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...

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The plant signaling molecule auxin controls a variety of growth and developmental processes in land plants. Auxin regulates gene expression through a nuclear auxin signaling pathway (NAP) consisting of a ubiquitin ligase auxin receptor TIR1/AFB, its Aux/IAA degradation substrate, and the DNA-binding ARF transcription factors. While extensive qualitative understanding of the pathway and its interactions has been obtained by studying the flowering plant Arabidopsis thaliana, it is so far unknown how these translate to quantitative system behaviour in vivo, a problem that is confounded by large NAP gene families in this species. Here we used the minimal NAP of the liverwort Marchantia polymorpha to quantitatively map NAP protein accumulation and dynamics in vivo through the use of knock-in fluorescent fusion proteins. Beyond revealing the native accumulation profile of the entire NAP protein network, we discovered that the two central ARFs MpARF1 and MpARF2 are proteasomally degraded. This degradation serves two functions: it tunes the stoichiometry of auxin-responsive, positively acting MpARF1 and auxin-independent, negatively acting MpARF2, thereby permitting auxin response. Secondly, through mapping a minimal degradation motif, we found that degradation is likely selective for MpARF2 monomers and favours accumulation of dimers. Interfering with MpARF1:MpARF2 stoichiometry or preventing degradation of MpARF2 monomers caused strong growth defects associated with auxin response defects. Thus, quantitative analysis of the entire Marchantia NAP, allowed to identify a novel regulatory mechanism in auxin response, built on regulated ARF degradation.

Auxin is a well-studied plant hormone, the spatial distribution of which remains incompletely understood. Here, we investigate the effects of cell growth and divisions on the dynamics of auxin patterning, using a combination of mathematical modelling and experimental observations. In contrast to most prior work, models are not designed or tuned with the aim to produce a specific auxin pattern. Instead, we use well-established techniques from dynamical systems theory to uncover and classify ranges of auxin patterns as exhaustively as possible, as parameters are varied. Previous work using these techniques has shown how a multitude of stable auxin patterns may coexist, each attainable from a specific ensemble of initial conditions. When a key parameter spans a range of values, these steady patterns form a geometric curve with successive folds, often nicknamed a snaking diagram. As we introduce growth and cell divisions into a one-dimensional model of auxin distribution, we observe new behaviour which can be conveniently explained in terms of this diagram. Cell growth changes the shape of the snaking diagram, corresponding to deformations of auxin patterns. As divisions occur this can lead to abrupt creation or annihilation of auxin peaks. We term this phenomenon ‘snake-jumping’. Under rhythmic cell divisions, we show how this can lead to stable oscillations of auxin. However, we also show that this requires a high level of synchronisation between cell divisions. Using 18 hour time-lapse imaging of the auxin reporter DII:Venus in roots ofArabidopsis thaliana, we show auxin fluctuates greatly, both in terms of amplitude and periodicity, consistent with the snake-jumping events observed with non-synchronised cell divisions. Periodic signals downstream the auxin signalling pathway have previously been recorded in plant roots. The present work shows that auxin alone is unlikely to play the role of a pacemaker in this context.Author summaryAuxin is a crucial plant hormone, the function of which underpins almost every known plant development process. The complexity of its transport and signalling mechanisms, alongside the inability to image directly, make mathematical modelling an integral part of research on auxin. One particularly intriguing phenomenon is the experimental observation of oscillations downstream of auxin pathway, which serve as initiator for lateral organ formation. Existing literature, with the aid of modelling, has presented both auxin transport and signalling as potential drivers for these oscillations. In this study, we demonstrate how growth and cell divisions may trigger fluctuations of auxin with significant amplitude, which may lead to regular oscillations in situations where cell divisions are highly synchronised. More physiological conditions including variations in the timing of cell divisions lead to much less temporal regularity in auxin variations. Time-lapse microscope images confirm this lack of regularity of auxin fluctuations in the root apical meristem. Together our findings indicate that auxin changes are unlikely to be strictly periodic in tissues that do not undergo synchronous cell divisions and that other factors may have a robust ability to convert irregular auxin inputs into the periodic outputs underpinning root development.