Can Fiber-seq be used to study DNA-binding proteins?

Yes, Fiber-seq provides near-nucleotide resolution of chromatin accessibility, enabling detection of protein footprints.

Important Notes:

• Success depends on protein binding dynamics, occupancy, and footprint size.

• Multiple labs have successfully published on TF and polymerase footprinting using Fiber-seq.

• EpiCypher recommends using fibertools and fiberseq-qc (https://github.com/fiberseq) for Fiber-seq data analysis.

Check out these papers for real-world examples:

• Tullius et al., Mol. Cell (2024)

• Dubocanin et al., Cell Genomics (2025)

• Vollger et al., bioRxiv (2024)