Spatiotemporal control of gene expression by a light-switchable transgene system

Abstract Site-specific DNA recombinases are important genome engineering tools. Chemical- and light-inducible recombinases, in particular, enable spatiotemporal control of gene expression. However, inducible recombinases are scarce due to the challenge of engineering high performance systems, thus constraining the sophistication of genetic circuits and animal models that can be created. Here we present a library of >20 orthogonal inducible split recombinases that can be activated by small molecules, light and temperature in mammalian cells and mice. Furthermore, we engineer inducible split Cre systems with better performance than existing systems. Using our orthogonal inducible recombinases, we create a genetic switchboard that can independently regulate the expression of 3 different cytokines in the same cell, a tripartite inducible Flp, and a 4-input AND gate. We quantitatively characterize the inducible recombinases for benchmarking their performances, including computation of distinguishability of outputs. This library expands capabilities for multiplexed mammalian gene expression control.

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Spatiotemporal control of gene expression boundaries using a feedforward loop

10.1101/806620 ◽

2019 ◽

Author(s):

Prasad U. Bandodkar ◽

Hadel Al Asafen ◽

Gregory T. Reeves

Keyword(s):

Gene Expression ◽

Biological Networks ◽

Target Gene ◽

Network Motif ◽

Control Of Gene Expression ◽

Intermediate Node ◽

Morphogen Gradients ◽

Spatially Distributed ◽

Spatiotemporal Behavior ◽

Spatiotemporal Control

AbstractA feed forward loop (FFL) is commonly observed in several biological networks. The FFL network motif has been mostly been studied with respect to variation of the input signal in time, with only a few studies of FFL activity in a spatially distributed system such as morphogen-mediated tissue patterning. However, most morphogen gradients also evolve in time. We studied the spatiotemporal behavior of a coherent FFL in two contexts: (1) a generic, oscillating morphogen gradient and (2) the dorsal-ventral patterning of the early Drosophila embryo by a gradient of the NF-κB homolog Dorsal with its early target Twist. In both models, we found features in the dynamics of the intermediate node – phase difference and noise filtering – that were largely independent of the parameterization of the models, and thus were functions of the structure of the FFL itself. In the Dorsal gradient model, we also found that the dynamics of Dorsal require maternal pioneering factor Zelda for proper target gene expression.

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A collection of genetic mouse lines and related tools for inducible and reversible intersectional misexpression

10.1101/754192 ◽

2019 ◽

Author(s):

Elham Ahmadzadeh ◽

N. Sumru Bayin ◽

Xinli Qu ◽

Aditi Singh ◽

Linda Madisen ◽

...

Keyword(s):

Gene Expression ◽

Target Gene ◽

Genetic Manipulation ◽

Cell Types ◽

Biological Processes ◽

Control Of Gene Expression ◽

A Cell ◽

Summary Statement ◽

Spatiotemporal Control ◽

Mouse Lines

AbstractThanks to many advances in genetic manipulation, mouse models have become very powerful in their ability to interrogate biological processes. In order to precisely target expression of a gene of interest to particular cell types, intersectional genetic approaches utilizing two promoter/enhancers unique to a cell type are ideal. Within these methodologies, variants that add temporal control of gene expression are the most powerful. We describe the development, validation and application of an intersectional approach that involves three transgenes, requiring the intersection of two promoter/enhancers to target gene expression to precise cell types. Furthermore, the approach utilizes available lines expressing tTA/rTA to control timing of gene expression based on whether doxycycline is absent or present, respectively. We also show that the approach can be extended to other animal models, using chicken embryos. We generated three mouse lines targeted at the Tigre (Igs7) locus with TRE-loxP-tdTomato-loxP upstream of three genes (p21, DTA and Ctgf) and combined them with Cre and tTA/rtTA lines that target expression to the cerebellum and limbs. Our tools will facilitate unraveling biological questions in multiple fields and organisms.Summary statementAhmadzadeh et al. present a collection of four mouse lines and genetic tools for misexpression-mediated manipulation of cellular activity with high spatiotemporal control, in a reversible manner.

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Spatiotemporal control of gene expression boundaries using a feedforward loop

Developmental Dynamics ◽

10.1002/dvdy.150 ◽

2020 ◽

Vol 249 (3) ◽

pp. 369-382

Author(s):

Prasad U. Bandodkar ◽

Hadel Al Asafen ◽

Gregory T. Reeves

Keyword(s):

Gene Expression ◽

Control Of Gene Expression ◽

Feedforward Loop ◽

Spatiotemporal Control

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Stable integration of an optimized inducible promoter system enables spatiotemporal control of gene expression throughout avian development

Biology Open ◽

10.1242/bio.055343 ◽

2020 ◽

Vol 9 (10) ◽

pp. bio055343 ◽

Cited By ~ 1

Author(s):

Daniel Chu ◽

An Nguyen ◽

Spenser S. Smith ◽

Zuzana Vavrušová ◽

Richard A. Schneider

Keyword(s):

Gene Expression ◽

Embryonic Development ◽

Inducible Promoter ◽

In Ovo ◽

Control Of Gene Expression ◽

Promoter Construct ◽

Avian Development ◽

Spatiotemporal Control ◽

Promoter System

ABSTRACTPrecisely altering gene expression is critical for understanding molecular processes of embryogenesis. Although some tools exist for transgene misexpression in developing chick embryos, we have refined and advanced them by simplifying and optimizing constructs for spatiotemporal control. To maintain expression over the entire course of embryonic development we use an enhanced piggyBac transposon system that efficiently integrates sequences into the host genome. We also incorporate a DNA targeting sequence to direct plasmid translocation into the nucleus and a D4Z4 insulator sequence to prevent epigenetic silencing. We designed these constructs to minimize their size and maximize cellular uptake, and to simplify usage by placing all of the integrating sequences on a single plasmid. Following electroporation of stage HH8.5 embryos, our tetracycline-inducible promoter construct produces robust transgene expression in the presence of doxycycline at any point during embryonic development in ovo or in culture. Moreover, expression levels can be modulated by titrating doxycycline concentrations and spatial control can be achieved using beads or gels. Thus, we have generated a novel, sensitive, tunable, and stable inducible-promoter system for high-resolution gene manipulation in vivo.

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