Boundary Formation through a Direct Threshold-Based Readout of Mobile Small RNA Gradients

Skopelitis, Damianos S.; Benkovics, Anna Hangyáné; Husbands, Aman Y.; Timmermans, Marja C.P.

doi:10.1016/j.devcel.2017.10.003

Cited by 92 publications

(104 citation statements)

References 65 publications

(108 reference statements)

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“…In Arabidopsis, the ta-siARF pathway was first described as a mechanism for vegetative phase change, although studies in rice and maize have revealed adaxial-abaxial patterning defects in monocot ta-siARF mutants (Bohmert et al, 1998;Timmermans et al, 1998;Peragine et al, 2004;Pekker et al, 2005;Hunter et al, 2006;Nagasaki et al, 2007;Nogueira et al, 2007;Itoh et al, 2008;Douglas et al, 2010). However, recent work in tomato and Arabidopsis has confirmed that a role for ta-siARF in leaf polarity is conserved in both monocots and eudicots (Yifhar et al, 2012;Skopelitis et al, 2017). Thus, many of the observed phenotypic differences of ta-siARF mutants are probably confounded by the lack of investigations in diverse angiosperms.…”

Section: Flat Laminar Growth: Patterning and Coordination Of Adaximentioning

confidence: 99%

On the mechanisms of development in monocot and eudicot leaves

Conklin

Strable

et al. 2018

New Phytologist

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Contents Summary I. Introduction II. Leaf zones in monocot and eudicot leaves III. Monocot and eudicot leaf initiation: differences in degree and timing, but not kind IV. Reticulate and parallel venation: extending the model? V. Flat laminar growth: patterning and coordination of adaxial-abaxial and mediolateral axes VI. Stipules and ligules: ontogeny of primordial elaborations VII. Leaf architecture VIII. Stomatal development: shared and diverged mechanisms for making epidermal pores IX. Conclusion Acknowledgements References SUMMARY: Comparisons of concepts in monocot and eudicot leaf development are presented, with attention to the morphologies and mechanisms separating these angiosperm lineages. Monocot and eudicot leaves are distinguished by the differential elaborations of upper and lower leaf zones, the formation of sheathing/nonsheathing leaf bases and vasculature patterning. We propose that monocot and eudicot leaves undergo expansion of mediolateral domains at different times in ontogeny, directly impacting features such as venation and leaf bases. Furthermore, lineage-specific mechanisms in compound leaf development are discussed. Although models for the homologies of enigmatic tissues, such as ligules and stipules, are proposed, tests of these hypotheses are rare. Likewise, comparisons of stomatal development are limited to Arabidopsis and a few grasses. Future studies may investigate correlations in the ontogenies of parallel venation and linear stomatal files in monocots, and the reticulate patterning of veins and dispersed stoma in eudicots. Although many fundamental mechanisms of leaf development are shared in eudicots and monocots, variations in the timing, degree and duration of these ontogenetic events may contribute to key differences in morphology. We anticipate that the incorporation of an ever-expanding number of sequenced genomes will enrich our understanding of the developmental mechanisms generating eudicot and monocot leaves.

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Section: Flat Laminar Growth: Patterning and Coordination Of Adaximentioning

confidence: 99%

On the mechanisms of development in monocot and eudicot leaves

Conklin

Strable

et al. 2018

New Phytologist

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“…Testing SPL and TCP binding in multiple tissues would help in assessing these possibilities; such data would aid evaluation of the possibility that the AGO7 promoter integrates both temporal and spatial signals. More broadly, linking such TF binding events to changes at the cellular level in diverse plants should remain a challenging but productive approach (Fouracre & Poethig, 2016;Skopelitis, Benkovics, Husbands, & Timmermans, 2017).…”

Section: Discussionmentioning

confidence: 99%

Functional dissection of the ARGONAUTE7 promoter

et al. 2019

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ARGONAUTES are the central effector proteins of RNA silencing which bind target transcripts in a small RNA ‐guided manner. Arabidopsis thaliana has 10 ARGONAUTE ( AGO ) genes, with specialized roles in RNA ‐directed DNA methylation, post‐transcriptional gene silencing, and antiviral defense. To better understand specialization among AGO genes at the level of transcriptional regulation we tested a library of 1497 transcription factors for binding to the promoters of AGO 1 , AGO 10 , and AGO 7 using yeast 1‐hybrid assays. A ranked list of candidate DNA ‐binding TF s revealed binding of the AGO 7 promoter by a number of proteins in two families: the miR156‐regulated SPL family and the miR319‐regulated TCP family, both of which have roles in developmental timing and leaf morphology. Possible functions for SPL and TCP binding are unclear: we showed that these binding sites are not required for the polar expression pattern of AGO 7 , nor for the function of AGO 7 in leaf shape. Normal AGO 7 transcription levels and function appear to depend instead on an adjacent 124‐bp region. Progress in understanding the structure of this promoter may aid efforts to understand how the conserved AGO 7‐triggered TAS 3 pathway functions in timing and polarity.

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“…Past work understanding natural morphogenesis and engineering synthetic morphogenesis largely focused on genetic systems implementing reaction-diffusion mechanisms as the primary means of temporal and spatial patterning (Basu et al, 2005;Cooper et al, 2015;Danino et al, 2010;Gregor et al, 2007;Raspopovic et al, 2014;Skopelitis et al, 2017;Sohka et al, 2009;Tabor et al, 2009). However, there is an opportunity to take advantage of a holistic approach to patterning.…”

Section: Towards Engineering the Growth Of More Complex Biological Pamentioning

confidence: 99%

Abstracted functions for engineering the autonomous growth and formation of patterns

Choksi

Endy

2019

Preprint

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Natural biological patterns arise via the growth, differentiation, death, differential adhesion, communication, and movement of or among cells. Synthetic biologists typically impose explicit genetic control of cell-cell communication and programmable cell state to realize engineered biological patterns. Such engineering approaches do not usually consider the underlying physical properties of individual cells that inevitably contribute to pattern development. To better integrate synthetic genetic systems engineering with natural growth and patterning we derived abstract functions that relate how changes in basic cell properties such as growth rate, length, and radius of curvature result in differences in the curvature, end-point reliability, and texture of borders that define boundaries among growing cell lineages. Each abstracted border function is derived holistically as an emergent consequence of underlying cell physical properties. We experimentally demonstrate control of border curvature to angles of 60° from initial trajectories, control of end-point variability to within 15° of desired target endpoints, and control of border texture between 10 to 60 unit cell lengths. In combination with synthetic genetic control systems, we grow arbitrary two-dimensional patterns including phases of the moon, PacMen, and a yinyang-like pattern. Differences between the idealized and observed behavior of abstracted border functions highlight opportunities for realizing more precise control of growth and form, including better integration of synthetic genetic systems with native cellular properties and processes. plasmid segregation, Tim Rudge and Anton Kan for their help with CellModeller, and Jonathan Calles for his help editing.

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Boundary Formation through a Direct Threshold-Based Readout of Mobile Small RNA Gradients

Cited by 92 publications

References 65 publications

On the mechanisms of development in monocot and eudicot leaves

On the mechanisms of development in monocot and eudicot leaves

Functional dissection of the ARGONAUTE7 promoter

Abstracted functions for engineering the autonomous growth and formation of patterns

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