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RNA binding proteins and their recognition elements within the transcriptome

Guest Editors: John Rinn and Jernej Ule

In this issue of Genome Biology we present a special collection of Research, Method, Software, Review, Research Highlight and Editorial articles focusing on the theme of ‘the RBPome’, a term we use to describe RNA-binding proteins (RBPs) and their recognition elements within the transcriptome. The issue provides a number of new insights into the role of RBPs in gene regulation and incorporates studies using a variety of different approaches to assay RNA-protein interactions. Advances in computational analyses for the study of RBPome data are also reported. More information and perspective on our RBPome issue can be found on the BioMed Central blog.

  1. Content type: Method

    RNA-binding proteins (RBPs) regulate splicing according to position-dependent principles, which can be exploited for analysis of regulatory motifs. Here we present RNAmotifs, a method that evaluates the sequen...

    Authors: Matteo Cereda, Uberto Pozzoli, Gregor Rot, Peter Juvan, Anthony Schweitzer, Tyson Clark and Jernej Ule

    Citation: Genome Biology 2014 15:R20

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  2. Content type: Research

    Retention of a subset of introns in spliced polyadenylated mRNA is emerging as a frequent, unexplained finding from RNA deep sequencing in mammalian cells.

    Authors: Vicky Cho, Yan Mei, Arleen Sanny, Stephanie Chan, Anselm Enders, Edward M Bertram, Andy Tan, Christopher C Goodnow and T Daniel Andrews

    Citation: Genome Biology 2014 15:R26

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  3. Content type: Research highlight

    Smaug, a protein repressing translation and inducing mRNA decay, directly controls an unexpectedly large number of maternal mRNAs driving early Drosophila development.

    Authors: Michael Götze and Elmar Wahle

    Citation: Genome Biology 2014 15:101

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  4. Content type: Review

    High-throughput sequencing of RNAs crosslinked to Argonaute proteins reveals not only a multitude of atypical miRNA binding sites but also of miRNA targets with atypical functions, and can be used to infer qua...

    Authors: Nitish Mittal and Mihaela Zavolan

    Citation: Genome Biology 2014 15:202

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  5. Content type: Software

    CLIP-seq is widely used to study genome-wide interactions between RNA-binding proteins and RNAs. However, there are few tools available to analyze CLIP-seq data, thus creating a bottleneck to the implementatio...

    Authors: Beibei Chen, Jonghyun Yun, Min Soo Kim, Joshua T Mendell and Yang Xie

    Citation: Genome Biology 2014 15:R18

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  6. Content type: Method

    We present GraphProt, a computational framework for learning sequence- and structure-binding preferences of RNA-binding proteins (RBPs) from high-throughput experimental data. We benchmark GraphProt, demonstra...

    Authors: Daniel Maticzka, Sita J Lange, Fabrizio Costa and Rolf Backofen

    Citation: Genome Biology 2014 15:R17

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  7. Content type: Method

    RNA-binding proteins (RBPs) bind to their target RNA molecules by recognizing specific RNA sequences and structural contexts. The development of CLIP-seq and related protocols has made it possible to exhaustiv...

    Authors: Tsukasa Fukunaga, Haruka Ozaki, Goro Terai, Kiyoshi Asai, Wataru Iwasaki and Hisanori Kiryu

    Citation: Genome Biology 2014 15:R16

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  8. Content type: Software

    We have developed a novel machine-learning approach, MutPred Splice, for the identification of coding region substitutions that disrupt pre-mRNA splicing. Applying MutPred Splice to human disease-causing exoni...

    Authors: Matthew Mort, Timothy Sterne-Weiler, Biao Li, Edward V Ball, David N Cooper, Predrag Radivojac, Jeremy R Sanford and Sean D Mooney

    Citation: Genome Biology 2014 15:R19

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  9. Content type: Research

    RNA-binding proteins (RBPs) mediate mRNA biogenesis, translation and decay. We recently developed an approach to profile transcriptome-wide RBP contacts on polyadenylated transcripts by next-generation sequenc...

    Authors: Markus Schueler, Mathias Munschauer, Lea Haarup Gregersen, Ana Finzel, Alexander Loewer, Wei Chen, Markus Landthaler and Christoph Dieterich

    Citation: Genome Biology 2014 15:R15

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  10. Content type: Research

    Light is one of the most important factors regulating plant growth and development. Light-sensing photoreceptors tightly regulate gene expression to control photomorphogenic responses. Although many levels of ...

    Authors: Hshin-Ping Wu, Yi-shin Su, Hsiu-Chen Chen, Yu-Rong Chen, Chia-Chen Wu, Wen-Dar Lin and Shih-Long Tu

    Citation: Genome Biology 2014 15:R10

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  11. Content type: Research

    Various microRNAs (miRNAs) are up- or downregulated in tumors. However, the repression of cognate miRNA targets responsible for the phenotypic effects of this dysregulation in patients remains largely unexplor...

    Authors: Thalia A Farazi, Jelle J ten Hoeve, Miguel Brown, Aleksandra Mihailovic, Hugo M Horlings, Marc J van de Vijver, Thomas Tuschl and Lodewyk FA Wessels

    Citation: Genome Biology 2014 15:R9

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  12. Content type: Research

    Nrd1 and Nab3 are essential sequence-specific yeast RNA binding proteins that function as a heterodimer in the processing and degradation of diverse classes of RNAs. These proteins also regulate several mRNA c...

    Authors: Shaun Webb, Ralph D Hector, Grzegorz Kudla and Sander Granneman

    Citation: Genome Biology 2014 15:R8

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  13. Content type: Research

    Sm proteins are multimeric RNA-binding factors, found in all three domains of life. Eukaryotic Sm proteins, together with their associated RNAs, form small ribonucleoprotein (RNP) complexes important in multip...

    Authors: Zhipeng Lu, Xiaojun Guan, Casey A Schmidt and A Gregory Matera

    Citation: Genome Biology 2014 15:R7

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  14. Content type: Research

    Long noncoding RNAs (lncRNAs) form an abundant class of transcripts, but the function of the majority of them remains elusive. While it has been shown that some lncRNAs are bound by ribosomes, it has also been...

    Authors: Sebastiaan van Heesch, Maarten van Iterson, Jetse Jacobi, Sander Boymans, Paul B Essers, Ewart de Bruijn, Wensi Hao, Alyson W MacInnes, Edwin Cuppen and Marieke Simonis

    Citation: Genome Biology 2014 15:R6

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  15. Content type: Research

    Smaug is an RNA-binding protein that induces the degradation and represses the translation of mRNAs in the early Drosophila embryo. Smaug has two identified direct target mRNAs that it differentially regulates: n...

    Authors: Linan Chen, Jason G Dumelie, Xiao Li, Matthew HK Cheng, Zhiyong Yang, John D Laver, Najeeb U Siddiqui, J Timothy Westwood, Quaid Morris, Howard D Lipshitz and Craig A Smibert

    Citation: Genome Biology 2014 15:R4

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  16. Content type: Method

    Although numerous approaches have been developed to map RNA-binding sites of individual RNA-binding proteins (RBPs), few methods exist that allow assessment of global RBP–RNA interactions. Here, we describe PI...

    Authors: Ian M Silverman, Fan Li, Anissa Alexander, Loyal Goff, Cole Trapnell, John L Rinn and Brian D Gregory

    Citation: Genome Biology 2014 15:R3

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  17. Content type: Research

    Sm-like proteins are highly conserved proteins that form the core of the U6 ribonucleoprotein and function in several mRNA metabolism processes, including pre-mRNA splicing. Despite their wide occurrence in al...

    Authors: Peng Cui, Shoudong Zhang, Feng Ding, Shahjahan Ali and Liming Xiong

    Citation: Genome Biology 2014 15:R1

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  18. Content type: Research

    RNA-binding proteins regulate a number of cellular processes, including synthesis, folding, translocation, assembly and clearance of RNAs. Recent studies have reported that an unexpectedly large number of prot...

    Authors: Davide Cirillo, Domenica Marchese, Federico Agostini, Carmen Maria Livi, Teresa Botta-Orfila and Gian Gaetano Tartaglia

    Citation: Genome Biology 2014 15:R13

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