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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.

Sliced microRNA targets and precise loop-first processing of MIR319 hairpins revealed by analysis of the Physcomitrella patens degradome