Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences (original) (raw)

Abstract

Motivation: Most non-coding RNAs are characterized by a specific secondary and tertiary structure that determines their function. Here, we investigate the folding energy of the secondary structure of non-coding RNA sequences, such as microRNA precursors, transfer RNAs and ribosomal RNAs in several eukaryotic taxa. Statistical biases are assessed by a randomization test, in which the predicted minimum free energy of folding is compared with values obtained for structures inferred from randomly shuffling the original sequences.

Results: In contrast with transfer RNAs and ribosomal RNAs, the majority of the microRNA sequences clearly exhibit a folding free energy that is considerably lower than that for shuffled sequences, indicating a high tendency in the sequence towards a stable secondary structure. A possible usage of this statistical test in the framework of the detection of genuine miRNA sequences is discussed.

Availability: The dataset, software and additional data files are freely available as supplementary information on our Website.

Supplementary information: http://www.psb.ugent.be/bioinformatics/

To whom correspondence should be addressed.

Author notes

1Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB), Ghent University, Technologiepark 927, B-9052 Ghent, Belgium and 2Laboratoire associé de l'INRA, France