Integrated analysis of lncRNAs and mRNA expression profiles reveals the potential role of lncRNAs in different bovine lactation stages

Long non-coding RNAs (lncRNAs) play a critical role in mammary development and breast cancer biology. Despite their important role in the mammary gland, little is known on the roles of lncRNAs in bovine lactation, particularly regarding the molecular processes underlying it. To characterize the role of lncRNAs in bovine lactation, four samples of Holstein cow mammary gland tissue at peak and late lactation stages were examined after biopsy. We then profiled the transcriptome of mammary gland using RNA sequencing technology. Further, functional lncRNA-mRNA co-expression pairs were constructed to infer the function of lncRNAs using a generalized linear model, followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Over 1000 putative lncRNAs were identified, 117 of which were differentially expressed between peak and late lactation stages. Bovine lncRNAs were shorter, with fewer exon numbers, and expressed at significantly lower levels than protein-coding genes. Seventy-two differentially expressed lncRNAs (DE-lncRNAs) were co-expressed with 340 different protein-coding genes. The KEGG pathway analysis showed that target mRNAs for DE-lncRNAs were mainly related to lipid and glucose metabolism, including the peroxisome proliferator-activated receptors (PPAR) and 5' adenosine monophosphate-activated protein kinase (AMPK) signaling pathways. Further bioinformatics and integrative analyses revealed that 12 DE-lncRNAs potentially played important roles in bovine lactation. Our findings provide a valuable resource for future bovine transcriptome studies, facilitate the understanding of bovine lactation biology, and offer functional information for cattle lactation.Keywords: Long non-coding RNA, bovine lactation, mammary gland, co-expression, RNA sequencing长链非编码RNA（Long non-coding RNAs，lncRNAs）在乳腺发育与乳腺癌生物学过程中发挥关键调控作用。尽管lncRNAs在乳腺组织中具有重要功能，但目前对其在奶牛泌乳过程中的作用机制，尤其是其介导的分子生物学进程，仍知之甚少。为解析lncRNAs在奶牛泌乳中的功能，本研究通过活检获取了泌乳盛期与泌乳后期的荷斯坦奶牛乳腺组织样本（共4份）并开展检测。随后，本研究利用RNA测序（RNA sequencing）技术对乳腺转录组进行了测序分析。进一步，本研究通过广义线性模型构建功能性lncRNA-mRNA共表达对以预测lncRNAs的潜在功能，并依次开展基因本体（Gene Ontology，GO）与京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes，KEGG）通路富集分析。本研究共鉴定出超过1000条推定的lncRNAs，其中117条在泌乳盛期与泌乳后期之间呈现显著差异表达。与蛋白编码基因相比，奶牛lncRNAs的转录本长度更短、外显子数目更少，且表达水平显著更低。72个差异表达lncRNAs（DE-lncRNAs）与340个不同的蛋白编码基因存在共表达关联。KEGG通路富集分析结果显示，DE-lncRNAs的靶mRNA主要参与脂质与葡萄糖代谢过程，涵盖过氧化物酶体增殖物激活受体（peroxisome proliferator-activated receptors，PPAR）以及5'腺苷单磷酸活化蛋白激酶（5' adenosine monophosphate-activated protein kinase，AMPK）信号通路。进一步的生物信息学整合分析表明，其中12个DE-lncRNAs可能在奶牛泌乳过程中发挥重要调控作用。本研究结果为后续奶牛转录组学研究提供了宝贵的参考资源，有助于加深对奶牛泌乳生物学机制的理解，并为奶牛泌乳功能研究提供了功能性参考信息。关键词：长链非编码RNA，奶牛泌乳，乳腺，共表达，RNA测序