Biswas Tathagata, Hassan Huzaifa, Rohner Nicolas
Stowers Institute for Medical Research, Kansas City, Missouri, USA.
Institute for Integrative Cell Biology and Physiology, University of Münster, Münster, Germany.
Ann N Y Acad Sci. 2025 Apr;1546(1):173-181. doi: 10.1111/nyas.15300. Epub 2025 Mar 13.
Astyanax mexicanus, a species with both surface-dwelling and multiple cave-dwelling populations, offers a unique opportunity to study repeated adaptation to dark and resource-scarce environments. While previous work has identified large-scale gene expression changes between morphs under even identical laboratory conditions, the regulatory basis of these expression differences remains largely unexplored. In this study, we focus on microRNAs (miRNAs) as key regulators of gene expression. Our analysis identified 683 mature miRNAs, establishing the first comprehensive catalog of miRNAs for this species. We identified a unique subset of differentially expressed miRNAs common to all studied cave-dwelling populations, potentially orchestrating the nuanced gene expression patterns required for survival in the cave milieu. Furthermore, we performed in silico target prediction of these miRNAs, revealing possible roles in developmental and metabolic pathways pivotal for thriving in nutrient-limited cave conditions. Interestingly, we also observed that Molino, which is the "youngest" of the three cavefish analyzed in this study, exhibited the most abundant number of differentially expressed mature miRNAs among the cave morphs. The comprehensive miRNA catalog generated, along with the insight into their differential expression across different morphs, will guide future investigations into the intricate world of miRNA-mediated evolution of complex traits.
墨西哥丽脂鲤有生活在地表和多种生活在洞穴中的种群，这为研究对黑暗和资源稀缺环境的反复适应提供了独特的机会。虽然之前的研究已经确定，即使在相同的实验室条件下，不同形态之间也存在大规模的基因表达变化，但这些表达差异的调控基础在很大程度上仍未被探索。在这项研究中，我们聚焦于微小RNA（miRNA）作为基因表达的关键调节因子。我们的分析鉴定出了683个成熟的miRNA，建立了该物种首个全面的miRNA目录。我们鉴定出了所有研究的洞穴种群共有的一组独特的差异表达miRNA，它们可能协调了在洞穴环境中生存所需的细微基因表达模式。此外，我们对这些miRNA进行了计算机靶标预测，揭示了它们在发育和代谢途径中的可能作用，这些途径对于在营养有限的洞穴条件下茁壮成长至关重要。有趣的是，我们还观察到，在本研究分析的三种洞穴鱼中“最年轻”的莫利诺洞穴鱼，在洞穴形态中表现出数量最多的差异表达成熟miRNA。生成的全面miRNA目录，以及对它们在不同形态间差异表达的深入了解，将为未来研究miRNA介导的复杂性状进化的复杂世界提供指导。
