Protein–RNA interactions: new genomic technologies and perspectives

RNA-binding proteins are key players in the regulation of gene expression. In this Progress article, we discuss state-of-the-art technologies that can be used to study individual RNA-binding proteins or large complexes such as the ribosome. We also describe how these approaches can be used to study interactions with different types of RNAs, including nascent transcripts, mRNAs, microRNAs and ribosomal RNAs, in order to investigate transcription, RNA processing and translation. Finally, we highlight current challenges in data analysis and the future steps that are needed to obtain a quantitative and high-resolution picture of protein–RNA interactions on a genome-wide scale.

[1]  M. Kiledjian,et al.  Finding the right RNA: identification of cellular mRNA substrates for RNA-binding proteins. , 1999, RNA.

[2]  W F Rigby,et al.  Characterization of the mRNA ligands bound by the RNA binding protein hnRNP A2 utilizing a novel in vivo technique. , 2000, Nucleic acids research.

[3]  S. Tenenbaum,et al.  Identifying mRNA subsets in messenger ribonucleoprotein complexes by using cDNA arrays. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[4]  H. Urlaub,et al.  A two-tracked approach to analyze RNA-protein crosslinking sites in native, nonlabeled small nuclear ribonucleoprotein particles. , 2002, Methods.

[5]  Jernej Ule,et al.  CLIP Identifies Nova-Regulated RNA Networks in the Brain , 2003, Science.

[6]  J. Steitz,et al.  Evidence for reassociation of RNA-binding proteins after cell lysis: implications for the interpretation of immunoprecipitation analyses. , 2004, RNA.

[7]  Jernej Ule,et al.  CLIP: a method for identifying protein-RNA interaction sites in living cells. , 2005, Methods.

[8]  Erik van Nimwegen,et al.  PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny , 2005, PLoS Comput. Biol..

[9]  M. Moore.  From Birth to Death: The Complex Lives of Eukaryotic mRNAs , 2005, Science.

[10]  B. Blencowe,et al.  An RNA map predicting Nova-dependent splicing regulation , 2006, Nature.

[11]  S. Guil,et al.  The multifunctional RNA-binding protein hnRNP A1 is required for processing of miR-18a , 2007, Nature Structural &Molecular Biology.

[12]  J. Keene.  RNA regulons: coordination of post-transcriptional events , 2007, Nature Reviews Genetics.

[13]  Tyson A. Clark,et al.  HITS-CLIP yields genome-wide insights into brain alternative RNA processing , 2008, Nature.

[14]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[15]  M. Kiebler,et al.  Faculty Opinions recommendation of Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. , 2009 .

[16]  Nicholas T. Ingolia,et al.  Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling , 2009, Science.

[17]  Peter F. Stadler,et al.  Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures , 2009, PLoS Comput. Biol..

[18]  David Tollervey,et al.  Identification of protein binding sites on U3 snoRNA and pre-rRNA by UV cross-linking and high-throughput analysis of cDNAs , 2009, Proceedings of the National Academy of Sciences.

[19]  Lior Pachter,et al.  Sequence Analysis , 2020, Definitions.

[20]  T. Pohlmann,et al.  The fungal RNA‐binding protein Rrm4 mediates long‐distance transport of ubi1 and rho3 mRNAs , 2009, The EMBO journal.

[21]  John T. Lis,et al.  Defining mechanisms that regulate RNA polymerase II transcription in vivo , 2009, Nature.

[22]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[23]  Gene W. Yeo,et al.  An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells , 2009, Nature Structural &Molecular Biology.

[24]  Mikael Bodén,et al.  MEME Suite: tools for motif discovery and searching , 2009, Nucleic Acids Res..

[25]  A. Kasarskis,et al.  A window into third-generation sequencing. , 2010, Human molecular genetics.

[26]  Scott B. Dewell,et al.  Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP , 2010, Cell.

[27]  Serban Nacu,et al.  Fast and SNP-tolerant detection of complex variants and splicing in short reads , 2010, Bioinform..

[28]  Michael Briese,et al.  iCLIP Predicts the Dual Splicing Effects of TIA-RNA Interactions , 2010, PLoS biology.

[29]  Gene W. Yeo,et al.  Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans , 2010, Nature Structural &Molecular Biology.

[30]  Robert B Darnell,et al.  HITS‐CLIP: panoramic views of protein–RNA regulation in living cells , 2010, Wiley interdisciplinary reviews. RNA.

[31]  Nicholas T. Ingolia,et al.  Mammalian microRNAs predominantly act to decrease target mRNA levels , 2010, Nature.

[32]  J. Ule,et al.  iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution , 2010, Nature Structural &Molecular Biology.

[33]  M. Zavolan,et al.  A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins , 2011, Nature Methods.

[34]  Hui Zhou,et al.  starBase: a database for exploring microRNA–mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data , 2010, Nucleic Acids Res..

[35]  R. Darnell,et al.  Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data , 2011, Nature Biotechnology.

[36]  Jernej Ule,et al.  Understanding splicing regulation through RNA splicing maps , 2011, Trends in genetics : TIG.

[37]  Uwe Ohler,et al.  Integrative regulatory mapping indicates that the RNA-binding protein HuR couples pre-mRNA processing and mRNA stability. , 2011, Molecular cell.

[38]  Mohsen Khorshid,et al.  CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins , 2010, Nucleic Acids Res..

[39]  David Tollervey,et al.  Cross-linking, ligation, and sequencing of hybrids reveals RNA–RNA interactions in yeast , 2011, Proceedings of the National Academy of Sciences.

[40]  Grace X. Y. Zheng,et al.  Genome-wide identification of Ago2 binding sites from mouse embryonic stem cells with and without mature microRNAs , 2010, Nature Structural &Molecular Biology.

[41]  Uwe Ohler,et al.  PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data , 2011, Genome Biology.

[42]  N. Rajewsky,et al.  Transcriptome-wide analysis of regulatory interactions of the RNA-binding protein HuR. , 2011, Molecular cell.

[43]  J. Weissman,et al.  Nascent transcript sequencing visualizes transcription at nucleotide resolution , 2011, Nature.

[44]  Grace X. Y. Zheng,et al.  Erratum: Genome-wide identification of Ago2 binding sites from mouse embryonic stem cells with and without mature microRNAs (Nature Structural and Molecular Biology (2011) 18 (237-244)) , 2011 .

[45]  S. Luo,et al.  RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries. , 2011, RNA.

[46]  S. Linnarsson,et al.  Counting absolute numbers of molecules using unique molecular identifiers , 2011, Nature Methods.