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

ABSTRACT

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.

KEYWORDS:

• Chicken
• skin
• melanogenesis
• lncRNA
• Gene
• RNA sequencing

Acknowledgments

This study was supported by Sichuan Science and Technology Program (2022YFN0039), and A Scientific Research Project of Leshan Normal University (LZD008). This work was also funded by Scientific Research Project of Leshan Normal University (DGZZ202002), and the Science and Technology Plan Project of Leshan (20NZD005). The dataset supporting the conclusions of this article is available in the NCBI Sequence Read Archive (SRA) repository [Accession number PRJNA842174].

Disclosure statement

No potential conflict of interest was reported by the author(s).

Supplementary material

Supplemental data for this article can be accessed online at https://doi.org/10.1080/00071668.2022.2113506

Additional information

Funding

This work was supported by the Scientific Research Project of Leshan Normal University [DGZZ202002,LZD008]; Sichuan Science and Technology Program [2022YFN0039]; Science and Technology Plan Project of Leshan [20NZD005].