title: Genome-Wide Analysis of lncRNA and mRNA Expression During Differentiation of Abdominal Preadipocytes in the Chicken.
abstract: 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 reported for the first time, including the propanoate metabolism, fatty acid metabolism, and oxidative phosphorylation 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, includingXLOC_068731,XLOC_022661,XLOC_045161,XLOC_070302,CHD6,LLGL1,NEURL1B,KLHL38, andACTR6This study provides a valuable resource for further study of chicken lncRNA and facilitates a better understanding of preadipocyte differentiation in the chicken.
authors.affiliation: College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009 Jiangsu, China.
authors.forename: Tao
authors.initials: T
authors.lastname: Zhang
authors.affiliation: College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009 Jiangsu, China.
authors.forename: Xiangqian
authors.initials: X
authors.lastname: Zhang
authors.affiliation: College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009 Jiangsu, China.
authors.forename: Kunpeng
authors.initials: K
authors.lastname: Han
authors.affiliation: College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009 Jiangsu, China.
authors.forename: Genxi
authors.initials: G
authors.lastname: Zhang
authors.affiliation: College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009 Jiangsu, China jywang@yzu.edu.cn.
authors.forename: Jinyu
authors.identifier: 0000-0002-5706-0624
authors.initials: J
authors.lastname: Wang
authors.affiliation: College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009 Jiangsu, China.
authors.forename: Kaizhou
authors.initials: K
authors.lastname: Xie
authors.affiliation: College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009 Jiangsu, China.
authors.forename: Qian
authors.initials: Q
authors.lastname: Xue
mesh_terms: D000005:Abdomen; D017667:Adipocytes / Q000166:cytology* / Q000378:metabolism*; D000818:Animals; D002454:Cell Differentiation / Q000235:genetics*; D002645:Chickens / Q000235:genetics*; D016000:Cluster Analysis; D005091:Exons / Q000235:genetics; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D058977:Molecular Sequence Annotation; D011786:Quality Control; D062085:RNA, Long Noncoding / Q000235:genetics* / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D060888:Real-Time Polymerase Chain Reaction; D015203:Reproducibility of Results
chemical_list: D062085:RNA, Long Noncoding; D012333:RNA, Messenger
keywords: Chicken; GenPred; Preadipocyte differentiation; RNA-sequencing; Shared data resources; Stage-specific module; genomic selection