Stress-Induced Alternative Splicing Provides a Mechanism for the Regulation of MicroRNA Processing in Arabidopsis thaliana

Abstract

MicroRNAs (miRNAs) have emerged as a class of regulators of gene expression through posttranscriptional degradation or translational repression in living cells. Increasing evidence points to the important relationship between miRNAs and environmental stress responses, but the regulatory mechanisms in plants are poorly understood. Here, we found that Arabidopsis thaliana intronic miR400 was cotranscribed with its host gene (At1g32583) and downregulated by heat treatment. Intriguingly, an alternative splicing (AS) event that occurred in the intron (306 bp) where MIR400 was located was specifically induced by heat stress. A 100 bp fragment was excised, and the remaining 206 bp intron containing MIR400 transcripts was retained in the host gene. The stress-induced AS event thus resulted in greater accumulation of miR400 primary transcripts and a low level of mature miR400. Together, these results provide the direct evidence that AS acts as a regulatory mechanism linking miRNAs and environmental stress in plants.

Genome-Wide Analysis of Alternative Splicing during Development and Drought Stress in Maize

“…Alternative splicing has recently been implicated as playing a major role in these processes during stresses, including disease, heat, drought, and others (Deom et al, 1987;Iida et al, 2004;Jeong et al, 2011;Kakumanu et al, 2012;Chang et al, 2014;Mandadi and Scholthof, 2015). Gene expression changes in splicing factors are a major factor in determining stress-induced alternative splicing changes (Yan et al, 2012;Leviatan et al, 2013;Staiger and Brown, 2013). For example, Cui et al (2014) recently showed that overexpression of the splicing factor SAD1 conferred increased splicing precision and resulted in increased tolerance to salt stress in Arabidopsis (Arabidopsis thaliana).…”

In silico identification and characterization of conserved plant microRNAs in barley

“…Intronic miRNAs can be subject to inefficient splicing or alternative splicing which can affect the miRNA production. Expression of intronic miR400 is downregulated by heat treatment due to an alternative splicing event which causes the miRNA to be retained in the host gene [49]. To investigate miRNA origins, we first added introns to the barley annotation file from the International Barley Sequencing Consortium (ftp://ftpmips.helmholtz-muenchen.de/plants/barley/ p u b l i c _ d a t a / g e n e s / b a r l e y _ H i g h C o n f _ g e n e s _ MIPS_21Aug12_Transcript_and_CDS_structure.gff) using Genome Tools (version 1.4.1) and converted the .gff file into .bed format.…”

The crosstalk between plant microRNA biogenesis factors and the spliceosome

“…Until now, 12 intronic miRNAs have been found in the genome of Arabidopsis thaliana. 37,38 Our bioinformatic and experimental studies revealed that 17 more miRNAs of A. thaliana are also encoded within introns of protein -and noncoding genes (manuscript in preparation). Thus, in the A. thaliana genome approximately 8% of miRNAs are encoded within introns of host genes, while the remaining represent independent transcriptional units.…”

“…17,18,39,40 These introns undergo complex alternative splicing, providing a possible mechanism for the regulation of miRNA processing in A. thaliana. 38,41 Our estimations have shown that approximately 50% of A. thaliana miRNA genes contains intron(s). In the majority of intron-containing precursors, the miRNA-enclosing hairpin loop structure is located within the first exon.…”

“…Thus, exonic localization of miR400 inhibits its efficient processing from the stress-induced mRNA isoform. 38 Alternative splicing of pri-miRNAs has been observed in many cases of intron-containing miRNA genes. The picture that emerges is that introns and alternative splicing have highly relevant roles in regulating the miRNA levels in very specific conditions, and also contribute to proper plant response to stress conditions (Fig.…”