Fluctuations of the transcription factor ATML1 generate the pattern of giant cells in the Arabidopsis sepal

Meyer, Heather M; Teles, José; Formosa-Jordan, Pau; Refahi, Yassin; San-Bento, Rita; Ingram, Gwyneth; Jönsson, Henrik; Locke, James; Roeder, Adrienne

doi:10.7554/elife.19131

Cited by 96 publications

(146 citation statements)

References 107 publications

(192 reference statements)

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“…In growing organisms, developmental decisions are robust, although biochemical processes and phenotypic traits present an important degree of stochasticity (Oates, 2003;Eldar & Elowitz, 2010;Balázsi et al, 2011;Garcia-Ojalvo & Martinez Arias, 2012;Meyer & Roeder, 2014). This is also the case for plant development and growing roots (Roeder et al, 2010;Hong et al, 2016;Meyer et al, 2017). For instance, the mitotic events at the root meristem or the size cells need to reach before dividing, all show variability (Roeder, 2012;Mä et al, 2014).…”

Section: Discussionmentioning

confidence: 99%

A Sizer model for cell differentiation in Arabidopsis thaliana root growth

Pavelescu

Vilarrasa-Blasi

Planas-Riverola

et al. 2018

Molecular Systems Biology

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Plant roots grow due to cell division in the meristem and subsequent cell elongation and differentiation, a tightly coordinated process that ensures growth and adaptation to the changing environment. How the newly formed cells decide to stop elongating becoming fully differentiated is not yet understood. To address this question, we established a novel approach that combines the quantitative phenotypic variability of wild‐type Arabidopsis roots with computational data from mathematical models. Our analyses reveal that primary root growth is consistent with a Sizer mechanism, in which cells sense their length and stop elongating when reaching a threshold value. The local expression of brassinosteroid receptors only in the meristem is sufficient to set this value. Analysis of roots insensitive to BR signaling and of roots with gibberellin biosynthesis inhibited suggests distinct roles of these hormones on cell expansion termination. Overall, our study underscores the value of using computational modeling together with quantitative data to understand root growth.

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Section: Discussionmentioning

confidence: 99%

A Sizer model for cell differentiation in Arabidopsis thaliana root growth

Pavelescu

Vilarrasa-Blasi

Planas-Riverola

et al. 2018

Molecular Systems Biology

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“…It has also been observed in multiple pathways in mammalian cells (Yin et al, 2009;Mantsoki et al, 2016;Riddle et al, 2018), in Drosophila cells (Pare et al, 2009) and between individuals in Drosophila (Lin et al, 2016). However, gene expression variability has mostly been analysed for a few individual genes in plants at a single-cell resolution (Angel et al, 2015;Araujo et al, 2017;Meyer et al, 2017;Gould et al, 2018). Several studies suggest that transcriptional variability between cells can be exploited during development in multiple organisms (Wernet et al, 2006;Chang et al, 2008;Pare et al, 2009;Meyer et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

“…However, gene expression variability has mostly been analysed for a few individual genes in plants at a single-cell resolution (Angel et al, 2015;Araujo et al, 2017;Meyer et al, 2017;Gould et al, 2018). Several studies suggest that transcriptional variability between cells can be exploited during development in multiple organisms (Wernet et al, 2006;Chang et al, 2008;Pare et al, 2009;Meyer et al, 2017). On the other hand, the identification of mutants in which transcriptional and/or phenotypic variability is increased indicates that variability is at least partly buffered or controlled (Rutherford & Lindquist, 1998;Queitsch et al, 2002;Raj et al, 2010;Folta et al, 2014;Schaefer et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

Widespread inter‐individual gene expression variability in Arabidopsis thaliana

Cortijo

Aydın

Ahnert

et al. 2019

Molecular Systems Biology

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A fundamental question in biology is how gene expression is regulated to give rise to a phenotype. However, transcriptional variability is rarely considered although it could influence the relationship between genotype and phenotype. It is known in unicellular organisms that gene expression is often noisy rather than uniform, and this has been proposed to be beneficial when environmental conditions are unpredictable. However, little is known about inter‐individual transcriptional variability in multicellular organisms. Using transcriptomic approaches, we analysed gene expression variability between individual Arabidopsis thaliana plants growing in identical conditions over a 24‐h time course. We identified hundreds of genes that exhibit high inter‐individual variability and found that many are involved in environmental responses, with different classes of genes variable between the day and night. We also identified factors that might facilitate gene expression variability, such as gene length, the number of transcription factors regulating the genes and the chromatin environment. These results shed new light on the impact of transcriptional variability in gene expression regulation in plants.

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“…Noise in gene expression has been shown to have a significant impact on the design and function of genetic circuits in unicellular organisms 4,5 , and has been observed in multiple pathways in cell cultures of mammalian cells 6 . However, gene expression variability in growing multicellular organisms has only been analysed for a few individual genes in plants 7-9 and animals 10 . It is not known at a genome-wide scale to what extent gene expression can be variable during plant development.…”

Section: Introductionmentioning

confidence: 99%