CUT and RUNTools

CUT and RUNTools processes and analyzes data from Cleavage Under Targets and Release Using Nuclease (CUT&RUN) experiments to identify chromatin-associated protein binding sites and generate genomic footprinting information.

Key Features:

• Flexible Pipeline: Provides a general, adaptable computational framework for CUT&RUN data analysis across genomics applications.
• Endonuclease Cut Site Extraction: Extracts endonuclease cut-site information from short-read fragments generated by CUT&RUN experiments.
• Single-Locus Binding Estimates: Computes precise estimates of protein binding at individual genomic loci.
• Aggregate Motif Footprints: Generates aggregated motif footprint analyses across multiple genomic sites to characterize binding patterns.
• Informative Visualizations: Produces detailed visual representations of cut-site distributions, footprints, and binding estimates.

Scientific Applications:

• High-resolution mapping of protein–DNA interactions: Resolves chromatin-associated protein binding sites at high spatial resolution from CUT&RUN data.
• Transcription factor binding and motif analysis: Identifies motif-associated footprints and supports transcription factor footprinting studies.
• Gene regulation and epigenetic studies: Supports investigation of regulatory mechanisms and epigenetic modifications linked to protein-DNA interactions.
• Chromatin organization analysis: Enables locus-specific analysis of chromatin-associated protein binding and structural genome organization.

Methodology:

Processes antibody-targeted CUT&RUN primary cleavage data, extracts cut-site information from short-read sequences, and uses those cut sites to compute single-locus binding estimates and aggregate motif footprint analyses.