Modulation Unit for RNA Translation Characterization

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Solution Overview

Problem

Current methods are inadequate for rapidly and efficiently assigning molecular functions to the majority of uncharacterized RNA binding proteins (RBPs), which hinders a comprehensive understanding of gene expression regulation.

Innovation Solution

The development of methods involving the assembly of a modulation unit comprising an RNA binding protein, an exogenous RNA binding moiety, and a gene-editing agent, which is delivered into cells to modulate gene expression and identify functions by detecting changes in target RNA translation.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Productivity

If traditional methods are used to characterize RNA binding proteins, then the process is slow and inefficient, but the molecular functions can be identified with high accuracy

Engineering Contradiction:

Improverate of RBP characterizationVSAvoidtime required for functional assignment

Core Design Contradiction:

ProductivityVSLoss of time

Solution Approach 1:

The method segments the RBP characterization process into modular components: (1) RBP expression constructs with specific domains, (2) tethering to RNA structural motifs, (3) functional profiling assays. This segmentation enables parallel processing of multiple RBPs simultaneously, dramatically increasing throughput while maintaining systematic rigor for accurate functional identification.

Inventive Principle:

Principle #1Segmentation

Solution Approach 2:

The invention creates a universal platform that can characterize any RBP with an RNA-binding domain using the same standardized workflow. The method uses universal RNA structural motifs and common profiling assays that work across diverse RBP families, enabling high-throughput characterization without requiring protein-specific optimization, thus resolving the contradiction between speed and accuracy.

Inventive Principle:

Principle #6Universality (Multi-functionality)

2Loss of information

If comprehensive functional profiling is performed on all RBPs, then complete understanding of gene regulation is achieved, but the resource requirements and experimental complexity increase significantly

Engineering Contradiction:

Improvecompleteness of RBP functional knowledgeVSAvoidexperimental system complexity

Core Design Contradiction:

Loss of informationVSDevice complexity

Solution Approach 1:

The comprehensive profiling is segmented into discrete, standardized modules including specific RNA structural motifs (stem-loops, hairpins), defined RBP domain categories, and systematic functional assays. This modular segmentation reduces experimental complexity by providing a reproducible framework that can be systematically applied across all RBPs to achieve complete functional understanding.

Inventive Principle:

Principle #1Segmentation

Solution Approach 2:

The invention introduces standardized RNA structural motifs as intermediaries between the diverse RBPs and the functional profiling system. These motif-containing reporter constructs serve as universal mediators that translate various RBP specificities into comparable functional readouts, enabling comprehensive profiling without proportionally increasing system complexity.

Inventive Principle:

Principle #24Intermediary (Mediator)

Data Source

PatentUS20240417730A1Methods of modulating RNA translation

Publication Date: 2024.12.19 RGT UNIV OF CALIFORNIA

AI summary

Provided are methods of modulating gene expression of a target RNA in a cell comprising (a) recruiting a modulation unit, wherein the modulation unit comprises an RNA binding protein (RBP), an exogenous RNA binding moiety, and a gene-editing agent; (b) delivering the modulation unit into the cell; and (c) detecting change in the target RNA translation, wherein the modulation unit modulates gene expression of the target RNA in the cell.