Sakhawala Rima M, Tirgar Reyhaneh, Vieux Karl-Frédéric, Haskell Dustin, Yu Guoyun, Zinovyeva Anna, McJunkin Katherine
Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases Intramural Research Program, National Institutes of Health, Bethesda, Maryland 20892, USA.
Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA.
Genes Dev. 2025 Jul 14. doi: 10.1101/gad.352481.124.
MicroRNAs (miRNAs) are short RNAs that post-transcriptionally regulate gene expression. In canonical miRNA biogenesis, primary miRNAs are transcribed from intergenic loci or intronic regions by RNA polymerase II and sequentially cleaved by the Microprocessor complex and Dicer, and the resulting mature miRNAs are loaded into Argonaute to repress target mRNAs. A minority of miRNAs are generated via noncanonical biogenesis pathways that bypass the Microprocessor complex and/or Dicer. Here, we describe a new Pol III-dependent, Microprocessor-independent, and Dicer-dependent biogenesis pathway exemplified by the family in Although the family loci reside in intronic regions of protein-coding genes, we show that the miRNAs are derived from independent Pol III transcripts. Unlike other Pol III-dependent miRNAs, the family small RNAs are the dominant species derived from their loci rather than fragments of a larger functional noncoding RNA. These germline-enriched miRNAs are loaded in multiple miRNA Argonautes, including the recently characterized germline Argonaute ALG-5, which we demonstrated is repressive when tethered to a reporter transcript. We extend these findings, identifying additional Pol III transcribed and noncanonical small RNAs in and human data sets, including human miR-4521. These young, noncanonical miRNAs may represent an early snapshot in the evolution of de novo miRNA genes.
微小RNA（miRNA）是一类在转录后调控基因表达的短RNA。在经典的miRNA生物合成过程中，初级miRNA由RNA聚合酶II从基因间区域或内含子区域转录而来，随后依次被微处理器复合体和Dicer切割，产生的成熟miRNA被装载到AGO蛋白中以抑制靶标mRNA。少数miRNA通过非经典生物合成途径产生，这些途径绕过了微处理器复合体和/或Dicer。在此，我们描述了一种新的由RNA聚合酶III依赖、不依赖微处理器复合体且依赖Dicer的生物合成途径，以秀丽隐杆线虫中的miRNA家族为例。尽管该miRNA家族基因座位于蛋白质编码基因的内含子区域，但我们发现这些miRNA来源于独立的RNA聚合酶III转录本。与其他RNA聚合酶III依赖的miRNA不同，该miRNA家族的小RNA是其基因座产生的主要物种，而非来自更大功能非编码RNA的片段。这些在生殖系中富集的miRNA被装载到多种miRNA AGO蛋白中，包括最近鉴定出的生殖系AGO蛋白ALG-5，我们证明当它与报告转录本相连时具有抑制作用。我们扩展了这些发现，在秀丽隐杆线虫和人类数据集中鉴定出了其他由RNA聚合酶III转录的非经典小RNA，包括人类miR-4521。这些年轻的非经典miRNA可能代表了从头产生的miRNA基因进化过程中的早期状态。
