Small Genetic Circuits and MicroRNAs: Big Players in Polymerase II Transcriptional Control in Plants

Abstract

ORCID IDs: 0000-0001-6793-6151 (M.M.); 0000-0002-0105-6431 (S.A.F.)RNA Polymerase II (Pol II) regulatory cascades involving transcription factors (TFs) and their targets orchestrate the genetic circuitry of every eukaryotic organism. In order to understand how these cascades function, they can be dissected into small genetic networks, each containing just a few Pol II transcribed genes, that generate specific signal-processing outcomes. Small RNA regulatory circuits involve direct regulation of a small RNA by a TF and/or direct regulation of a TF by a small RNA and have been shown to play unique roles in many organisms. Here, we will focus on small RNA regulatory circuits containing Pol II transcribed microRNAs (miRNAs). While the role of miRNA-containing regulatory circuits as modular building blocks for the function of complex networks has long been on the forefront of studies in the animal kingdom, plant studies are poised to take a lead role in this area because of their advantages in probing transcriptional and posttranscriptional control of Pol II genes. The relative simplicity of tissue-and cell-type organization, miRNA targeting, and genomic structure make the Arabidopsis thaliana plant model uniquely amenable for small RNA regulatory circuit studies in a multicellular organism. In this Review, we cover analysis, tools, and validation methods for probing the component interactions in miRNA-containing regulatory circuits. We then review the important roles that plant miRNAs are playing in these circuits and summarize methods for the identification of small genetic circuits that strongly influence plant function. We conclude by noting areas of opportunity where new plant studies are imminently needed.

Impact of small RNAs in retrograde signalling pathways inArabidopsis thaliana

“…The effect of these miRNAs might be visible on the protein level due to inhibition of translation. If the target mRNA encodes a transcription factor, we should then see the miRNA dependent regulation in the expression of downstream targets of this transcription factor (Figure 11b), as has been reported before (Megraw et al, 2016). As an example, the transcription factor AT4G36920 can act as an activator or repressor on its targets.…”

The Legume miR1514a modulates a NAC transcription factor transcript to trigger phasiRNA formation in response to drought

“…In addition, miRNAs can act in cell–cell or organ–organ communication (Megraw et al , 2016), and they can even work at long distances from where they are produced, being transported through phloem (Buhtz et al , 2008; Lin et al , 2008; Pant et al , 2008), thus effectively amplifying their regulatory effects. Upon cleavage of an initial transcript, production of secondary small RNAs may represent another way of signal amplification, as could be the case for phasiRNAs.…”

Systems biology study of transcriptional and post-transcriptional co-regulatory network sheds light on key regulators involved in important biological processes in Citrus sinensis

“…Deciphering complicated coregulatory network is a crucial issue in the post-genomic era for understanding the intracellular mechanism of complex biological processes such as development, growth and responses to biotic and abiotic stresses in all plants (Berri et al 2009;Dodds and Rathjen 2010;Leyva-González et al 2012;Megraw et al 2016). Coregulatory network includes transcription regulators and post transcription regulators that can regulate each other as well as themselves.…”