A network of transcriptional repressors modulates auxin responses

Abstract

Alongside spatio-temporal distribution of developmental signals themselves, the regulation of signalling capacity plays a pivotal role in setting developmental responses in both plants and animals (1). The hormone auxin is a key signal for plant growth and development that acts through the AUXIN RESPONSE FACTOR (ARF) transcription factors (2-4). Subsets of ARFs, the conserved Class A ARFs (abbreviated ARF ClassA ) (5), are transcriptional activators of auxin-responsive target genes, and are essential for regulating auxin signalling throughout the plant lifecycle (2,3). While ARF ClassA show tissue-specific expression patterns, it is unknown how their expression is regulated. By investigating chromatin modifications and accessibility, we show that loci encoding ARF ClassA are constitutively open for transcription. Using a yeast one-hybrid (Y1H) approach, we identify transcriptional regulators of ARF ClassA activator genes from Arabidopsis thaliana, and demonstrate that each ARF ClassA is controlled by specific sets of transcriptional regulators. Transient transformation assays and expression analyses in mutants reveal that the majority of these regulators act as repressors of ARF ClassA transcription in planta. Taken together these observations support a scenario whereby the default configuration of open chromatin enables a network of transcriptional repressors to regulate expression level of ARF ClassA and modulate auxin signalling output throughout development. Transcriptional regulation of ARF ClassA Amongst the 23 Arabidopsis ARFs, ARF5, 6, 7, 8 and 19 are ARF ClassA activators of transcription (3) and are key regulators of both embryonic and post-embryonic development (6-12). In the stem cell niches driving post-embryonic plant development, the root and shoot apical meristems (RAM and SAM) ( 6), tissue-specific variation of ARF ClassA expression (Fig. 1a,b), is thought to be a key determinant of the diversity of auxin responses (14,15). ARF ClassA are encoded by genes with 11-14 introns and the first intron of ARF7 and 19 is 3 around 3 times bigger than the other introns. We tested the role of upstream sequences in determining ARF ClassA expression by comparing patterns in meristems from transcriptional reporter lines (Fig. 1a,b, Extended Fig. 1a-j) using either sequences 3-5 kb 5' of the ATG and 3' up to the end of the first intron for ARF6, 7 and 19 or the 5' sequences alone (designated respectively pARF and pARF -intron ). A difference between the two reporters was only seen for ARF7 (Fig. 1a,b, Extended Fig. 1c,h). Only the ARF7 transcriptional reporter including the first intron showed a strong expression in the RAM (Fig. 1b). The 3' sequence thus contains regulatory information required for ARF7 expression in the root. Comparison with patterns of ARF ClassA reporters with shorter 2 kb promoters (Extended Fig. 1k-o, ( 14)) and with patterns observed with RNA in situ hybridization (Extended Fig. 1p-r; (15,16)) further showed that sequences upstream of the first 2 kb 5' of the ATG are necessary for regulat...

Hormonal Regulation of Stem Cell Proliferation at the Arabidopsis thaliana Root Stem Cell Niche

“…Interestingly, MP and ARF10 are not expressed homogenously in the RAM (Rademacher et al, 2011), suggesting that the cellular context could be important to define the effect of auxin over WOX5 (García-Gómez et al, 2017). Particularly, MP is expressed in the QC cells but not ARF10 (Rademacher et al, 2011;Truskina et al, 2020), which raises the hypothesis that particular ARF profiles could be important for the auxin regulation of WOX5 expression in these cells. Hence, it is of interest to uncover the mechanisms behind the expression patterns of these ARFs in the RAM in order to understand the specificity of auxin responses in the root meristem; however, there is still no evidence about it.…”

“…The proposed links between patterning mechanisms and hormonal signaling pathways may be critical for understanding how cells will respond to auxin and may constitute a generic mechanism for the spatial specificity of hormonal responses in plant development. Interestingly, it has been shown that the chromatin of several ARFs is constitutively open for transcription, and a series of transcriptional repressors affect their expression (Truskina et al, 2020). Under such a scenario, SHR-JKD and SHR-MGP could act as the repressors that are behind the expression patterns of ARF10 and MP, respectively, and that underlie the spatial specificity of their activity in the RAM.…”

Unraveling Root Development Through Single-Cell Omics and Reconstruction of Gene Regulatory Networks

“…Particularly, GRN inferred from yeast one- and two-hybrid approaches have greatly contributed to our understanding of development and stress in Arabidopsis. These GRN have provided new insights into secondary cell wall gene regulation under abiotic stress ( Taylor-Teeples et al, 2014 ), showed coordinated transcriptional regulation of enzymes involved in nitrogen metabolism ( Gaudinier et al, 2018 ) and identified upstream regulation of AUXIN RESPONSE FACTORS to modulate auxin signaling throughout development ( Truskina et al, 2020 ).…”

Information Content Differentiates Enhancers From Silencers in Mouse Photoreceptors

“…Another challenge is that both enhancers and silencers often respond to the same TFs (Alexandre and Vincent, 2003;Iype et al, 2004;Liu et al, 2014;Martínez-Montañés et al, 2013;Peng et al, 2005;Stampfel et al, 2015;White et al, 2016). Many TF-bound sequences act as silencers (Clyde et al, 2003;Doni Jayavelu et al, 2020;Gisselbrecht et al, 2020;Grossman et al, 2017;Kwasnieski et al, 2014;Truskina et al, 2020;White et al, 2013), but predictions of cis-regulatory sequences based on TF binding or chromatin state often do not make a distinction between these two classes of sequence. Since enhancers in one cell type are often silencers in other cell types (Barolo and Posakony, 2002;Clyde et al, 2003;Gisselbrecht et al, 2020;Junion et al, 2012;Parker et al, 2011;Rachmin et al, 2015;Swanson et al, 2010), enhancers and silencers likely share similar sequence features.…”