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MicroRNAs (miRNAs) and natural antisense transcripts (NATs) control many biological processes and have been broadly applied for genetic manipulation of eukaryotic gene expression. Still unclear, however, are whether and how NATs regulate miRNA production. Here, we report that the  cis -NATs of  MIR398  genes repress the processing of their pri-miRNAs. Through genome-wide analysis of RNA sequencing data, we identify  cis -NATs of  MIRNA  genes in Arabidopsis and Brassica. In Arabidopsis,  MIR398b  and  MIR398c  are coexpressed in vascular tissues with their antisense genes  NAT398b  and  NAT398c , respectively. Knock down of  NAT398b  and  NAT398c  promotes miR398 processing, resulting in stronger plant thermotolerance owing to silencing of miR398-targeted genes; in contrast, their overexpression activates  NAT398b  and  NAT398c , causing poorer thermotolerance due to the upregulation of miR398-targeted genes. Unexpectedly, overexpression of  MIR398b  and  MIR398c  activates  NAT398b  and  NAT398c . Taken together, these results suggest that  NAT398b/c  repress miR398 biogenesis and attenuate plant thermotolerance via a regulatory loop.

Natural antisense transcripts of MIR398 genes suppress microR398 processing and attenuate plant thermotolerance