Precise transcriptional control of cellular quiescence by BRAVO/WOX5 complex in Arabidopsis roots

Betegón‐Putze, Isabel; Mercadal, Josep; Bosch, Nadja; Planas-Riverola, Ainoa; Marquès-Bueno, Mar; Vilarrasa-Blasi, Josep; Frigola, David; Burkart, Rebecca C.; Martı́nez, Consuelo; Stahl, Yvonne; Prat, Salomé; Ibañes, Marta; Caño‐Delgado, Ana I.

doi:10.1101/2020.07.15.203638

Cited by 3 publications

(38 citation statements)

References 32 publications

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“…it cannot diffuse. To be consistent with the regulatory interactions between BRAVO and WOX5 reported previously [28], we further require the complex to be inactive, i.e. it does not transcriptionally regulate BRAVO nor WOX5.…”

Section: Bravo Can Confine Its Own Expression Domain By Immobilizing Wox5mentioning

confidence: 88%

“…(either directly or through WOX5-targets) [28] and that WOX5 proteins are able to move from the QC to the VI [22,23]. Thus, WOX5, by moving to the VI cells and shootwards, is able to induce BRAVO expression in those cells.…”

Section: Bravo Can Confine Its Own Expression Domain By Immobilizing Wox5mentioning

confidence: 99%

“…The R2R3-MYB transcription factor BRAVO (BRASSINOSTEROIDS AT VASCULAR AND OR-GANIZING CENTER) has recently been linked to the maintenance of SCN homeostasis [27,28].…”

Section: Introductionmentioning

confidence: 99%

“…We have recently shown that BRAVO and WOX5 are codependent, as evidenced by the mutual regulation of each other promoter expression and the physical interaction of their corresponding proteins, presumably into a protein (e.g. heterodimer) complex [28]. These data also showed that the expression of the BRAVO promoter, restricted to the QC and VI in WT plants, expands towards the vasculature, cortex and endodermis in the bravo loss-of-function mutant [28] (Figure 1B,C), suggesting that BRAVO actively confines its own expression domain.…”

Section: Introductionmentioning

confidence: 99%

“…The expansion is not observed in wox5-1 mutants nor in bravo-2 wox5-1 mutants, suggesting that such confinement requires WOX5. B-E from experiments in [28].…”

Section: Introductionmentioning

confidence: 99%

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Self-confined expression in theArabidopsisroot stem cell niche

Mercadal

Betegón‐Putze

Bosch

et al. 2021

Preprint

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Stem cell niches are local microenvironments that preserve their unique identity while communicating with adjacent tissues. In the primary root of Arabidopsis thaliana, the stem cell niche comprises the expression of two transcription factors, BRAVO and WOX5, among others. Intriguingly, these proteins confine their own gene expression to the niche, as evidenced in each mutant background. Here we propose through mathematical modeling that BRAVO confines its own expression domain to the stem cell niche by attenuating its WOX5-dependent diffusible activator. This negative feedback drives WOX5 action to be spatially restricted as well. The results show that WOX5 diffusion and sequestration by binding to BRAVO is sufficient to drive realistic confined BRAVO expression at the stem cell niche. We propose that attenuation of a diffusible activator can be a general mechanism to confine genetic activity to a small region while at the same time maintain signaling within it and with the surrounding cells.

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Section: Bravo Can Confine Its Own Expression Domain By Immobilizing Wox5mentioning

confidence: 88%

Section: Bravo Can Confine Its Own Expression Domain By Immobilizing Wox5mentioning

confidence: 99%

“…The R2R3-MYB transcription factor BRAVO (BRASSINOSTEROIDS AT VASCULAR AND OR-GANIZING CENTER) has recently been linked to the maintenance of SCN homeostasis [27,28].…”

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

“…The expansion is not observed in wox5-1 mutants nor in bravo-2 wox5-1 mutants, suggesting that such confinement requires WOX5. B-E from experiments in [28].…”

Section: Introductionmentioning

confidence: 99%

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Self-confined expression in theArabidopsisroot stem cell niche

Mercadal

Betegón‐Putze

Bosch

et al. 2021

Preprint

Self Cite

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MINI-EX: Integrative inference of single-cell gene regulatory networks in plants

Ferrari

Pérez

Vandepoele

2022

Preprint

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Multicellular organisms, such as plants, are characterized by highly specialized and tightly regulated cell populations, establishing specific morphological structures and executing distinct functions. Gene regulatory networks (GRNs) describe condition-specific interactions of transcription factor (TF) regulating the expression of target genes, underpinning these specific functions. As efficient and validated methods to identify cell-type specific GRNs from single-cell data in plants are lacking, limiting our understanding of the organization of specific cell-types in both model species and crops, we developed MINI-EX (Motif-Informed Network Inference based on single-cell EXpression data), an integrative approach to infer cell-type specific networks in plants. MINI-EX uses single-cell transcriptomic data to define expression-based networks and integrates TF motif information to filter the inferred regulons, resulting in networks with increased accuracy. Next, regulons are assigned to different cell-types, leveraging cell-specific expression, and candidate regulators are prioritized using network centrality measures, functional annotations, and expression specificity. This embedded prioritization strategy offers a unique and efficient means to unravel signaling cascades in specific cell-types controlling a biological process of interest. We demonstrate MINI-EX's stability towards input data sets with low number of cells and its robustness towards missing data, and we show it infers state-of-the-art networks with a better performance compared to related single-cell network tools. MINI-EX successfully identifies key regulators controlling root development in Arabidopsis and rice, and governing ear development in maize, enhancing our understanding of cell-type specific regulation and unraveling the role of different regulators controlling the development of specific cell-types in plants.

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Brassinosteroid gene regulatory networks at cellular resolution

Nolan

Vukašinović

Hsu

et al. 2022

Preprint

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Brassinosteroids (BRs) are plant steroid hormones that regulate diverse processes such as cell division and cell elongation. BRs control thousands of genes through gene regulatory networks (GRNs) that vary in space and time. We used time series single-cell RNA-sequencing to identify BR-responsive gene expression specific to different cell types and developmental stages of the Arabidopsis root, uncovering the elongating cortex as a site where BRs trigger a shift from proliferation to elongation associated with increased expression of cell wall-related genes. Our analysis revealed HAT7 and GTL1 as BR-responsive transcription factors that regulate cell elongation in the cortex. These results establish the cortex as an important site for BR-mediated gene expression and unveil a BR signaling network regulating the transition from proliferation to elongation, illuminating new aspects of spatiotemporal hormone response.

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Precise transcriptional control of cellular quiescence by BRAVO/WOX5 complex in Arabidopsis roots

Cited by 3 publications

References 32 publications

Self-confined expression in theArabidopsisroot stem cell niche

Self-confined expression in theArabidopsisroot stem cell niche

MINI-EX: Integrative inference of single-cell gene regulatory networks in plants

Brassinosteroid gene regulatory networks at cellular resolution

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