Small noncoding RNAs (ncRNAs) play a vital role in a broad range of biological processes both in health and disease. A comprehensive quantitative reference of small ncRNA expression would significantly advance our understanding of ncRNA roles in shaping tissue functions. Here, we systematically profiled the levels of five ncRNA classes (microRNA [miRNA], small nucleolar RNA [snoRNA], small nuclear RNA [snRNA], small Cajal body-specific RNA [scaRNA], and transfer RNA [tRNA] fragments) across 11 mouse tissues by deep sequencing. Using 14 biological replicates spanning both sexes, we identified that ∼30% of small ncRNAs are distributed across the body in a tissue-specific manner with some also being sexually dimorphic. We found that some miRNAs are subject to “arm switching” between healthy tissues and that tRNA fragments are retained within tissues in both a gene- and a tissue-specific manner. Out of 11 profiled tissues, we confirmed that brain contains the largest number of unique small ncRNA transcripts, some of which were previously annotated while others are identified in this study. Furthermore, by combining these findings with single-cell chromatin accessibility (scATAC-seq) data, we were able to connect identified brain-specific ncRNAs with their cell types of origin. These results yield the most comprehensive characterization of specific and ubiquitous small RNAs in individual murine tissues to date, and we expect that these data will be a resource for the further identification of ncRNAs involved in tissue function in health and dysfunction in disease.

小型非编码RNA（ncRNA）在健康和疾病的广泛生物学过程中起着至关重要的作用。小型ncRNA表达的全面定量参考将大大提高我们对ncRNA在塑造组织功能中的作用的了解。在这里，我们系统地分析了五个ncRNA类（microRNA [miRNA]，小核仁RNA [snoRNA]，小核RNA [snRNA]，小Cajal体特异性RNA [scaRNA]和转移RNA [tRNA]片段）的水平。通过深度测序获得11种小鼠组织。我们使用14个跨性别的生物学复制品，我们发现约有30％的小型ncRNA以组织特异性的方式分布在体内，其中有些也具有两性性。我们发现一些miRNA受到健康组织之间的“臂转换”，并且tRNA片段以基因和组织特异性方式保留在组织内。在11个有轮廓的组织中，我们确认大脑包含最多数量的独特小ncRNA转录本，其中一些先前已被注释，而另一些已在本研究中鉴定。此外，通过将这些发现与单细胞染色质可及性（scATAC-seq）数据相结合，我们能够将已鉴定的脑特异性ncRNA与它们的细胞来源联系起来。这些结果迄今可对单个鼠组织中的特定和普遍存在的小RNA进行最全面的表征，我们希望这些数据将为进一步鉴定参与健康和疾病功能的组织中的ncRNA提供资源。