RT Journal Article
SR Electronic
T1 Investigating the concept of accessibility for predicting novel RNA-RNA interactions
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.06.03.446902
DO 10.1101/2021.06.03.446902
A1 Sabine Reißer
A1 Irmtraud M Meyer
YR 2021
UL http://biorxiv.org/content/early/2021/06/03/2021.06.03.446902.abstract
AB State-of-the-art methods for predicting novel trans RNA-RNA interactions use the so-called accessibility as key concept. It estimates whether a region in a given RNA sequence is accessible for forming trans interactions, using a thermodynamic model which quantifies its secondary structure features. RNA-RNA interactions are then predicted by finding the minimum free energy base-pairing between the two transcripts, taking into account the accessibility as energy penalty.We investigated the underlying assumptions of this approach using the two methods RNAplex and IntaRNA on two datasets, containing sRNA-mRNA and snoRNA-rRNA interactions, respectively.We find that (1) known trans RNA-RNA interactions frequently overlap regions containing RNA structure features, (2) the estimated accessibility reflects sRNA structures fairly well, but often disagrees with structure annotations of longer transcripts, (3) the prediction performance of RNA-RNA interaction prediction methods is independent of the quality of the estimated accessibility profiles, and (4) one important overall effect of accessibility profiles is to prevent the thermodynamic model from predicting too long interactions.Based on our findings, we conclude that the accessibility concept to the minimum free energy approach to predicting novel RNA-RNA interactions has conceptual limitations and discuss potential ways of improving the field in the future.Competing Interest StatementThe authors have declared no competing interest.