A computational model for non-conserved mature miRNAs from the rice genome

作者：Kumar S P; Pandya H A; Jasrai Y T^*

来源：SAR and QSAR in Environmental Research, 2014, 25(3): 205-220.

DOI：10.1080/1062936X.2013.875941

• scoring model
• Oryza sativa
• mature miRNA modelling
• non-conserved miRNAs
• Argonaute protein

Several computational approaches employ the high complementarity of plant miRNAs to target mRNAs as a filter to recognize miRNA. Numerous non-conserved miRNAs are known with more recent evolutionary origin as a result of target gene duplication events. We present here a computational model with knowledge inputs from reported non-conserved mature miRNAs of Oryza sativa (rice). Sequence- and structure-based approaches were used to retrieve miRNA features based on rice Argonaute protein and develop a multiple linear regression (MLR) model (r(2) = 0.996, q(cv)(2) = 0.989) which scored mature miRNAs as predicted by the MaturePred program. The model was validated by scoring test set (q(2) = 0.990) and computationally predicted mature miRNAs as external test set (q(test)(2) = 0.895). This strategy successfully enhanced the confidence of retrieving most probable non-conserved miRNAs from the rice genome. We anticipate that this computational model would recognize unknown non-conserved miRNA candidates and nurture the current mechanistic understanding of miRNA sorting to unveil the role of non-conserved miRNAs in gene silencing.

• 出版日期2014-3-4