Transposome Assembly for Simultaneous ATAC-Seq and 5' RNA-Seq

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Solution Overview

Problem

Current methods for analyzing cancer development and progression at the single-cell level often require difficult trade-offs between studying immune components and genetic or epigenetic triggers, and lack a platform for simultaneously profiling chromatin accessibility alongside B and T lymphocytes antigen repertoire analysis.

Innovation Solution

A method involving tagmentation of genomic DNA using a transposome assembly with a transposase, adaptors, and oligonucleotides, allowing for simultaneous measurement of transcription, 5' end of RNA transcripts, chromatin accessibility, surface markers, and immune receptor sequences at the single-cell level.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Measurement precision

If conventional single-cell analysis methods are used to study immune components, then immune cell characterization is improved, but the ability to simultaneously profile chromatin accessibility and antigen repertoire is lost

Engineering Contradiction:

Improveimmune cell characterizationVSAvoidmulti-modal profiling capability

Core Design Contradiction:

Measurement precisionVSAdaptability or versatility

Solution Approach 1:

The patent combines chromatin accessibility profiling (ATAC-seq) and antigen repertoire analysis (scRNA-seq) into a single integrated workflow. The transposome assembly simultaneously performs Tn5 tagmentation for chromatin accessibility and captures 5' RNA transcripts, enabling both modalities to be measured from the same single-cell lysate without requiring separate experiments.

Inventive Principle:

Principle #5Merging (Combining)

Solution Approach 2:

The transposome assembly serves multiple functions simultaneously: it acts as a Tn5 transposase for chromatin accessibility profiling, a capture probe for 5' RNA sequencing, and a barcode carrier for cell identification. This multi-functional design allows a single reagent to enable comprehensive multi-modal single-cell analysis.

Inventive Principle:

Principle #6Universality (Multi-functionality)

2Measurement precision

If repertoire profiling is performed to capture the 5' end of transcripts, then immune receptor analysis is improved, but chromatin accessibility profiling becomes incompatible

Engineering Contradiction:

Improveimmune receptor analysisVSAvoidchromatin accessibility compatibility

Core Design Contradiction:

Measurement precisionVSAdaptability or versatility

Solution Approach 1:

Instead of using conventional 3' RNA sequencing adapters, the patent inverts the approach by designing transposome adapters with 5' overhangs that are complementary to the 5' capture sequence. This inversion allows the same transposome assembly to simultaneously capture 5' RNA transcripts and perform chromatin accessibility profiling, making repertoire profiling and ATAC-seq compatible.

Inventive Principle:

Principle #13The other way round (Inversion)

3Measurement precision

If multiple separate assays are used to profile different biological parameters, then measurement comprehensiveness is improved, but experimental complexity and time increase

Engineering Contradiction:

Improvebiological parameter coverageVSAvoidexperimental workflow complexity

Core Design Contradiction:

Measurement precisionVSDevice complexity

Solution Approach 1:

The patent merges chromatin accessibility profiling, RNA sequencing, surface marker detection, and immune receptor sequencing into a single unified experiment. The transposome assembly enables simultaneous measurement of all these parameters from the same single-cell lysate, eliminating the need for multiple separate assays and reducing experimental complexity.

Inventive Principle:

Principle #5Merging (Combining)

Solution Approach 2:

The transposome assembly is designed as a universal reagent that can simultaneously perform multiple functions: chromatin accessibility profiling, RNA capture, surface marker detection, and immune receptor sequencing. This multi-functionality allows comprehensive biological parameter coverage without requiring separate specialized assays for each modality.

Inventive Principle:

Principle #6Universality (Multi-functionality)

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 comprehensive and simultaneous analysis of multiple biological parameters at the single-cell level, providing insights into cancer development and immune responses without the need for trade-offs.

Implementation Method 1

incubating the permeabilized cell with a transposome assembly comprising a transposase, a first oligonucleotide, and a second oligonucleotide wherein the transposase makes double-strand breaks in genomic DNA and attaches adaptors at the ends of the genomic DNA fragments that are produced

Methodology Applied

Scientific EffectTransposase-mediated tagmentation: Enzyme

Implementation Method 2

a second oligonucleotide comprising a 3' single-stranded overhang on the non-transfer strand... producing tagmented genomic DNA with a transposase recognition site and a complementary sequence to a capture sequence of a third oligonucleotide

Methodology Applied

Scientific EffectNucleic acid hybridization: Chemical Bonding

Data Source

PatentUS20250066859A1Single-cell ATAC-SEQ compatible with 5' RNA-seq

Publication Date: 2025.02.27 NEW YORK UNIV

AI summary

The invention relates to methods for simultaneously measuring transcription, chromatin accessibility, surface markers, and immune receptor sequence of a biological sample at the single-cell level, comprising one or more cells.