The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites
Open accessAbstract
We describe Cleavage Under Targets and Release Using Nuclease (CUT&RUN), a chromatin profiling strategy in which antibody-targeted controlled cleavage by micrococcal nuclease releases specific protein-DNA complexes into the supernatant for paired-end DNA sequencing. Unlike Chromatin Immunoprecipitation (ChIP), which fragments and solubilizes total chromatin, CUT&RUN is performed in situ, allowing for both quantitative high-resolution chromatin mapping and probing of the local chromatin environment. When applied to yeast and human nuclei, CUT&RUN yielded precise transcription factor profiles while avoiding crosslinking and solubilization issues. CUT&RUN is simple to perform and is inherently robust, with extremely low backgrounds requiring only ~1/10th the sequencing depth as ChIP, making CUT&RUN especially cost-effective for transcription factor and chromatin profiling. When used in conjunction with native ChIP-seq and applied to human CTCF, CUT&RUN mapped directional long range contact sites at high resolution. We conclude that in situ mapping of protein-DNA interactions by CUT&RUN is an attractive alternative to ChIP-seq.
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Thorvaldsdottir, H., Robinson, J. T., & Mesirov, J. P. (2013) · Briefings in Bioinformatics · doi:10.1093/bib/bbs017 · Cited by 9,049
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Quantitative ChIP-Seq normalization reveals global modulation of the epigenome
Orlando, D. A., Chen, M. W., Brown, V. E., Solanki, S., Choi, Y. J., Olson, E. R., Fritz, C. C., Bradner, J. E., & Guenther, M. G. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.10.018 · Cited by 503
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
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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-citationJASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles
Castro-Mondragon, J. A., Riudavets-Puig, R., Rauluseviciute, I., Berhanu Lemma, R., Turchi, L., Blanc-Mathieu, R., Lucas, J., Boddie, P., Khan, A., Manosalva Pérez, N., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkab1113 · Cited by 1,935
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The technological landscape and applications of single-cell multi-omics
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Reprogramming human T cell function and specificity with non-viral genome targeting
Roth, T. L., Puig-Saus, C., Yu, R., Shifrut, E., Carnevale, J., Li, P. J., Hiatt, J., Saco, J., Krystofinski, P., Li, H., et al. (2018) · Nature · doi:10.1038/s41586-018-0326-5 · Cited by 839
Metadata
- Authors
- Skene, P. J., & Henikoff, S.
- Venue
- eLife
- Publisher
- eLife Sciences Publications, Ltd
- Published
- 2017-01-16
- Volume
- 6
- ISSN
- 2050-084X (ISSN-L)
- OpenAlex
- W2562443513
- Cited by
- 1,776
- References
- 5
- FWCI
- 28.63
- Type
- journal article
- Language
- en
- Open access
- gold
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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