High-Throughput Multiomics DNA Barcoding for Chromatin Accessibility
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Solution Overview
Problem
Current methods for multiomics analysis of single cells, such as molecular barcoding for single cell transcriptomics and proteomics, lack efficient techniques for comprehensive analysis of genomic DNA and organelle DNA, particularly in determining chromatin accessibility and methylome information.
Innovation Solution
A method involving transposomes with double-strand nucleases to induce DNA breaks, generating barcoded DNA fragments with capture sequences, followed by sequencing and denaturation to produce single-stranded barcoded fragments, allowing for the determination of chromatin accessibility and methylome information.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Adaptability or versatility
If molecular barcoding is used for single cell transcriptomics and proteomics analysis, then gene expression profiles can be deciphered, but efficient techniques for comprehensive analysis of genomic DNA and organelle DNA are lacking
Solution Approach 1:
The transposome system is designed to perform multiple functions: it fragments DNA, adds barcodes, and enables sequencing of both genomic DNA and organelle DNA through a single unified method, making the system versatile for multiomics analysis across different DNA types and cellular compartments
Solution Approach 2:
The method segments DNA analysis into distinct barcoded fragments, where each fragment carries unique molecular and cellular barcodes. This segmentation allows simultaneous tracking and analysis of different DNA sources (nuclear vs. mitochondrial) within the same cell, enabling comprehensive multiomics analysis
2Measurement precision
If transposomes with double-strand nucleases are used to induce DNA breaks and generate barcoded fragments, then chromatin accessibility and methylome information can be determined, but the process requires multiple steps including fragmentation, barcoding, and sequencing
Solution Approach 1:
The transposome is pre-loaded with barcoded adaptors before being introduced to the DNA sample. This preliminary preparation allows the barcoding and fragmentation to occur simultaneously in a single reaction step, reducing the number of subsequent processing steps while maintaining precise measurement of chromatin accessibility
Solution Approach 2:
The method combines DNA fragmentation, barcode attachment, and sample labeling into a single transposome reaction step. By merging these previously separate operations into one unified process, the method achieves precise chromatin accessibility measurement without requiring multiple sequential steps
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 high-throughput multiomics analysis by providing detailed insights into chromatin accessibility and methylome information of single cells, enhancing the understanding of cellular structures and DNA sequences.
Implementation Method 1
a double-strand nuclease configured to induce a double-stranded DNA break at a structure comprising dsDNA
Implementation Method 2
contacting the plurality of overhang dsDNA fragments with a polymerase to generate a plurality of complementary dsDNA fragments each comprising a complementary sequence to at least a portion of the 5′ overhang
Implementation Method 3
denaturing the plurality of complementary dsDNA fragments to generate a plurality of single stranded DNA (ssDNA) fragments
Data Source
AI summary
Disclosed herein include systems, methods, compositions, and kits for sample analysis. Nucleic acid fragments comprising a capture sequence (or a complement thereof) can be generated from double-stranded genomic deoxyribonucleic acid (gDNA), barcoded to generate single-stranded DNA (ssDNA) fragments, and sequenced. Information relating to the gDNA (e.g., genome, chromatin accessibility, methylome) can be determined based on the sequences of the ssDNA fragments in the sequencing data obtained.