Exploring Evidence of Non-coding RNA Translation With Trips-Viz and GWIPS-Viz Browsers

Abstract

Detection of translation in so-called non-coding RNA provides an opportunity for identification of novel bioactive peptides and microproteins. The main methods used for these purposes are ribosome profiling and mass spectrometry. A number of publicly available datasets already exist for a substantial number of different cell types grown under various conditions, and public data mining is an attractive strategy for identification of translation in non-coding RNAs. Since the analysis of publicly available data requires intensive data processing, several data resources have been created recently for exploring processed publicly available data, such as OpenProt, GWIPS-viz, and Trips-Viz. In this work we provide a detailed demonstration of how to use the latter two tools for exploring experimental evidence for translation of RNAs hitherto classified as non-coding. For this purpose, we use a set of transcripts with substantially different patterns of ribosome footprint distributions. We discuss how certain features of these patterns can be used as evidence for or against genuine translation. During our analysis we concluded that the MTLN mRNA, previously misannotated as lncRNA LINC000116, likely encodes only a short proteoform expressed from shorter RNA transcript variants.

Streptomyces rare codon UUA: from features associated with 2 adpA related locations to candidate phage regulatory translational bypassing

“…We examined published ribosome profiling data to determine if it contains unidentified pertinent information about UUA decoding. We started by analysing the S. coelicolor ribosome profiling data [ 88 ] available from the GWIPS database [ 89 , 90 ]. A relatively high peak at the UUA codon inside adpA confirmed ribosome pausing at this rare codon during mRNA translation (Supplementary Figure 7A).…”

A review of Ribosome profiling and tools used in Ribo-seq data analysis

“…The blue circles contained keywords that served as focal points of Ribo-seq research in the past, such as small open reading frames, mouse and human. Items that appear more orange indicate their recent emergence, for example, crispr [22] , differential gene expression [23] , non-coding RNA [24] and apoptosis [25] , and therefore, showcase the current trends in Ribo-seq and RNA-seq research.…”

LncRNA NEAT1 in the pathogenesis of liver‐related diseases

“…12 However, hundreds of lncRNAs are polyadenylated, present in the cytoplasm, and capable of attaching themselves to ribosomes, suggesting that they may be translated and produce micro-peptides. 13 LncRNAs exert significant influence over protein expression and crucial intracellular signaling pathways. 14 Extensive research has been conducted to investigate the involvement of lncRNAs in the pathogenesis of various diseases, revealing their contribution to disease development.…”

“…LncRNAs encompass a diverse range of RNA molecules, typically more than 200 bp in length, which do not commonly undergo translation to produce proteins 12 . However, hundreds of lncRNAs are polyadenylated, present in the cytoplasm, and capable of attaching themselves to ribosomes, suggesting that they may be translated and produce micro‐peptides 13 . LncRNAs exert significant influence over protein expression and crucial intracellular signaling pathways 14 .…”