Regulation of Small RNA Accumulation in the Maize Shoot Apex

Abstract

MicroRNAs (miRNAs) and trans-acting siRNAs (ta-siRNAs) are essential to the establishment of adaxial–abaxial (dorsoventral) leaf polarity. Tas3-derived ta-siRNAs define the adaxial side of the leaf by restricting the expression domain of miRNA miR166, which in turn demarcates the abaxial side of leaves by restricting the expression of adaxial determinants. To investigate the regulatory mechanisms that allow for the precise spatiotemporal accumulation of these polarizing small RNAs, we used laser-microdissection coupled to RT-PCR to determine the expression profiles of their precursor transcripts within the maize shoot apex. Our data reveal that the pattern of mature miR166 accumulation results, in part, from intricate transcriptional regulation of its precursor loci and that only a subset of mir166 family members contribute to the establishment of leaf polarity. We show that miR390, an upstream determinant in leaf polarity whose activity triggers tas3 ta-siRNA biogenesis, accumulates adaxially in leaves. The polar expression of miR390 is established and maintained independent of the ta-siRNA pathway. The comparison of small RNA localization data with the expression profiles of precursor transcripts suggests that miR166 and miR390 accumulation is also regulated at the level of biogenesis and/or stability. Furthermore, mir390 precursors accumulate exclusively within the epidermal layer of the incipient leaf, whereas mature miR390 accumulates in sub-epidermal layers as well. Regulation of miR390 biogenesis, stability, or even discrete trafficking of miR390 from the epidermis to underlying cell layers provide possible mechanisms that define the extent of miR390 accumulation within the incipient leaf, which patterns this small field of cells into adaxial and abaxial domains via the production of tas3-derived ta-siRNAs.

An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions

“…A r t i c l e s establishment of biological axes in stem, root and leaf 62,63 . Both MIR166A and MIR166B were surrounded by a cluster of intergenic CNSs, including six with clear homologs beyond the Brassicaceae as well as conservation between the two A. thaliana loci.…”

RBE controls microRNA164 expression to effect floral organogenesis

“…Because miRNA gene families usually produce similar or identical mature miRNAs, the functional specificity of each miRNA gene largely results from its distinct spatial and temporal expression pattern. For instance, the maize miR166 gene family includes nine members that are localized in distinct patterns in the shoot apex, with only some of these genes contributing to the function of miR166 in the specification of the abaxial side of leaves (Nogueira et al, 2009). …”

Ontogeny of the Maize Shoot Apical Meristem

“…Similar to the SAM, lateral shoot meristems undergo vegetative growth, first initiating a bikeeled prophyll followed by foliar husk leaves before transitioning into an inflorescence meristem or undergoing senescence ( Figures 1F and 1L) (Kiesselbach, 1949). Previous studies have analyzed transcripts encoded in various hand-dissected and laser-microdissected shoot apices from 14-d-old seedlings using microarray analysis, as well as 454-based and Illumina-based RNA sequencing (RNA-seq) (Emrich et al, 2007;Ohtsu et al, 2007;Brooks et al, 2009;Jia et al, 2009;Nogueira et al, 2009). However, as yet, no transcriptomic analyses of maize SAM ontogeny during embryogenesis have been described.…”