4.8 Article

Optogenetic control of the Bicoid morphogen reveals fast and slow modes of gap gene regulation

Related references

Note: Only part of the references are listed.
Article Cell Biology

Rapid and robust optogenetic control of gene expression in Drosophila

Florencia di Pietro et al.

Summary: Gene function deciphering requires precise control of gene expression in both space and time. The ShineGal4/UAS system, based on light-inducible Magnet photoswitches, allows efficient activation of transgenes in Drosophila, enabling generation of gain and loss-of-function phenotypes at various levels. This system enriches the genetic toolkit, providing high temporal and spatial resolution control over gene expression in vivo.

DEVELOPMENTAL CELL (2021)

Review Engineering, Biomedical

Signaling, Deconstructed: Using Optogenetics to Dissect and Direct Information Flow in Biological Systems

Payam E. Farahani et al.

Summary: Cells receive information from their environment and use optogenetic tools to study how they decode signals and produce appropriate responses. Optogenetics helps researchers manipulate protein interactions and activities with precision, leading to a better understanding and engineering of biology.

ANNUAL REVIEW OF BIOMEDICAL ENGINEERING, VOL 23, 2021 (2021)

Article Genetics & Heredity

Independence of chromatin conformation and gene regulation during Drosophila dorsoventral patterning

Elizabeth Ing-Simmons et al.

Summary: Chromatin organization is largely independent of dorsoventral gene expression in early Drosophila embryonic development, with tissue-specific chromatin states and gene expression being maintained across tissues. Tissue-specific chromatin conformation is not necessary for tissue-specific gene expression, but rather acts as a scaffold facilitating gene expression when enhancers become active.

NATURE GENETICS (2021)

Article Multidisciplinary Sciences

The nuclear to cytoplasmic ratio directly regulates zygotic transcription in Drosophila through multiple modalities

Sahla Syed et al.

Summary: The research found that the N/C ratio affects the number of cell divisions and the timing of zygotic genome activation, influencing transcription through multiple modes of action.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

Article Cell Biology

Extremely rapid and reversible optogenetic perturbation of nuclear proteins in living embryos

Anna C. Koegler et al.

Summary: Many developmental regulators have complex and context-specific roles in different tissues and stages, making the dissection of their function extremely challenging. The improved light-inducible nuclear export system (iLEXY) enables rapid, efficient, and reversible nuclear protein depletion in embryos, and is generalizable to proteins of diverse sizes and functions, highlighting its power in dissecting the function of pleiotropic factors during embryogenesis with unprecedented temporal precision.

DEVELOPMENTAL CELL (2021)

Article Biochemistry & Molecular Biology

Desensitisation of Notch signalling through dynamic adaptation in the nucleus

Ranjith Viswanathan et al.

Summary: This study uses optogenetics to control Notch signaling activation with high precision during Drosophila embryogenesis and observes dynamic adaptation of target gene transcription over time. The results reveal a novel mechanism of dynamic nuclear adaptation in controlling Notch signaling output during tissue differentiation, providing insights into the translation of signaling inputs into gene expression outputs.

EMBO JOURNAL (2021)

Article Cell Biology

An optogenetic method for interrogating YAP1 and TAZ nuclear-cytoplasmic shuttling

Anna M. Dowbaj et al.

Summary: The shuttle of transcription factors and transcriptional regulators is crucial for the regulation of biological processes. A new method involving optogenetic release of YAP1 and TAZ from sequestration demonstrates the correlation between their rates of entry and exit. Phosphorylation influences YAP1's rate of nuclear export, indicating a complex regulatory mechanism for protein dynamics.

JOURNAL OF CELL SCIENCE (2021)

Article Multidisciplinary Sciences

Temporal integration of inductive cues on the way to gastrulation

Sarah McFann et al.

Summary: Markers for endoderm and mesoderm germ layers are commonly expressed together in the early embryo, reflecting cells' ability to explore potential fates before fully committing. In Drosophila, applying endoderm-inducing signals to the ventral embryo reveals a critical time window during which mesodermal cell movements and gene expression are suppressed by proendoderm signaling. Computational modeling shows that repression of the mesoderm-associated gene snail by the ERK target gene huckebein is sufficient to account for a broad range of transcriptional and morphogenetic effects.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

Article Genetics & Heredity

Two promoters integrate multiple enhancer inputs to drive wild-type knirps expression in the Drosophila melanogaster embryo

Lily Li et al.

Summary: The study reveals that the expression of developmental genes is regulated by multiple enhancers and core promoters, which provide both redundancy and specificity. Specific burst properties during transcription, such as burst size and frequency, are most strongly tuned by the combination of promoters and enhancers. The presence of multiple promoters in a locus is due to enhancer preference and a need for redundancy, with broad promoters being common among developmental genes.

GENETICS (2021)

Article Biochemistry & Molecular Biology

Optogenetic Rescue of a Patterning Mutant

Heath E. Johnson et al.

CURRENT BIOLOGY (2020)

Article Biochemistry & Molecular Biology

Optimal Decoding of Cellular Identities in a Genetic Network

Mariela D. Petkova et al.

Article Biochemical Research Methods

FRET-assisted photoactivation of flavoproteins for in vivo two-photon optogenetics

Tomoaki Kinjo et al.

NATURE METHODS (2019)

Article Multidisciplinary Sciences

Optimizing photoswitchable MEK

Aleena L. Patel et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

Article Biochemistry & Molecular Biology

An Optogenetic Platform for Real-Time, Single-Cell Interrogation of Stochastic Transcriptional Regulation

Marc Rullan et al.

MOLECULAR CELL (2018)

Article Chemistry, Physical

Two photon spectroscopy and microscopy of the fluorescent flavoprotein, iLOV

Rachael J. Homans et al.

PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2018)

Review Genetics & Heredity

Bringing Light to Transcription: The Optogenetics Repertoire

Lorena de Mena et al.

FRONTIERS IN GENETICS (2018)

Article Biochemistry & Molecular Biology

Tracing Information Flow from Erk to Target Gene Induction Reveals Mechanisms of Dynamic and Combinatorial Control

Maxwell Z. Wilson et al.

MOLECULAR CELL (2017)

Article Cell Biology

The Spatiotemporal Limits of Developmental Erk Signaling

Heath E. Johnson et al.

DEVELOPMENTAL CELL (2017)

Article Biochemistry & Molecular Biology

Shadow Enhancers Mediate Dynamic Shifts of Gap Gene Expression in the Drosophila Embryo

Ezzat El-Sherif et al.

CURRENT BIOLOGY (2016)

Article Multidisciplinary Sciences

Optogenetic control of nuclear protein export

Dominik Niopek et al.

NATURE COMMUNICATIONS (2016)

Review Developmental Biology

Morphogen rules: design principles of gradient-mediated embryo patterning

James Briscoe et al.

DEVELOPMENT (2015)

Article Biochemistry & Molecular Biology

Live Imaging of Bicoid-Dependent Transcription in Drosophila Embryos

Tanguy Lucas et al.

CURRENT BIOLOGY (2013)

Article Biochemistry & Molecular Biology

Quantitative Imaging of Transcription in Living Drosophila Embryos Links Polymerase Activity to Patterning

Hernan G. Garcia et al.

CURRENT BIOLOGY (2013)

Article Biochemistry & Molecular Biology

MicroRNAs Act as Cofactors in Bicoid-Mediated Translational Repression

Claudia J. Roedel et al.

CURRENT BIOLOGY (2013)

Article Multidisciplinary Sciences

Dynamic interpretation of maternal inputs by the Drosophila segmentation gene network

Feng Liu et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Article Biochemical Research Methods

Fiji: an open-source platform for biological-image analysis

Johannes Schindelin et al.

NATURE METHODS (2012)

Review Biochemistry & Molecular Biology

The gap gene network

Johannes Jaeger

CELLULAR AND MOLECULAR LIFE SCIENCES (2011)

Article Genetics & Heredity

STAT Is an Essential Activator of the Zygotic Genome in the Early Drosophila Embryo

Amy Tsurumi et al.

PLOS GENETICS (2011)

Article Genetics & Heredity

Temporal Coordination of Gene Networks by Zelda in the Early Drosophila Embryo

Chung-Yi Nien et al.

PLOS GENETICS (2011)

Article Computer Science, Interdisciplinary Applications

Robust smoothing of gridded data in one and higher dimensions with missing values

Damien Garcia

COMPUTATIONAL STATISTICS & DATA ANALYSIS (2010)

Article Developmental Biology

The Bicoid gradient is shaped independently of nuclei

Oliver Grimm et al.

DEVELOPMENT (2010)

Article Multidisciplinary Sciences

Anterior-posterior positional information in the absence of a strong Bicoid gradient

Amanda Ochoa-Espinosa et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

Article Developmental Biology

Dispensability of nanos mRNA localization for abdominal patterning but not for germ cell development

Elizabeth R. Gavis et al.

MECHANISMS OF DEVELOPMENT (2008)

Article Biochemistry & Molecular Biology

Probing the limits to positional information

Thomas Gregor et al.

Review Genetics & Heredity

Network motifs: theory and experimental approaches

Uri Alon

NATURE REVIEWS GENETICS (2007)

Article Multidisciplinary Sciences

An optimized transgenesis system for Drosophila using germ-line-specific φC31 integrases

Johannes Bischof et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Multidisciplinary Sciences

The role of binding site cluster strength in Bicoid-dependent patterning in Drosophila

A Ochoa-Espinosa et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

Article Multidisciplinary Sciences

Dynamic control of positional information in the early Drosophila embryo

J Jaeger et al.

NATURE (2004)