Guizhou Fisheries Research Institute, Guizhou Academy of Agriculture Sciences, Guiyang, Guizhou, China.
Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, Ministry of Agriculture and Rural Affairs, Wuxi, Jiangsu, China.
BMC Genomics. 2023 Feb 10;24(1):70. doi: 10.1186/s12864-023-09168-w.
MicroRNAs (miRNAs) are endogenous small non-coding RNAs (21-25 nucleotides) that act as essential components of several biological processes. Golden-back crucian carp (GBCrC, Carassius auratus) is a naturally mutant species of carp that has two distinct body skin color types (golden and greenish-grey), making it an excellent model for research on the genetic basis of pigmentation. Here, we performed small RNA (sRNA) analysis on the two different skin colors via Illumina sequencing.
A total of 679 known miRNAs and 254 novel miRNAs were identified, of which 32 were detected as miRNAs with significant differential expression (DEMs). 23,577 genes were projected to be the targets of 32 DEMs, primarily those involved in melanogenesis, adrenergic signaling in cardiomyocytes, MAPK signaling pathway and wnt signaling pathway by functional enrichment. Furthermore, we built an interaction module of mRNAs, proteins and miRNAs based on 10 up-regulated and 13 down-regulated miRNAs in golden skin. In addition to transcriptional destabilization and translational suppression, we discovered that miRNAs and their target genes were expressed in the same trend at both the transcriptional and translational levels. Finally, we discovered that miR-196d could be indirectly implicated in regulating melanocyte synthesis and motility in the skin by targeting to myh7 (myosin-7) gene through the luciferase reporter assay, antagomir silencing in vivo and qRT-PCR techniques.
Our study gives a systematic examination of the miRNA profiles expressed in the skin of GBCrC, assisting in the comprehension of the intricate molecular regulation of body color polymorphism and providing insights for C. auratus breeding research.
微小 RNA（miRNA）是内源性的小非编码 RNA（21-25 个核苷酸），作为几个生物过程的必需组成部分发挥作用。金背鲫鱼（GBCrC，Carassius auratus）是鲫鱼的一种自然突变种，具有两种截然不同的体肤颜色类型（金黄色和灰绿色），是研究色素沉着遗传基础的理想模型。在这里，我们通过 Illumina 测序对两种不同的肤色进行了小 RNA（sRNA）分析。
共鉴定出 679 个已知 miRNA 和 254 个新 miRNA，其中 32 个被检测为差异表达（DEMs）的 miRNA。32 个 DEMs 的靶基因共预测到 23577 个，主要涉及黑色素生成、心肌细胞肾上腺素能信号、MAPK 信号通路和 wnt 信号通路，通过功能富集分析。此外，我们基于 10 个上调和 13 个下调 miRNA 在金黄色皮肤中构建了一个 mRNA、蛋白质和 miRNA 的互作模块。除了转录不稳定和翻译抑制外，我们还发现 miRNA 和其靶基因在转录和翻译水平上表达趋势一致。最后，我们发现 miR-196d 可以通过靶向 myh7（肌球蛋白-7）基因，通过荧光素酶报告基因检测、体内反义寡核苷酸沉默和 qRT-PCR 技术，间接参与调节皮肤中黑素细胞的合成和运动。
本研究系统地研究了 GBCrC 皮肤中表达的 miRNA 谱，有助于理解体色多态性的复杂分子调控，并为 C. auratus 养殖研究提供了见解。
