The whole-transcriptome landscape of muscle and adipose tissues reveals the ceRNA regulation network related to intramuscular fat deposition in yak
The whole-transcriptome landscape of muscle and adipose tissues reveals the ceRNA regulation network related to intramuscular fat deposition in yak
复制标题
肌肉和脂肪组织的全转录组图谱揭示了牦牛肌内脂肪沉积相关的ceRNA调控网络
DOI：
10.1186/s12864-020-6757-z
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发表时间：
2020-05-07
期刊：
影响因子：
4.4
通讯作者：
Ji, Qiumei
中科院分区：
文献类型：
--
作者：
Wang, Hui;Zhong, Jincheng;Ji, Qiumei
研究背景肉制品中肌内脂肪(IMF)含量与肉类品质呈正相关，是消费者关注的重要指标。IMF沉积的调节是物种特有的。然而，牦牛(Bos Grunniens)中与IMF沉积相关的mRNA和非编码RNA及其调控网络仍不清楚。高通量测序技术为分析动物转录组相关差异和特定性状之间的关系提供了一种强有力的方法。因此，我们对牦牛肌肉和脂肪组织的全部转录本进行了筛选和分析，以阐明与IMF沉积相关的基因。结果0.5岁和2.5岁的牦牛肌肉组织中IMF含量有显著差异。几种mRNAs、miRNAs、lncRNAs和CircRNAs普遍在肌肉和脂肪组织中表达。在0.5和2.5年龄的牦牛中，149个mRNAs、62个miRNAs、4个lncRNAs和223个CircRNAs在肌肉组织中差异表达，72个mRNAs、15个miRNAs、9个lncRNAs和211个CircRNAs在脂肪组织中差异表达。KEGG注释揭示了这些差异表达的基因与维持肌肉和脂肪组织正常生物功能的途径有关。此外，16个mRNAs、5个miRNAs、3个lncRNAs和5个CircRNAs在两种类型的组织中共表达。我们怀疑这些共同差异表达的基因与牦牛体内的IMF沉积有关。此外，在以IMF沉积相关基因为基础构建的竞争内源RNA(CerNA)调控网络中，发现了LPL、ACADL、SCD和FASN，它们以前被证明与IMF的含量有关。3个CENA子网络还揭示了TCONS-00016416及其靶SIRT1通过相同的miR-381-y和miR-208反应元件相互“对话”，而TCONS-00061798及其靶PRKCA和TCONS-00084092及其靶LPL分别通过miR-122-x和miR-499-y反应元件相互“对话”。结论本研究结果揭示了参与牦牛IMF沉积的潜在mRNA和非编码RNA，为进一步研究该物种的IMF沉积提供了有用的资源。
BackgroundThe Intramuscular fat (IMF) content in meat products, which is positively correlated with meat quality, is an important trait considered by consumers. The regulation of IMF deposition is species specific. However, the IMF-deposition-related mRNA and non-coding RNA and their regulatory network in yak (Bos grunniens) remain unknown. High-throughput sequencing technology provides a powerful approach for analyzing the association between transcriptome-related differences and specific traits in animals. Thus, the whole transcriptomes of yak muscle and adipose tissues were screened and analyzed to elucidate the IMF deposition-related genes. The muscle tissues were used for IMF content measurements.ResultsSignificant differences were observed between the 0.5- and 2.5-year-old yaks. Several mRNAs, miRNAs, lncRNAs and circRNAs were generally expressed in both muscle and adipose tissues. Between the 0.5- and 2.5-year-old yaks, 149 mRNAs, 62 miRNAs, 4 lncRNAs, and 223 circRNAs were differentially expressed in muscle tissue, and 72 mRNAs, 15 miRNAs, 9 lncRNAs, and 211 circRNAs were differentially expressed in adipose tissue. KEGG annotation revelved that these differentially expressed genes were related to pathways that maintain normal biological functions of muscle and adipose tissues. Moreover, 16 mRNAs, 5 miRNAs, 3 lncRNAs, and 5 circRNAs were co-differentially expressed in both types of tissue. We suspected that these co-differentially expressed genes were involved in IMF-deposition in the yak. Additionally,LPL,ACADL,SCD, andFASN, which were previously shown to be associated with the IMF content, were identified in the competing endogenous RNA (ceRNA) regulatory network that was constructed on the basis of the IMF deposition-related genes. Three ceRNA subnetworks also revealed thatTCONS-00016416and its targetSIRT1“talk” to each other through the same miR-381-y and miR-208 response elements, whereasTCONS-00061798and its targetPRKCA, andTCONS-00084092and its targetLPL“talk” to each other through miR-122-x and miR-499-y response elements, respectively.ConclusionTaken together, our results reveal the potential mRNA and noncoding RNAs involved in IMF deposition in the yak, providing a useful resource for further research on IMF deposition in this animal species.