Comparative Transcriptome Analysis Reveals Regulatory Mechanism of Long Non-Coding RNAs during Abdominal Preadipocyte Adipogenic Differentiation in Chickens

SIMPLE SUMMARY: Excessive fat deposition, particularly abdominal fat, negatively affects meat quality, feed utilization, and reproduction performance in chickens. Adipogenesis is a well-orchestrated process that involves a network of regulatory molecules. Emerging evidence has shown that long non-coding RNAs (lncRNAs) participate in mammalian adipogenesis. However, limited information is available about their role in adipogenesis in chickens. Therefore, we investigated the genome-wide identification, expression profiles, and regulatory networks of lncRNAs during adipogenic differentiation of chicken abdominal preadipocytes. We found that lncRNAs were expressed in chicken abdominal adipocytes, characterized by their differentiation stage-specific expression pattern and were involved in multiple lipid metabolism-related pathways. Several lncRNAs were identified as key lncRNAs responsible for adipogenic differentiation. These key lncRNAs could regulate lipid-related protein-encoding genes in cis- and trans-regulation manners, and/or competitively sponge miRNA to sequester it away from lipid-related genes, thereby functioning as regulators of chicken adipogenesis. These findings provide valuable information that improves our understanding of functional mechanisms of lncRNAs underlying adipogenesis and contributes to the genetic improvement of excessive abdominal fat in chickens. ABSTRACT: Long non-coding RNAs (lncRNAs) are implicated in mammalian adipogenesis and obesity. However, their genome-wide distribution, expression profiles, and regulatory mechanisms during chicken adipogenesis remain rarely understood. In the present study, lncRNAs associated with adipogenesis were identified from chicken abdominal adipocytes at multiple differentiation stages using Ribo-Zero RNA-seq. A total of 15,179 lncRNAs were identified and characterized by stage-specific expression patterns. Of these, 840 differentially expressed lncRNAs were detected, and their cis- and trans-target genes were significantly enriched in multiple lipid-related pathways. Through weighted gene co-expression network analysis (WGCNA) and time-series expression profile clustering analysis, 14 key lncRNAs were identified as candidate regulatory lncRNAs in chicken adipogenic differentiation. The cis- and trans-regulatory interactions of key lncRNAs were constructed based on their differentially expressed cis- and trans-target genes, respectively. We also constructed a competing endogenous RNA (ceRNA) network based on the key lncRNAs, differentially expressed miRNAs, and differentially expressed mRNAs. MSTRG.25116.1 was identified as a potential regulator of chicken abdominal preadipocyte adipogenic differentiation by acting as a transcriptional trans-regulator of fatty acid amide hydrolase (FAAH) gene expression and/or a ceRNA that post-transcriptionally mediates FAAH gene expression by sponging gga-miR-1635.