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, 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

Genome-Wide Analysis of mRNAs and lncRNAs of Intramuscular Fat Related to Lipid Metabolism in Two Pig Breeds

“…It was inferred that the 11 key lncRNAs such as XLOC_004398, XLOC_0053194, and XLOC_046142 could regulate the proliferation and differentiation of intramuscular adipocytes as well as lipogenesis in LW and LY pigs by target regulating these genes involved in p38 MAPK signaling pathway. The results were similar to those of Zhang et al, who found that the target genes of lncRNAs in abdominal fat tissue of chicken were significantly enriched in MAPK signaling pathway [18]. Note that XLOC_046142 might play a critical role in MAPK signaling pathway by trans-acting on MAPKAPK2.…”

“…LncRNAs, nonprotein coding transcripts longer than 200 nucleotides, have important regulatory functions in adipogenesis and lipid metabolism. With the development of high throughput sequencing technology, RNA-seq has been widely applied in the identification and functional analysis of lncRNAs and mRNAs of adipose tissues in pig [7,13,16,17], chicken [18], sheep [19,20] and cattle [21]. Ramayo et al [22] identified 270 and 186 lncRNAs in the liver tissues of female pigs with high and low intramuscular fatty acid contents, respectively.…”

“…analyzed the methylation of lncRNAs and found the expression level of linc-sscg3623 varied with pig breeds and developmental stages, affecting fat synthesis. By identifying the lncRNA and mRNA expression profiles of preadipocytes at different stages in abdominal adipose tissue of Jinghai Yellow chicken, Zhang et al found that the target genes of lncRNAs were significantly enriched in MAPK and PPAR signaling pathway associated with adipocyte differentiation [18]. These studies indicate that lncRNAs might determine fat deposition and fatty acid composition, and regulate adipogenic differentiation and lipid metabolism in livestock and poultry.…”

The Landscape of Non-Coding RNA in an Adult Pig Model of Intrauterine Growth Restriction

“…6B). Interestingly, previous studies have shown that ATF4 related to positively regulating hepatic gluconeogenesis [39]. This agrees with the increased hepatic gluconeogenesis capacity observed in IUGR pigs.…”

Sequencing and characterization of lncRNAs in the breast muscle of Gushi and Arbor Acres chickens

“…GO enrichment revealed the functions of genes in stage-specific modules, and KEGG analysis revealed signaling pathways and metabolic networks vital for breast muscle development (Zhang et al 2017a). In the current study, the GO terms for the target lncRNA genes were related primarily to biological processes and molecular functions (Fig 4).…”