Analysis of the mechanism of lncRNA_89636 in the regulation of asip by targeting miR-200a in koi carp skin color differentiation.

As a globally renowned ornamental fish, the body color and patterns of koi carp play a decisive role in their market value. Although genetic factors drive color diversity, the non-coding regulatory mechanisms underlying koi color variation are poorly understood. This study focused on two color patterns (red and black) in Hi-Utsuri koi. Histological analysis revealed that black skin primarily consists of dendritic melanocytes, whereas red skin contains numerous granular erythrophores. Whole transcriptome and small RNA sequencing identified many differentially expressed non-coding RNAs (lncRNAs, circRNAs, miRNAs) and mRNAs associated with skin pigmentation. Key regulatory factors involved in pigment differentiation and formation were identified, including lncRNA_89636, asip, mc1r, miR-200a and miR-144. A combination of bioinformatic analysis and experimental techniques (in situ hybridization, dual luciferase reporter assays, cell vector construction, gene editing, lentiviral vector construction, qPCR and western blotting) was used to investigate the molecular regulatory mechanisms among lncRNA_89636, miR-200a and asip. The results showed significantly higher expression of lncRNA_89636 and asip in red skin compared to black skin, while miR-200a was markedly elevated in black skin relative to red skin. A key finding was that lncRNA_89636 regulates asip expression by competitively binding to miR-200a, thereby influencing melanocyte function. Gene editing experiments confirmed that knockout the asip gene disrupts melanocyte distribution and alters the expression levels of both lncRNA_89636 and miR-200a. This work preliminarily elucidates the molecular mechanism regulating skin pigmentation in koi carp via the lncRNA_89636/miR-200a/asip axis and provides a theoretical basis for breeding superior Hi-Utsuri koi.