Table_1_Using Pan RNA-Seq Analysis to Reveal the Ubiquitous Existence of 5′ and 3′ End Small RNAs.XLSX

In this study, we used pan RNA-seq analysis to reveal the ubiquitous existence of both 5′ and 3′ end small RNAs (5′ and 3′ sRNAs). 5′ and 3′ sRNAs alone can be used to annotate nuclear non-coding and mitochondrial genes at 1-bp resolution and identify new steady RNAs, which are usually transcribed from functional genes. Then, we provided a simple and cost effective way for the annotation of nuclear non-coding and mitochondrial genes and the identification of new steady RNAs, particularly long non-coding RNAs (lncRNAs). Using 5′ and 3′ sRNAs, the annotation of human mitochondrial was corrected and a novel ncRNA named non-coding mitochondrial RNA 1 (ncMT1) was reported for the first time in this study. We also found that most of human tRNA genes have downstream lncRNA genes as lncTRS-TGA1-1 and corrected the misunderstanding of them in previous studies. Using 5′, 3′, and intronic sRNAs, we reported for the first time that enzymatic double-stranded RNA (dsRNA) cleavage and RNA interference (RNAi) might be involved in the RNA degradation and gene expression regulation of U1 snRNA in human. We provided a different perspective on the regulation of gene expression in U1 snRNA. We also provided a novel view on cancer and virus-induced diseases, leading to find diagnostics or therapy targets from the ribonuclease III (RNase III) family and its related pathways. Our findings pave the way toward a rediscovery of dsRNA cleavage and RNAi, challenging classical theories.

本研究采用泛RNA测序（pan RNA-seq）分析，揭示了5'端与3'端小RNA（5′ and 3′ sRNAs）普遍存在的现象。仅依靠5'端与3'端小RNA，即可实现1碱基分辨率下的核非编码基因与线粒体基因注释，并鉴定出通常由功能基因转录产生的新型稳定RNA。据此，我们开发了一种简便且经济高效的方法，用于核非编码基因与线粒体基因的注释，以及新型稳定RNA的鉴定，尤其是长链非编码RNA（long non-coding RNAs, lncRNAs）。借助5'与3'端小RNA，我们修正了人类线粒体基因的注释，并首次报道了一种新型非编码RNA——非编码线粒体RNA1（non-coding mitochondrial RNA 1, ncMT1）。我们还发现，绝大多数人类转运RNA（tRNA）基因下游均存在长链非编码RNA基因lncTRS-TGA1-1，并纠正了既往研究对该类基因的认知偏差。通过5'端、3'端与内含子小RNA，我们首次提出，酶促双链RNA（double-stranded RNA, dsRNA）切割与RNA干扰（RNA interference, RNAi）可能参与人类U1小核RNA（U1 snRNA）的RNA降解与基因表达调控，为U1小核RNA的基因表达调控研究提供了全新视角。此外，我们针对癌症与病毒诱导性疾病提出了全新见解，有望从核糖核酸酶III（ribonuclease III, RNase III）家族及其相关通路中筛选诊断或治疗靶点。本研究的发现为双链RNA切割与RNA干扰的重新认识铺平了道路，对经典理论提出了挑战。