MicroRNAs (miRNAs) play an essential role in the post-transcriptional regulation of animal development and physiology. However, in vivo studies aimed at linking miRNA function to the biology of distinct cell types within complex tissues remain challenging, partly because in vivo miRNA-profiling methods lack cellular resolution. We report microRNome by methylation-dependent sequencing (mime-seq), an in vivo enzymatic small-RNA-tagging approach that enables high-throughput sequencing of tissue- and cell-type-specific miRNAs in animals. The method combines cell-type-specific 3′-terminal 2′-O-methylation of animal miRNAs by a genetically encoded, plant-specific methyltransferase (HEN1), with chemoselective small-RNA cloning and high-throughput sequencing. We show that mime-seq uncovers the miRNomes of specific cells within Caenorhabditis elegans and Drosophila at unprecedented specificity and sensitivity, enabling miRNA profiling with single-cell resolution in whole animals. Mime-seq overcomes current challenges in cell-type-specific small-RNA profiling and provides novel entry points for understanding the function of miRNAs in spatially restricted physiological settings.

MicroRNAs (miRNAs) 在动物发育和生理的转录后调控中发挥着重要作用。然而，旨在将 miRNA 功能与复杂组织内不同细胞类型的生物学联系起来的体内研究仍然具有挑战性，部分原因是体内miRNA 分析方法缺乏细胞分辨率。我们通过甲基化依赖性测序 (mime-seq) 报告 microRNome，这是一种体内酶促小 RNA 标记方法，可对动物中的组织和细胞类型特异性 miRNA 进行高通量测序。该方法通过基因编码的植物特异性甲基转移酶 (HEN1) 将动物 miRNA 的细胞类型特异性 3'-末端 2'-O-甲基化与化学选择性小 RNA 克隆和高通量测序相结合。我们表明，mime-seq 以前所未有的特异性和敏感性揭示了秀丽隐杆线虫和果蝇中特定细胞的 miRNomes ，从而能够在整个动物中以单细胞分辨率进行 miRNA 分析。Mime-seq 克服了当前在细胞类型特异性小 RNA 分析方面的挑战，并为理解 miRNA 在空间受限的生理环境中的功能提供了新的切入点。