Identification and expression analysis of miRNAs in fast-growing transgenic Arabidopsis thaliana

Abstract

In higher eukaryotes small RNAs play a role in regulating gene expression. In Arabidopsis, about 190 microRNAs (miRNAs) have been identified but only a few of them have their biological functions determined. Overexpression of one of the Arabidopsis thaliana purple acid phosphatases AtPAP2 in Arabidopsis was shown to promote plant growth. The overexpression lines grew faster and produced higher seed yield (http://www.youtube.com/watch?v=Yq842GWKdYw). Shoot microarray data showed that many genes involved in miRNAi biogenesis were significantly changed. The purpose of this research is to study the changes in miRNAs expression profiles in 20-day-old plants by sequencing sRNAs and investigate if there are any relationship between miRNAs biogenesis and the fast-growing phenotypes. In the shoot of OE lines, the expression levels of 37 known miRNAs were up-regulated and 11 miRNAs were down-regulated, whereas in the root of OE lines, 16 known miRNAs were up-regulated and 26 miRNAs were down-regulated. Up-regulated miRNAs in both shoot and root samples of the two OE lines include ath-miR158b ,ath-miR160, and ath-miR172a/b, which are predicted to target mRNAs coding for Dof zinc finger protein, auxin response factors and Apetala 2 (AP2) proteins, respectively. Down-regulated miRNAs in the shoot and root samples of both OE lines include ath-miR167a/b, ath-miR773, ath-miR775 and ath-miR848. Furthermore, the levels of miR161.2, ath-miR172c/d, ath-miR173, ath-miR780.1/2, ath-miR822, ath-miR841, ath-miR850 were higher in the shoots of both OE lines. A number of novel miRNAs were identified,of which some were predicted to target to novel genes, including a chromomethylase 1 (CMT1) and an F-box family protein.