Comparative analyses of ChIP-seq, CUT&RUN and CUT&Tag for Polycomb chromatin profiling.

Yoonji Oh, Hanbyeol Kim, Sanghyun Lee, Soon-Jung Park, Yun-Gwi Park, Sung-Hwan Moon, Inkyung Jung, Chul-Hwan Lee

Abstract readComparative Study

In one paragraph

Article in BMB reports, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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8 authors.

Yoonji OhDepartment of Biomedical Sciences and Pharmacology, Seoul National University College of Medicine, Seoul 03080, Korea.

Hanbyeol KimDepartment of Biomedical Sciences and Pharmacology, Seoul National University College of Medicine, Seoul 03080, Korea.

Sanghyun LeeDepartment of Biological Sciences, KAIST, Daejeon 34141, Korea.

Soon-Jung ParkDepartment of Animal Science and Technology, Chung-Ang University, Anseong 17546, Korea.

Yun-Gwi ParkDepartment of Animal Science and Technology, Chung-Ang University, Anseong 17546, Korea.

Sung-Hwan MoonDepartment of Animal Science and Technology, Chung-Ang University, Anseong 17546, Korea.

Inkyung JungDepartment of Biological Sciences, KAIST, Daejeon 34141, Korea.

Chul-Hwan LeeDepartment of Biomedical Sciences and Pharmacology, Seoul National University College of Medicine, Seoul 03080; Cancer Research Institute, Ischemic/hypoxic Disease Institute, Medical Research Center, Seoul National University, Seoul 03080; Wide River Institute of Immunology, Seoul National University, Hongcheon 25159, Korea.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Chromatin profiling methods such as ChIP-seq, CUT&RUN, and CUT&Tag differ substantially in background structure, signal distribution, and resolution, complicating direct quantitative comparison across platforms. In this study, we systematically compared conventional and double-crosslink ChIP-seq, CUT&RUN, and CUT&Tag by profiling the Polycomb-associated histone modification H3K27me3 in human cardiomyocytes and the PRC2 catalytic subunit EZH2 in pluripotent stem cells. To enable cross-assay comparison, we developed a biologically informed normalization strategy based on stable Polycomb reference loci, allowing harmonization of signal scales while preserving assay-intrinsic signal architecture. This approach revealed CUT&RUN to preferentially capture broad H3K27me3 domains, whereas CUT&Tag provides sharper and more localized enrichment for both H3K27me3 and EZH2. Together, our results establish a practical framework for cross-platform epigenomic comparison and guide the selection of chromatin profiling strategies. [BMB Reports 2026; 59(4): 242-252].

Indexed as

ChromatinChromatin Immunoprecipitation SequencingPolycomb-Group ProteinsChromatin ImmunoprecipitationEnhancer of Zeste Homolog 2 ProteinHistonesHumansMyocytes, CardiacPluripotent Stem CellsChromatinEnhancer of Zeste Homolog 2 ProteinEZH2 protein, humanHistonesPolycomb-Group Proteins

Identifiers

PMID41781185

PMCPMC13126067

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.