Targeted Transposon Epigenetic Analysis Multiplexing
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Solution Overview
Problem
Current epigenetic analysis methods, such as ChIP, are limited by high sample requirements, inability to analyze multiple proteins concurrently, and the need for ultra-high affinity antibodies, which restricts research in fields like stem cells and clinical applications where sample numbers are limited and cost is a concern.
Innovation Solution
The development of methods using protein-oligonucleotide conjugates and oligonucleotide-transposome constructs that allow for the concurrent analysis of multiple chromatin-associated proteins without immunoprecipitation, reducing sample needs and enabling the use of antibodies that fail in traditional ChIP methods.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If traditional ChIP methods are used, then specific chromatin regions can be identified, but large sample numbers are required
Solution Approach 1:
The patent combines multiple ChIP experiments into a single multiplexed assay by incorporating unique barcodes onto antibodies or oligonucleotides that target different chromatin regions or proteins. This merging allows simultaneous analysis of multiple targets in one experiment, dramatically reducing the total sample numbers required while maintaining identification accuracy.
Solution Approach 2:
The invention creates a universal platform that can analyze multiple chromatin-associated proteins and regions concurrently using a common set of reagents and procedures. The multiplexed approach enables a single experimental setup to perform functions that traditionally required separate experiments, reducing sample consumption across the board.
2Measurement precision
If traditional ChIP methods are used, then chromatin-protein interactions can be analyzed, but only single protein analysis is possible
Solution Approach 1:
The patent merges multiple single-protein ChIP analyses into a single multiplexed experiment by using antibody-oligonucleotide conjugates with unique barcodes for each target protein. This allows concurrent detection and differentiation of multiple chromatin-associated proteins within the same sample, maintaining interaction detection precision while enabling multi-protein analysis.
Solution Approach 2:
The invention introduces barcode oligonucleotides as intermediaries that link multiple antibody targets to a common detection platform. These barcoded intermediaries allow distinct proteins to be simultaneously tracked and identified through their unique molecular tags, enabling multi-protein analysis without compromising interaction detection accuracy.
3Measurement precision
If traditional ChIP methods are used, then chromatin regions can be mapped, but ultra-high affinity antibodies are required
Solution Approach 1:
The patent combines multiple low-to-moderate affinity antibodies into a multiplexed assay where each antibody is conjugated to a unique barcode. The collective signal from multiple antibodies targeting the same or different regions provides sufficient mapping accuracy, reducing the requirement for any single antibody to have ultra-high affinity while maintaining overall chromatin region mapping precision.
Solution Approach 2:
The invention creates a universal detection system using standardized barcode oligonucleotides that can work with a broad range of antibodies regardless of their individual affinity levels. This universal platform allows chromatin region mapping using diverse antibody reagents, reducing the stringency requirement for ultra-high affinity antibodies while preserving mapping accuracy through aggregated signal detection.
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 methods significantly reduce sample requirements, enable multi-analyte capabilities, and streamline the analysis process, making them more efficient and cost-effective for high-throughput applications across various life sciences research.
Implementation Method 1
mediating the transposition of a transposome complex into a chromatin sample
Data Source
AI summary
Disclosed herein are compositions, methods and kits useful for epigenetic analysis based on the use of transposons that are targeted to specific regions of chromatin based on DNA-DNA interactions, protein-protein interactions, RNA-RNA interactions, and nucleic acid-protein interactions.