LlamaTags: A Versatile Tool to Image Transcription Factor Dynamics in Live Embryos

Bothma, Jacques P.; Norstad, Matthew; Álamos, Simón; García, Hernán G.

doi:10.1016/j.cell.2018.03.069

Cited by 118 publications

(160 citation statements)

References 54 publications

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“…We predicted that the 'flattening' of the Bcd profile in response to decreasing aspect ratio of the embryo should result in a slight but measurable shift in the downstream gap gene expression domains. We first measured Hunchback (Hb) expression boundary at mid n.c. 14 using live imaging of hb>LlamaTag [27]. In control embryos, the Hb expression boundary locates at 49.0% EL with variation of 1.3% EL, consistent with previous reports [28].…”

Section: Developmental Reproducibility Is Preserved In a Wide Range Osupporting

confidence: 89%

Embryonic geometry underlies phenotypic variation in decanalized conditions

Huang

Saunders

2019

Preprint

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During development, many mutations cause increased variation in phenotypic outcomes, a phenomenon termed decanalization. Such variations can often be attributed to genetic and environmental perturbations. However, phenotypic discordance remains even in isogenic model organisms raised in homogeneous environments. To understand the mechanisms underlying phenotypic variation, we used as a model the highly precise anterior-posterior (AP) patterning of the early Drosophila embryo. We decanalized the system by depleting the maternal bcd product and found that in contrast to the highly scaled patterning in the wild-type, the segmentation gene boundaries shift away from the scaled positions according to the total embryonic length. Embryonic geometry is hence a key factor predetermining patterning outcomes in such decanalized conditions. Embryonic geometry was also found to predict individual patterning outcomes under bcd overexpression, another decanalizing condition. Further analysis of the gene regulatory network acting downstream of the morphogen identified vulnerable points in the networks due to limitations in the available physical space.

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Section: Developmental Reproducibility Is Preserved In a Wide Range Osupporting

confidence: 89%

Embryonic geometry underlies phenotypic variation in decanalized conditions

Huang

Saunders

2019

Preprint

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“…All imaged embryos that managed to start gastrulation were included in the analysis. Embryo 2 is the same from ª 2018 The Authors Molecular Systems Biology 14: e8355 | 2018 (Bothma et al, 2018) Bcd activity, the challenge of extracting dynamic information from the early Drosophila embryo is increasingly tractable. Related to the above points, the tandem reporter enables a characterization of the stability of the system.…”

Section: Discussionmentioning

confidence: 99%

Bicoid gradient formation mechanism and dynamics revealed by protein lifetime analysis

Durrieu

Kirrmaier

Schneidt

et al. 2018

Molecular Systems Biology

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Embryogenesis relies on instructions provided by spatially organized signaling molecules known as morphogens. Understanding the principles behind morphogen distribution and how cells interpret locally this information remains a major challenge in developmental biology. Here, we introduce morphogen‐age measurements as a novel approach to test models of morphogen gradient formation. Using a tandem fluorescent timer as a protein age sensor, we find a gradient of increasing age of Bicoid along the anterior–posterior axis in the early Drosophila embryo. Quantitative analysis of the protein age distribution across the embryo reveals that the synthesis–diffusion–degradation model is the most likely model underlying Bicoid gradient formation, and rules out other hypotheses for gradient formation. Moreover, we show that the timer can detect transitions in the dynamics associated with syncytial cellularization. Our results provide new insight into Bicoid gradient formation and demonstrate how morphogen‐age information can complement knowledge about movement, abundance, and distribution, which should be widely applicable to other systems.

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“…In some cases this may be circumvented by averaging mechanisms that allow cells to produce homogeneous patterns of gene expression (Little et al 2013). For example, cells that express the mesodermal determinant Snail average their transcriptional output over a period of 20 minutes by mRNA diffusion to produce a homogeneous field of cells and a sharp boundary in Drosophila syncytial embryos (Bothma et al 2018). However it is only in rare circumstances that mRNA diffusion can operate and it is unclear whether other averaging mechanisms would be effective over shorter time intervals.…”

Section: Introductionmentioning

confidence: 99%

Enhancer priming enables fast and sustained transcriptional responses to Notch signaling

Falo‐Sanjuan

Lammers

García

et al. 2018

Preprint

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Information from developmental signaling pathways must be accurately decoded to generate transcriptional outcomes. In the case of Notch, the intracellular domain (NICD) transduces the signal directly to the nucleus.How enhancers decipher NICD in the real time of developmental decisions is not known. Using the MS2/MCP system to visualize nascent transcripts in single cells in Drosophila embryos we reveal how two target enhancers read Notch activity to produce synchronized and sustained profiles of transcription. By manipulating the levels of NICD and altering specific motifs within the enhancers we uncover two key principles. First, increased NICD levels alter transcription by increasing duration rather than frequency of transcriptional bursts. Second, priming of enhancers by tissue-specific transcription factors is required for NICD to confer synchronized and sustained activity; in their absence, transcription is stochastic and bursty. The dynamic response of an individual enhancer to NICD thus differs depending on the cellular context.

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LlamaTags: A Versatile Tool to Image Transcription Factor Dynamics in Live Embryos

Cited by 118 publications

References 54 publications

Embryonic geometry underlies phenotypic variation in decanalized conditions

Embryonic geometry underlies phenotypic variation in decanalized conditions

Bicoid gradient formation mechanism and dynamics revealed by protein lifetime analysis

Enhancer priming enables fast and sustained transcriptional responses to Notch signaling

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