Genetic interactions between RNA interference and abscisic acid response

RNA-interference is a conserved process in eukaryotes in which 21-24nt small RNAs (sRNAs) direct cleavage or translational inhibition of target mRNAs by Watson-Crick complementarity. MicroRNAs are a subclass of sRNAs processed from hairpin-forming, non-coding RNA-PolymeraseII transcripts which play crucial roles in development and stress responses. Abscisic acid (ABA) is a hormone associated with flowering, nutrient signaling, and post-transcriptional processes including miRNAs, but unlike auxin its molecular interactions with siRNAs are unknown. We show that At-MIR842 and At-MIR846 are transcribed as a cistron repressed by ABA and subject to alternative splicing. One target of miR846, At5g28520 encoding a jacalin-lectin, is highly up-regulated by ABA in roots. Cleavage of its transcript is directed by miR846, the major species produced by alternative At-MIR842-846 transcript splicing, but only in the absence of exogenous ABA. Mutants of ABA HYPERSENSITIVE1/CAP-BINDING-PROTEIN80 affect splicing, ABA signaling and the biogenesis of miRNAs. We show that double mutants of ABA hypersensitive1 and suppressor of gene silencing3, which encodes a zinc-finger protein required for RNAi, manifest novel phenotypes including early flowering, fused cotyledons, altered inflorescence phyllotaxy, bent siliques, poor pollen adherence to the stigma, reduced seed set, and resistance to fungal infection. A custom microarray was designed to probe the molecular bases of these phenotypes. Results confirmed documented effects of abh1on MIRNA expression and identified miRNA precursors and targets (e.g. pre-MIR168a, pre-MIR395c, pre-MIR824, pre-MIR2936,LACCASE12) induced by ABA and/or elevated in abh1 sgs3 double mutant (pre-MIR156ac, pre-MIR164b, pre-MIR166a,At5g15845/CONSTANS-LIKE1-cis-NAT-RNA). miR156 targets SQUAMOSA-PROMOTER-BINDING-PROTEIN-LIKE genes that spawn siRNAs and control flowering time; miR164 targets CUP-SHAPED-COTYLEDON1 and -2 genes; miR166 methylates target PHABULOSA gDNA in trans; miR168 targets ARGONAUTE1; miR2936 is pollen-specific. We also found abh1 or sgs3 by ABA interactions (e.g.At4g35770/SENESCENCE-ASSOCIATED1, At1g11260/SUGAR-TRANSPORTER1). We have uncovered new nodes in regulatory networks linking ABA and nutrient signaling, flowering, mRNA processing and RNAi.