Comparative transcriptome analysis of rumen papillae in suckling and weaned Japanese Black calves using RNA sequencing
Comparative transcriptome analysis of rumen papillae in suckling and weaned Japanese Black calves using RNA sequencing
复制标题
使用 RNA 测序对哺乳期和断奶日本黑牛犊瘤胃乳头进行比较转录组分析
DOI：
10.1093/jas/skx016
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发表时间：
2018
影响因子：
3.3
通讯作者：
Roh S
中科院分区：
文献类型：
--
作者：
Nishihara K;Kato D;Suzuki Y;Kim D;Nakano M;Yajima Y;Haga S;Nakano M;Ishizaki H;Kawahara-Miki R;Kono T;Katoh K;Roh S
在反刍动物断奶和生长过程中，瘤胃乳头的长度和密度开始增加。这一重大进展增加了瘤胃内表面积和 VFA（乙酸盐、丙酸盐、丁酸盐等）的吸收效率。因此，研究断奶期间瘤胃乳头生长发育的控制因素具有重要意义。本研究旨在比较哺乳和断奶犊牛瘤胃乳头的转录组。从 10 头雄性日本黑牛犊（5 头哺乳牛，5 周龄；5 头断奶牛，15 周龄）的瘤胃乳头中提取总 RNA，并用于 RNA 测序。估计转录本丰度并鉴定差异表达基因，然后将这些数据用于 Ingenuity Pathway Analysis (IPA)，以预测主要的规范途径和上游调节因子。 IPA筛选出的871个差异表达基因中，断奶组有466个基因上调，405个基因下调。典型途径分析表明，“动脉粥样硬化”是最重要的途径，而“维甲酸”（维生素 A 的衍生物）被预测为断奶期间最活跃的上游调节因子。分析还预测 IgG、脂多糖和肿瘤坏死因子-α 作为微生物-上皮相互作用的调节剂，从而激活瘤胃相关的免疫反应。本研究中发现的功能类别和上调因子为研究与日本黑犊牛从哺乳到断奶期间瘤胃乳头增殖和发育相关的新候选基因提供了宝贵的资源。
The length and density of rumen papillae starts to increase during weaning and growth of ruminants. This significant development increases the intraruminal surface area and the efficiency of VFA (acetate, propionate, butyrate, etc.) uptake. Thus, it is important to investigate the factors controlling the growth and development of rumen papillae during weaning. This study aimed to compare the transcriptomes of rumen papillae in suckling and weaned calves. Total RNA was extracted from the rumen papillae of 10 male Japanese Black calves (5 suckling calves, 5 wk old; 5 weaned calves, 15 wk old) and used in RNA-sequencing. Transcript abundance was estimated and differentially expressed genes were identified and these data were then used in Ingenuity Pathway Analysis (IPA) to predict the major canonical pathways and upstream regulators. Among the 871 differentially expressed genes screened by IPA, 466 genes were upregulated and 405 were downregulated in the weaned group. Canonical pathway analysis showed that “atherosclerosis” was the most significant pathway, and “tretinoin,” a derivative of vitamin A, was predicted as the most active upstream regulator during weaning. Analyses also predicted IgG, lipopolysaccharides, and tumor-necrosis factor-α as regulators of the microbe-epithelium interaction that activates rumen-related immune responses. The functional category and the up-regulators found in this study provide a valuable resource for studying new candidate genes related to the proliferation and development of rumen papillae from suckling to weaning Japanese Black calves.