A network of transcriptional repressors modulates auxin responses.

Jekaterina Truskina ,Silvana Porco ,Jingyi Han ,Margot E Smit ,Etienne Farcot ,Arnaud Stigliani ,Ondřej Smetana ,Géraldine Brunoud ,François Roudier ,Anthony Bishopp ,Carlos Galván‐Ampudia ,Siobhán M Brady ,Elina Chrysanthou ,François Parcy ,Ari Pekka Mähönen ,Stéphanie Lainé ,Malcolm Bennett ,Jonathan Legrand ,Julien Macé ,Simon Bellows ,Anne Maarit Bågman ,Teva Vernoux

doi:10.1038/s41586-020-2940-2

Abstract

The regulation of signalling capacity, combined with the spatiotemporal distribution of developmental signals themselves, is pivotal in setting developmental responses in both plants and animals1. The hormone auxin is a key signal for plant growth and development that acts through the AUXIN RESPONSE FACTOR (ARF) transcription factors2-4. A subset of these, the conserved class A ARFs5, are transcriptional activators of auxin-responsive target genes that are essential for regulating auxin signalling throughout the plant lifecycle2,3. Although class A ARFs have tissue-specific expression patterns, how their expression is regulated is unknown. Here we show, by investigating chromatin modifications and accessibility, that loci encoding these proteins are constitutively open for transcription. Through yeast one-hybrid screening, we identify the transcriptional regulators of the genes encoding class A ARFs from Arabidopsis thaliana and demonstrate that each gene is controlled by specific sets of transcriptional regulators. Transient transformation assays and expression analyses in mutants reveal that, in planta, the majority of these regulators repress the transcription of genes encoding class A ARFs. These observations support a scenario in which the default configuration of open chromatin enables a network of transcriptional repressors to regulate expression levels of class A ARF proteins and modulate auxin signalling output throughout development.

Highlights

Transcriptional regulation of ARFClassA Amongst the 23 Arabidopsis AUXIN RESPONSE FACTOR (ARF), ARF5, 6, 7, 8 and 19 are ARFClassA activators of transcription [3] and are key regulators of both embryonic and post-embryonic development [6,7,8,9,10,11,12]
Meta-analysis of published datasets covering a whole range of tissues and developmental stages shows H3K27me3 is largely absent from all ARFClassA loci while H3K4me3 is detected at these loci (Fig.1c, Extended Data Fig.2a-c, Supplementary Table 1)
The assay yielded 42 novel putative transcriptional regulators of ARFClassA (Fig.2, Extended Fig.3a,b, Supplementary Table 2). This candidate gene regulatory network revealed that individual ARFClassA loci are likely regulated by specific sets of transcription factors (TFs), with only 4 TFs identified that bind multiple ARFClassA sequences

Summary

Discussion

Despite a general role of Polycomb-mediated gene repression in tissue-specific expression [25], the general absence of H3K27me at ARFClassA loci indicates that their regulation does not rely on this epigenetic mechanism. This may be because such a system would not allow for rapid changes in signalling output. The network we characterise resembles the early scenario proposed by Jacob and Monod [29] for transcriptional regulation by repressors only, indicating that there may be a place for the concept of controlling the expression of key developmental regulators via transcriptional repression

Methods

Findings