Analysis of long noncoding RNA and mRNA using RNA sequencing during the differentiation of intramuscular preadipocytes in chicken

Long noncoding RNAs (lncRNAs) regulate metabolic tissue development and function, including adipogenesis. However, little is known about the function and profile of lncRNAs in intramuscular preadipocyte differentiation in chicken. Here, we identified lncRNAs in chicken intramuscular preadipocytes at different differentiation stages using RNA sequencing. A total of 1,311,382,604 clean reads and 25,435 lncRNAs were obtained from 12 samples. In total, 7,433 differentially expressed genes (4,698 lncRNAs and 2,735 mRNAs) were identified by pairwise comparison. These 7,433 differentially expressed genes were grouped into 11 clusters based on their expression patterns by K-means clustering. Using Weighted Gene Coexpression Network Analysis, we identified four stage-specific modules positively related to I0, I2, I4, and I6 stages and two stage-specific modules negatively related to I0 and I2 stages, respectively. Many well-known and novel pathways associated with intramuscular preadipocyte differentiation were identified. We also identified hub genes in each stage-specific module and visualized them in Cytoscape. Our analysis revealed many highly-connected genes, including XLOC_058593, BMP3, MYOD1, and LAMP3. This study provides a valuable resource for chicken lncRNA study and improves our understanding of the biology of preadipocyte differentiation in chicken.

长链非编码RNA（long noncoding RNAs，lncRNAs）可调控代谢组织的发育与功能，涵盖脂肪生成过程。然而，目前针对鸡肌内前体脂肪细胞分化过程中lncRNAs的功能与表达谱的研究仍较为匮乏。本研究通过RNA测序（RNA sequencing），对不同分化阶段的鸡肌内前体脂肪细胞中的lncRNAs进行了鉴定。本研究从12份样本中共获得1,311,382,604条清洁读段（clean reads）与25,435条lncRNAs。通过两两比对分析，共鉴定得到7,433个差异表达基因（differentially expressed genes），其中4,698个为lncRNAs，2,735个为信使RNA（mRNA）。基于这些差异表达基因的表达模式，通过K-means聚类（K-means clustering）将其划分为11个聚类簇。本研究采用加权基因共表达网络分析（Weighted Gene Coexpression Network Analysis），分别鉴定得到4个与I0、I2、I4及I6阶段呈正相关的阶段特异性模块，以及2个与I0和I2阶段呈负相关的阶段特异性模块。本研究鉴定得到诸多与鸡肌内前体脂肪细胞分化相关的经典通路与全新通路。此外，本研究还对每个阶段特异性模块中的核心基因（hub genes）进行了鉴定，并通过Cytoscape软件对其进行了可视化展示。分析结果显示诸多连接度较高的基因，包括XLOC_058593、BMP3、MYOD1及LAMP3。本研究为鸡lncRNAs相关研究提供了宝贵的资源，并加深了我们对鸡肌内前体脂肪细胞分化生物学机制的理解。