title: Introduction to Bioinformatics Resources for Post-transcriptional Regulation of Gene Expression.
abstract: Untranslated regions (UTRs) and, to a lesser extent, coding sequences of mRNAs are involved in defining the fate of the mature transcripts through the modulation of three primary control processes, mRNA localization, degradation and translation; the action of trans-factors such as RNA-binding proteins (RBPs) and noncoding RNAs (ncRNAs) combined with the presence of defined sequence and structural cis-elements ultimately determines translation levels. Identifying functional regions in UTRs and uncovering post-transcriptional regulators acting upon these regions is thus of paramount importance to understand the spectrum of regulatory possibilities for any given mRNA. This tasks can now be approached computationally, to reduce the space of testable hypotheses and to drive experimental validation.This chapter focuses on presenting databases and tools allowing to study the various aspects of post-transcriptional regulation, including motif search (sequence and secondary structure), prediction of regulatory networks (e.g., RBP and ncRNA binding sites), profiling of the mRNAs translational state, and other aspects of this level of gene expression regulation. Two analysis pipelines are also presented as practical examples of how the described tools could be integrated and effectively employed.
authors.affiliation: Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Via Delle Regole n. 101, 38123, Mattarello, Trento, Italy.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Quattrone
authors.affiliation: Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Via Delle Regole n. 101, 38123, Mattarello, Trento, Italy. erik.dassi@unitn.it.
authors.forename: Erik
authors.initials: E
authors.lastname: Dassi
mesh_terms: D019295:Computational Biology / Q000379:methods*; D005786:Gene Expression Regulation / Q000235:genetics*; D012333:RNA, Messenger / Q000096:biosynthesis / Q000235:genetics*; D022661:RNA, Untranslated / Q000235:genetics; D016601:RNA-Binding Proteins / Q000235:genetics; D020506:Untranslated Regions / Q000235:genetics
chemical_list: D012333:RNA, Messenger; D022661:RNA, Untranslated; D016601:RNA-Binding Proteins; D020506:Untranslated Regions
keywords: Binding site; Bioinformatics; Data analysis; Database; Motif; Omics; Pipeline; Polysomal profiling; Prediction; RBP; Secondary structure; UTR; ncRNA