Finding Missing Interactions of the Arabidopsis thaliana Root Stem Cell Niche Gene Regulatory Network

Abstract

Over the last few decades, the Arabidopsis thaliana root stem cell niche (RSCN) has become a model system for the study of plant development and stem cell niche dynamics. Currently, many of the molecular mechanisms involved in RSCN maintenance and development have been described. A few years ago, we published a gene regulatory network (GRN) model integrating this information. This model suggested that there were missing components or interactions. Upon updating the model, the observed stable gene configurations of the RSCN could not be recovered, indicating that there are additional missing components or interactions in the model. In fact, due to the lack of experimental data, GRNs inferred from published data are usually incomplete. However, predicting the location and nature of the missing data is a not trivial task. Here, we propose a set of procedures for detecting and predicting missing interactions in Boolean networks. We used these procedures to predict putative missing interactions in the A. thaliana RSCN network model. Using our approach, we identified three necessary interactions to recover the reported gene activation configurations that have been experimentally uncovered for the different cell types within the RSCN: (1) a regulation of PHABULOSA to restrict its expression domain to the vascular cells, (2) a self-regulation of WOX5, possibly by an indirect mechanism through the auxin signaling pathway, and (3) a positive regulation of JACKDAW by MAGPIE. The procedures proposed here greatly reduce the number of possible Boolean functions that are biologically meaningful and experimentally testable and that do not contradict previous data. We believe that these procedures can be used on any Boolean network. However, because the procedures were designed for the specific case of the RSCN, formal demonstrations of the procedures should be shown in future efforts.

The MADS-boxXAANTAL1increases proliferation at the Arabidopsis root stem-cell niche and participates in transition to differentiation by regulating cell-cycle components

“…Therefore, it is likely that XAL1 is a component of the complex regulatory network that underlies stem-cell divisions in the Arabidopsis roots. Among other transcription factors, the PLT genes are important components of such a network (Azpeitia et al, 2013;Davila-Velderrain et al, 2014a, b). PLTs are necessary for stem-cell maintenance and cell division in the root (Aida et al, 2004;Galinha et al, 2007) and also their proteins accumulation level define the location of developmental zones (proliferation, elongation and differentiation) (Mahonen et al, 2014).…”

Role of transcriptional regulation in the evolution of plant phenotype: A dynamic systems approach

“…The first GRN that was grounded on experimental data and formally analyzed was proposed for floral organ specification during early flower development (Mendoza and Álvarez‐Buylla, ) and since then, the same approach has been used for other cases (Mendoza et al, , 2000; Benítez et al, ; Azpeitia et al, ; Alvarez‐Buylla et al, ). Once such GRNs are established, uncovering the emergence and maintenance of the dynamical behavior from the concerted action of the molecular components being considered and their regulatory interactions, requires the use of mathematical/computational models (see Davila and Álvarez‐Buylla, , for a description of methods used and examples).…”

PP2A-3 interacts with ACR4 and regulates formative cell division in the Arabidopsis root

“…S1A). Several plant hormones and proteins that play a role in this process have been identified, and small regulatory networks have been proposed (3)(4)(5)(6)(7)(8)(9)(10)(11). However, our knowledge of the mechanisms and signaling networks mediating formative cell divisions is sparse and is largely derived from transcriptional data (12).…”