考基因组的读段数 Mapped reads	参考基因组上有唯一比对位置的读段数 Uniq mapped reads	参考基因组上有多个比对位置的读段数 Multiple mapped reads	GC /%	Q30 /%
M.C	128 303 002	108 631 698 （84.67%）	97 000 181 （89.29%）	11 631 517 （10.71%）	52.30	85.60
M.S	108 776 484	91 300 177 （83.93%）	84 635 626 （92.70%）	6 664 551 （7.30%）	50.84	85.16