Genetic activation of canonical RNA interference in mice [liver]

Canonical RNA interference (RNAi) is sequence-specific mRNA degradation guided by small interfering RNAs (siRNAs) made from long double-stranded RNA (dsRNA) by RNase III Dicer. RNAi has different functions in eukaryotes including gene regulation, antiviral innate immunity or defense against transposable elements. In mammals, RNAi is constrained by inefficient cleavage of dsRNA by Dicer because it is adapted to produce microRNAs, a different class of small RNAs. An exception of the rule is highly active RNAi in mouse oocytes, which employs a truncated Dicer isoform (ΔHEL1). A homozygous mutation of murine Dicer to express only the truncated variant causes major dysregulation of microRNAs and perinatal lethality. Here, we report the phenotype and RNAi activity in DicerΔHEL1/wt mice, which are viable, fertile, slightly smaller, and show minimal miRNome changes. At the same time, endogenous siRNA levels are increased by an order of magnitude in DicerΔHEL1/wt mice. We show that siRNA abundance is limited by available dsRNA but not by the Protein Kinase R, an innate immunity factor shown to limit siRNA biogenesis in cultured cells. Using dsRNA expressed from a transgene, functional RNAi in vivo was successfully induced in the heart. DicerΔHEL1/wt mice thus represent a new model for researching mammalian canonical RNAi in vivo and offer an unprecedented platform for addressing earlier claims about its biological roles. Bulk small RNA-seq of 15 mouse liver samples in five different genotypes: - 3x wt - 3x DicerSOM/wt Pkr+/– Tg(MosIR) - 3x DicerSOM/wt Pkr–/– Tg(MosIR) - 3x DicerΔHEL1/wt Pkr+/– Tg(MosIR) - 3x DicerΔHEL1/wt Pkr–/– Tg(MosIR)

经典RNA干扰（RNA interference, RNAi）是由核糖核酸酶III Dicer从长双链RNA（long double-stranded RNA, dsRNA）生成的小干扰RNA（small interfering RNAs, siRNAs）所介导的序列特异性mRNA降解过程。RNAi在真核生物（eukaryotes）中具备多种功能，涵盖基因调控、抗病毒先天免疫以及抵御转座因子（transposable elements）的防御机制。在哺乳动物（mammals）体内，RNAi的活性受限于Dicer对dsRNA的低效切割——这是因为Dicer的演化适配性使其主要用于生成另一类小RNA：微小RNA（microRNAs, miRNAs）。该规律的一个例外是小鼠卵母细胞中高度活跃的RNAi，此类RNAi依赖于截短型Dicer同工型（ΔHEL1）。若小鼠Dicer发生纯合突变，仅表达该截短变体，则会引发微小RNA谱的严重失调，并导致围产期致死。

本研究报道了DicerΔHEL1/wt小鼠的表型与RNAi活性：该品系小鼠可正常存活、可育，体型略小于野生型个体，且微小RNA组（miRNome）仅存在极细微的变化。与此同时，DicerΔHEL1/wt小鼠体内的内源性siRNA水平提升了一个数量级。本研究证实，siRNA的丰度受限于可获取的dsRNA，而非蛋白激酶R（Protein Kinase R, PKR）——后者是一种先天免疫因子，既往研究显示其可在培养细胞中限制siRNA的生物发生。利用由转基因（transgene）表达的dsRNA，本研究成功在小鼠心脏中诱导出具有功能的体内RNAi。因此，DicerΔHEL1/wt小鼠为研究哺乳动物体内的经典RNA干扰提供了全新的动物模型，也为验证此前关于其生物学功能的相关论断提供了前所未有的研究平台。

本数据集包含5种不同基因型的15份小鼠肝脏样本的批量小RNA测序（bulk small RNA-seq）数据：
- 3份野生型（wt）样本
- 3份DicerSOM/wt Pkr+/– Tg(MosIR)样本
- 3份DicerSOM/wt Pkr–/– Tg(MosIR)样本
- 3份DicerΔHEL1/wt Pkr+/– Tg(MosIR)样本
- 3份DicerΔHEL1/wt Pkr–/– Tg(MosIR)样本