BIND&MODIFY: a long-range method for single-molecule mapping of chromatin modifications in eukaryotes.

Area of Science:

• Molecular Biology
• Genomics
• Epigenetics

Background:

• Epigenetic histone modifications are crucial in development and disease.
• Current methods average chromatin states and miss long-range interactions.

Purpose of the Study:

• To introduce BIND&MODIFY, a novel method for single-molecule profiling of epigenetic marks.
• To enable simultaneous measurement of histone modifications, transcription factor binding, and DNA methylation.

Main Methods:

• Utilizes long-read sequencing combined with a custom-engineered protein (A-M.EcoGII) for targeted DNA labeling.
• Employs methyltransferase M.EcoGII tethered to protein binding sites to mark neighboring DNA regions.
• Enables single-molecule resolution analysis of chromatin architecture.

Main Results:

• BIND&MODIFY accurately reflects bulk measurements like ChIP-seq and CUT&TAG when aggregated.
• The method successfully measures histone modification status, transcription factor binding, and CpG 5mC methylation simultaneously.
• Quantifies correlations between local and distal genomic elements at single-molecule resolution.

Conclusions:

• BIND&MODIFY provides unprecedented single-molecule resolution for epigenetic profiling.
• This technique overcomes limitations of bulk methods, offering insights into chromatin interactions and disease mechanisms.
• Enables comprehensive analysis of epigenetic landscapes and their functional correlations.