RNAnue: efficient data analysis for RNA-RNA interactomics.
Nucleic Acids Res
; 49(10): 5493-5501, 2021 06 04.
Article
em En
| MEDLINE
| ID: mdl-34019662
ABSTRACT
RNA-RNA inter- and intramolecular interactions are fundamental for numerous biological processes. While there are reasonable approaches to map RNA secondary structures genome-wide, understanding how different RNAs interact to carry out their regulatory functions requires mapping of intermolecular base pairs. Recently, different strategies to detect RNA-RNA duplexes in living cells, so called direct duplex detection (DDD) methods, have been developed. Common to all is the Psoralen-mediated in vivo RNA crosslinking followed by RNA Proximity Ligation to join the two interacting RNA strands. Sequencing of the RNA via classical RNA-seq and subsequent specialised bioinformatic analyses the result in the prediction of inter- and intramolecular RNA-RNA interactions. Existing approaches adapt standard RNA-seq analysis pipelines, but often neglect inherent features of RNA-RNA interactions that are useful for filtering and statistical assessment. Here we present RNAnue, a general pipeline for the inference of RNA-RNA interactions from DDD experiments that takes into account hybridisation potential and statistical significance to improve prediction accuracy. We applied RNAnue to data from different DDD studies and compared our results to those of the original methods. This showed that RNAnue performs better in terms of quantity and quality of predictions.
Texto completo:
1
Base de dados:
MEDLINE
Assunto principal:
RNA
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Análise de Sequência de RNA
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Biologia Computacional
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Sequenciamento de Nucleotídeos em Larga Escala
Idioma:
En
Ano de publicação:
2021
Tipo de documento:
Article