Efficiency and precision of miRNA biogenesis modes in plants

Abstract

Many evolutionarily conserved microRNAs (miRNAs) in plants regulate transcription factorswith key functions in development. Hence, mutations in the core components of the miRNA biogenesis machinery cause strong growth defects. An essential aspect of miRNA biogenesis is the precise excision of the small RNA from its precursor. In plants, miRNA precursors are largely variable in size and shape and can be processed by different modes. Here, we optimized an approach to detect intermediates during miRNA biogenesis. We characterized a miRNA whose processing is triggered by a terminal branched loop. Plant miRNA processing can be initiated by internal bubbles, small terminal loops or branched loops followed by dsRNA segments of 15-17 bp. Interestingly, precision and efficiency vary with the processing modes.Despite the various potential structural determinants present in a single a miRNA precursor, DCL1 is mostly guided by a predominant structural region in each precursor in wild-type plants.However, our studies in fiery1, hyl1 and se mutants revealed the existence of cleavage signatures consistent with the recognition of alternative processing determinants. The results provide a general view of the mechanisms underlying the specificity of miRNA biogenesis in plants.

A conserved SNP variation in the pre-miR396c flanking region in Oryza sativa indica landraces correlates with mature miRNA abundance

“…BTLs seen in Arabidopsis pri- miR166 alter processing direction from a base-to-loop mode to a bidirectional mode that has implications on miRNA abundance 26 . BTLs reduce the efficiency of Arabidopsis miR157c processing and replacement by a 4 nucleotides loop increases processing efficiency 27 . Group 2 members show a common conserved 10 bp terminal loop (TL) in the UR.…”