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Research: H3K27 and H3K9 methylation mask potential CTCF binding sites to maintain 3D genome integrity
- Kei Fukuda,
- Chikako Shimura,
- and Yoichi Shinkai
Genome Res. October 2025 35: 2199-2210; Published in Advance August 5, 2025, doi:10.1101/gr.280732.125
...in Class 2 upon TKO (adj. P = 9.2 × 10−14) (Supplemental Fig. S1F,G). This suggests that the reorganization of H3K9 methylation states due to the loss of each H3K9 methyltransferase inhibits CTCF binding.Because certain fractions of CTCF binding are sensitive to DNA methylation (Wang et al. 2012; Kim et al...
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Research: DNA (de)methylation in embryonic stem cells controls CTCF-dependent chromatin boundaries
- Laura Wiehle,
- Graeme J. Thorn,
- Günter Raddatz,
- Christopher T. Clarkson,
- Karsten Rippe,
- Frank Lyko,
- Achim Breiling,
- and Vladimir B. Teif
Genome Res. May 2019 29: 750-761; Published in Advance April 4, 2019, doi:10.1101/gr.239707.118
...display a -wide loss of 5hmC and a severe deregulation of the 5mC landscape (Dawlaty et al. 2013). In the present study, we link CTCF binding, DNA (de)methylation, and nucleosome occupancy by comparing WT ESCs with DKO ESCs that lack Tet1/2. The resulting cascade of downstream events can be summarized...
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Research: The aberrant epigenome of DNMT3B-mutated ICF1 patient iPSCs is amenable to correction, with the exception of a subset of regions with H3K4me3- and/or CTCF-based epigenetic memory
- Varsha Poondi Krishnan,
- Barbara Morone,
- Shir Toubiana,
- Monika Krzak,
- Salvatore Fioriniello,
- Floriana Della Ragione,
- Maria Strazzullo,
- Claudia Angelini,
- Sara Selig,
- and Maria R. Matarazzo
Genome Res. February 2023 33: 169-183; Published in Advance February 24, 2023, doi:10.1101/gr.276986.122
...that the majority of phenotype-related hypomethylated regions reacquire normal DNA methylation levels following editing. However, at the most severely hypomethylated regions in ICF1 iPSCs, which also display the highest increases in H3K4me3 levels and/or abnormal CTCF binding, the epigenetic memory persists...
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Research: Nucleosome repositioning links DNA (de)methylation and differential CTCF binding during stem cell development
- Vladimir B. Teif,
- Daria A. Beshnova,
- Yevhen Vainshtein,
- Caroline Marth,
- Jan-Philipp Mallm,
- Thomas Höfer,
- and Karsten Rippe
Genome Res. August 2014 24: 1285-1295; Published in Advance May 8, 2014, doi:10.1101/gr.164418.113
...and Odom2013; Van Bortle and Corces 2013). About 40% of the several thousands of potential cell typespecific CTCF binding sites in the human were linked to changes in DNA methylation (Wang et al. 2012). On the other hand, it was concluded that in most cases, differential DNA methylation is not a cause...
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Research: Enhancer methylation dynamics contribute to cancer plasticity and patient mortality
- Rachel E. Bell,
- Tamar Golan,
- Danna Sheinboim,
- Hagar Malcov,
- David Amar,
- Avi Salamon,
- Tamar Liron,
- Sahar Gelfman,
- Yankel Gabet,
- Ron Shamir,
- and Carmit Levy
Genome Res. May 2016 26: 601-611; Published in Advance February 23, 2016, doi:10.1101/gr.197194.115
...and Beland 2009). Since widespread DNA methylation changes are associated with aging (Richardson 2003), we calculated the correlations between patient ages and accumulation of enhancer methylation changes. Encouragingly, we found no significant correlation between eDMR methylation changes in metastatic...
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Research: YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment
- Jonathan A. Beagan,
- Michael T. Duong,
- Katelyn R. Titus,
- Linda Zhou,
- Zhendong Cao,
- Jingjing Ma,
- Caroline V. Lachanski,
- Daniel R. Gillis,
- and Jennifer E. Phillips-Cremins
Genome Res. July 2017 27: 1139-1152; Published in Advance May 23, 2017, doi:10.1101/gr.215160.116
.... 2016). Importantly, a large proportion of genomic loci that are methylated in NPCs maintain the mark through the duration of neural development (Ziller et al. 2015; Sharma et al. 2016). Because CTCF binding is anti-correlated with DNA methylation, we posit that a notable proportion of the large class...
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Method: A pooling-based approach to mapping genetic variants associated with DNA methylation
- Irene M. Kaplow,
- Julia L. MacIsaac,
- Sarah M. Mah,
- Lisa M. McEwen,
- Michael S. Kobor,
- and Hunter B. Fraser
Genome Res. June 2015 25: 907-917; Published in Advance April 24, 2015, doi:10.1101/gr.183749.114
...for associations with chromatin accessibility and CTCF binding but are less likely to be associated with traits indirectly linked to DNA, such as gene expression and disease phenotypes. In summary, our approach allows genome-wide mapping of genetic variants associated with DNA methylation in any tissue of any...
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Research: DNA methylation contributes to natural human variation
- Holger Heyn,
- Sebastian Moran,
- Irene Hernando-Herraez,
- Sergi Sayols,
- Antonio Gomez,
- Juan Sandoval,
- Dave Monk,
- Kenichiro Hata,
- Tomas Marques-Bonet,
- Liewei Wang,
- and Manel Esteller
Genome Res. September 2013 23: 1363-1372; Published in Advance August 1, 2013, doi:10.1101/gr.154187.112
..., intragenic methylation has been linked to transcriptional and splicing activities ( Jones 2012), suggesting a sophisticated regulatory potential for this epigenetic modification. DNA methylation levels are closely related to the genomic context, with CpG-rich regions (CpG islands) located in the 59 endof...
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Research: The role of DNA methylation in directing the functional organization of the cancer epigenome
- Fides D. Lay,
- Yaping Liu,
- Theresa K. Kelly,
- Heather Witt,
- Peggy J. Farnham,
- Peter A. Jones,
- and Benjamin P. Berman
Genome Res. April 2015 25: 467-477; Published in Advance March 6, 2015, doi:10.1101/gr.183368.114
...(Supplemental Fig. 1E). NDRs in cluster C4 consisted of weak enhancers or insulators characterized by CTCF binding sites (Supplemental Fig. 1E). The highly consistent phasing patterns around the C4 CTCF sites (Supplemental Fig. 1D) substantiated our earlier findings that DNA methylation rates are significantly...
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Research: Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer
- Phillippa C. Taberlay,
- Aaron L. Statham,
- Theresa K. Kelly,
- Susan J. Clark,
- and Peter A. Jones
Genome Res. September 2014 24: 1421-1432; Published in Advance June 10, 2014, doi:10.1101/gr.163485.113
...cells, we needed to consider NDRs in the context of epi maps extending beyond DNA methylation and nucleosome occupancy using NOMe-seq. We therefore performed ChIP-seq to generate signatures of key histone modifications (H3K4me1, H3K27ac, H3K4me3, H3K27me3) and regulatory factors (CTCF, RNAPol II...
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