CUT&RUNTools: a flexible pipeline for CUT&RUN processing and footprint analysis.

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a common method for mapping protein-DNA interactions.
• Cleavage under minimal conditions with sonication (CUT&RUN) offers an alternative with potentially higher signal-to-noise ratios.
• Analyzing CUT&RUN data requires specialized tools to accurately identify protein binding sites and genomic footprints.

Purpose of the Study:

• To introduce CUT&RUNTools, a flexible and general bioinformatics pipeline.
• To facilitate the identification of chromatin-associated protein binding.
• To enable genomic footprinting analysis from antibody-targeted CUT&RUN primary cleavage data.

Main Methods:

• CUT&RUNTools processes short-read sequencing fragments to extract endonuclease cut site information.
• The pipeline generates single-locus binding estimates.
• It also produces aggregate motif footprints and informative visualizations.

Main Results:

• CUT&RUNTools supports the high-resolution mapping capabilities of CUT&RUN experiments.
• The software provides a comprehensive analysis of protein binding and genomic footprints.
• Visualizations aid in the interpretation of high-resolution mapping data.

Conclusions:

• CUT&RUNTools is a valuable resource for researchers studying chromatin organization and protein-DNA interactions.
• The pipeline offers a robust solution for analyzing CUT&RUN data.
• It enhances the ability to perform high-resolution mapping of epigenetic modifications and protein binding events.