Collins, KM;
Oregioni, A;
Robertson, LE;
Kelly, G;
Ramos, A;
(2015)
Protein-RNA specificity by high-throughput principal component analysis of NMR spectra.
Nucleic Acids Research
, 43
(6)
, Article e41. 10.1093/nar/gku1372.
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Abstract
Defining the RNA target selectivity of the proteins regulating mRNA metabolism is a key issue in RNA biology. Here we present a novel use of principal component analysis (PCA) to extract the RNA sequence preference of RNA binding proteins. We show that PCA can be used to compare the changes in the nuclear magnetic resonance (NMR) spectrum of a protein upon binding a set of quasi-degenerate RNAs and define the nucleobase specificity. We couple this application of PCA to an automated NMR spectra recording and processing protocol and obtain an unbiased and high-throughput NMR method for the analysis of nucleobase preference in protein–RNA interactions. We test the method on the RNA binding domains of three important regulators of RNA metabolism.
| Type: | Article |
|---|---|
| Title: | Protein-RNA specificity by high-throughput principal component analysis of NMR spectra |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1093/nar/gku1372 |
| Publisher version: | http://doi.org/10.1093/nar/gku1372 |
| Language: | English |
| Additional information: | © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
| Keywords: | Science & Technology, Life Sciences & Biomedicine, Biochemistry & Molecular Biology, MOLECULAR-BASIS, LET-7 MICRORNAS, PRE-MICRORNA, RECOGNITION, COMPLEX, URIDYLATION, BIOGENESIS, SIGNAL, LIN28, STEP, principal component analysis, rna, rna-binding motifs, nucleic acid structure, Protein-nucleic acid interaction, RNA characterisation and manipulation |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Structural and Molecular Biology |
| URI: | https://discovery.ucl.ac.uk/id/eprint/1460880 |
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