Introduction to Bioinformatics Resources for Post-transcriptional Regulation of Gene Expression

Abstract

Untranslated regions of mRNA (UTRs) are involved in defining the fate of the transcript through processes such as mRNA localization, degradation, translation initiation regulation, and several others: the action of trans-factors such as RNA-binding proteins and non-coding RNAs, combined with the presence of defined sequence and structural cis-elements, ultimately determines protein synthesis levels. Identifying functional regions in UTRs and uncovering post-transcriptional regulators acting upon these is thus of paramount importance to understand this regulatory layer: these tasks can now be approached computationally to reduce the testable hypothesis space and drive the experimental validation in a more effective way.This chapter will focus on presenting databases and tools allowing to study the various aspects of post-transcriptional regulation, including the profiling of actively translated mRNAs, regulatory network analysis (e.g., RBP and ncRNA binding sites), trans-factor binding sites prediction, motif search (sequence and secondary structure), and other aspects of this regulatory layer: two potential analysis pipelines are also presented as practical examples of how these tools could be integrated and effectively employed.

Keywords: Binding site; Bioinformatics; Data analysis; Database; Motif; Omics; Pipeline; Polysomal profiling; Prediction; RBP; Secondary structure; UTR; ncRNA.