Modular RNA Recognition Complexes for Host–Virus RNA Mapping
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Solution Overview
Problem
The understanding of the RNA interactome of viral proteins, particularly SARS-CoV-2, is limited, and there is a lack of comprehensive interrogation of viral protein-host RNA interactions, which are crucial for understanding the virus's replication and host gene expression suppression.
Innovation Solution
RNA recognition complexes comprising an RNA-targeting agent, such as CRISPR/Cas9 components or PUF proteins, and a coronavirus-derived protein are used to modulate gene expression by binding to target RNA, either upregulating or downregulating it, with methods involving delivery into cells and profiling gene expression.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Loss of information
If comprehensive interrogation of viral protein-host RNA interactions is performed, then understanding of virus replication and host gene suppression is improved, but current methods lack sufficient capability to achieve this comprehensive understanding
Solution Approach 1:
The patent combines an RNA-targeting agent (such as CRISPR/Cas9 or PUF protein) with a coronavirus-derived protein to create a fusion complex. This merging allows the complex to simultaneously target specific RNA sequences and modulate gene expression, thereby achieving comprehensive interrogation of viral protein-host RNA interactions that neither component could accomplish alone.
Solution Approach 2:
The RNA recognition complex is designed with multi-functionality, capable of both targeting specific RNA sequences through the RNA-targeting agent and modulating gene expression through the coronavirus-derived protein. This universal design allows a single complex to perform multiple functions: RNA binding, gene upregulation, and gene downregulation, enabling comprehensive study of viral-host interactions.
2Adaptability or versatility
If RNA recognition complexes are used to modulate gene expression, then gene expression can be upregulated or downregulated, but the complexity of the complex increases
Solution Approach 1:
The RNA recognition complex is segmented into distinct functional modules: an RNA-targeting agent (CRISPR/Cas9 or PUF protein) and a coronavirus-derived protein. This segmentation allows each component to perform its specific function while maintaining modularity, making the complex easier to design, assemble, and study despite its multi-functional capability.
Applied Scientific Principles
This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.
Function Achieved in This Case
These complexes effectively upregulate or downregulate target RNA expression, providing insights into host-virus interactions and potential therapeutic interventions for diseases associated with reduced gene expression.
Implementation Method 1
the RNA-targeting agent comprises CRISPR/Cas9 components
Implementation Method 2
the sgRNA is targeted to an individual gene of a cell
Implementation Method 3
the RNA recognition complex binds to the target RNA and upregulates gene expression of the target RNA
Data Source
AI summary
Provided are RNA recognition complexes that include an RNA-targeting agent; and a coronavirus-derived protein. In some embodiments, the RNA recognition complex further includes a linker. In some embodiments, the RNA-targeting agent includes CRISPR/Cas9 components (e.g., a Cas9 protein, a Cas 13b protein, or a Cas 13d protein). Also provided herein are methods of upregulating gene expression of a target RNA that include delivering a RNA recognition complex into a cell, wherein the RNA recognition complex comprises a RNA-targeting agent, and a coronavirus-derived protein, and wherein the RNA recognition complex binds to the target RNA and upregulates gene expression of the target RNA in the cell.