Small RNAs from MITE‐derived stem‐loop precursors regulate abscisic acid signaling and abiotic stress responses in rice

Abstract

SUMMARYSmall silencing RNAs (sRNAs) are non-coding RNA regulators that negatively regulate gene expression by guiding mRNA degradation, translation repression or chromatin modification. Plant sRNAs play crucial roles in various developmental processes, hormone signaling, immune responses and adaptation to a variety of abiotic stresses. miR441 and miR446 were previously annotated as microRNAs (miRNAs) because their precursors can form typical stem-loop structures, but are not considered as real miRNAs because of inconsistency with some ancillary criteria of the recent guidelines for annotation of plant miRNAs. We tentatively rename them small interfering (si)R441 and siR446, respectively, in this study. It has recently been shown that the precursors of siR441 and siR446 might originate from the miniature inverted-repeat transposable element (MITE) Stowaway1. In this report, we show that, in contrast with Dicer-like (DCL)3-and RNA-dependent RNA polymerase (RDR)2-dependent MITE-derived ra-siRNAs, siR441 and siR446 are processed by OsDCL3a but independent of OsRDR2, indicating that siR441 and siR446 are generated from single-stranded stem-loop precursors. We also show that abscisic acid (ABA) and abiotic stresses downregulate the expression of siR441 and siR446 but, surprisingly, increase the accumulation of their precursors in rice plants, implying that processing of siRNA precursors is inhibited. We provide evidence to show that this defective processing is due to increased precursor accumulation per se, possibly by intermolecular self-pairing of the processing intermediate sequences, thus hindering their normal processing. Functional examinations indicate that siR441 and siR446 are positive regulators of rice ABA signaling and tolerance to abiotic stress, possibly by regulating MAIF1 expression.

Continuing analysis of microRNA origins

“…31 Through these analyses, we were able to define the molecular events responsible for 1,213 miR origins. In agreement with previous studies, 17,18,20,[24][25][26][27] our results indicate that the predominant mechanism for miR formation from TE sequences occurred via the model illustrated in Figure 1. Encouragingly, we find the results of our current analysis of 7,321 miRs to be strikingly similar to our previous analysis of over 15,000 distinct miR loci.…”

“…1). Now confirmed in several subsequent analyses, [16][17][18][19][20][25][26][27] their model indicates that transcription across neighboring TE insertions on opposite strands, followed by DICER processing and RISC incorporation, was initially responsible for the formation of the majority of functional miR loci. In addition, a transposable element-based miR origin suggests an additionally advantageous role for continued genome colonization-the miRs formed by this mechanism would likely be able to repress any mRNAs bearing sequences obtained from that miR's progenitor TE.…”

The effect of transposable elements on phenotypic variation: insights from plants to humans

“…In rice, the MITE-derived 24-nt siR441 and siR446 function as positive regulators of abscisic acid signaling and abiotic stress responses by repressing their target, MAIF1 (miRNAs regulated and abiotic stress induced F-box gene) (Yan et al, 2011). In Arabidopsis, the transcripts of Athila LTR retrotransposons produce double-stranded RNAs that are then processed into 21-and 22-nt siRNAs.…”

Epigenetic Chromatin Regulators as Mediators of Abiotic Stress Responses in Cereals

“…The validated target of siR441 and siR446, MAIF1(encoding an F-box protein), was previously shown to be up regulated under abiotic www.intechopen.com stress conditions. In addition, transgenic rice plants with decreased accumulation of siR441 and siR446 had the same phenotype as MAIF1 overexpressing plants [ 108 Yan et al, 2010]. Together these observations point to a role for rice siR441 and siR446 in abiotic stress response through regulation of MAIF1.…”

“…For example siRNA 002061_0636_3054.1 shows down-regulation under conditions of increased heat, salinity and dehydration, whereas siRNA 005047_0654_19041.1 is substantially induced by cold. SiRNAs have been also implicated in abiotic stress response in rice [ 108 Yan et al, 2011]. Rice siR441 and siR446 accumulation was down-regulated by cold, drought, high salinity and by ABA treatment.…”