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

Abstract

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.

Precise annotation of tick mitochondrial genomes reveals multiple copy number variation of short tandem repeats and one transposon-like element

“…One of tRNA Ser s(mtDNA: 5713:5769) and tRNA Cys ( Figure 2B) had no D-arms, whereas tRNA Ala ( Figure 2B), tRNA Glu , tRNA Tyr and tRNA Phe had unstable T-arms. Another new nding was that the intergenic regions between tick mt tRNA genes are longer than those in mammalian except a novel 31-nt ncRNA [4], which was generated in the gene order rearrangement of mammalian mt tRNA genes. Although these intergenic regions in ticks were cleaved between their neighbouring tRNAs to form small RNAs (sRNAs) shorter than 10 bp, they are not likely to have biological functions, in our view.…”

“…Based on these ndings, we proposed the uninterrupted transcription of mammal mt genomes [3]. In addition, we proposed that long antisense transcripts degrade quickly as transient RNAs, making them unlikely to perform speci c functions [4], although all antisense transcripts are processed from two primary transcripts. The second contribution concerned the use 5′ and 3′ end small RNAs (5′ and 3′ sRNAs) [4] to annotate mt genes to a resolution of 1 bp, subsequently dubbed "precise annotation" [5].…”

“…In addition, we proposed that long antisense transcripts degrade quickly as transient RNAs, making them unlikely to perform speci c functions [4], although all antisense transcripts are processed from two primary transcripts. The second contribution concerned the use 5′ and 3′ end small RNAs (5′ and 3′ sRNAs) [4] to annotate mt genes to a resolution of 1 bp, subsequently dubbed "precise annotation" [5]. Precise annotation of these accurate genomes led us to discover a novel 31-nt ncRNA in mammalian mt DNA [4] and that the copy numbers of tandem repeats exhibit great diversity within an E. fullo individual [5].…”

“…The second contribution concerned the use 5′ and 3′ end small RNAs (5′ and 3′ sRNAs) [4] to annotate mt genes to a resolution of 1 bp, subsequently dubbed "precise annotation" [5]. Precise annotation of these accurate genomes led us to discover a novel 31-nt ncRNA in mammalian mt DNA [4] and that the copy numbers of tandem repeats exhibit great diversity within an E. fullo individual [5]. Recently, precise annotation of human, chimpanzee, rhesus macaque and mouse mt genomes has been performed to study ve Conserved Sequence Blocks (CSBs) in the mt D-loop region [6]; this ultimately led to a deep understanding of the mechanisms involved in the RNA-DNA transition and even the functions of the D-loop.…”

A negative feedback model to explain regulation of SARS-CoV-2 replication and transcription

“…The genomic RNA, as a positive-sense RNA [gRNA(+)], is used as a template for the translation of ORF1a and ORF1b, and the replication and transcription of the SARS-CoV-2 genome. Recently, the translation of 10 other proteins (S, E, M, N, ORF3a, 6, 7a, 7b, 8 and 10) of SARS-CoV-2 has been reported in a study [2] that directly validates the prevailing "leader-to-body fusion" model using Nanopore RNA-seq-a direct RNA sequencing method [3]. In the model validated in that study (Figure 1A with varied length is located immediately upstream of ORFs except ORF1a and 1b ( Figure 1A).…”