The DOI matches its Crossref record; 12 of the 12 references it cites were found in a registry or an index.
The interaction landscape between transcription factors and the nucleosome
Open accessAbstract
Nucleosomes cover most of the genome and are thought to be displaced by transcription factors in regions that direct gene expression. However, the modes of interaction between transcription factors and nucleosomal DNA remain largely unknown. Here we systematically explore interactions between the nucleosome and 220 transcription factors representing diverse structural families. Consistent with earlier observations, we find that the majority of the studied transcription factors have less access to nucleosomal DNA than to free DNA. The motifs recovered from transcription factors bound to nucleosomal and free DNA are generally similar. However, steric hindrance and scaffolding by the nucleosome result in specific positioning and orientation of the motifs. Many transcription factors preferentially bind close to the end of nucleosomal DNA, or to periodic positions on the solvent-exposed side of the DNA. In addition, several transcription factors usually bind to nucleosomal DNA in a particular orientation. Some transcription factors specifically interact with DNA located at the dyad position at which only one DNA gyre is wound, whereas other transcription factors prefer sites spanning two DNA gyres and bind specifically to each of them. Our work reveals notable differences in the binding of transcription factors to free and nucleosomal DNA, and uncovers a diverse interaction landscape between transcription factors and the nucleosome. A method for systematically exploring interactions between the nucleosome and transcription factors identifies five major interaction patterns.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
An integrated encyclopedia of DNA elements in the human genome
The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072
The accessible chromatin landscape of the human genome
Thurman, R. E., Rynes, E., Humbert, R., Vierstra, J., Maurano, M. T., Haugen, E., Sheffield, N. C., Stergachis, A. B., Wang, H., Vernot, B., et al. (2012) · Nature · doi:10.1038/nature11232 · Cited by 2,679
A census of human transcription factors: function, expression and evolution
Vaquerizas, J. M., Kummerfeld, S. K., Teichmann, S. A., & Luscombe, N. M. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2538 · Cited by 1,573
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
Self-citationPioneer Transcription Factors Target Partial DNA Motifs on Nucleosomes to Initiate Reprogramming
Soufi, A., Garcia, M. F., Jaroszewicz, A., Osman, N., Pellegrini, M., & Zaret, K. S. (2015) · Cell · doi:10.1016/j.cell.2015.03.017 · Cited by 780
Nucleosome structure and function
McGinty, R. K., & Tan, S. (2015) · Chemical Reviews · doi:10.1021/cr500373h · Cited by 530
Jolma, A., Kivioja, T., Toivonen, J., Cheng, L., Wei, G., Enge, M., Taipale, M., Vaquerizas, J. M., Yan, J., Sillanpää, M. J., et al. (2010) · Genome Research · doi:10.1101/gr.100552.109 · Cited by 441
Self-citationIwafuchi-Doi, M., Donahue, G., Kakumanu, A., Watts, J. A., Mahony, S., Pugh, B. F., Lee, D., Kaestner, K. H., & Zaret, K. S. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.03.001 · Cited by 390
Nucleosome breathing and remodeling constrain CRISPR-Cas9 function
Isaac, R. S., Jiang, F., Doudna, J. A., Lim, W. A., Narlikar, G. J., & Almeida, R. (2016) · eLife · doi:10.7554/elife.13450 · Cited by 234
Sekiya, T., Muthurajan, U. M., Luger, K., Tulin, A. V., & Zaret, K. S. (2009) · Genes & Development · doi:10.1101/gad.1775509 · Cited by 221
Cited by
JASPAR 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
Base-resolution models of transcription-factor binding reveal soft motif syntax
Avsec, Ž., Weilert, M., Shrikumar, A., Krueger, S., Alexandari, A., Dalal, K., Fropf, R., McAnany, C., Gagneur, J., Kundaje, A., et al. (2021) · Nature Genetics · doi:10.1038/s41588-021-00782-6 · Cited by 610
Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function
Dodonova, S. O., Zhu, F., Dienemann, C., Taipale, J., & Cramer, P. (2020) · Nature · doi:10.1038/s41586-020-2195-y · Cited by 265
Self-citationPioneer factors as master regulators of the epigenome and cell fate
Balsalobre, A., & Drouin, J. (2022) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-022-00464-z · Cited by 251
Chromatin accessibility profiling methods
Minnoye, L., Marinov, G. K., Krausgruber, T., Pan, L., Marand, A. P., Secchia, S., Greenleaf, W. J., Furlong, E. E. M., Zhao, K., Schmitz, R. J., et al. (2021) · Nature Reviews Methods Primers · doi:10.1038/s43586-020-00008-9 · Cited by 206
Metadata
- Authors
- Zhu, F., Farnung, L., Kaasinen, E., Sahu, B., Yin, Y., Wei, B., Dodonova, S. O., Nitta, K. R., Morgunova, E., Taipale, M., Cramer, P., & Taipale, J.
- Venue
- Nature
- Published
- 2018-09-24
- Volume
- 562
- Issue
- 7725
- Pages
- 76-81
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W2951091094
- Cited by
- 368
- References
- 12
- FWCI
- 11.07
- Type
- journal article
- Language
- en
- Open access
- green
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: The interaction landscape between transcription factors and the nucleosome. https://app.cochat.ai/papers/10.1038/s41586-018-0549-5
- The paper
- Zhu, F., Farnung, L., Kaasinen, E., Sahu, B., Yin, Y., Wei, B., Dodonova, S. O., Nitta, K. R., Morgunova, E., Taipale, M., Cramer, P., & Taipale, J. (2018). The interaction landscape between transcription factors and the nucleosome. Nature. https://doi.org/10.1038/s41586-018-0549-5
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
