Enhanced microRNA accumulation through stemloop‐adjacent introns

Abstract

MicroRNAs (miRNAs) originate from stemloop-forming precursor RNAs found in longer primary transcripts that often contain introns. We show that in plants, those introns, when located 3 0 of the stemloop, can promote mature miRNA accumulation, through a mechanism that likely operates at the level of miRNA processing or stability. Reversely, when miRNA production is reduced such as in dicer-like 1 mutants, splicing of introns that promote miRNA processing is considerably increased, pointing to a tight physical and temporal coordination of intron splicing and miRNA processing in plants. Our findings further suggest that miRNA transcripts without introns generated through alternative polyA-site usage might contribute to the differential adjustment of miRNA levels, possibly at a tissue-specific level.

The crosstalk between plant microRNA biogenesis factors and the spliceosome

“…Interestingly, Schwab and colleagues did not observe such a significant reduction of miRNA levels when the donor splice site of the MIR163 transgene was mutated. 42 As discussed in their paper, 2 different explanations are possible: 1) the mutations introduced into the donor splice sites abolished splicing but did not prevent inefficient U1snRNP binding, or 2) the difference between promoters used (CaMV35S vs. the native MIR163 promoter) may exert some effects on co-transcriptional splicing and dicing of the pri-miR163. The second hypothesis is supported by the experiments that we have reported in our recently published paper, in which we used the CaMV35S promoter for all MIR161 splice variants: we do not observe such dramatic effects of donor splice site mutations on the miR163 accumulation.…”

“…42,43 All of these genes contain at least one intron located 3′ to the miRNA stem-loop. In the case of transgenic Arabidopsis lines in which MIR163 gene construct without intron has been introduced into the genetic background of the mir163-2 null mutant, the level of mature miR163 was strongly reduced.…”

“…Introduction of unrelated introns derived from protein coding genes or from other MIR genes at the original MIR163 intron site restores the mature miR163 accumulation to the level of wild type plants. 42 Thus, the presence of introns, regardless of their origin, sequence, and length plays a stimulatory role in miRNA biogenesis, and points to defined, conserved intronic sequences as crucial elements in this process. Moreover, other experiments performed by Schwab and colleagues demonstrated that introns located upstream of the miRNA hairpin structure did not stimulate miRNA accumulation.…”

“…Moreover, other experiments performed by Schwab and colleagues demonstrated that introns located upstream of the miRNA hairpin structure did not stimulate miRNA accumulation. 42 Thus, the location of intron with respect to the miRNA stem-loop structure seems to be important for boosting the accumulation of miRNAs. This observation implies a possible stimulatory contact of splicing machinery elements with the pri-miRNA processing complex, when located downstream from the miRNA stem-loop.…”

“…Schwab et al as well as Hajheidari et almade an interesting observation that in Arabidopsis dcl1 mutants in which miRNA biogenesis is impaired, the efficiency of splicing of introns located downstream of the miRNA stem-loop is increased. 42,45 This provides an additional argument for a close interplay between splicing and miRNA biogenesis. Moreover, this may suggest that U1 snRNP is not involved anymore in the interactions with the miRNA biogenesis machinery that slows down splicing.…”