title: Hyper conserved elements in vertebrate mRNA 3'-UTRs reveal a translational network of RNA-binding proteins controlled by HuR.
abstract: Little is known regarding the post-transcriptional networks that control gene expression in eukaryotes. Additionally, we still need to understand how these networks evolve, and the relative role played in them by their sequence-dependent regulatory factors, non-coding RNAs (ncRNAs) and RNA-binding proteins (RBPs). Here, we used an approach that relied on both phylogenetic sequence sharing and conservation in the whole mapped 3'-untranslated regions (3'-UTRs) of vertebrate species to gain knowledge on core post-transcriptional networks. The identified human hyper conserved elements (HCEs) were predicted to be preferred binding sites for RBPs and not for ncRNAs, namely microRNAs and long ncRNAs. We found that the HCE map identified a well-known network that post-transcriptionally regulates histone mRNAs. We were then able to discover and experimentally confirm a translational network composed of RNA Recognition Motif (RRM)-type RBP mRNAs that are positively controlled by HuR, another RRM-type RBP. HuR shows a preference for these RBP mRNAs bound in stem-loop motifs, confirming its role as a 'regulator of regulators'. Analysis of the transcriptome-wide HCE distribution revealed a profile of prevalently small clusters separated by unconserved intercluster RNA stretches, which predicts the formation of discrete small ribonucleoprotein complexes in the 3'-UTRs.
authors: Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Trento, via delle Regole, 101 38123 Mattarello (TN) Italy.
authors: Erik
authors: E
authors: Dassi
authors: Paola
authors: P
authors: Zuccotti
authors: Sara
authors: S
authors: Leo
authors: Alessandro
authors: A
authors: Provenzani
authors: Michael
authors: M
authors: Assfalg
authors: Mariapina
authors: M
authors: D'Onofrio
authors: Paola
authors: P
authors: Riva
authors: Alessandro
authors: A
authors: Quattrone
mesh_terms: D020413:3' Untranslated Regions; D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D017124:Conserved Sequence; D051959:ELAV Proteins / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D006657:Histones / Q000235:genetics; D006801:Humans; D055029:Inverted Repeat Sequences; D061986:MCF-7 Cells; D014176:Protein Biosynthesis; D012333:RNA, Messenger / Q000235:genetics*; D016601:RNA-Binding Proteins / Q000235:genetics*; D016415:Sequence Alignment; D014714:Vertebrates
chemical_list: D020413:3' Untranslated Regions; D051959:ELAV Proteins; D006657:Histones; D012333:RNA, Messenger; D016601:RNA-Binding Proteins
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