Spatial control of gene expression within a scaffold by localized inducer release

ABSTRACTLocalization of RNAs to various subcellular destinations is a widely used mechanism that regulates a large proportion of transcripts in polarized cells. In many cases, such localized transcripts mediate spatial control of gene expression by being translationally silent while in transit and locally activated at their destination. Here, we investigate the translation of RNAs localized at dynamic cellular protrusions of human and mouse, migrating, mesenchymal cells. In contrast to the model described above, we find that protrusion-localized RNAs are not locally activated solely at protrusions, but can be translated with similar efficiency in both internal and peripheral locations. Interestingly, protrusion-localized RNAs are translated at extending protrusions, they become translationally silenced in retracting protrusions and this silencing is accompanied by coalescence of single RNAs into larger heterogeneous RNA clusters. This work describes a distinct mode of translational regulation of localized RNAs, which we propose is used to regulate protein activities during dynamic cellular responses.

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CreLite: An Optogenetically Controlled Cre/loxP System Using Red Light

10.1101/823971 ◽

2019 ◽

Author(s):

Shuo-Ting Yen ◽

Kenneth A. Trimmer ◽

Nader Aboul ◽

Rachel D. Mullen ◽

James C. Culver ◽

...

Keyword(s):

Gene Expression ◽

Light Exposure ◽

Red Light ◽

Regulatory Elements ◽

Cell Labeling ◽

P System ◽

Zebrafish Embryos ◽

Control Of Gene Expression ◽

Spatial Control ◽

Temporal And Spatial

ABSTRACTPrecise manipulation of gene expression with temporal and spatial control is essential for functional studies and the determination of cell lineage relationships in complex biological systems. The Cre-loxP system is commonly used for gene manipulation at desired times and places. However, specificity is dependent on the availability of tissue- or cell-specific regulatory elements used in combination with Cre or CreER (tamoxifen-inducible). Here we present CreLite, an optogenetically-controlled Cre system using red light in developing zebrafish embryos. Cre activity is disabled by splitting Cre and fusing the inactive halves with the Arabidopsis thaliana red light-inducible binding partners, PhyB and PIF6. In addition, PhyB-PIF6 binding requires phycocyanobilin (PCB), providing an additional layer of control. Upon exposure to red light (660 nm) illumination, the PhyB-CreC and PIF6-CreN fusion proteins come together in the presence of PCB to restore Cre activity. Red-light exposure of transgenic zebrafish embryos harboring a Cre-dependent multi-color fluorescent protein reporter (ubi:zebrabow) injected with CreLite mRNAs and PCB, resulted in Cre activity as measured by the generation of multi-spectral cell labeling in various tissues, including heart, skeletal muscle and epithelium. We show that CreLite can be used for gene manipulations in whole embryos or small groups of cells at different stages of development. CreLite provides a novel optogenetic tool for precise temporal and spatial control of gene expression in zebrafish embryos that may also be useful in cell culture, ex vivo organ culture, and other animal models for developmental biology studies.

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Spatial Control of Gene Expression by Nanocarriers Using Heparin Masking and Ultrasound-Targeted Microbubble Destruction

ACS Nano ◽

10.1021/acsnano.6b01199 ◽

2016 ◽

Vol 10 (8) ◽

pp. 7267-7278 ◽

Cited By ~ 20

Author(s):

Beata Chertok ◽

Robert Langer ◽

Daniel G. Anderson

Keyword(s):

Gene Expression ◽

Control Of Gene Expression ◽

Spatial Control

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A conserved choreography of mRNAs at centrosomes reveals a localization mechanism involving active polysome transport

10.1101/2020.09.04.282038 ◽

2020 ◽

Cited By ~ 1

Author(s):

Adham Safieddine ◽

Emeline Coleno ◽

Abdel-Meneem Traboulsi ◽

Oh Sung Kwon ◽

Frederic Lionneton ◽

...

Keyword(s):

Gene Expression ◽

Cell Cycle ◽

High Throughput ◽

Local Translation ◽

Protein Coding ◽

Control Of Gene Expression ◽

Spatial Control ◽

Centrosomal Protein ◽

Protein Coding Genes ◽

Drug Treatments

AbstractLocal translation allows for a spatial control of gene expression. Here, we used high-throughput smFISH to screen centrosomal protein-coding genes, and we describe 8 human mRNAs accumulating at centrosomes. These mRNAs localize at different stages during cell cycle with a remarkable choreography, indicating a finely regulated translational program at centrosomes. Interestingly, drug treatments and reporter analyses revealed a common translation-dependent localization mechanism requiring the nascent protein. Using ASPM and NUMA1 as models, single mRNA and polysome imaging revealed active movements of endogenous polysomes towards the centrosome at the onset of mitosis, when these mRNAs start localizing. ASPM polysomes associate with microtubules and localize by either motor-driven transport or microtubule pulling. Remarkably, the Drosophila orthologs of the human centrosomal mRNAs also localize to centrosomes and also require translation. These data identify a conserved family of centrosomal mRNAs that localize by active polysomes transport mediated by nascent proteins.

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Temporal and spatial control of gene expression in horticultural crops

Horticulture Research ◽

10.1038/hortres.2014.47 ◽

2014 ◽

Vol 1 (1) ◽

Cited By ~ 53

Author(s):

Manjul Dutt ◽

Sadanand A Dhekney ◽

Leonardo Soriano ◽

Raju Kandel ◽

Jude W Grosser

Keyword(s):

Gene Expression ◽

Control Of Gene Expression ◽

Spatial Control ◽

Horticultural Crops ◽

Temporal And Spatial

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Translational regulation of protrusion-localized RNAs involves silencing and clustering after transport

eLife ◽

10.7554/elife.44752 ◽

2019 ◽

Vol 8 ◽

Cited By ~ 1

Author(s):

Konstadinos Moissoglu ◽

Kyota Yasuda ◽

Tianhong Wang ◽

George Chrisafis ◽

Stavroula Mili

Keyword(s):

Gene Expression ◽

Translational Regulation ◽

Cellular Responses ◽

Distinct Mode ◽

Control Of Gene Expression ◽

Spatial Control ◽

Polarized Cells ◽

Regulate Protein ◽

In Transit ◽

Human And Mouse

Localization of RNAs to various subcellular destinations is a widely used mechanism that regulates a large proportion of transcripts in polarized cells. In many cases, such localized transcripts mediate spatial control of gene expression by being translationally silent while in transit and locally activated at their destination. Here, we investigate the translation of RNAs localized at dynamic cellular protrusions of human and mouse, migrating, mesenchymal cells. In contrast to the model described above, we find that protrusion-localized RNAs are not locally activated solely at protrusions, but can be translated with similar efficiency in both internal and peripheral locations. Interestingly, protrusion-localized RNAs are translated at extending protrusions, they become translationally silenced in retracting protrusions and this silencing is accompanied by coalescence of single RNAs into larger heterogeneous RNA clusters. This work describes a distinct mode of translational regulation of localized RNAs, which we propose is used to regulate protein activities during dynamic cellular responses.

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Spatial control of gene expression in flies using bacterially derived binary transactivation systems

Insect Molecular Biology ◽

10.1111/imb.12717 ◽

2021 ◽

Author(s):

S. Gamez ◽

L. C. Vesga ◽

S. C. Mendez‐Sanchez ◽

O. S. Akbari

Keyword(s):

Gene Expression ◽

Control Of Gene Expression ◽

Spatial Control

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A choreography of centrosomal mRNAs reveals a conserved localization mechanism involving active polysome transport

Nature Communications ◽

10.1038/s41467-021-21585-7 ◽

2021 ◽

Vol 12 (1) ◽

Cited By ~ 2

Author(s):

Adham Safieddine ◽

Emeline Coleno ◽

Soha Salloum ◽

Arthur Imbert ◽

Abdel-Meneem Traboulsi ◽

...

Keyword(s):

Gene Expression ◽

Cell Cycle ◽

High Throughput ◽

Local Translation ◽

Protein Coding ◽

Control Of Gene Expression ◽

Spatial Control ◽

Centrosomal Protein ◽

Protein Coding Genes ◽

Drug Treatments

AbstractLocal translation allows for a spatial control of gene expression. Here, we use high-throughput smFISH to screen centrosomal protein-coding genes, and we describe 8 human mRNAs accumulating at centrosomes. These mRNAs localize at different stages during cell cycle with a remarkable choreography, indicating a finely regulated translational program at centrosomes. Interestingly, drug treatments and reporter analyses reveal a common translation-dependent localization mechanism requiring the nascent protein. UsingASPMandNUMA1as models, single mRNA and polysome imaging reveals active movements of endogenous polysomes towards the centrosome at the onset of mitosis, when these mRNAs start localizing. ASPM polysomes associate with microtubules and localize by either motor-driven transport or microtubule pulling. Remarkably, theDrosophilaorthologs of the human centrosomal mRNAs also localize to centrosomes and also require translation. These data identify a conserved family of centrosomal mRNAs that localize by active polysome transport mediated by nascent proteins.

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