CUT&Tag recovers up to half of ENCODE ChIP-seq histone acetylation peaks

Leyla Abbasova, Paulina Urbanaviciute, Di Hu, Joy N. Ismail, Brian M. Schilder, Alexi Nott, Nathan G. Skene and Sarah J. Marzi ()
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Leyla Abbasova: UK Dementia Research Institute at Imperial College London
Paulina Urbanaviciute: UK Dementia Research Institute at King’s College London
Di Hu: UK Dementia Research Institute at Imperial College London
Joy N. Ismail: UK Dementia Research Institute at King’s College London
Brian M. Schilder: UK Dementia Research Institute at Imperial College London
Alexi Nott: UK Dementia Research Institute at Imperial College London
Nathan G. Skene: UK Dementia Research Institute at Imperial College London
Sarah J. Marzi: Imperial College London

Nature Communications, 2025, vol. 16, issue 1, 1-15

Abstract: Abstract DNA-protein interactions have traditionally been profiled via chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq). Cleavage Under Targets & Tagmentation (CUT&Tag) is a rapidly expanding technique that enables the profiling of such interactions in situ at high sensitivity. However, thorough evaluation and benchmarking against established ChIP-seq datasets are lacking. Here, we comprehensively benchmarked CUT&Tag for H3K27ac and H3K27me3 against published ChIP-seq profiles from ENCODE in K562 cells. Combining multiple new and published CUT&Tag datasets, there was an average recall of 54% known ENCODE peaks for both histone modifications. We tested peak callers MACS2 and SEACR and identified optimal peak calling parameters. Overall, peaks identified by CUT&Tag represent the strongest ENCODE peaks and show the same functional and biological enrichments as ChIP-seq peaks identified by ENCODE. Our workflow systematically evaluates the merits of methodological adjustments, providing a benchmarking framework for the experimental design and analysis of CUT&Tag studies.

Date: 2025
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DOI: 10.1038/s41467-025-58137-2

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