Structural features of microRNA (miRNA) precursors and their relevance to miRNA biogenesis and small interfering RNA/short hairpin RNA design.
We have established the structures of 10 human microRNA (miRNA) precursors using biochemical methods. Eight of these structures turned out to be different from those that were computer-predicted. The differences localized in the terminal loop region and at the opposite side of the precursor hairpin stem. We have analyzed the features of these structures from the perspectives of miRNA biogenesis and active strand selection. We demonstrated the different thermodynamic stability profiles for pre-miRNA hairpins harboring miRNAs at their 5'- and 3'-sides and discussed their functional implications. Our results showed that miRNA prediction based on predicted precursor structures may give ambiguous results, and the success rate is significantly higher for the experimentally determined structures. On the other hand, the differences between the predicted and experimentally determined structures did not affect the stability of termini produced through "conceptual dicing." This result confirms the value of thermodynamic analysis based on mfold as a predictor of strand section by RNAi-induced silencing complex (RISC).
Krol
Jacek
J
Laboratory of Cancer Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.
Sobczak
Krzysztof
K
Wilczynska
Urszula
U
Drath
Maria
M
Jasinska
Anna
A
Kaczynska
Danuta
D
Krzyzosiak
Wlodzimierz J
WJ
D001483:Base Sequence; D035683:MicroRNAs / Q000096:biosynthesis / Q000737:chemistry*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012322:RNA Precursors / Q000737:chemistry*; D034741:RNA, Small Interfering / Q000737:chemistry*; D034743:RNA-Induced Silencing Complex; D013816:Thermodynamics
D035683:MicroRNAs; D012322:RNA Precursors; D034741:RNA, Small Interfering; D034743:RNA-Induced Silencing Complex