Integrated analysis of long non-coding RNAs and mRNA expression profiles identified potential interactions regulating melanogenesis in chicken skin

1. Long non-coding RNAs (lncRNAs) play important roles in various physiological functions. However, the mechanisms underlying the regulation of lncRNAs in melanogenesis remain unclear. To determine the molecular mechanisms involved in skin melanogenesis, the present study depicted the expression profiles of lncRNAs and messenger RNAs (mRNAs) in black- (B group) and white- (W group) skinned chickens using RNA sequencing. 2. In total, 373 differentially expressed lncRNAs (DELs; 203 up-regulated and 170 down-regulated) and 253 differentially expressed genes (DEGs; 152 up-regulated and 101 down-regulated) were identified between the B and W groups. A total of eight known melanogenesis-related genes were identified (KIT, TYRP1, DCT (TYRP2), SLC45A2, OCA2, EDNRB2, TRPM1 and RAB38). 3. Functional annotation of the co-expressed DEGs and DELs was performed using Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analyses. The co-expressed DEGs were mainly involved in melanogenesis and the co-expressed genes of 117 and 108 DELs were significantly enriched in the melanogenesis and tyrosine metabolism pathways, respectively. 4. The DEL-DEG interaction network revealed that three lncRNAs (XR_003072387.1, XR_003075112.1, and XR_003077033.1) and DCT genes may have key roles in regulating melanogenesis in chicken skin. This data provides the groundwork for studying the lncRNA regulatory mechanisms of skin melanogenesis and suggested a new perspective on the modulation of melanogenesis in chicken skin based on a lncRNA-mRNA causal regulatory network.

1. 长链非编码RNA（long non-coding RNAs, lncRNAs）在诸多生理功能中发挥重要调控作用。然而，lncRNA调控黑色素生成的具体分子机制仍未明确。为探明皮肤黑色素生成的相关分子机制，本研究通过RNA测序技术，分析了黑皮（B组）与白皮（W组）鸡皮肤组织中lncRNA及信使RNA（messenger RNAs, mRNA）的表达谱。
2. 共计在B组与W组间鉴定出373个差异表达长链非编码RNA（differentially expressed lncRNAs, DELs；其中203个上调、170个下调）以及253个差异表达基因（differentially expressed genes, DEGs；其中152个上调、101个下调）。此外，共鉴定得到8个已知的黑色素生成相关基因，分别为KIT、TYRP1、DCT（TYRP2）、SLC45A2、OCA2、EDNRB2、TRPM1及RAB38。
3. 本研究通过基因本体论（Gene Ontology, GO）及京都基因与基因组百科全书（Kyoto Encyclopaedia of Genes and Genomes, KEGG）通路富集分析，对共表达的DEGs与DELs进行了功能注释。结果显示，共表达的DEGs主要富集于黑色素生成通路；117个与108个DELs的共表达基因分别显著富集于黑色素生成通路与酪氨酸代谢通路。
4. 通过构建DEL-DEG互作网络，本研究发现3个lncRNA（XR_003072387.1、XR_003075112.1及XR_003077033.1）与DCT基因可能在鸡皮肤黑色素生成调控中扮演核心角色。本数据集为研究皮肤黑色素生成的lncRNA调控机制奠定了研究基础，并为基于lncRNA-mRNA因果调控网络解析鸡皮肤黑色素生成调控机制提供了全新视角。