Genome-wide profiling of histone modifications and transcription factor binding at single-cell resolution by...

Area of Science:

• Epigenomics
• Molecular Biology
• Genomics

Background:

• Mapping protein-DNA interactions at single-cell resolution is challenging, especially for sparse transcription factors (TFs).
• Existing methods struggle with reliable detection of TF binding due to its sparse nature.

Purpose of the Study:

• To establish a novel method, DeChIC-seq, for direct recording of protein-DNA interactions.
• To enable sensitive detection of transcription factor binding and chromatin profiling at single-cell resolution.

Main Methods:

• DeChIC-seq utilizes a protein A-DddAtox fusion to induce localized C-to-U conversions near antibody-bound chromatin.
• The method retains genome-wide sequence information without immunoprecipitation.
• Integration with single-cell whole-genome amplification (scDeChIC-seq) allows for individual cell chromatin profiling.

Main Results:

• DeChIC-seq enables profiling of histone modifications and sensitive TF binding detection.
• scDeChIC-seq successfully resolved lineage-specific chromatin states in mouse embryogenesis using limited blastomere inputs.
• The method sensitively detected TF binding of NR5A2, TFAP2C, and KLF5 in scarce samples.

Conclusions:

• DeChIC-seq provides a conversion-based framework for chromatin profiling.
• This technique facilitates mechanistic dissection of TF-driven gene regulation in rare cells, developmental systems, and disease contexts.
• DeChIC-seq shows strong potential for TF-binding site detection in limited biological samples.