Graphical Abstract Highlights d Tocopherols positively regulate miRNA biogenesis d Tocopherols are required for PAP accumulation d PAP positively regulates miRNA biogenesis d Retrograde regulation of miR398 confers heat tolerance In Brief As key regulators of gene expression, miRNAs themselves are subjected to sophisticated regulation. Fang et al. report that chloroplast retrograde signaling involving tocopherols (vitamin E) and PAP, a retrograde inhibitor of the nuclear XRN exonucleases, regulates miRNA biogenesis in Arabidopsis and confers heat tolerance.

RNA polymerases IV and V (Pol IV and Pol V) are required for the generation of noncoding RNAs in RNA-directed DNA methylation (RdDM). Their subunit compositions resemble that of Pol II. The mechanism and accessory factors involved in their assembly remain largely unknown. In this study, we identified mutant alleles of (), (), and () that cause defects in RdDM in We found that Pol IV-dependent small interfering RNAs and Pol V-dependent transcripts were greatly reduced in the mutants. NRPE1, the largest subunit of Pol V, failed to associate with other Pol V subunits in the and mutants, suggesting the involvement of IYO and QQT2 in Pol V assembly. In addition, we found that IYO and QQT2 were mutually dependent for their association with the NRPE3 subassembly prior to the assembly of Pol V holoenzyme. Finally, we show that IYO and QQT2 are similarly required for the assembly of Pol II and Pol IV. Our findings reveal IYO and QQT2 as cofactors for the assembly of Pol II, Pol IV, and Pol V and provide mechanistic insights into how RNA polymerases are assembled in plants.