Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP

By M. Hafner, Markus Landthaler, Lukas Burger, Mohsen Khorshid, Jean Hausser, Philipp Berninger, Andrea Rothballer, M. Ascano, Anna-Carina Jungkamp, Mathias Munschauer and 5 more. Cell, 2010

2,917 citations recorded by the source corpus.

Summary RNA transcripts are subject to post-transcriptional gene regulation involving hundreds of RNA-binding proteins (RBPs) and microRNA-containing ribonucleoprotein complexes (miRNPs) expressed in a cell-type dependent fashion. We developed a cell-based crosslinking approach to determine at high resolution and transcriptome-wide the binding sites of cellular RBPs and miRNPs. The crosslinked sites are revealed by thymidine to cytidine transitions in the cDNAs prepared from immunopurified RNPs of 4-thiouridine-treated cells. We determined the binding sites and regulatory consequences for several intensely studied RBPs and miRNPs, including PUM2, QKI, IGF2BP1-3, AGO/EIF2C1-4 and TNRC6A-C. Our study revealed that these factors bind thousands of sites containing defined sequence motifs and have distinct preferences for exonic versus intronic or coding versus untranslated transcript regions. The precise mapping of binding sites across the transcriptome will be critical to the interpretation of the rapidly emerging data on genetic variation between individuals and how these variations contribute to complex genetic diseases.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/4e15a268586023e6e6ba6a49eedd4a33e98d531d

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

Citations in the corpus

The biochemical basis of microRNA targeting efficacy (2018, background): “Additional analyses showed that the biochemical+model performed at least as well as in vivo cross-linking immunoprecipitation sequencing (CLIP-seq) approaches in identifying the mRNAs most repressed upon miRNA transfection or most derepressed upon miRNA knockout (25, 38, 39) (fig.”
A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins (2011, neutral): “, photoactivatable ribonucleoside–enhanced CLIP (PAR-CLIP”
DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions (2014, methodology): “immunoprecipitates HITS-CLIP (10) High Sequencing of AGO binding regions on targeted transcripts PAR-CLIP (11) High Sequencing of AGO binding regions on targeted transcripts”
RNA-protein binding motifs mining with a new hybrid deep learning based cross-domain knowledge integration approach (2016, background): “Although there are many genome-wide RNA-binding protein detection techniques, such as RNAcompete [3], PAR-CLIP [4], they are still cost-heavy and time-intensive.”
Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA (2012, methodology): “Furthermore, we overlaid our mapping data with publicly available transcriptome-wide maps of binding sites for major regulatory RNA-binding proteins in human cells generated by PAR-CLIP-Seq (47).”
The miR-17/92 cluster: a comprehensive update on its genomics, genetics, functions and increasingly important and numerous roles in health and disease (2013, neutral): “On a related note, miRNAs were recently shown to also target intergenic and intronic regions, pseudogenes and long ncRNAs.(119,121,123,135,136) Another dimension of the miRNA target prediction problem relates to the observation of conservation of miRNA sequences across animals and plants (and viruse”
MicroRNAs and their targets: recognition, regulation and an emerging reciprocal relationship (2012, methodology): “However, it is now possible to identify endogenous target sites by sequencing those that co-immunoprecipitate with miRISC factors using techniques such as CLIP coupled with high-throughput sequencing (CLIP–seq) or high-throughput sequencing together with CLIP (HITS–CLIP”
Expanded identification and characterization of mammalian circular RNAs (2014, background): “Using data from high-throughput in vivo crosslinking experiments, which identified clusters of AGO2crosslinking sites that indicated AGO2 binding [24-26], we compared the density of AGO2-crosslinking clusters within exons that can form circRNAs to the density within their neighboring linear exons.”
MicroRNA Functions in Stress Responses (2010, positive): “In particular, these miRNA binding sites can be located near sites containing rare codons (Hafner et al., 2010).”