Hyper conserved elements in vertebrate mRNA 3′-UTRs reveal a translational network of RNA-binding proteins controlled by HuR

被引:27
|
作者
Dassi, Erik [1 ]
Zuccotti, Paola [2 ]
Leo, Sara [1 ]
Provenzani, Alessandro [3 ]
Assfalg, Michael [4 ]
D'Onofrio, Mariapina [4 ]
Riva, Paola [2 ]
Quattrone, Alessandro [1 ]
机构
[1] Univ Trento, Ctr Integrat Biol, Lab Translat Genom, I-38123 Mattarello, TN, Italy
[2] Univ Milan, Dept Med Biotechnol & Translat Med, I-20133 Milan, Italy
[3] Univ Trento, Ctr Integrat Biol, Lab Genom Screening, I-38123 Mattarello, TN, Italy
[4] Univ Verona, Dept Biotechnol, I-37134 Verona, Italy
关键词
KINASE-REGULATED PHOSPHORYLATION; ULTRACONSERVED ELEMENTS; POSTTRANSCRIPTIONAL REGULATION; RIBONUCLEOPROTEIN COMPLEXES; UNTRANSLATED REGIONS; WIDE ANALYSIS; MICRORNAS; SEQUENCES; DATABASE; TRANSCRIPTOME;
D O I
10.1093/nar/gkt017
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
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.
引用
收藏
页码:3201 / 3216
页数:16
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