Abstract
BackgroundmRNA degradation plays an important role in the determination of mRNA abundance and can quickly regulate gene expression. The production of uncapped mRNAs, an important mechanism of mRNA degradation, can be initiated by decapping enzymes, endonucleases or small RNAs such as microRNAs (miRNAs). Little is known, however, about the role of uncapped mRNAs in plants under environmental stress.ResultsUsing a novel approach called parallel analysis of RNA ends (PARE), we performed a global study of uncapped mRNAs under drought stress in foxtail millet (Setaria italica [L.] P. Beauv.). When both gene degradation (PARE) and gene transcription (RNA-sequencing) data were considered, four types of mRNA decay patterns were identified under drought stress. In addition, 385 miRNA–target interactions were identified in the PARE data using PAREsnip. The PARE analysis also suggested that two miRNA hairpin processing mechanisms—loop-last and loop-first processing—operate in foxtail millet, with both miR319 and miR156 gene families undergoing precise processing via the unusual loop-first mechanism. Finally, we found 11 C4 photosynthesis-related enzymes encoded by drought-responsive genes.ConclusionsWe performed a global analysis of mRNA degradation under drought stress and uncovered diverse drought-response mechanisms in foxtail millet. This information will deepen our understanding of mRNA expression under stressful environmental conditions in gramineous plants. In addition, PARE analysis identified many miRNA targets and revealed miRNA-precursor processing modes in foxtail millet.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0632-0) contains supplementary material, which is available to authorized users.
Highlights
MRNA degradation plays an important role in the determination of mRNA abundance and can quickly regulate gene expression
parallel analysis of RNA ends (PARE) libraries were prepared from seedlings subjected to polyethylene glycol (PEG)-simulated drought (Dd) and control (Dc) conditions, with two independent biological replicates for each group
The mapped reads, which accounted for about 68.06–76.35 % of the total reads from different PARE-seq libraries, were used to measure gene degradation levels calculated as reads per million (RPM)
Summary
MRNA degradation plays an important role in the determination of mRNA abundance and can quickly regulate gene expression. Genome-wide profiling methods, such as RNA-sequencing (RNA-seq) [1] and gene-chip analysis [2], have been used to study mRNA expression and to identify genes expressed in specific tissues and developmental processes [3] and in response to environmental stimuli [4] Such studies are generally designed to capture aspects of steady-state mRNA abundance. One such pathway proceeds in the 3′ to 5′ direction, with mRNA decay beginning with deadenylation catalyzed by mRNA deadenylases [6, 7] Another mRNA degradation pathway, from 5′ to 3′, is often initiated with cleavage of the monomethyl guanosine (m7G) by the Dcp decapping enzyme [8, 9]. Some internal cleavages, such as those involving the RNA-induced silencing complex (RISC) directed by microRNAs (miRNAs) or small interfering RNAs, can initiate mRNA
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