PT  - JOURNAL ARTICLE
AU  - Zheng Yan
AU  - Bin Zhang
AU  - Haiyang Hu
AU  - Gangcai Xie
AU  - Song Guo
AU  - Philipp Khaitovich
AU  - Yi-Ping Phoebe Chen
TI  - An alternative class of targets for microRNAs containing CG dinucleotide
AID  - 10.1101/026708
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 026708
4099  - http://biorxiv.org/content/early/2016/02/28/026708.short
4100  - http://biorxiv.org/content/early/2016/02/28/026708.full
AB  - Background MicroRNAs are endogenous ∼23nt RNAs which regulate mRNA targets mainly through perfect pairing with their seed region (positions 2-7). Several instances of bulge UTR sequence can also be recognized by miRNA as their target. But such non-Watson-Crick base pairings are incompletely understood.Results We found a group of miRNAs which had very few conservative targets while potentially having a subclass of bulge message RNA targets. Compared with the canonical target, these bulge targets had a lower negative correlation with the miRNA expression, and either were downregulated in the miRNA overexpression experiment or upregulated in the miRNA knock-down experiment.Conclusions We proved that the bulge target exists widely in certain groups of miRNAs and such non-canonical targets can be recoginized by miRNA. Incorporating these bulge targets, combined with evolutionary conservation, will reduce the false-positive rate of microRNA computational target prediction.