Tissue-dependent regulation of miRNA activity

miRNAs play important roles in every aspect of plant development. Small RNA regulation confers sensitivity and robustness onto gene regulatory networks, and the morphogen-like readout of small RNA mobility gradients yields sharply delineated domains of target gene expression. However, how the spatiotemporal patterns of miRNA activity are attained is less well understood. We used the high-resolution maize shoot apex transcriptome atlas (Knauer et al., 2019) together with data from small RNA-Seq, PARE analysis, small RNA in-situ hybridization, and RNAseq of weak dcl1 mutant tissues to demonstrate that miRNA accumulation and function during development is regulated in a tiissue dependent manner at the transcriptional and post-transcriptional level. Overall design: small RNA-seq, 1 replicate, of maize shoot apices (SAM and up to four leaf primordia); Bulk RNA-seq, 2x replicates, of the SAM center zone of wild type or dcl1-2 captured by LCM (Knauer et al., 2019); Bulk RNA-seq, 2x replicates, of leaf primordia (P3) of wild type or dcl1-2 captured by LCM (Knauer et al., 2019).