Long-range single-molecule mapping of chromatin accessibility in eukaryotes.

Area of Science:

• Genomics
• Epigenetics
• Molecular Biology

Background:

• Mapping open chromatin regions identifies active eukaryotic regulatory elements.
• Current methods using DNA fragmentation and short-read sequencing lack large-scale chromatin state information and fail to show distal regulatory element coordination.

Purpose of the Study:

• To develop a single-molecule, long-read sequencing assay for profiling individual chromatin fiber accessibility.
• To enable high-resolution, single-molecule assessment of chromatin states at multikilobase scales.

Main Methods:

• Developed single-molecule long-read accessible chromatin mapping sequencing assay (SMAC-seq).
• Combined preferential open chromatin methylation (using EcoGII m6A methyltransferase) with nanopore sequencing's ability to read DNA modifications.

Main Results:

• Aggregate SMAC-seq signals align with bulk-level accessibility measurements.
• Observed single-molecule nucleosome and transcription factor protection footprints.
• Quantified correlations between chromatin states of distal genomic elements.

Conclusions:

• SMAC-seq provides high-resolution, single-molecule insights into chromatin accessibility and organization.
• This method overcomes limitations of previous techniques, enabling study of large-scale chromatin states and distal element coordination.