Lighting up the central dogma for predictive developmental biology

García, Hernán G.; Berrocal, Augusto; Kim, Yang Joon; Martini, Gabriella; Zhao, Jiaxi

doi:10.1016/bs.ctdb.2019.10.010

Cited by 20 publications

(21 citation statements)

References 190 publications

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“…Transcriptionally silent loci that remain inactive throughout interphase, such as those revealed by our experiment (Fig. 3F), have been observed using MS2 (and its sister mRNA labeling tool, PP7) in live-imaging experiments in flies (Garcia et al, 2013;Lammers et al, 2020;Berrocal et al, 2020), plants (Alamos et al, 2020), and mammalian cells (Hafner et al, 2020). However, it has not been possible to determine whether these inactive loci correspond to a separate transcriptional state from active loci, or whether they are an artifact of the fluorescence detection thresholds associated with various microscopy techniques.…”

Section: Transcriptionally Active and Inactive Loci Correspond To Functionally Distinct Populationssupporting

confidence: 66%

“…A major obstacle to uncovering the mechanistic and quantitative underpinnings of enhancer action is the inherent complexity of endogenous regulatory sequences. Synthetic minimal enhancers are powerful alternatives to the complex experimental reality faced by modeling efforts in endogenous enhancers (Garcia et al, 2016(Garcia et al, , 2020. Synthetic minimal enhancers contain binding sites for one or a handful of transcription factors, making them more amenable to theoretical dissection (Fakhouri et al, 2010;Sayal et al, 2016;Crocker and Ilsley, 2017) and revealing the complex interplay among activators, repressors, and pioneer factors, as well as their contribution to mRNA transcript accumulation (Fakhouri et al, 2010;Sayal et al, 2016;Crocker and Ilsley, 2017).…”

Section: Discussionmentioning

confidence: 99%

“…1A) whose concentrations are interpreted by enhancer DNA sequences that, in turn, regulate transcription of developmental genes (Wolpert, 1969;Briscoe and Small, 2015). A long-standing goal in quantitative developmental biology is to precisely predict gene expression from knowledge of the DNA regulatory sequence and morphogen concentration (Garcia et al, 2020;Vincent et al, 2016). Achieving this predictive understanding requires theoretical models that calculate how DNA sequence dictates the functional relation between input morphogen concentration and output transcriptional activity, and calls for testing these predictions by measuring input-output functions (Garcia et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

“…A long-standing goal in quantitative developmental biology is to precisely predict gene expression from knowledge of the DNA regulatory sequence and morphogen concentration (Garcia et al, 2020;Vincent et al, 2016). Achieving this predictive understanding requires theoretical models that calculate how DNA sequence dictates the functional relation between input morphogen concentration and output transcriptional activity, and calls for testing these predictions by measuring input-output functions (Garcia et al, 2020). Precise genetic manipulations (Venken and Bellen, 2005;Bier et al, 2018) and powerful imaging technologies (Gregor et al, 2005;Garcia et al, 2013;Mir et al, 2017) have rendered the early embryo of the fruit fly Drosophila melanogaster (Drosophila) a prime model system for quantitatively dissecting these input-output functions in development.…”

Section: Introductionmentioning

confidence: 99%

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Minimal synthetic enhancers reveal control of the probability of transcriptional engagement and its timing by a morphogen gradient

Reimer

Álamos

Westrum

et al. 2021

Preprint

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How enhancers interpret morphogen gradients to generate spatial patterns of gene expression is a central question in developmental biology. Although recent studies have begun to elucidate that enhancers can dictate whether, when, and at what rate a promoter will engage in transcription, the complexity of endogenous enhancers calls for theoretical models with too many free parameters to quantitatively dissect these regulatory strategies. To overcome this limitation, we established a minimal synthetic enhancer system in embryos of the fruit 2y Drosophila melanogaster. Here, a gradient of the Dorsal activator is read by a single Dorsal binding site. By quantifying transcriptional activity using live imaging, our experiments revealed that this single Dorsal binding site is capable of regulating whether promoters engage in transcription in a Dorsal concentration-speci1c manner. By modulating binding-site aZnity, we determined that a gene’s decision to engage in transcription and its transcriptional onset time can be explained by a simple theoretical model where the promoter has to traverse multiple kinetic barriers before transcription can ensue. The experimental platform developed here pushes the boundaries of live-imaging in studying gene regulation in the early embryo by enabling the quanti1cation of the transcriptional activity driven by a single transcription factor binding site, and making it possible to build more complex enhancers from the ground up in the context of a dialogue between theory and experiment.

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Section: Transcriptionally Active and Inactive Loci Correspond To Functionally Distinct Populationssupporting

confidence: 66%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Minimal synthetic enhancers reveal control of the probability of transcriptional engagement and its timing by a morphogen gradient

Reimer

Álamos

Westrum

et al. 2021

Preprint

Self Cite

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show abstract

“…However the spatial aspects of transcription have dominated the study of developmental gene expression, with the role of temporal processes in shaping patterns receiving comparably little attention (J. Bothma and Levine 2013;Garcia et al 2020).…”

Section: Introductionmentioning

confidence: 99%

Kinetic sculpting of the seven stripes of the Drosophila even-skipped gene

Berrocal

Lammers²,

García

et al. 2020

eLife

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We used live imaging to visualize the transcriptional dynamics of the Drosophila melanogaster even-skipped gene at single-cell and high-temporal resolution as its seven stripe expression pattern forms, and developed tools to characterize and visualize how transcriptional bursting varies over time and space. We find that despite being created by the independent activity of five enhancers, even-skipped stripes are sculpted by the same kinetic phenomena: a coupled increase of burst frequency and amplitude. By tracking the position and activity of individual nuclei, we show that stripe movement is driven by the exchange of bursting nuclei from the posterior to anterior stripe flanks. Our work provides a conceptual, theoretical and computational framework for dissecting pattern formation in space and time, and reveals how the coordinated transcriptional activity of individual nuclei shapes complex developmental patterns.

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Single‐Cell Microgels for Diagnostics and Therapeutics

Dubay

Urban

Darling

2021

Adv Funct Materials

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Cell encapsulation within hydrogel droplets is transforming what is feasible in multiple fields of biomedical science such as tissue engineering and regenerative medicine, in vitro modeling, and cell-based therapies. Recent advances have allowed researchers to miniaturize material encapsulation complexes down to single-cell scales, where each complex, termed a singlecell microgel, contains only one cell surrounded by a hydrogel matrix while remaining <100 μm in size. With this achievement, studies requiring singlecell resolution are now possible, similar to those done using liquid droplet encapsulation. Of particular note, applications involving long-term in vitro cultures, modular bioinks, high-throughput screenings, and formation of 3D cellular microenvironments can be tuned independently to suit the needs of individual cells and experimental goals. In this progress report, an overview of established materials and techniques used to fabricate single-cell microgels, as well as insight into potential alternatives is provided. This focused review is concluded by discussing applications that have already benefited from single-cell microgel technologies, as well as prospective applications on the cusp of achieving important new capabilities.

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Lighting up the central dogma for predictive developmental biology

Cited by 20 publications

References 190 publications

Minimal synthetic enhancers reveal control of the probability of transcriptional engagement and its timing by a morphogen gradient

Minimal synthetic enhancers reveal control of the probability of transcriptional engagement and its timing by a morphogen gradient

Kinetic sculpting of the seven stripes of the Drosophila even-skipped gene

Single‐Cell Microgels for Diagnostics and Therapeutics

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