ZBTB33 binds unmethylated regions of the genome associated with actively expressed genes
Open accessAbstract
Background: DNA methylation and repressive histone modifications cooperate to silence promoters. One mechanism by which regions of methylated DNA could acquire repressive histone modifications is via methyl DNA-binding transcription factors. The zinc finger protein ZBTB33 (also known as Kaiso) has been shown in vitro to bind preferentially to methylated DNA and to interact with the SMRT/NCoR histone deacetylase complexes. We have performed bioinformatic analyses of Kaiso ChIP-seq and DNA methylation datasets to test a model whereby binding of Kaiso to methylated CpGs leads to loss of acetylated histones at target promoters. Results: Our results suggest that, contrary to expectations, Kaiso does not bind to methylated DNA in vivo but instead binds to highly active promoters that are marked with high levels of acetylated histones. In addition, our studies suggest that DNA methylation and nucleosome occupancy patterns restrict access of Kaiso to potential binding sites and influence cell type-specific binding. Conclusions: We propose a new model for the genome-wide binding and function of Kaiso whereby Kaiso binds to unmethylated regulatory regions and contributes to the active state of target promoters.
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Kaiso is not associated with highly methylated promoters in GM12878 lymphoblastoid cells or K562 human myeloid leukaemia cell lines.
“a different study discovered that Kaiso was not associated with highly methylated promoters in GM12878 lympho-blastoid cells or in K562 human myeloid leukaemia cell lines64.”
From Transcription factors as readers and effectors of DNA methylation (2016) · cites this paper as [64]
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- Authors
- Blattler, A., Yao, L., Wang, Y., Ye, Z., Jin, V. X., & Farnham, P. J.
- Affiliations
- University of Southern California (US)
- The Ohio State University (US)
- Corresponding author
- Farnham, Peggy J
- Venue
- Epigenetics & Chromatin
- Published
- 2013-05-21
- Volume
- 6
- Issue
- 1
- Pages
- 13-13
- ISSN
- 1756-8935 (ISSN-L)
- PMC
- PMC3663758
- OpenAlex
- W2152609389
- Cited by
- 82
- References
- 39
- Citations by year
- 2026: 3 · 2025: 3 · 2024: 16 · 2023: 3 · 2022: 6 · 2021: 2 · 2020: 2 · 2019: 9 · 2018: 9 · 2017: 6 · 2016: 5 · 2015: 10 · 2014: 6 · 2013: 2
- FWCI
- 3.44
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- Epigenetics & Chromatin (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- National Institutes of Health
- National Human Genome Research Institute (U54HG004558)
- National Cancer Institute (P30CA014089)
- 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 › Chromatin Remodeling and Cancer
- Keywords
- ZBTB33, Kaiso, DNA methylation, histone acetylation, transcription factor binding, nucleosome occupancy, cell type-specific binding, chromatin regulation
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