Differential sensitivity to methylated DNA by ETS-family transcription factors is intrinsically encoded in their DNA-binding domains
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Transactivation by the ETS family of transcription factors, whose members share structurally conserved DNA-binding domains, is variably sensitive to methylation of their target genes. The mechanism by which DNA methylation controls ETS proteins remains poorly understood. Uncertainly also pervades the effects of hemi-methylated DNA, which occurs following DNA replication and in response to hypomethylating agents, on site recognition by ETS proteins. To address these questions, we measured the affinities of two sequence-divergent ETS homologs, PU.1 and Ets-1, to DNA sites harboring a hemi- and fully methylated CpG dinucleotide. While the two proteins bound unmethylated DNA with indistinguishable affinity, their affinities to methylated DNA are markedly heterogeneous and exhibit major energetic coupling between the two CpG methylcytosines. Analysis of simulated DNA and existing co-crystal structures revealed that hemi-methylation induced non-local backbone and groove geometries that were not conserved in the fully methylated state. Indirect readout of these perturbations was differentially achieved by the two ETS homologs, with the distinctive interfacial hydration in PU.1/DNA binding moderating the inhibitory effects of DNA methylation on binding. This data established a biophysical basis for the pioneering properties associated with PU.1, which robustly bound fully methylated DNA, but not Ets-1, which was substantially inhibited.
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The ability of PU.1 to bind 5mC, unlike other E-twenty-six family members, is consistent with the lack of increase in PU.1 binding upon vitC treatment.
“consistent with the ability of PU.1 to bind 5mC, unlike other E-twenty-six family members.48”
From Vitamin C-induced epigenomic remodelling in IDH1 mutant acute myeloid leukaemia (2018) · cites this paper as [48]
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Systematic DNA nicking reveals the structural logic of protein recognitionPreprint
Yao, Y. M., O’Hagan, M., Onoon, K., Givon, L., Hamer-Rogotner, S., Salinas, R., Kessler, N., Dym, O., Pipatpolkai, T., Schumacher, M. A., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.06.30.662289
An epigenomic investigation of atrial fibrillation in a matched left and right atrial human cohort
Rodriguez, A., Frost, S., Thomas, A., Fernández‐Aroca, D. M., Choudhury, J., Tikkas, G., Tinker, A., Munroe, P. B., Bell, C. G., & Villar, D. (2026) · Clinical Epigenetics · doi:10.1186/s13148-026-02076-2
Roos‐Weil, D. (2018) · doi:10.70675/1030cb13z12b8z4f7cz8f8az165206a6209a
Prasasya, R. D., Kim, J. J., Liu, Z., Kohli, R. M., & Bartolomei, M. S. (2026) · Genes & Development · doi:10.1101/gad.353483.125
- Authors
- Stephens, D. C., & Poon, G. M. K.
- Affiliations
- Georgia State University (US)
- Corresponding author
- Poon, Gregory M. K.
- ORCID
- Poon, Gregory M. K.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2016-06-07
- Volume
- 44
- Issue
- 18
- Pages
- 8671-8681
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC5062964
- OpenAlex
- W2416365174
- Cited by
- 37
- References
- 63
- Citations by year
- 2026: 3 · 2025: 3 · 2024: 2 · 2023: 2 · 2022: 3 · 2021: 4 · 2020: 5 · 2019: 2 · 2018: 6 · 2017: 7
- FWCI
- 2.60
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- HighWire Press Open Archive (submittedVersion)
- Funders
- National Heart, Lung, and Blood Institute (R21HL129063)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- ETS transcription factors, DNA methylation, CpG, PU.1, ETS1, DNA binding affinity, DNA-binding domain, pioneer transcription factors, DNA replication, interfacial hydration, transcriptional repression
- MeSH terms
- Protein Domains, Proto-Oncogene Protein Spi-1, Animals, Binding Sites, DNA, Nucleic Acid Conformation, Protein Binding, Proto-Oncogene Proteins, Thermodynamics, Trans-Activators, CpG Islands, DNA Methylation, Principal Component Analysis, 5-Methylcytosine, Proto-Oncogene Proteins c-ets, Mice
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.
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