Chromatin Affinity Handle for Protein Profiling

Resolve Bottlenecks,
Find Innovative SolutionsGenerate Solutions

Solution Overview

Problem

Current methodologies, such as chromatin immunoprecipitation (ChIP) assays, are limited in determining all proteins and post-translational modifications specifically associated with a defined small region of chromatin, as they primarily focus on singular histone modifications and lack the ability to detect co-occupancy of multiple targets or enrich for specific genomic loci, thereby failing to provide a comprehensive understanding of chromatin-templated events.

Innovation Solution

A method involving the use of tagged and untagged cell samples, where one sample contains chromatin tagged with a specific affinity handle and the other does not, allows for the enrichment and identification of proteins specifically associated with a target chromatin region through affinity purification and mass spectrometry, enabling the determination of both proteins and their post-translational modifications.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Measurement precision

If chromatin immunoprecipitation (ChIP) assays are used to examine histone modifications and proteins, then understanding of genome-wide distribution is improved, but the ability to determine all proteins and post-translational modifications specifically associated with a defined small region of chromatin is limited

Engineering Contradiction:

Improvespecificity of protein-chromatin association detectionVSAvoidcomprehensive profiling capability

Core Design Contradiction:

Measurement precisionVSAdaptability or versatility

Solution Approach 1:

The method segments the chromatin analysis into two distinct approaches: (1) targeted enrichment of specific genomic loci using locus-specific probes, and (2) global chromatin analysis. This segmentation allows simultaneous achievement of high specificity for defined regions and comprehensive profiling of multiple proteins and modifications, resolving the contradiction between measurement precision and adaptability

Inventive Principle:

Principle #1Segmentation

Solution Approach 2:

The patent introduces an intermediary affinity handle system that bridges the chromatin and detection components. The affinity handle can be specifically targeted to defined chromatin regions while also enabling comprehensive protein and modification detection through affinity purification, thus mediating between the need for region-specific precision and comprehensive profiling capability

Inventive Principle:

Principle #24Intermediary (Mediator)

2Measurement precision

If ChIP assays focus on singular histone PTMs or proteins, then depth of analysis for individual targets is improved, but the ability to detect co-occupancy of multiple targets is lost

Engineering Contradiction:

Improvedetection sensitivity for individual targetsVSAvoidnumber of proteins and modifications detected

Core Design Contradiction:

Measurement precisionVSQuantity of substance

Solution Approach 1:

The affinity handle system is designed with multi-functionality, serving as a universal platform that can simultaneously detect multiple proteins and post-translational modifications. The system maintains high detection sensitivity for individual targets while enabling comprehensive multi-target profiling, thus resolving the contradiction between measurement precision and quantity of substances detected

Inventive Principle:

Principle #6Universality (Multi-functionality)

Solution Approach 2:

The method merges multiple detection capabilities into a single affinity purification workflow. By combining the ability to detect singular targets with comprehensive multi-protein and multi-modification profiling in one assay, the patent resolves the contradiction between depth of individual target analysis and breadth of overall detection

Inventive Principle:

Principle #5Merging (Combining)

3Measurement precision

If ChIP methods are used to enrich for chromatin regions, then localization of defined proteins to chromosomal sites is improved, but the ability to determine all proteins present at a defined small region of chromatin is insufficient

Engineering Contradiction:

Improvelocalization accuracyVSAvoidcomprehensive protein identification capability

Core Design Contradiction:

Measurement precisionVSDevice complexity

Solution Approach 1:

The affinity handle acts as an intermediary that connects locus-specific targeting with comprehensive protein identification. It enables precise localization to defined chromatin regions while simultaneously facilitating the detection of all associated proteins and modifications, thus resolving the contradiction between localization accuracy and comprehensive identification capability

Inventive Principle:

Principle #24Intermediary (Mediator)

Solution Approach 2:

The methodology segments the complex analysis into targeted enrichment followed by comprehensive profiling. This segmentation allows precise localization to small chromatin regions while maintaining the capability to identify all proteins present, resolving the contradiction between measurement precision and device complexity

Inventive Principle:

Principle #1Segmentation

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

This approach enables the specific identification and quantification of proteins and post-translational modifications associated with a target chromatin region, providing a comprehensive understanding of chromatin-templated events and overcoming the limitations of existing ChIP assays.

Implementation Method 1

a tag capable of specifically recognizing and binding one or more portions of the target chromatin and wherein the tag comprises an affinity handle

Methodology Applied

Scientific EffectAffinity binding: Adsorption

Implementation Method 2

isolating the affinity handle from each cell sample wherein affinity handle isolated from the first cell sample consists of affinity handle bound to tagged target chromatin

Methodology Applied

Scientific EffectAffinity purification: Adsorption