摘要
MicroRNAs(miRNAs)and small interfering RNAs(siRNAs)regulate gene expression in eukaryotes.Plant miRNAs modulate their targets mainly via messenger RNA(mRNA)cleavage.Small RNA(sRNA)targets have been extensively investigated in Arabidopsis using computational prediction,experimental validation,and degradome sequencing.However,small RNA targets are largely unknown in rice(Oryza sativa).Here,we report global identification of small RNA targets using high throughput degradome sequencing in the rice indica cultivar 93-11(Oryza sativa L.ssp.indica).One hundred and seventy-seven transcripts targeted by a total of 87 unique miRNAs were identified.Of targets for the conserved miRNAs between Arabidopsis and rice,transcription factors comprise around 70%(58 in 82),indicating that these miRNAs act as masters of gene regulatory nodes in rice.In contrast,non-conserved miRNAs targeted diverse genes which provide more complex regulatory networks.In addition,5 AUXIN RESPONSE FACTORs(ARFs)cleaved by the TAS3 derived ta-siRNAs were also detected.A total of 40 sRNA targets were further validated via RNA ligasemediated 5′rapid amplification of cDNA ends(RLM 5′-RACE).Our degradome results present a detailed sRNAtarget interaction atlas,which provides a guide for the study of the roles of sRNAs and their targets in rice.
基金
This work was supported by National Basic Research Program of China(Nos.2009CB941500 and 2005CB522400 to X.C.)
by National Natural Science Foundation of China(Grant Nos.30870534 and 30621001 to X.C.).
