Sliced microRNA targets and precise loop-first processing of MIR319 hairpins revealed by analysis of the Physcomitrella patens degradome.
Expression profiling of the 5' ends of uncapped mRNAs ("degradome" sequencing) can be used to empirically catalog microRNA (miRNA) targets, to probe patterns of miRNA hairpin processing, to examine mRNA decay, and to analyze accumulation of endogenous short interfering RNA (siRNA) precursors. We sequenced and analyzed the degradome of the moss Physcomitrella patens, an important model system for functional genomic analyses in plant evolution. A total of 52 target mRNAs of 27 different Physcomitrella miRNA families were identified. Many targets of both more conserved and less conserved miRNA families encoded putative regulatory proteins. Remnants of MIRNA hairpin processing also populated the degradome data and indicated an unusual "loop-first" mode of precise processing for the MIR319 gene family. Precise loop-first processing was confirmed for native Physcomitrella, rice, and Arabidopsis MIR319 hairpins, as well as an Arabidopsis artificial MIRNA (aMIRNA) based upon a MIR319 backbone. MIR319 is thus a conserved exception to the general rule of loop-last processing of MIRNA hairpins. Loop-first MIR319 processing may contribute to the high efficacy of a widely used MIR319-based strategy for aMIRNA production in plants.
Addo-Quaye
Charles
C
Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA.
Snyder
Jo Ann
JA
Park
Yong Bum
YB
Li
Yong-Fang
YF
Sunkar
Ramanjulu
R
Axtell
Michael J
MJ
D001483:Base Sequence; D019068:Bryopsida / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D055442:Metabolome; D035683:MicroRNAs / Q000737:chemistry* / Q000235:genetics; D009690:Nucleic Acid Conformation; D020871:RNA Stability; D018749:RNA, Plant / Q000737:chemistry* / Q000235:genetics; D017422:Sequence Analysis, DNA
D035683:MicroRNAs; D018749:RNA, Plant