Journal
RNA
Volume 15, Issue 12, Pages 2112-2121Publisher
COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT
DOI: 10.1261/rna.1774909
Keywords
microRNA; uncapped mRNAs; plants; Physcomitrella; genomics; second-generation sequencing
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Funding
- US National Science Foundation [0718051]
- Oklahoma Agricultural Experiment Station
- Department of Energy [FG02-84ER13179]
- Direct For Biological Sciences
- Div Of Molecular and Cellular Bioscience [0718051] Funding Source: National Science Foundation
- Office of Advanced Cyberinfrastructure (OAC)
- Direct For Computer & Info Scie & Enginr [821527] Funding Source: National Science Foundation
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Expression profiling of the 59 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.
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