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Automated in situ profiling of chromatin modifications resolves cell types and gene regulatory programs

Derek H. Janssens, Steven J. Wu, Jay F. Sarthy, Michael P. Meers, Carrie H. Myers, James M. Olson, Kami Ahmad, View ORCID ProfileSteven Henikoff
doi: https://doi.org/10.1101/418681
Derek H. Janssens
1Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA, 98105
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Steven J. Wu
1Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA, 98105
2Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA, 98195 USA
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Jay F. Sarthy
1Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA, 98105
3Cancer and Blood Disorders, 4800 Sand Point Way, Seattle Children’s Hospital, Seattle, WA, 98105
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Michael P. Meers
1Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA, 98105
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Carrie H. Myers
4Clinical Research Division Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA, 98105
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James M. Olson
3Cancer and Blood Disorders, 4800 Sand Point Way, Seattle Children’s Hospital, Seattle, WA, 98105
4Clinical Research Division Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA, 98105
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Kami Ahmad
1Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA, 98105
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Steven Henikoff
1Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA, 98105
5Howard Hughes Medical Institute, USA
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  • ORCID record for Steven Henikoff
  • For correspondence: steveh@fredhutch.org
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Abstract

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. Here we describe an automated CUT&RUN platform and apply it to characterize the chromatin landscapes of human cell lines. We find that 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 diffuse midline gliomas by their subtype-specific gene expression programs. The easy, cost-effective workflow makes automated CUT&RUN an attractive tool for high-throughput characterization of cell types and patient samples.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted September 16, 2018.
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Automated in situ profiling of chromatin modifications resolves cell types and gene regulatory programs
Derek H. Janssens, Steven J. Wu, Jay F. Sarthy, Michael P. Meers, Carrie H. Myers, James M. Olson, Kami Ahmad, Steven Henikoff
bioRxiv 418681; doi: https://doi.org/10.1101/418681
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Automated in situ profiling of chromatin modifications resolves cell types and gene regulatory programs
Derek H. Janssens, Steven J. Wu, Jay F. Sarthy, Michael P. Meers, Carrie H. Myers, James M. Olson, Kami Ahmad, Steven Henikoff
bioRxiv 418681; doi: https://doi.org/10.1101/418681

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