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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. Method

    RNAmotifs: prediction of multivalent RNA motifs that control alternative splicing

    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...

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

    Genome Biology 2014 15:R20

    Published on: 31 January 2014

  2. Research

    The RNA-binding protein hnRNPLL induces a T cell alternative splicing program delineated by differential intron retention in polyadenylated RNA

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

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

    Genome Biology 2014 15:R26

    Published on: 29 January 2014

  3. Research highlight

    Smaug destroys a huge treasure

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

    Michael Götze and Elmar Wahle

    Genome Biology 2014 15:101

    Published on: 27 January 2014

  4. Review

    To be or not to be a piRNA: genomic origin and processing of piRNAs

    Piwi-interacting RNAs (piRNAs) originate from genomic regions dubbed piRNA clusters. How cluster transcripts are selected for processing into piRNAs is not understood. We discuss evidence for the involvement o...

    Adrien Le Thomas, Katalin Fejes Tóth and Alexei A Aravin

    Genome Biology 2014 15:204

    Published on: 27 January 2014

  5. Review

    Seq and CLIP through the miRNA world

    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...

    Nitish Mittal and Mihaela Zavolan

    Genome Biology 2014 15:202

    Published on: 25 January 2014

  6. Software

    PIPE-CLIP: a comprehensive online tool for CLIP-seq data analysis

    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...

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

    Genome Biology 2014 15:R18

    Published on: 22 January 2014

  7. Method

    GraphProt: modeling binding preferences of RNA-binding proteins

    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...

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

    Genome Biology 2014 15:R17

    Published on: 22 January 2014

  8. Software

    MutPred Splice: machine learning-based prediction of exonic variants that disrupt splicing

    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...

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

    Genome Biology 2014 15:R19

    Published on: 13 January 2014

  9. Research

    Differential protein occupancy profiling of the mRNA transcriptome

    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...

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

    Genome Biology 2014 15:R15

    Published on: 13 January 2014

  10. Research

    Genome-wide analysis of light-regulated alternative splicing mediated by photoreceptors in Physcomitrella patens

    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 ...

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

    Genome Biology 2014 15:R10

    Published on: 7 January 2014

  11. Method

    RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome

    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...

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

    Genome Biology 2014 15:R3

    Published on: 7 January 2014

  12. Software

    dCLIP: a computational approach for comparative CLIP-seq analyses

    Although comparison of RNA-protein interaction profiles across different conditions has become increasingly important to understanding the function of RNA-binding proteins (RBPs), few computational approaches ...

    Tao Wang, Yang Xie and Guanghua Xiao

    Genome Biology 2014 15:R11

    Published on: 7 January 2014

  13. Research

    Extensive localization of long noncoding RNAs to the cytosol and mono- and polyribosomal complexes

    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...

    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

    Genome Biology 2014 15:R6

    Published on: 7 January 2014

  14. Research

    Global regulation of mRNA translation and stability in the early Drosophilaembryo by the Smaug RNA-binding protein

    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...

    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

    Genome Biology 2014 15:R4

    Published on: 7 January 2014

  15. Research

    Identification of distinct miRNA target regulation between breast cancer molecular subtypes using AGO2-PAR-CLIP and patient datasets

    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...

    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

    Genome Biology 2014 15:R9

    Published on: 7 January 2014

  16. Research

    Constitutive patterns of gene expression regulated by RNA-binding proteins

    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...

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

    Genome Biology 2014 15:R13

    Published on: 2 January 2014