LNCediting: a database for functional effects of RNA editing in lncRNAs

Abstract

RNA editing is a widespread post-transcriptional mechanism that can make a single base change on specific nucleotide sequence in an RNA transcript. RNA editing events can result in missense codon changes and modulation of alternative splicing in mRNA, and modification of regulatory RNAs and their binding sites in noncoding RNAs. Recent computational studies accurately detected more than 2 million A-to-I RNA editing sites from next-generation sequencing (NGS). However, the vast majority of these RNA editing sites have unknown functions and are in noncoding regions of the genome. To provide a useful resource for the functional effects of RNA editing in long noncoding RNAs (lncRNAs), we systematically analyzed the A-to-I editing sites in lncRNAs across human, rhesus, mouse, and fly, and observed an appreciable number of RNA editing sites which can significantly impact the secondary structures of lncRNAs and lncRNA–miRNA interactions. All the data were compiled into LNCediting, a user-friendly database (http://bioinfo.life.hust.edu.cn/LNCediting/). LNCediting provides customized tools to predict functional effects of novel editing sites in lncRNAs. We hope that it will become an important resource for exploring functions of RNA editing sites in lncRNAs.

Systematic characterization of A-to-I RNA editing hotspots in microRNAs across human cancers

“…In addition to protein-coding genes, RNA editing can occur in noncoding genes, such as lncRNAs and microRNAs (miRNAs) (Gong et al 2014(Gong et al , 2017. miRNAs are ∼22-nt small RNAs that function in post-transcriptional gene regulation and participate in various cellular pathways and pathological processes, including cancer (Bartel 2004;Garzon et al 2009).…”

State of the art technologies to explore long non‐coding RNAs in cancer

“…LncRNAs have been shown to undergo A‐to‐I editing with important effects on their secondary structures and interaction with other RNA species 13. As deregulation of such editing events may perturb lncRNA interaction networks and lead to disease conditions including cancer, a complete picture of normal or abnormal A‐to‐I editing is of paramount importance 115.…”

“…Deamination of Adenosine to inosine is a common RNA modification, which plays important regulatory roles and has been implicated in several disorders including cancer [114]. LncRNAs have been shown to undergo A-to-I editing with important effects on their secondary structures and interaction with other RNA species [13]. As deregulation of such editing events may perturb lncRNA interaction networks and lead to disease conditions including cancer, a complete picture of normal or abnormal A-to-I editing is of paramount importance [115].…”

“…Among transcripts encoded by these regions are long non-coding RNAs [5]. Most lncRNAs are transcribed by RNA polymerase II [1], and similar to protein-coding RNAs, can be subjected to post-transcriptional modifications, including 5 0 -end capping, 3 0 -end polyadenylation, splicing [6][7][8][9][10][11] N 6 adenosine methylation (m 6 A) [12] and A-to-I editing [13]. Due to not having a comprehensive knowledge of their function, LncRNAs are categorized based on their location relative to the protein-coding genes as: sense (which are transcribed from sense strand of protein-coding genes and overlap one or more exons and introns), antisense (which are transcribed from the antisense strand of protein-coding genes), bidirectional (which are located 1 kb away from promoters of protein-coding genes in the opposite direction), intronic (which are located between exons of protein-coding genes) and intergenic (which are located between two protein-coding genes) [5,7,14,15].…”

The Butterfly Effect of RNA Alterations on Transcriptomic Equilibrium

“…In addition to editing of mRNAs and miRNAs, global analysis of A-to-I RNA editing events in 17 cancer types from TCGA detected widespread RNA editing on lncRNAs across different cancers [126,145]. Recent development of LNCediting, a lncRNA secondary structure prediction tool, could predict the impact of A-to-I RNA editing on lncRNA secondary structures, as well as the potential alterations in miRNA-lncRNA interactions [145]. The functional implications of RNA editing on lncRNAs have yet to be discovered, but with our current knowledge of the importance of lncRNAs in cancer, we postulate that RNA editing of lncRNA may contribute to tumorigenesis.…”