Exploring the landscape of tools and resources for the analysis of long non-coding RNAs

Abstract

In recent years, research on long non-coding RNAs (lncRNAs) has gained considerable attention due to the increasing number of newly identified transcripts. Several characteristics make their functional evaluation challenging, which called for the urgent need to combine molecular biology with other disciplines, including bioinformatics. Indeed, the recent development of computational pipelines and resources has greatly facilitated both the discovery and the mechanisms of action of lncRNAs. In this review, we present a curated collection of the most recent computational resources, which have been categorized into distinct groups: databases and annotation, identification and classification, interaction prediction, and structure prediction. As the repertoire of lncRNAs and their analysis tools continues to expand over the years, standardizing the computational pipelines and improving the existing annotation of lncRNAs will be crucial to facilitate functional genomics studies.

Keywords: Bioinformatics; Genomics; LncRNA; NcRNA; RNA; Transcriptomics.

Graphical abstract

Fig. 1

Mechanisms of action of lncRNAs. Cytoplasmic-enriched lncRNAs (a, b) can regulate mRNA translation and stability , , , or act as templates for micro-peptides , . Nuclear-enriched lncRNAs (c-i) can act as enhancers , guides , decoy molecules , or chromatin architects , , by the interaction with a variety of transcription factors and epigenetic effectors, typically including DNA methyltransferases, histone-modifying, or chromatin remodeling enzymes.