The DOI matches its Crossref record; 11 of the 11 references it cites were found in a registry or an index.
Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution
Open accessAbstract
SUMMARY Chromatin immunoprecipitation (ChIP-chip and ChIP-seq) assays identify where proteins bind throughout a genome. However, DNA contamination and DNA fragmentation heterogeneity produce false positives (erroneous calls) and imprecision in mapping. Consequently, stringent data filtering produces false negatives (missed calls). Here we describe ChIP-exo, where an exonuclease trims ChIP DNA to a precise distance from the crosslinking site. Bound locations are detectable as peak-pairs by deep sequencing. Contaminating DNA is degraded or fails to form complementary peak-pairs. With the single bp accuracy provided by ChIP-exo, we show an unprecedented view into genome-wide binding of the yeast transcription factors Reb1, Gal4, Phd1, Rap1, and human CTCF. Each of these factors was chosen to address potential limitations of ChIP-exo. We found that binding sites become unambiguous and reveal diverse tendencies governing in vivo DNA binding specificity that include sequence variants, functionally distinct motifs, motif clustering, secondary interactions, and combinatorial modules within a compound motif.
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Cites
High-Resolution Profiling of Histone Methylations in the Human Genome
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“Estimates range from 13,000 to 29,000 binding locations across mammalian genomes (Cuddapah et al., 2009; Dion et al., 2007).”
BackgroundInfluentialCTCF is a uniquely versatile transcription regulator linked to epigenetics and disease
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Global mapping of protein-DNA interactions in vivo by digital genomic footprinting
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Cited by
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
Annotation of functional variation in personal genomes using RegulomeDB
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CUT&Tag for efficient epigenomic profiling of small samples and single cells
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
Transcriptional enhancers: from properties to genome-wide predictions
Shlyueva, D., Stampfel, G., & Stark, A. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3682 · Cited by 1,356
Impact of cytosine methylation on DNA binding specificities of human transcription factors
Yin, Y., Morgunova, E., Jolma, A., Kaasinen, E., Sahu, B., Khund-Sayeed, S., Das, P. K., Kivioja, T., Dave, K., Zhong, F., et al. (2017) · Science · doi:10.1126/science.aaj2239 · Cited by 1,257
Metadata
- Authors
- Rhee, H. S., & Pugh, B. F.
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2011-12
- Volume
- 147
- Issue
- 6
- Pages
- 1408-1419
- ISSN
- 0092-8674 (ISSN-L)
- OpenAlex
- W1989419347
- Cited by
- 757
- References
- 11
- FWCI
- 23.16
- Type
- journal article
- Language
- en
- Open access
- bronze
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