Protocol for genomic mapping of chromatin targets using high-throughput CUT&RUN.

Viswakalyan Kotapalli, Polina Iakova, Yue Lu, Abhinav K Jain

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Article in STAR protocols, 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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4 authors.

Viswakalyan KotapalliDepartment of Epigenetics and Molecular Carcinogenesis, Houston, TX 77030, USA; Center for Cancer Epigenetics, The UT MD Anderson Cancer Center, Houston, TX 77030, USA. Electronic address: VKotapalli@mdanderson.org.

Polina IakovaDepartment of Epigenetics and Molecular Carcinogenesis, Houston, TX 77030, USA; Center for Cancer Epigenetics, The UT MD Anderson Cancer Center, Houston, TX 77030, USA.

Yue LuDepartment of Epigenetics and Molecular Carcinogenesis, Houston, TX 77030, USA; Epigenomics Profiling Core, Houston, TX 77030, USA; Center for Cancer Epigenetics, The UT MD Anderson Cancer Center, Houston, TX 77030, USA.

Abhinav K JainDepartment of Epigenetics and Molecular Carcinogenesis, Houston, TX 77030, USA; Epigenomics Profiling Core, Houston, TX 77030, USA; Center for Cancer Epigenetics, The UT MD Anderson Cancer Center, Houston, TX 77030, USA. Electronic address: ajain@mdanderson.org.

Funding

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6 · The paper itself

Abstract

The genomic distribution of proteins that define chromatin state, including transcription factors, chromatin modifiers, and histone modifications, is critical for understanding gene regulation, cellular identity, and disease development. Here, we present a high-throughput cleavage under targets and release using nuclease (CUT&RUN) protocol performed in 96-well plate format. We describe steps for targeted DNA enrichment, high-quality library preparation, sequencing, and data analysis. This protocol enables high-resolution genomic mapping of proteins of interest and factors that define the epigenome. For complete details on the use and execution of this protocol, please refer to Skene and Henikoff

Indexed as

AntibodyChIPseqChromatin immunoprecipitation ChIP

Identifiers

PMID42364106

DOI10.1016/j.xpro.2026.104631

PMCPMC13321014

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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.