05月03 【成功案例】百迈客云 真核生物有参考基因组的转录组分析平台 助力 王金玉老师 发表《鸡中腹部前脂肪细胞分化过程中lncRNA和mRNA表达的全基因组分析》
摘要：
长非编码RNA（lncRNA）调节脂肪形成和其他与代谢组织发育和功能相关的过程。然而，关于鸡中前脂肪细胞分化期间lncRNAs的功能和特征却知道的很少，本文使用RNA测序分析不同分化阶段的前脂肪细胞中的lncRNA和mRNA表达。从12个样本总共获得了1,300,074,528 clean reads和27,023个新的LncRNA，在各个阶段差异表达的基因（1,336个lncRNA和1,759个mRNA；总共3,095个）的数量随着细胞分化而下降。这些差异基因参与前脂肪细胞分化的几个广泛研究的途径，包括甘油脂代谢，哺乳动物中雷帕霉素的靶标，过氧化物酶体增殖物激活受体和丝裂原活化蛋白激酶信号通路，而在本研究中，首次报道了一些与前脂肪细胞分化相关的通路，包括丙酸代谢，脂肪酸代谢和氧化磷酸化途径。此外，通过k-means均值聚类，3,095个差异基因被聚成8个表达模式。其中，K2这一簇基因中在前脂肪细胞分化中起着重要作用，使用加权共表达网络分析（WGCNA），鉴定了与A0（第0天），A2（第2天）和A6（第6天）阶段相关的6个阶段特异性模块，随后从阶段特异性模块鉴定了9个中心，高度相关的基因，包括：XLOC_068731, XLOC_022661, XLOC_045161, LOC_070302, CHD6, LLGL1, NEURL1B, KLHL38, 和ACTR6。本研究为进一步研究鸡的lncRNA提供了宝贵的资源，有利于更好的了解鸡的前脂肪细胞分化。
本文主要用了云平台中的WGCNA和k-means均值聚类。
英文摘要：
Long noncoding RNAs (lncRNAs) regulate adipogenesis and other processes associated with metabolic tissue development and function. However, little is known about the function and profile of lncRNAs during preadipocyte differentiation in the chicken (Gallus gallus). Herein, lncRNA and mRNA expression in preadipocytes at different stages of differentiation were analyzed using RNA sequencing. A total of 1,300,074,528 clean reads and 27,023 novel lncRNAs were obtained from 12 samples. The number of genes (1336 lncRNAs and 1759 mRNAs; 3095 in total) differentially expressed across various stages declined as differentiation progressed. Differentially expressed genes were found to be involved in several pathways related to preadipocyte differentiation that have been extensively studied, including glycerolipid metabolism, and the mammalian target of rapamycin, peroxisome proliferator-activated receptor, and mitogen-activated protein kinase signaling pathways. To our knowledge, some pathways are being report- ed for the first time, including the propanoate metabolism, fatty acid metabolism, and oxidative phosphor- ylation pathways. Furthermore, 3095 differentially expressed genes were clustered into eight clusters, and their expression patterns were determined through K-means clustering. Genes involved in the K2 cluster likely play important roles in preadipocyte differentiation. Six stage-specific modules related to A0 (day 0), A2 (day 2), and A6 (day 6) stages were identified, using weighted coexpression network analysis. Nine central, highly connected .genes in stage-specific modules were subsequently identified, including XLOC_068731, XLOC_022661, XLOC_045161, XLOC_070302, CHD6, LLGL1, NEURL1B, KLHL38, and ACTR6. This study provides a valuable resource for further study of chicken lncRNA and facilitates a better understanding of preadipocyte differentiation in the chicken.