Barcoded Chromatin Profiling for Multiplex Histone Modification Mapping
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Solution Overview
Problem
Existing methods for histone modification analysis are limited in their ability to analyze multiple modifications concurrently without splitting the sample and do not provide spatial information on chromatin and nucleosome modifications within a tissue context.
Innovation Solution
Highly parallelized, sensitive, and accurate methods for profiling nucleosome modifications and DNA binding proteins using target-binding conjugates with specific binding domains and nucleic acid barcodes, allowing simultaneous analysis and spatial localization of histone modifications.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Adaptability or versatility
If traditional ChIP-seq or ACT-seq methods are used to analyze histone modifications, then specific DNA sequences corresponding to modified nucleosomes can be identified, but the analysis of multiple modifications concurrently is limited and requires sample splitting
Solution Approach 1:
The invention segments the analysis process by assigning unique barcodes to different histone modifications, allowing multiple modifications to be analyzed in parallel within the same sample. Each modification type receives a distinct barcode identifier, enabling concurrent profiling without sample splitting.
Solution Approach 2:
The chromatin tagmentation method uses universal barcode-loaded transposomes that can recognize and tag multiple different histone modifications simultaneously. This multi-functional approach allows a single reagent system to profile various modifications (acetylation, methylation, phosphorylation, ubiquitination) in the same reaction.
2Loss of information
If ChIP-seq methods are used to determine histone modifications, then DNA sequences of modified nucleosomes can be identified, but spatial information on chromatin and nucleosome modifications within tissue context is not provided
Solution Approach 1:
The invention adds a spatial dimension to the existing ChIP-seq approach by incorporating spatial barcodes that encode location information within tissue sections. This dimensional expansion allows simultaneous retrieval of both sequence information and spatial context, eliminating the loss of spatial data while maintaining analytical capability.
3Productivity
If multiple histone modifications are analyzed using traditional methods, then modification types can be identified, but the throughput and efficiency are reduced due to sample splitting
Solution Approach 1:
The invention merges multiple separate modification analysis experiments into a single integrated assay. By using barcode-loaded transposomes that can tag multiple modification types simultaneously, the method combines what were previously separate workflows into one parallelized process, dramatically increasing throughput and reducing time loss.
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
Enables simultaneous profiling of multiple nucleosome modifications and DNA binding proteins with high throughput, providing spatial information and potential applications in cancer diagnosis and monitoring epigenetic changes.
Implementation Method 1
a binding domain that binds specifically to a histone modification or to a DNA binding protein
Implementation Method 2
ligating an adapter with the nucleic acid barcode to the target DNA of the nucleosome
Data Source
AI summary
Compositions and methods for single reaction and multiplexed profiling of histone modifications. Compositions include a binding domain and adaptor or a nucleosome binding conjugate comprising a binding domain conjugated to an adapter. Methods include analyzing a plurality of nucleosomes comprising (i) contacting a plurality of substrates comprising a binding domain and adaptor composition with a solution comprising the plurality of nucleosomes, wherein a nucleosome comprising a histone modification or DNA binding protein binds to the binding domain; (ii) ligating an adapter with the nucleic acid barcode to the target DNA of the nucleosome comprising the histone modification or DNA binding protein; (iii) introducing universal sequences for amplifying the target DNA; (iv) amplifying the barcoded target DNA; and (v) analyzing the amplified barcoded target DNA by sequencing.