Snapshot: a package for clustering and visualizing epigenetic history during cell differentiation

Area of Science:

• Genomics
• Epigenetics
• Computational Biology

Background:

• Epigenetic modifications regulate gene expression during cell differentiation.
• Analyzing large epigenetic datasets to find regulatory events is challenging.

Purpose of the Study:

• To develop a computational tool for simplifying and analyzing epigenetic data during cell differentiation.
• To aid biologists in identifying regulatory elements controlling cell differentiation.

Main Methods:

• Developed the Snapshot package for clustering and visualizing candidate cis-regulatory elements (cCREs).
• Utilized a binarized indexing strategy for cCRE clustering.
• Generated interpretable figures to visualize epigenetic signal and state patterns.

Main Results:

• Snapshot effectively clusters genomic locations based on distinct epigenetic patterns during cell differentiation.
• The tool visualizes epigenetic signals and states, aiding in understanding cell lineage-specific histories.
• Demonstrated utility with epigenomic data from hematopoiesis studies.

Conclusions:

• Snapshot successfully identifies distinct clusters of genomic locations with unique epigenetic profiles.
• The package offers superior interpretation and reproducibility of cCRE clusters compared to other methods.
• Snapshot is publicly available on GitHub for broader research application.