Identification and Annotation of Potential Function of Regulatory Antisense Long Non-Coding RNAs Related to Feed Efficiency in Bos taurus Bulls
Identification and Annotation of Potential Function of Regulatory Antisense Long Non-Coding RNAs Related to Feed Efficiency in Bos taurus Bulls
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DOI：
10.3390/ijms21093292
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发表时间：
2020-05
影响因子：
5.6
通讯作者：
W. Nolte;R. Weikard;R. Brunner;E. Albrecht;H. Hammon;A. Reverter;C. Kühn
中科院分区：
文献类型：
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作者：
W. Nolte;R. Weikard;R. Brunner;E. Albrecht;H. Hammon;A. Reverter;C. Kühn
长非编码 RNA (lncRNA) 可以影响哺乳动物细胞的转录和翻译过程，并与各种发育、生理和表型条件相关。然而，人们对它们在牲畜物种中的了解和注释仍然知之甚少。我们结合了公牛的表型、代谢组学和肝脏转录组学数据，了解残余采食量 (RFI) 和脂肪堆积的差异。基于牛参考基因组 ARS-UCD.1.2 的项目特异性转录组注释和多组织总 RNA 测序数据，我们预测 3590 个基因座为 lncRNA。为了识别对表型和基因表达具有潜在调控影响的lncRNA，我们对一组功能优先的基因座应用了调控影响因子算法（n = 4666）。应用偏相关和信息论算法，计算显着且独立的成对相关性并建立共表达网络，包括与lncRNA相关的血浆代谢物。评估网络中心 lncRNA 的潜在顺式作用，并进行生物途径富集分析。我们的结果揭示了反义lncRNA的普遍存在与邻近的蛋白质编码基因呈正相关，并表明它们参与线粒体功能、急性期反应信号、TCA循环、脂肪酸β-氧化和可能的糖异生。这些反义 lncRNA 表明其顺式相关基因具有稳定功能，并且在基因表达中具有假定的调节作用。
Long non-coding RNAs (lncRNAs) can influence transcriptional and translational processes in mammalian cells and are associated with various developmental, physiological and phenotypic conditions. However, they remain poorly understood and annotated in livestock species. We combined phenotypic, metabolomics and liver transcriptomic data of bulls divergent for residual feed intake (RFI) and fat accretion. Based on a project-specific transcriptome annotation for the bovine reference genome ARS-UCD.1.2 and multiple-tissue total RNA sequencing data, we predicted 3590 loci to be lncRNAs. To identify lncRNAs with potential regulatory influence on phenotype and gene expression, we applied the regulatory impact factor algorithm on a functionally prioritized set of loci (n = 4666). Applying the algorithm of partial correlation and information theory, significant and independent pairwise correlations were calculated and co-expression networks were established, including plasma metabolites correlated with lncRNAs. The network hub lncRNAs were assessed for potential cis-actions and subjected to biological pathway enrichment analyses. Our results reveal a prevalence of antisense lncRNAs positively correlated with adjacent protein-coding genes and suggest their participation in mitochondrial function, acute phase response signalling, TCA-cycle, fatty acid β-oxidation and presumably gluconeogenesis. These antisense lncRNAs indicate a stabilizing function for their cis-correlated genes and a putative regulatory role in gene expression.