Control of somatic tissue differentiation by the long non-coding RNA TINCR. Structures of the human and Drosophila 80S ribosome. Molecular mapping of the determinants involved in human Staufen-ribosome association. iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. RNA targets and specificity of Staufen, a double-stranded RNA-binding protein in Caenorhabditis elegans. Functional signature for the recognition of specific target mRNAs by human Staufen1 protein. Genome-wide analysis of Staufen-associated mRNAs identifies secondary structures that confer target specificity. Staufen1 regulates diverse classes of mammalian transcripts. Staufen1 senses overall transcript secondary structure to regulate translation. Mammalian Staufen1 recruits Upf1 to specific mRNA 3′ UTRs so as to elicit mRNA decay. lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3′ UTRs via Alu elements. The multifunctional Staufen proteins: conserved roles from neurogenesis to synaptic plasticity. Unambiguous identification of miRNA:target site interactions by different types of ligation reactions. Cross-linking, ligation, and sequencing of hybrids reveals RNA–RNA interactions in yeast. Kudla, G., Granneman, S., Hahn, D., Beggs, J. Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges. Metastasis-suppressor transcript destabilization through TARBP2 binding of mRNA hairpins. Global analysis of RNA secondary structure in two metazoans. Landscape and variation of RNA secondary structure across the human transcriptome. Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo. Rouskin, S., Zubradt, M., Washietl, S., Kellis, M. In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features. Understanding the transcriptome through RNA structure. Our study reveals the fundamental role of mRNA secondary structures in gene expression and introduces hiCLIP as a widely applicable method for discovering new, especially long-range, RNA duplexes. We also discover a duplex spanning 858 nucleotides in the 3′ UTR of the X-box binding protein 1 ( XBP1) mRNA that regulates its cytoplasmic splicing and stability. Using this technique to investigate RNA structures bound by Staufen 1 (STAU1) in human cells, we uncover a dominance of intra-molecular RNA duplexes, a depletion of duplexes from coding regions of highly translated mRNAs, an unexpected prevalence of long-range duplexes in 3′ untranslated regions (UTRs), and a decreased incidence of single nucleotide polymorphisms in duplex-forming regions. Here we present hiCLIP, a biochemical technique for transcriptome-wide identification of RNA secondary structures interacting with RNA-binding proteins (RBPs). However, little is known about the in vivo structure of full-length mRNAs. The structure of messenger RNA is important for post-transcriptional regulation, mainly because it affects binding of trans-acting factors 1.
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