Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends.
MicroRNAs (miRNAs) are important regulatory molecules in most eukaryotes and identification of their target mRNAs is essential for their functional analysis. Whereas conventional methods rely on computational prediction and subsequent experimental validation of target RNAs, we directly sequenced >28,000,000 signatures from the 5' ends of polyadenylated products of miRNA-mediated mRNA decay, isolated from inflorescence tissue of Arabidopsis thaliana, to discover novel miRNA-target RNA pairs. Within the set of approximately 27,000 transcripts included in the 8,000,000 nonredundant signatures, several previously predicted but nonvalidated targets of miRNAs were found. Like validated targets, most showed a single abundant signature at the miRNA cleavage site, particularly in libraries from a mutant deficient in the 5'-to-3' exonuclease AtXRN4. Although miRNAs in Arabidopsis have been extensively investigated, working in reverse from the cleaved targets resulted in the identification and validation of novel miRNAs. This versatile approach will affect the study of other aspects of RNA processing beyond miRNA-target RNA pairs.
Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA.
Marcelo A
MA
German
Manoj
M
Pillay
Dong-Hoon
DH
Jeong
Amit
A
Hetawal
Shujun
S
Luo
Prakash
P
Janardhanan
Vimal
V
Kannan
Linda A
LA
Rymarquis
Kan
K
Nobuta
Rana
R
German
Emanuele
E
De Paoli
Cheng
C
Lu
Gary
G
Schroth
Blake C
BC
Meyers
Pamela J
PJ
Green
D017360:Arabidopsis / Q000235:genetics*; D019295:Computational Biology / Q000379:methods; D015723:Gene Library; D035683:MicroRNAs / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*
D035683:MicroRNAs; D012333:RNA, Messenger; D018749:RNA, Plant