Combinatorial single-cell profiling of major chromatin types with MAbID

Area of Science:

• Epigenetics and Gene Regulation
• Genomics and Molecular Biology
• Biotechnology

Background:

• Gene expression is controlled by complex interactions of regulatory factors.
• Simultaneously measuring these factors within a single sample is technically challenging.
• Understanding cooperative regulatory factor action is crucial for gene regulation insights.

Purpose of the Study:

• Introduce Multiplexing Antibodies by barcode Identification (MAbID), a novel method for combinatorial genomic profiling.
• Enable simultaneous measurement of multiple histone modifications and chromatin-binding proteins.
• Facilitate deeper understanding of gene regulatory mechanisms.

Main Methods:

• Developed MAbID utilizing antibody-DNA conjugates to integrate genomic barcodes at epitope locations.
• Enabled combined incubation of multiple antibodies for simultaneous epigenetic marker detection.
• Applied MAbID for profiling chromatin types and performing multiplexed measurements.

Main Results:

• Demonstrated successful multiplexed measurements of multiple epigenetic markers without compromising data quality.
• Achieved joint measurements of six epitopes in single mouse bone marrow cells.
• Captured associated changes in multifactorial chromatin states during in vitro differentiation.

Conclusions:

• MAbID offers a powerful approach for combinatorial genomic profiling of epigenetic markers.
• The method facilitates unique insights into the interplay of gene regulatory mechanisms.
• MAbID is particularly valuable for low-input samples and single-cell analyses.