DiMeLo-seq

DiMeLo-seq maps protein–DNA interactions genome-wide by directing exogenous methylation with antibody-tethered enzymes and detecting both introduced methylation and endogenous CpG methylation using long-read, single-molecule sequencing.

Key Features:

• Long-read, single-molecule sequencing: Detects exogenous methylation marks and native CpG methylation on unamplified DNA to enable single-molecule resolution.
• Antibody-tethered enzymes: Uses antibody-tethered enzymes to introduce targeted methylation near protein binding sites in situ.
• Multimodal genomic mapping: Simultaneously profiles chromatin-binding proteins and histone modifications across the human genome.
• Repetitive-region mapping: Enables mapping within highly repetitive regions, including estimation of centromere protein A (CENP-A) density along single chromatin fibers.

Scientific Applications:

• Genome regulation and epigenetics: Characterizes protein–DNA interactions and histone modifications to study regulatory mechanisms across genomic contexts.
• Centromere and repetitive-sequence studies: Maps binding events and estimates protein density within centromeres and other repetitive regions that are refractory to short-read methods.
• Single-molecule quantitative analysis: Provides single-molecule measurements of protein occupancy and methylation states for quantitative analyses.

Methodology:

Antibody-tethered enzymes introduce targeted methylation near protein binding sites, long-read single-molecule sequencing detects the introduced exogenous methylation together with native CpG methylation on unamplified DNA, and the approach has been optimized and benchmarked by mapping chromatin-binding proteins and histone modifications across the human genome.