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.
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This work was supported by the Medical Research Council, the European Molecular Biology Laboratory (grant number U105185858), the European Research Council (206726-CLIP) and by a Human Frontiers Science Program Long-Term fellowship and an EMBL EIPOD fellowship to J.K. and K.Z., respectively.
The authors declare no competing financial interests.
- Argonaute proteins
Core components of the RNA-mediated silencing pathways. They provide the platform for target mRNA recognition by small non-coding RNAs and harbour the catalytic activity for mRNA cleavage.
- Differential display
A PCR-based approach that was used to study differences in RNA populations. It has now been superseded by microarray and RNA sequencing approaches.
- Global run-on sequencing
(GRO-seq). A technique that combines nuclear run-on assays with high-throughput sequencing to obtain genome-wide information about active transcription.
- Heterogeneous nuclear ribonucleoprotein
(HNRNP). The core protein components of heterogeneous nuclear ribonucleoprotein particles that associate with all nascent transcripts. They are involved in diverse aspects of post-transcriptional regulation.
Nucleic acid sequences with a number of nucleotides of length k.
A regulator of a biologically coherent set of RNAs important for synaptic function. It is involved in the neurological disorder paraneoplastic opsoclonus myoclonus ataxia.
The genome-scale study of protein–RNA interactions and their functional consequences.
- Ribonucleoprotein particles
(RNPs). Complexes consisting of protein and RNA components.
- Small nuclear RNAs
(snRNAs). A class of non-coding RNAs that are found in the nucleus of eukaryotic cells and that constitute core components of all subunits of the spliceosome.
- Small nucleolar RNAs
(snoRNAs). A class of small non-coding RNAs that are involved in guiding chemical modifications of other RNAs, such as ribosomal or transfer RNAs.
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König, J., Zarnack, K., Luscombe, N. et al. Protein–RNA interactions: new genomic technologies and perspectives. Nat Rev Genet 13, 77–83 (2012) doi:10.1038/nrg3141
SCRIBER: accurate and partner type-specific prediction of protein-binding residues from proteins sequences
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