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      Advances in the characterization of RNA‐binding proteins

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          Abstract

          From transcription, to transport, storage, and translation, RNA depends on association with different RNA‐binding proteins ( RBPs). Methods based on next‐generation sequencing and protein mass‐spectrometry have started to unveil genome‐wide interactions of RBPs but many aspects still remain out of sight. How many of the binding sites identified in high‐throughput screenings are functional? A number of computational methods have been developed to analyze experimental data and to obtain insights into the specificity of protein– RNA interactions. How can theoretical models be exploited to identify RBPs? In addition to oligomeric complexes, protein and RNA molecules can associate into granular assemblies whose physical properties are still poorly understood. What protein features promote granule formation and what effects do these assemblies have on cell function? Here, we describe the newest in silico, in vitro, and in vivo advances in the field of protein– RNA interactions. We also present the challenges that experimental and computational approaches will have to face in future studies. WIREs RNA 2016, 7:793–810. doi: 10.1002/wrna.1378

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          HITS-CLIP yields genome-wide insights into brain alternative RNA processing

          Summary Protein-RNA interactions play critical roles in all aspects of gene expression. Here we develop a genome-wide means of mapping protein-RNA binding sites in vivo, by high throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP). HITS-CLIP analysis of the neuron-specific splicing factor Nova2 revealed extremely reproducible RNA binding maps in multiple mouse brains. These maps provide genome-wide in vivo biochemical footprints confirming the previous prediction that the position of Nova binding determines the outcome of alternative splicing; moreover, they are sufficiently powerful to predict Nova action de novo. HITS-CLIP revealed a large number of Nova-RNA interactions in 3′ UTRs, leading to the discovery that Nova regulates alternative polyadenylation in the brain. HITS-CLIP, therefore, provides a robust, unbiased means to identify functional protein-RNA interactions in vivo.
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            HMMER web server: 2015 update

            The HMMER website, available at http://www.ebi.ac.uk/Tools/hmmer/, provides access to the protein homology search algorithms found in the HMMER software suite. Since the first release of the website in 2011, the search repertoire has been expanded to include the iterative search algorithm, jackhmmer. The continued growth of the target sequence databases means that traditional tabular representations of significant sequence hits can be overwhelming to the user. Consequently, additional ways of presenting homology search results have been developed, allowing them to be summarised according to taxonomic distribution or domain architecture. The taxonomy and domain architecture representations can be used in combination to filter the results according to the needs of a user. Searches can also be restricted prior to submission using a new taxonomic filter, which not only ensures that the results are specific to the requested taxonomic group, but also improves search performance. The repertoire of profile hidden Markov model libraries, which are used for annotation of query sequences with protein families and domains, has been expanded to include the libraries from CATH-Gene3D, PIRSF, Superfamily and TIGRFAMs. Finally, we discuss the relocation of the HMMER webserver to the European Bioinformatics Institute and the potential impact that this will have.
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              The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome.

              Many large noncoding RNAs (lncRNAs) regulate chromatin, but the mechanisms by which they localize to genomic targets remain unexplored. We investigated the localization mechanisms of the Xist lncRNA during X-chromosome inactivation (XCI), a paradigm of lncRNA-mediated chromatin regulation. During the maintenance of XCI, Xist binds broadly across the X chromosome. During initiation of XCI, Xist initially transfers to distal regions across the X chromosome that are not defined by specific sequences. Instead, Xist identifies these regions by exploiting the three-dimensional conformation of the X chromosome. Xist requires its silencing domain to spread across actively transcribed regions and thereby access the entire chromosome. These findings suggest a model in which Xist coats the X chromosome by searching in three dimensions, modifying chromosome structure, and spreading to newly accessible locations.
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                Author and article information

                Contributors
                gian.tartaglia@crg.es
                Journal
                Wiley Interdiscip Rev RNA
                Wiley Interdiscip Rev RNA
                10.1002/(ISSN)1757-7012
                WRNA
                Wiley Interdisciplinary Reviews. RNA
                John Wiley & Sons, Inc. (Hoboken, USA )
                1757-7004
                1757-7012
                08 August 2016
                Nov-Dec 2016
                : 7
                : 6 ( doiID: 10.1002/wrna.2016.7.issue-6 )
                : 793-810
                Affiliations
                [ 1 ] Centre for Genomic Regulation (CRG)The Barcelona Institute for Science and Technology, Dr. Aiguader 88 08003 BarcelonaSpain
                [ 2 ]Universitat Pompeu Fabra (UPF) BarcelonaSpain
                [ 3 ] IFOM FoundationFIRC Institute of Molecular Oncology Foundation MilanItaly
                [ 4 ]Institució Catalana de Recerca i Estudis Avançats (ICREA) BarcelonaSpain
                Author notes
                [*] [* ]Correspondence to: gian.tartaglia@ 123456crg.es
                [†]

                These authors contributed equally to this article.

                Article
                WRNA1378
                10.1002/wrna.1378
                5113702
                27503141
                9a4307ba-842a-473f-8d80-43047c6a1936
                © 2016 The Authors. WIREs RNA published by Wiley Periodicals, Inc.

                This is an open access article under the terms of the Creative Commons Attribution‐NonCommercial‐NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non‐commercial and no modifications or adaptations are made.

                History
                : 28 March 2016
                : 14 June 2016
                : 23 June 2016
                Page count
                Figures: 4, Tables: 3, Pages: 18, Words: 11306
                Funding
                Funded by: European Union Seventh Framework Programme
                Award ID: FP7/2007‐2013
                Funded by: European Research Council
                Award ID: RIBOMYLOME_309545
                Funded by: Spanish Ministry of Economy and Competitiveness
                Award ID: BFU2014‐55054‐P
                Funded by: AGAUR
                Award ID: 2014 SGR 00685
                Funded by: Centro de Excelencia Severo Ochoa 2013–2017
                Award ID: SEV‐2012‐0208
                Categories
                Protein‐RNA Recognition
                RNA‐Protein Complexes
                RNA in Disease
                Advanced Review
                Advanced Reviews
                Custom metadata
                2.0
                wrna1378
                wrna1378-hdr-0001
                November/December 2016
                Converter:WILEY_ML3GV2_TO_NLMPMC version:4.9.7 mode:remove_FC converted:17.11.2016

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