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. 2025 Apr 7;26(1):348.
doi: 10.1186/s12864-025-11543-8.

Integrated analysis of tyrosine-induced MiRNA and mRNA expression profiles in melanocytes reveals the regulatory role of miR-1560-3p in melanin deposition in Xichuan black-bone chickens

Zhiyuan Zhang #  1 , Pengwei Zhang #  1 , Fumin He  1 , Yingdong Hou  1 , Xiaowen Geng  1 , Ruilong Xu  1 , Ruiting Li  2 , Yadong Tian  1   3 , Wenting Li  1   3 , Guirong Sun  1   3 , Ruirui Jiang  1   3 , Xiaojun Liu  1   3 , Ruili Han  1   3 , Guoxi Li  1   3 , Xiangtao Kang  1   3 , Donghua Li  4   5
Affiliations

Integrated analysis of tyrosine-induced MiRNA and mRNA expression profiles in melanocytes reveals the regulatory role of miR-1560-3p in melanin deposition in Xichuan black-bone chickens

Zhiyuan Zhang et al. BMC Genomics. .

Abstract

Background: Tyrosine is a prerequisite for melanin biosynthesis and plays a crucial role in the growth and development of melanocytes, but the underlying mechanism is still unclear. In our previous research, we added 10- 9-10- 6 mol/L tyrosine to the melanocytes of black-bone chickens and found that 10- 6 mol/L tyrosine significantly increased the tyrosinase content in melanocytes.

Methods: In this study, melanocytes from Xichuan black-bone chickens were used as research objects, 10- 6 mol/L tyrosine was added for transcriptome sequencing. By analyzing miRNA and mRNA expression profiles, the miRNA-mRNA network was constructed, the targeting relationship was demonstrated by double luciferase reporting experiments, and the influence of tyrosine-mediated miRNA-mRNA network on melanin deposition was verified by constructing overexpression and interference vectors.

Results: We found that tyrosine promoted the proliferation and migration of melanocytes, and expression profile analysis identified 57 differentially expressed mRNAs (DEGs) and 19 differentially expressed miRNAs (DEMs). Fifty miRNA‒mRNA target gene pairs were identified via coexpression network analysis of the DEGs and the DEMs that were predicted to target various genes. Notably, VIP gene was reported to be involved in the development and deposition of melanoma cells. The binding of VIP to miR-1560-3p was further validated by a dual-luciferase reporter assay. In addition, test confirmed that miR-1560-3p inhibited the proliferation and migration of melanocytes and reduced the tyrosinase content. In conclusion, we found that tyrosine may affects melanin deposition in Xichuan black-bone chickens by affecting the miR-1560-3p-VIP axis. The results of this study provide experimental evidence for elucidating the mechanism of tyrosine in melanin deposition in black-bone chickens, and may serve as a reference for future investigations.

Keywords: miR-1560-3p-VIP; Melanin deposition; Transcriptomic analysis; Tyrosine.

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Conflict of interest statement

Declarations. Ethics approval and consent to participate: All of the animal experiments were approved by the Institutional Animal Care and Use Committee (IACUC) of Henan Agricultural University, Zhengzhou, China, and performed in strict accordance with the guidelines of the Animal Use Committee of the Chinese Ministry of Agriculture, Beijing, China (Approval number: 11–0085). All test animals in this study received informed consent from their owners to use these animals in the study. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests. Conflict of interest: No potential conflicts of interest were reported by any of the authors.

Figures

Fig. 1
Fig. 1
Transmission electron microscopy of melanocytes. The arrows indicate melanosomes
Fig. 2
Fig. 2
Effects of tyrosine on the proliferation, migration and tyrosinase synthesis of melanocytes. (A) The effect of tyrosine on melanocyte proliferation was determined via a CCK-8 assay. (B, C) The effect of tyrosine on the melanocyte cycle was determined by flow cytometry. (D) Effects of tyrosine on melanocyte proliferation-related genes. (E) Effects of tyrosine on melanocyte cycle-related genes. (F) Effect of tyrosine on melanocyte migration-related genes. (G) Effect of tyrosine on the tyrosinase content in melanocytes. * indicates P < 0.05, ** indicates P < 0.01
Fig. 3
Fig. 3
Analysis of mRNA expression differences. (A) Volcano map of DEGs. The red dots indicate upregulated genes, the blue dots indicate downregulated genes, and the gray dots indicate genes that were not significantly differentially expressed. (B) Coexpressed DEGs between the control group and the tyrosine treatment group. (C) DEG clustering. (D) GO enrichment analysis bubble map. (E) KEGG enrichment analysis bubble map
Fig. 4
Fig. 4
miRNA expression profile analysis. (A) Sequence length distribution diagram. The large figure shows the distribution of total reads with different lengths before weight removal, whereas the small figure at the upper right shows the distribution of unique reads with different lengths after weight removal. (B) Volcano map of DEMs. The red dots represent upregulated genes, the blue dots represent downregulated genes, and the gray dots represent nonsignificant DEGs. (C) Cluster map of DEMs. (D) Bubble map of GO enrichment analysis of DEM target genes. (E) Bubble map of KEGG enrichment analysis of DEM target genes
Fig. 5
Fig. 5
miRNA and mRNA screening and validation. (A, B) Differentially expressed miRNA‒mRNA coexpression network. (C) Validation of the miRNA sequencing results. (D) Verification of the mRNA sequencing results. * indicates P < 0.05, ** indicates P < 0.01
Fig. 6
Fig. 6
Verification of the targeting relationship between gga-miR-1560-3p and VIP. (A) Complementary base pairing site of the gga-miR-1560-3p seed sequence and VIP gene; (B) stem ring structure of the gga-miR-1560-3p and VIP genes; (C) results of the double-luciferase reporter gene assay
Fig. 7
Fig. 7
Analysis of tyrosine-mediated gga-miR-1560-3p targeting of VIP function. (A) gga-miR-1560-3p overexpression efficacy and determination of the influence of gga-miR-1560-3p overexpression on VIP genes. (B) gga-miR-1560-3p interference efficacy and determination of the effect of gga-miR-1560-3p interference on the VIP gene (C) The effects of overexpression and interference of gga-miR-1560-3p on melanocyte proliferation determined by CCK-8 assays. (D) The effect of gga-miR-1560-3p on melanocyte proliferation-related genes (E) Effects of gga-miR-1560-3p on melanocyte cycle-related genes (F) Effects of gga-miR-1560-3p on melanocyte migration-related genes (G) Effects of gga-miR-1560-3p and tyrosine cotreatment on the content of tyrosinase in melanocytes (H) Effect of VIP and tyrosine cotreatment on tyrosinase content in melanocytes * indicates P < 0.05, ** indicates P < 0.01
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