Synthetic Transcription Factors for Effector Domain Mapping
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
Existing methods for engineering synthetic transcription factors rely on a limited toolbox of effector domains, leading to incomplete mapping of transcriptional effector domains and a lack of understanding of sequence characteristics for activation or repression domains, particularly for human transcription factors.
Innovation Solution
Development of synthetic transcription factors comprising effector domains with specific amino acid sequences, including activator and repressor domains, fused to heterologous DNA binding domains, and their use in modulating gene expression.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Loss of information
If a limited toolbox of effector domains is used for engineering synthetic transcription factors, then the current knowledge base is sufficient for existing methods, but the mapping of transcriptional effector domains remains incomplete and sequence characteristics are not fully understood
Solution Approach 1:
The patent segments the effector domain identification process into systematic components by dividing human transcriptional proteins into discrete protein tiles (e.g., 100-amino acid segments) that can be independently screened and characterized. This segmentation enables comprehensive mapping of effector domains across thousands of proteins while maintaining manageable complexity through modular analysis units.
Solution Approach 2:
The patent creates synthetic transcription factor copies with standardized effector domains fused to heterologous DNA binding domains (such as dCas9). These synthetic factors serve as functional proxies for systematically testing and mapping effector domain activities across target genes, enabling high-throughput identification without requiring direct analysis of native transcription factors.
2Productivity
If high-throughput assays are used to screen effector domains, then productivity increases, but the complexity of systematically mapping effector domains across thousands of proteins increases
Solution Approach 1:
The patent employs a universal screening platform where synthetic transcription factors comprising standardized effector domains fused to heterologous DNA binding domains can be used to assess the activity of effector domains from diverse human transcriptional proteins. This multi-functional system enables high-throughput screening of effector domains across thousands of proteins using a single standardized assay framework, thereby achieving both high productivity and systematic coverage.
3Adaptability or versatility
If effector domains are fused to heterologous DNA binding domains, then the ability to modulate gene expression is enhanced, but the complexity of synthetic transcription factor design increases
Solution Approach 1:
The patent segments the synthetic transcription factor into distinct functional modules: effector domains (for activation or repression), heterologous DNA binding domains (for target localization), and optional linkers. This modular segmentation enables independent optimization of each component's function while simplifying the overall design process, as each module can be selected and combined based on specific gene expression modulation requirements.
Solution Approach 2:
The patent utilizes programmable DNA binding domains such as dCas9, where the binding specificity is determined by guide RNA sequences rather than protein sequence changes. This parameter change approach (using RNA instead of protein for DNA binding) simplifies the design of synthetic transcription factors, as the DNA binding specificity can be easily adjusted by changing guide RNA sequences without modifying the effector domain or DNA binding protein structure.
Data Source
AI summary
Provided herein are compositions, systems, and kits comprising effector domains for activating and silencing gene expression. In particular, synthetic transcription factors comprising the effector domains are provided.