scholarly journals Small Molecule-Inducible RNA-Targeting Systems for Temporal Control of RNA Regulation in Vivo

2020 ◽  
Author(s):  
Simone Rauch ◽  
Krysten A. Jones ◽  
Bryan Dickinson
Keyword(s):  
Gene Expression ◽  
Small Molecule ◽  
Rna Regulation ◽  
Base Editing ◽  
Expression Control ◽  
Gene Expression Control ◽  
Rna Targeting ◽  
Dynamics And Control ◽  
And Control

RNA regulation is critical for gene expression control, but tools to temporally manipulate RNA regulatory mechanisms are lacking. Here, we present small molecule-inducible RNA-targeting effectors based on our previously developed CRISPR/Cas-inspired RNA targeting system (CIRTS), which can trigger RNA editing, degradation, or translation on target transcripts. We go on to show the inducible CIRTS editor can be deployed for RNA base editing in vivo, providing a new set of tools to probe RNA regulatory dynamics and control gene expression.

scholarly journals Small Molecule-Inducible RNA-Targeting Systems for Temporal Control of RNA Regulation in Vivo

2020 ◽  
Author(s):  
Simone Rauch ◽  
Krysten A. Jones ◽  
Bryan Dickinson
Keyword(s):  
Gene Expression ◽  
Small Molecule ◽  
Rna Regulation ◽  
Base Editing ◽  
Expression Control ◽  
Gene Expression Control ◽  
Rna Targeting ◽  
Dynamics And Control ◽  
And Control

RNA regulation is critical for gene expression control, but tools to temporally manipulate RNA regulatory mechanisms are lacking. Here, we present small molecule-inducible RNA-targeting effectors based on our previously developed CRISPR/Cas-inspired RNA targeting system (CIRTS), which can trigger RNA editing, degradation, or translation on target transcripts. We go on to show the inducible CIRTS editor can be deployed for RNA base editing in vivo, providing a new set of tools to probe RNA regulatory dynamics and control gene expression.

scholarly journals Small Molecule-Inducible RNA-Targeting Systems for Temporal Control of RNA Regulation

2020 ◽  
Author(s):  
Simone Rauch ◽  
Krysten A. Jones ◽  
Bryan Dickinson
Keyword(s):  
Gene Expression ◽  
Small Molecule ◽  
Rna Binding ◽  
Effector Proteins ◽  
Dependent Manner ◽  
Rna Regulation ◽  
Biosensor System ◽  
Gene Expression Control ◽  
Rna Targeting ◽  
Target Transcript

<div>All aspects of mRNA lifetime and function, including its stability, translational to protein, and trafficking through the cell, are tightly regulated through coordinated post-transcriptional modifications and interactions with a multitude of effector proteins. Despite the increasing recognition of RNA regulation as a critical layer of mammalian gene expression control and its increasing excitement as a therapeutic target, tools to study and control RNA regulatory mechanisms with temporal precision in their endogenous environment are lacking. Here, we present small molecule-inducible RNA-targeting effectors based on our previously-developed CRISPR/Cas-inspired RNA targeting system (CIRTS). The CIRTS biosensor system is based on guide RNA (gRNA)-dependent RNA binding domains that interact with a target transcript using Watson-Crick-Franklin base pair interactions. Addition of a small molecule recruits an RNA effector to the target transcript, thereby eliciting a local effect on the transcript. In this work, we showcase that these CIRTS biosensors can trigger inducible RNA editing, degradation, or translation on target transcripts in a small molecule-dependent manner. We further go on to show that the new CIRTS editor can induce RNA base editing in a small molecule-dependent manner in vivo. Collectively this work provides a useful new set of tools to probe the dynamics of RNA regulatory systems and a new approach to control gene expression at the RNA level.</div>

scholarly journals Small Molecule-Inducible RNA-Targeting Systems for Temporal Control of RNA Regulation

2020 ◽  
Author(s):  
Simone Rauch ◽  
Krysten A. Jones ◽  
Bryan Dickinson
Keyword(s):  
Gene Expression ◽  
Small Molecule ◽  
Rna Binding ◽  
Effector Proteins ◽  
Dependent Manner ◽  
Rna Regulation ◽  
Biosensor System ◽  
Gene Expression Control ◽  
Rna Targeting ◽  
Target Transcript

<div>All aspects of mRNA lifetime and function, including its stability, translational to protein, and trafficking through the cell, are tightly regulated through coordinated post-transcriptional modifications and interactions with a multitude of effector proteins. Despite the increasing recognition of RNA regulation as a critical layer of mammalian gene expression control and its increasing excitement as a therapeutic target, tools to study and control RNA regulatory mechanisms with temporal precision in their endogenous environment are lacking. Here, we present small molecule-inducible RNA-targeting effectors based on our previously-developed CRISPR/Cas-inspired RNA targeting system (CIRTS). The CIRTS biosensor system is based on guide RNA (gRNA)-dependent RNA binding domains that interact with a target transcript using Watson-Crick-Franklin base pair interactions. Addition of a small molecule recruits an RNA effector to the target transcript, thereby eliciting a local effect on the transcript. In this work, we showcase that these CIRTS biosensors can trigger inducible RNA editing, degradation, or translation on target transcripts in a small molecule-dependent manner. We further go on to show that the new CIRTS editor can induce RNA base editing in a small molecule-dependent manner in vivo. Collectively this work provides a useful new set of tools to probe the dynamics of RNA regulatory systems and a new approach to control gene expression at the RNA level.</div>

scholarly journals Synthetic gene regulatory networks in the opportunistic human pathogen Streptococcus pneumoniae

2019 ◽  
Author(s):  
Robin A. Sorg ◽  
Clement Gallay ◽  
Jan-Willem Veening
Keyword(s):  
Gene Expression ◽  
Streptococcus Pneumoniae ◽  
Regulatory Networks ◽  
Expression Patterns ◽  
Combinatorial Libraries ◽  
Regulatory Elements ◽  
Expression Control ◽  
Gene Expression Control

AbstractStreptococcus pneumoniae can cause disease in various human tissues and organs, including the ear, the brain, the blood and the lung, and thus in highly diverse and dynamic environments. It is challenging to study how pneumococci control virulence factor expression, because cues of natural environments and the presence of an immune system are difficult to simulate in vitro. Here, we apply synthetic biology methods to reverse-engineer gene expression control in S. pneumoniae. A selection platform is described that allows for straightforward identification of transcriptional regulatory elements out of combinatorial libraries. We present TetR- and LacI-regulated promoters that show expression ranges of four orders of magnitude. Based on these promoters, regulatory networks of higher complexity are assembled, such as logic AND and IMPLY gates. Finally, we demonstrate single-copy genome-integrated toggle switches that give rise to bimodal population distributions. The tools described here can be used to mimic complex expression patterns, such as the ones found for pneumococcal virulence factors, paving the way for in vivo investigations of the importance of gene expression control on the pathogenicity of S. pneumoniae.

scholarly journals In vivo involvement of mutated initiation factor IF1 in gene expression control at the translational level

FEBS Letters ◽  
2005 ◽  
Vol 579 (5) ◽  
pp. 995-1000 ◽  
Author(s):  
Victor V. Croitoru ◽  
Margarete Bucheli-Witschel ◽  
Leif A. Isaksson
Keyword(s):  
Gene Expression ◽  
Initiation Factor ◽  
Expression Control ◽  
Gene Expression Control ◽  
Translational Level

scholarly journals New Putative Long Non-Coding RNAs (lncRNA) Revealed by Pan-Transcriptome of the Emerging Human Pathogenic Fungus Talaromyces Marneffei

2021 ◽  
Author(s):  
David Aciole Barbosa ◽  
Alexandre Santos Simeone ◽  
Ana Carolina Humberto ◽  
Yara Natercia Lima Faustino de Maria ◽  
Regina Costa de Oliveira ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcriptome Assembly ◽  
Pathogenic Fungus ◽  
The Novel ◽  
Talaromyces Marneffei ◽  
Expression Control ◽  
Gene Expression Control ◽  
Human Pathogenic Fungus ◽  
Non Coding Rnas

Abstract Previous genomic/transcriptomic analyses of Talaromyces marneffei (TM) unravelled relevant pathogenicity-related elements, as well as chromosomal regions potentially involved with the production of non-coding RNAs (ncRNAs), which have been parsimoniously reported in fungi. This manuscript describes a comprehensive pan-transcriptome assembly for TM that identifies a series of previously undetected genetic elements in this emerging pathogenic fungus. Our results confirm that ~58.28% of the 9,480 genes currently annotated in the TM genome are, in fact, transcribed in vivo and that ~23.6% of them may display alternative isomorphs. Moreover, we identified 585 transcripts that do not match any gene currently mapped in the genome, represented by 90 coding transcripts and 140 ncRNAs, including 48 long non-coding RNAs (lncRNAs). Overall, we expect that the novel elements described herein may contribute to improve the currently available Talaromyces databases and foster studies aiming at characterizing lncRNA-mediated gene expression control in fungi.

scholarly journals High-performance chemical- and light-inducible recombinases in mammalian cells and mice

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Benjamin H. Weinberg ◽  
Jang Hwan Cho ◽  
Yash Agarwal ◽  
N. T. Hang Pham ◽  
Leidy D. Caraballo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Mammalian Cells ◽  
High Performance ◽  
Genome Engineering ◽  
Genetic Circuits ◽  
Control Of Gene Expression ◽  
Expression Control ◽  
Gene Expression Control ◽  
High Performance Systems ◽  
Spatiotemporal Control

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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