MethylSeekR

MethylSeekR identifies DNA methylation footprints in bisulfite sequencing (Bis-seq) data to detect active regulatory elements associated with transcription factor binding in high-resolution methylomes.

Key Features:

• Footprint identification: Detects local reductions in DNA methylation (methylation footprints) indicative of transcription factor binding sites from Bis-seq data.
• High resolution: Operates on high-resolution methylome data to enable precise localization of regulatory regions.
• Broad applicability: Validated across diverse human methylomes, supporting analysis across multiple cell types and tissues.

Scientific Applications:

• Regulatory element discovery: Identification of active regulatory regions genome-wide based on methylation footprints.
• Transcription factor activity inference: Inferring transcription factor-associated activity by detecting local methylation depletion at binding sites.
• Comparative epigenomics: Comparing regulatory landscapes across cell types, tissues, differentiation states, and disease contexts using human methylomes.

Methodology:

Computational detection of methylation reduction patterns in bisulfite-sequencing data to infer transcription factor-associated footprints and active regulatory regions.