Argonaute CLIP--a method to identify in vivo targets of miRNAs.

microRNAs are important regulators of gene expression that guide translational repression and degradation of target mRNAs. Only relatively few miRNA targets have been characterized, and computational prediction is hampered by the relatively small number of nucleotides that seem to be involved in target recognition. Argonaute (Ago) crosslinking and immunoprecipitation (CLIP) in combination with next-generation sequencing proved to be a successful method for identifying targets of endogenous cellular miRNAs on a transcriptome-wide scale. Here we review various approaches to Ago CLIP, describe in detail the PAR-CLIP method and provide an outline of the necessary computational analysis for identification of in vivo miRNA binding sites.

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

[2]  Gene W. Yeo,et al.  High-Resolution Profiling and Analysis of Viral and Host Small RNAs during Human Cytomegalovirus Infection , 2011, Journal of Virology.

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

[4]  S. Chi,et al.  An alternative mode of microRNA target recognition , 2012, Nature Structural &Molecular Biology.

[5]  J. Ule,et al.  CLIP: construction of cDNA libraries for high-throughput sequencing from RNAs cross-linked to proteins in vivo. , 2009, Methods.

[6]  Uwe Ohler,et al.  Viral microRNA targetome of KSHV-infected primary effusion lymphoma cell lines. , 2011, Cell host & microbe.

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

[8]  Gunter Meister,et al.  A multifunctional human Argonaute2-specific monoclonal antibody. , 2008, RNA.

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

[10]  Thomas Tuschl,et al.  Identification of microRNAs and other small regulatory RNAs using cDNA library sequencing. , 2008, Methods.

[11]  D. Bartel.  MicroRNAs: Target Recognition and Regulatory Functions , 2009, Cell.

[12]  Mark B Gerstein,et al.  Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing , 2006, BMC Genomics.

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

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

[15]  Tatiana A. Tatusova,et al.  NCBI Reference Sequences: current status, policy and new initiatives , 2008, Nucleic Acids Res..

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

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

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

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

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

[21]  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.

[22]  A. Mele,et al.  Ago HITS-CLIP decodes miRNA-mRNA interaction maps , 2009, Nature.

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

[24]  T. Tuschl,et al.  Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex , 2008, Nature.

[25]  Paul Zhang,et al.  A novel monoclonal antibody against human Argonaute proteins reveals unexpected characteristics of miRNAs in human blood cells. , 2007, RNA.

[26]  Juliane C. Dohm,et al.  Substantial biases in ultra-short read data sets from high-throughput DNA sequencing , 2008, Nucleic acids research.