The DOI matches its Crossref record; 97 of the 97 references it cites were found in a registry or an index.
Impact of cytosine methylation on DNA binding specificities of human transcription factors
Open accessAbstract
Positives and negatives of methylated CpG: When the DNA bases cytosine and guanine are next to each other, a methyl group is generally added to the pyrimidine, generating a mCpG dinucleotide. This modification alters DNA structure but can also affect function by inhibiting transcription factor (TF) binding. Yin et al. systematically analyzed the effect of CpG methylation on the binding of 542 human TFs (see the Perspective by Hughes and Lambert). In addition to inhibiting binding of some TFs, they found that mCpGs can promote binding of others, particularly TFs involved in development, such as homeodomain proteins. Science , this issue p. eaaj2239 ; see also p. 489
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.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Of interest, the HNF4A binding motif does not contain a CG which can be methylated, thus making it a methylation-insensitive TF (11, 17).”
From Hepatocyte Nuclear Factor 4‐Alpha Is Essential for the Active Epigenetic State at Enhancers in Mouse Liver (2019) · cites this paper as [17]
Experimental — accuracy not yet measuredThe cited source says what the claim attributes to it.
In the citing paper
“Although many TF, including several members of the ETS family, display reduced binding affinities to DNA motifs containing methylated cytosine residues (44)”
From PU.1-Dependent Enhancer Inhibition Separates Tet2 -Deficient Hematopoiesis from Malignant Transformation (2022) · cites this paper as [44]
The cited source says what the claim attributes to it.
In the citing paper
“Given that the affinity of many transcription factors, including CTCF31, is negatively impacted by methylation of their binding sites32, it is possible that hypermethylation of DMR_394 disrupts binding of regulatory proteins and adversely affects the organization and regulation of genes nearby.”
From Integrated analysis of behavioral, epigenetic, and gut microbiome analyses in AppNL-G-F, AppNL-F, and wild type mice (2021) · cites this paper as [32]
The cited source says what the claim attributes to it.
In the citing paper
“DNA methylation (5-methylcytosine or 5mC) is associated with gene repression (16) and can disrupt the binding of many TFs (17, 18).”
From Hepatocyte Nuclear Factor 4‐Alpha Is Essential for the Active Epigenetic State at Enhancers in Mouse Liver (2019) · cites this paper as [17]
In the citing paper
“These studies unexpectedly uncovered that certain interactions between TFs and low affinity binding sites can be enhanced by the presence of 5mC.”
From Dynamic DNA methylation: In the right place at the right time (2018) · cites this paper as [28]
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
Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607
Fast gapped-read alignment with Bowtie 2
Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400
Coot : model-building tools for molecular graphics
Emsley, P., & Cowtan, K. (2004) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444904019158 · Cited by 30,571
Features and development of Coot
Emsley, P., Lohkamp, B., Scott, W. G., & Cowtan, K. (2010) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444910007493 · Cited by 29,915
Takahashi, K., & Yamanaka, S. (2006) · Cell · doi:10.1016/j.cell.2006.07.024 · Cited by 26,673
PHENIX : a comprehensive Python-based system for macromolecular structure solution
Adams, P. D., Afonine, P. V., Bunkóczi, G., Chen, V. B., Davis, I. W., Echols, N., Headd, J. J., Hung, L.-W., Kapral, G. J., Grosse-Kunstleve, R. W., et al. (2010) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444909052925 · Cited by 23,716
Phaser crystallographic software
McCoy, A. J., Grosse-Kunstleve, R. W., Adams, P. D., Winn, M. D., Storoni, L. C., & Read, R. J. (2007) · Journal of Applied Crystallography · doi:10.1107/s0021889807021206 · Cited by 20,612
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
Kabsch, W. (2010) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444909047337 · Cited by 16,463
Overview of the CCP 4 suite and current developments
Winn, M. D., Ballard, C. C., Cowtan, K. D., Dodson, E. J., Emsley, P., Evans, P. R., Keegan, R. M., Krissinel, E. B., Leslie, A. G. W., McCoy, A., et al. (2011) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444910045749 · Cited by 12,353
Flagged first, then by citations
Cited by
Sorted by citations
Items 1,001–1,002 of 1,002
Halter, T., Wang, J., Amesefe, D., Lastrucci, E., Charvin, M., Singla‐Rastogi, M., & Navarro, L. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.09.30.321257 · Cited by 1
Hou, H. (2019) · TSpace (University of Toronto) · Cited by 1
Metadata
- Authors
- Yin, Y., Morgunova, E., Jolma, A., Kaasinen, E., Sahu, B., Khund-Sayeed, S., Das, P. K., Kivioja, T., Dave, K., Zhong, F., Nitta, K. R., Taipale, M., Popov, A., Ginno, P. A., Domcke, S., Yan, J., Schübeler, D., Vinson, C., & Taipale, J.
- Affiliations
- Karolinska Institutet (SE)
- University of Helsinki (FI)
- National Institutes of Health (US)
- European Synchrotron Radiation Facility (FR)
- Friedrich Miescher Institute (CH)
- University of Basel (CH)
- Corresponding author
- Taipale, Jussi
- ORCID
- Venue
- Science
- Published
- 2017-05-05
- Volume
- 356
- Issue
- 6337
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC8009048
- OpenAlex
- W2610903912
- Cited by
- 1,257
- References
- 97
- Citations by year
- 2026: 92 · 2025: 138 · 2024: 148 · 2023: 159 · 2022: 166 · 2021: 150 · 2020: 125 · 2019: 125 · 2018: 113 · 2017: 37
- FWCI
- 44.66
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Academy of Finland Center of Excellence in Cancer Genetics
- European Research Area SynBio
- Center for Innovative Medicine at Karolinska Institutet
- Knut and Alice Wallenberg Foundation
- Göran Gustafsson Foundation
- Vetenskapsrådet
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Keywords
- cytosine methylation, CpG methylation, transcription factor binding specificity, DNA methylation, homeodomain transcription factor, 5-methylcytosine, hydrophobic interactions, epigenetic regulation, gene regulatory elements
- MeSH terms
- Protein Domains, Cytosine, DNA, Humans, Protein Binding, Transcription Factors, Dinucleoside Phosphates, Genome, Human, CpG Islands, DNA Methylation, Epigenesis, Genetic, SELEX Aptamer Technique
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
