Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences.

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.

Supplementary Data

• Non-coding RNA sequences used for the study. Download (tar.gz)
• Minimum free energy of folding randomization test software. Download (tar.gz)
• Minimum free energy of folding randomization test software - randfold version 2.0.1 (C version). Download (tar.gz)
• List of minimum free energy values and their associated probabilities for each non-coding RNA sequence. Download (Excel)
• Distribution of p-values. Download (.doc)