In this section
@article{Abbasova:2025:10.1038/s41467-025-58137-2,
author = {Abbasova, L and Urbanaviciute, P and Hu, D and Ismail, JN and Schilder, BM and Nott, A and Skene, NG and Marzi, SJ},
doi = {10.1038/s41467-025-58137-2},
journal = {Nature Communications},
title = {CUT&Tag recovers up to half of ENCODE ChIP-seq histone acetylation peaks},
url = {http://dx.doi.org/10.1038/s41467-025-58137-2},
volume = {16},
year = {2025}
}
TY - JOUR
AB - 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.
AU - Abbasova,L
AU - Urbanaviciute,P
AU - Hu,D
AU - Ismail,JN
AU - Schilder,BM
AU - Nott,A
AU - Skene,NG
AU - Marzi,SJ
DO - 10.1038/s41467-025-58137-2
PY - 2025///
SN - 2041-1723
TI - CUT&Tag recovers up to half of ENCODE ChIP-seq histone acetylation peaks
T2 - Nature Communications
UR - http://dx.doi.org/10.1038/s41467-025-58137-2
UR - https://doi.org/10.1038/s41467-025-58137-2
VL - 16
ER -