Background: It is very likely that RNA secondary structures, more so than the sequence
itself, are closely related to their functions, especially for mRNAs and even short noncoding RNAs.
However, secondary structure of most lncRNAs (long noncoding RNAs) remains poorly understood.
Method: Here, we perform a large-scale investigation of lncRNA secondary structures especially for
hairpin structural motif in human and mouse based on computational prediction using the RNAfold
Results: The main results show some difference between lncRNAs and mRNAs in various kinds of
local secondary structures. However, there are many hairpins in lncRNAs, even in those with short
sequence length, suggesting lncRNA as a highly structured RNA molecule. Furthermore, in both human
and mouse genome, there are more lncRNAs than mRNAs containing long-stem and big-loop hairpins.
It is important to note that these hairpins in lncRNAs are inclined to compact together and form a
junction-like structure motif which we call hairpin junction. Tetraloops are also analyzed to uncover the
probable associations with lncRNA functional stability.
Conclusion: Taken together, we find the secondary structure of lncRNAs has many characteristics,
most of which are similar with those in mRNAs. And we provide evidence of various lncRNA
secondary structural components, which can be exploited in lncRNA identification, the classification of
different types and the inference of function annotation.