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Epigenetics Chromatin. 2018 Dec 21;11(1):74. doi: 10.1186/s13072-018-0243-8.

Automated in situ chromatin profiling efficiently resolves cell types and gene regulatory programs.

Author information

1
Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA, 98109, USA.
2
Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, 98195, USA.
3
Cancer and Blood Disorder Center, Seattle Children's Hospital, 4800 Sand Point Way, Seattle, WA, 98105, USA.
4
Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA, 98109, USA.
5
Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA, 98109, USA. steveh@fredhutch.org.
6
Howard Hughes Medical Institute, Chevy Chase, MD, USA. steveh@fredhutch.org.

Abstract

BACKGROUND:

Our understanding of eukaryotic gene regulation is limited by the complexity of protein-DNA interactions that comprise the chromatin landscape and by inefficient methods for characterizing these interactions. We recently introduced CUT&RUN, an antibody-targeted nuclease cleavage method that profiles DNA-binding proteins, histones and chromatin-modifying proteins in situ with exceptional sensitivity and resolution.

RESULTS:

Here, we describe an automated CUT&RUN platform and apply it to characterize the chromatin landscapes of human cells. We find that automated CUT&RUN profiles of histone modifications crisply demarcate active and repressed chromatin regions, and we develop a continuous metric to identify cell-type-specific promoter and enhancer activities. We test the ability of automated CUT&RUN to profile frozen tumor samples and find that our method readily distinguishes two pediatric glioma xenografts by their subtype-specific gene expression programs.

CONCLUSIONS:

The easy, cost-effective workflow makes automated CUT&RUN an attractive tool for high-throughput characterization of cell types and patient samples.

KEYWORDS:

CUT&RUN; Chromatin regulators; Histone modifications; Transcription factors

PMID:
30577869
PMCID:
PMC6302505
DOI:
10.1186/s13072-018-0243-8
[Indexed for MEDLINE]
Free PMC Article

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