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Automated in situ chromatin profiling efficiently resolves cell types and gene regulatory programs
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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.
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Recent methods have overcome some limitations of ChIP.
“While ChIP is not equally adept at measuring all interactions (Baranello et al., 2016; Teytelman et al., 2013), recent methods have overcome some of these limitations (Janssens et al., 2018; Skene and Henikoff, 2017; Skene et al., 2018; Zhu et al., 2019).”
From Unraveling Hematopoiesis through the Lens of Genomics (2020) · cites this paper as Janssens et al., 2018
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Cites
Fast gapped-read alignment with Bowtie 2
Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400
BEDTools: a flexible suite of utilities for comparing genomic features
Quinlan, A. R., & Hall, I. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq033 · Cited by 27,437
Model-based Analysis of ChIP-Seq (MACS)
Zhang, Y., Liu, T., Meyer, C. A., Eeckhoute, J., Johnson, D. S., Bernstein, B. E., Nusbaum, C., Myers, R. M., Brown, M., Li, W., et al. (2008) · Genome Biology · doi:10.1186/gb-2008-9-9-r137 · Cited by 18,386
An integrated encyclopedia of DNA elements in the human genome
The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072
deepTools2: a next generation web server for deep-sequencing data analysis
Ramírez, F., Ryan, D. P., Grüning, B., Bhardwaj, V., Kilpert, F., Richter, A. S., Heyne, S., Dündar, F., & Manke, T. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw257 · Cited by 8,096
A bivalent chromatin structure marks key developmental genes in embryonic stem cells
Bernstein, B. E., Mikkelsen, T. S., Xie, X., Kamal, M., Huebert, D. J., Cuff, J., Fry, B., Meissner, A., Wernig, M., Plath, K., et al. (2006) · Cell · doi:10.1016/j.cell.2006.02.041 · Cited by 5,361
Histone H3K27ac separates active from poised enhancers and predicts developmental state
Creyghton, M. P., Cheng, A. W., Welstead, G. G., Kooistra, T., Carey, B. W., Steine, E. J., Hanna, J., Lodato, M. A., Frampton, G. M., Sharp, P. A., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1016071107 · Cited by 4,302
The Human Transcription Factors
Lambert, S. A., Jolma, A., Campitelli, L. F., Das, P. K., Yin, Y., Albu, M., Chen, X., Taipale, J., Hughes, T. R., & Weirauch, M. T. (2018) · Cell · doi:10.1016/j.cell.2018.01.029 · Cited by 3,399
Heintzman, N. D., Stuart, R. K., Hon, G., Fu, Y., Ching, C. W., Hawkins, R. D., Barrera, L. O., Van Calcar, S., Qu, C., Ching, K. A., et al. (2007) · Nature Genetics · doi:10.1038/ng1966 · Cited by 3,398
Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma
Schwartzentruber, J., Korshunov, A., Liu, X.-Y., Jones, D. T. W., Pfaff, E., Jacob, K., Sturm, D., Fontebasso, A. M., Quang, D.-A. K., Tönjes, M., et al. (2012) · Nature · doi:10.1038/nature10833 · Cited by 2,631
An atlas of active enhancers across human cell types and tissues
The FANTOM Consortium, Andersson, R., Gebhard, C., Miguel-Escalada, I., Hoof, I., Bornholdt, J., Boyd, M., Chen, Y., Zhao, X., Schmidl, C., et al. (2014) · Nature · doi:10.1038/nature12787 · Cited by 2,550
Histone modifications at human enhancers reflect global cell-type-specific gene expression
Heintzman, N. D., Hon, G. C., Hawkins, R. D., Kheradpour, P., Stark, A., Harp, L. F., Ye, Z., Lee, L. K., Stuart, R. K., Ching, C. W., et al. (2009) · Nature · doi:10.1038/nature07829 · Cited by 2,533
A unique chromatin signature uncovers early developmental enhancers in humans
Rada-Iglesias, A., Bajpai, R., Swigut, T., Brugmann, S. A., Flynn, R. A., & Wysocka, J. (2011) · Nature · doi:10.1038/nature09692 · Cited by 2,233
Regev, A., Teichmann, S. A., Lander, E. S., Amit, I., Benoist, C., Birney, E., Bodenmiller, B., Campbell, P., Carninci, P., Clatworthy, M., et al. (2017) · eLife · doi:10.7554/elife.27041 · Cited by 2,232
Tackling the widespread and critical impact of batch effects in high-throughput data
Leek, J. T., Scharpf, R. B., Bravo, H. C., Simcha, D., Langmead, B., Johnson, W. E., Geman, D., Baggerly, K., & Irizarry, R. A. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2825 · Cited by 2,196
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
Landt, S. G., Marinov, G. K., Kundaje, A., Kheradpour, P., Pauli, F., Batzoglou, S., Bernstein, B. E., Bickel, P., Brown, J. B., Cayting, P., et al. (2012) · Genome Research · doi:10.1101/gr.136184.111 · Cited by 2,033
Controlling TGF-beta signaling.
Massagué, J., & Chen, Y. (2000) · PubMed · Cited by 1,780
An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites
Skene, P. J., & Henikoff, S. (2017) · eLife · doi:10.7554/elife.21856 · Cited by 1,737
Self-citationControlling TGF-β signalingPreprint
Massagué, J., & Chen, Y. (2000) · Genes & Development · doi:10.1101/gad.14.6.627 · Cited by 1,589
Modification of Enhancer Chromatin: What, How, and Why?
Calo, E., & Wysocka, J. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.01.038 · Cited by 1,457
Regev, A., Teichmann, S. A., Lander, E. S., Amit, I., Benoist, C. O., Birney, E., Bodenmiller, B., & al, E. (2017) · Zurich Open Repository and Archive (University of Zurich) · doi:10.5167/uzh-162597 · Cited by 1,457
BigWig and BigBed: enabling browsing of large distributed datasets
Kent, W. J., Zweig, A. S., Barber, G. P., Hinrichs, A. S., & Karolchik, D. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq351 · Cited by 1,268
The chromatin accessibility landscape of primary human cancers
Corces, M. R., Granja, J. M., Shams, S., Louie, B. H., Seoane, J. A., Zhou, W., Silva, T. C., Groeneveld, C., Wong, C. K., Cho, S. W., et al. (2018) · Science · doi:10.1126/science.aav1898 · Cited by 1,230
Mackay, A., Burford, A., Carvalho, D., Izquierdo, E., Fazal-Salom, J., Taylor, K. R., Bjerke, L., Clarke, M., Vinci, M., Nandhabalan, M., et al. (2017) · Cancer Cell · doi:10.1016/j.ccell.2017.08.017 · Cited by 1,212
The selection and function of cell type-specific enhancers
Heinz, S., Romanoski, C. E., Benner, C., & Glass, C. K. (2015) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3949 · Cited by 1,010
Histone modification levels are predictive for gene expression
Karlić, R., Chung, H., Lasserre, J., Vlahoviček, K., & Vingron, M. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0909344107 · Cited by 809
Distinct epigenomic landscapes of pluripotent and lineage-committed human cells
Hawkins, R. D., Hon, G. C., Lee, L. K., Ngo, Q., Lister, R., Pelizzola, M., Edsall, L. E., Kuan, S., Luu, Y., Klugman, S., et al. (2010) · Cell stem cell · doi:10.1016/j.stem.2010.03.018 · Cited by 806
Targeted in situ genome-wide profiling with high efficiency for low cell numbers
Skene, P. J., Henikoff, J. G., & Henikoff, S. (2018) · Nature Protocols · doi:10.1038/nprot.2018.015 · Cited by 803
Self-citationDevelopmental and oncogenic programs in H3K27M gliomas dissected by single-cell RNA-seq
Filbin, M. G., Tirosh, I., Hovestadt, V., Shaw, M. L., Escalante, L. E., Mathewson, N. D., Neftel, C., Frank, N., Pelton, K., Hebert, C. M., et al. (2018) · Science · doi:10.1126/science.aao4750 · Cited by 694
NPAT links cyclin E–Cdk2 to the regulation of replication-dependent histone gene transcriptionPreprint
Zhao, J., Kennedy, B. K., Lawrence, B. D., Barbie, D. A., Matera, A. G., Fletcher, J. A., & Harlow, E. (2000) · Genes & Development · doi:10.1101/gad.827700 · Cited by 665
The Human Cell Atlas: from vision to reality
Rozenblatt-Rosen, O., Stubbington, M. J. T., Regev, A., & Teichmann, S. A. (2017) · Nature · doi:10.1038/550451a · Cited by 638
The Key Role of Epigenetics in Human Disease Prevention and Mitigation
Feinberg, A. P. (2018) · New England Journal of Medicine · doi:10.1056/nejmra1402513 · Cited by 638
Open chromatin in pluripotency and reprogramming
Gaspar‐Maia, A., Alajem, A., Meshorer, E., & Ramalho‐Santos, M. (2010) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3036 · Cited by 599
CTCF establishes discrete functional chromatin domains at the Hox clusters during differentiation
Narendra, V., Rocha, P. P., An, D., Raviram, R., Skok, J. A., Mazzoni, E. O., & Reinberg, D. (2015) · Science · doi:10.1126/science.1262088 · Cited by 535
Looping Back to Leap Forward: Transcription Enters a New Era
Levine, M., Cattoglio, C., & Tjian, R. (2014) · Cell · doi:10.1016/j.cell.2014.02.009 · Cited by 497
Direct promoter repression by BCL11A controls the fetal to adult hemoglobin switch
Liu, N., Hargreaves, V. V., Zhu, Q., Kurland, J. V., Hong, J., Kim, W., Sher, F., Macias-Trevino, C., Rogers, J. M., Kurita, R., et al. (2018) · Cell · doi:10.1016/j.cell.2018.03.016 · Cited by 478
The Nature of Embryonic Stem Cells
Martello, G., & Smith, A. G. (2014) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-100913-013116 · Cited by 444
Why Batch Effects Matter in Omics Data, and How to Avoid Them
Goh, W. W. B., Wang, W., & Wong, L. (2017) · Trends in biotechnology · doi:10.1016/j.tibtech.2017.02.012 · Cited by 419
Transcriptional Dependencies in Diffuse Intrinsic Pontine Glioma
Nagaraja, S., Vitanza, N. A., Woo, P. J., Taylor, K. R., Liu, F., Zhang, L., Li, M., Meng, W., Ponnuswami, A., Sun, W., et al. (2017) · Cancer Cell · doi:10.1016/j.ccell.2017.03.011 · Cited by 397
Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins
Teytelman, L., Thurtle, D. M., Rine, J., & van Oudenaarden, A. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1316064110 · Cited by 389
Cotney, J., Muhle, R. A., Sanders, S. J., Liu, L., Willsey, A. J., Niu, W., Liu, W., Klei, L., Lei, J., Yin, J., et al. (2015) · Nature Communications · doi:10.1038/ncomms7404 · Cited by 350
One mouse, one patient paradigm: New avatars of personalized cancer therapy
Malaney, P., Nicosia, S. V., & Davé, V. (2013) · Cancer Letters · doi:10.1016/j.canlet.2013.10.010 · Cited by 290
Profiling of Pluripotency Factors in Single Cells and Early Embryos
Hainer, S. J., Bošković, A., McCannell, K. N., Rando, O. J., & Fazzio, T. G. (2019) · Cell · doi:10.1016/j.cell.2019.03.014 · Cited by 203
Epigenetics of hematopoiesis and hematological malignanciesPreprint
Hu, D., & Shilatifard, A. (2016) · Genes & Development · doi:10.1101/gad.284109.116 · Cited by 175
Active promoters give rise to false positive ‘Phantom Peaks’ in ChIP-seq experiments
Jain, D., Baldi, S., Zabel, A., Straub, T., & Becker, P. B. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv637 · Cited by 156
Widespread Misinterpretable ChIP-seq Bias in Yeast
Park, D., Lee, Y., Bhupindersingh, G., & Iyer, V. R. (2013) · PLoS ONE · doi:10.1371/journal.pone.0083506 · Cited by 147
Liu, Q., Jiang, C., Xu, J., Zhao, M., Bortle, K. V., Cheng, X., Wang, G., Chang, H. Y., Wu, J. C., & Snyder, M. P. (2017) · Circulation Research · doi:10.1161/circresaha.116.310456 · Cited by 133
Regulatory network control of blood stem cells
Göttgens, B. (2015) · Blood · doi:10.1182/blood-2014-08-570226 · Cited by 82
Aldridge, S., Watt, S. B., Quail, M. A., Rayner, T. F., Lukk, M., Bimson, M. F., Gaffney, D., & Odom, D. T. (2013) · Genome biology · doi:10.1186/gb-2013-14-11-r124 · Cited by 41
Neiman, M., Sundling, S., Grönberg, H., Hall, P., Czene, K., Lindberg, J., & Klevebring, D. (2012) · PLoS ONE · doi:10.1371/journal.pone.0048616 · Cited by 35
Gasper, W. C., Marinov, G. K., Pauli, F., Scott, M. T., Newberry, K. M., DeSalvo, G., Ou, S. K.-H., Myers, R., Vielmetter, J., & Wold, B. J. (2014) · Scientific Reports · doi:10.1038/srep05152 · Cited by 34
lobChIP: from cells to sequencing ready ChIP libraries in a single day
Wallerman, O., Nord, H., Bysani, M., Borghini, L., & Wadelius, C. (2015) · Epigenetics & Chromatin · doi:10.1186/s13072-015-0017-5 · Cited by 17
Profiling of pluripotency factors in individual stem cells and early embryosPreprint
Hainer, S. J., Bošković, A., Rando, O. J., & Fazzio, T. G. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/286351 · Cited by 15
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Kaya-Okur, H. S., Wu, S. J., Codomo, C. A., Pledger, E. S., Bryson, T. D., Henikoff, J. G., Ahmad, K., & Henikoff, S. (2019) · Nature Communications · doi:10.1038/s41467-019-09982-5 · Cited by 2,187
Self-citationPeak calling by Sparse Enrichment Analysis for CUT&RUN chromatin profiling
Meers, M. P., Tenenbaum, D., & Henikoff, S. (2019) · Epigenetics & Chromatin · doi:10.1186/s13072-019-0287-4 · Cited by 556
Self-citationImproved CUT&RUN chromatin profiling tools
Meers, M. P., Bryson, T. D., Henikoff, J. G., & Henikoff, S. (2019) · eLife · doi:10.7554/elife.46314 · Cited by 474
Self-citationEfficient low-cost chromatin profiling with CUT&Tag
Kaya-Okur, H. S., Janssens, D. H., Henikoff, J. G., Ahmad, K., & Henikoff, S. (2020) · Nature Protocols · doi:10.1038/s41596-020-0373-x · Cited by 425
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Wang, W., Min, L., Qiu, X., Wu, X., Liu, C., Ma, J., Zhang, D., & Zhu, L. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.645647 · Cited by 248
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Oksuz, B. A., Yang, L., Abraham, S., Venev, S. V., Krietenstein, N., Parsi, K. M., Özadam, H., Oomen, M. E., Nand, A., Mao, H. Z., et al. (2021) · Nature Methods · doi:10.1038/s41592-021-01248-7 · Cited by 249
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Wu, S. J., Furlan, S. N., Mihalas, A. B., Kaya-Okur, H. S., Feroze, A. H., Emerson, S. N., Zheng, Y., Carson, K., Cimino, P. J., Keene, C. D., et al. (2021) · Nature Biotechnology · doi:10.1038/s41587-021-00865-z · Cited by 201
Self-citationUnraveling Hematopoiesis through the Lens of Genomics
Liggett, L. A., & Sankaran, V. G. (2020) · Cell · doi:10.1016/j.cell.2020.08.030 · Cited by 163
XSTREME: Comprehensive motif analysis of biological sequence datasetsPreprint
Grant, C. E., & Bailey, T. L. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.09.02.458722 · Cited by 140
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Meers, M. P., Janssens, D. H., & Henikoff, S. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.05.025 · Cited by 141
Self-citationZhang, L., Zhang, Y., Chen, Y., Gholamalamdari, O., Wang, Y., Ma, J., & Belmont, A. S. (2020) · Genome Research · doi:10.1101/gr.266239.120 · Cited by 142
High‐Resolution Chromatin Profiling Using CUT&RUN
Hainer, S. J., & Fazzio, T. G. (2019) · Current Protocols in Molecular Biology · doi:10.1002/cpmb.85 · Cited by 117
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Gopalan, S., Wang, Y., Harper, N. W., Garber, M. G., & Fazzio, T. G. (2021) · Molecular Cell · doi:10.1016/j.molcel.2021.09.019 · Cited by 112
Genomic methods in profiling DNA accessibility and factor localization
Klein, D. C., & Hainer, S. J. (2019) · Chromosome Research · doi:10.1007/s10577-019-09619-9 · Cited by 104
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Brahma, S., & Henikoff, S. (2019) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2019.09.003 · Cited by 91
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Self-citationSzulzewsky, F., Arora, S., Hoellerbauer, P., King, C., Nathan, E., Chan, M., Cimino, P. J., Ozawa, T., Kawauchi, D., Pajtler, K. W., et al. (2020) · Genes & Development · doi:10.1101/gad.338681.120 · Cited by 82
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Augert, A., Mathsyaraja, H., Ibrahim, A. H., Freie, B. W., Geuenich, M., Cheng, P.-F., Alibeckoff, S. P., Wu, N., Hiatt, J. B., Basom, R., et al. (2020) · Cancer Cell · doi:10.1016/j.ccell.2020.04.016 · Cited by 80
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Mitchell, K., Sprowls, S. A., Arora, S., Shakya, S., Silver, D. J., Goins, C. M., Wallace, L. C., Roversi, G. A., Schafer, R., Kay, K. E., et al. (2023) · Genes & Development · doi:10.1101/gad.349803.122 · Cited by 62
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Kita, K., Masayasu, S. E. G. A., Uchida, Y., Chiba, T., Matsushima, T., & Asahara, H. (2026) · STAR Protocols · doi:10.1016/j.xpro.2026.104889
Metadata
- Authors
- Janssens, D. H., Wu, S. J., Sarthy, J. F., Meers, M. P., Myers, C. H., Olson, J. M., Ahmad, K., & Henikoff, S.
- Affiliations
- Fred Hutch Cancer Center (US)
- University of Washington (US)
- Seattle Children's Hospital (US)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Henikoff, Steven
- ORCID
- Venue
- Epigenetics & Chromatin
- Published
- 2018-12
- Volume
- 11
- Issue
- 1
- Pages
- 74-74
- ISSN
- 1756-8935 (ISSN-L)
- PMC
- PMC6302505
- OpenAlex
- W2905640619
- Cited by
- 73
- References
- 53
- Citations by year
- 2026: 5 · 2025: 5 · 2024: 7 · 2023: 6 · 2022: 12 · 2021: 17 · 2020: 9 · 2019: 11
- FWCI
- 3.29
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Epigenetics & Chromatin (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- Europe PMC (PubMed Central) (publishedVersion, other-oa)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Howard Hughes Medical Institute
- Damon Runyon Cancer Research Foundation
- National Institutes of Health (1s10od020069-01)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Keywords
- CUT&RUN, chromatin profiling, histone modifications, promoter activity, chromatin accessibility, gene regulatory programs, protein-DNA interactions
- MeSH terms
- Binding Sites, Chromatin, DNA-Binding Proteins, Enhancer Elements, Genetic, Histones, Humans, Promoter Regions, Genetic, Protein Binding, Software, Transcription Factors, Gene Expression Regulation, Neoplastic, In Situ Hybridization, K562 Cells, Gene Expression Profiling, Histone Code, Chromatin Immunoprecipitation, High-Throughput Screening Assays
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