Precursor miRNAs show high degree of secondary structure conservation across diverse organisms. Can they interfere with the phylogenetic analysis?
The functions of miRNA (and various other types of functional non-coding RNA) molecules are mediated by their secondary structures. Therefore, selective pressure acts on these structures. However, secondary structure conservation is not necessarily mediated by sequence conservation. Thus, many sequences (slightly or strongly diverged) can fold into the same structure and hance may obscure phylogenetic signals and phylogeny reconstruction.
To overcome this problem one need to solve the problem for simultaneous optimization of alignment and self-folding - the so-called Sankoff's program for simultaneous prediction of secondary structure and alignment between nucleotide sequences. A simple reason behind the simultaneous optimization of alignment and self-folding is that strong structural consensus among related, but diverged sequences are a good indicator for preserved functional role. However, Up to now there is no a general solution for this long standing problem.
You can look at my site, I have some articles conserning this problem.
- Badges
- Science topic
- Similar topics
- Chemistry
- General Biochemistry
- Proteomics