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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
...and transcriptional regulation by mediating chromatin loop formation with cohesin, which acts as an insulator and contributes to the establishment of topologically associated domains (TADs) (Dixon et al. 2012; Nora et al. 2017). A large fraction of CTCF binding sites are shared across multiple cell types...
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Research: Wnt signaling activation induces CTCF binding and loop formation at cis-regulatory elements of target genes
- Anna Nordin,
- Chaitali Chakraborty,
- Mattias Jonasson,
- Orgena Dano,
- Gianluca Zambanini,
- Pierfrancesco Pagella,
- Silvia Remeseiro,
- and Claudio Cantù
Genome Res. August 2025 35: 1701-1716; Published in Advance June 23, 2025, doi:10.1101/gr.279684.124
...in size, similar processes also occur at a smaller and more transient scale during chromatin loop formation, often between enhancers and promoters or between regulatory elements (Guo et al. 2015). The binding profiles of CTCF have been extensively studied in various organisms and cell types, and despite...
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Method: BINDER achieves accurate identification of hierarchical TADs by comprehensively characterizing consensus TAD boundaries
- Yangyang Liu,
- Bingqiang Liu,
- and Juntao Liu
Genome Res. May 2025 35: 1194-1208; Published in Advance March 17, 2025, doi:10.1101/gr.279647.124
...by the enrichment of CTCF, SMC3, and RAD21 on GM12878 and K562 data (Fig. 3A–C). Additionally, the creation of insulating forces at TAD boundaries has been proposed to be associated with a common property of CTCF binding sites and transcription start sites (TSSs) of highly active housekeeping genes (Fu et al. 2008...
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Research: Cohesin organizes 3D DNA contacts surrounding active enhancers in C. elegans
- Jun Kim,
- Haoyu Wang,
- and Sevinç Ercan
Genome Res. May 2025 35: 1108-1123; Published in Advance April 10, 2025, doi:10.1101/gr.279365.124
...the frequency of cohesin-mediated loops, thus providing another layer of 3D folding with the potential to regulate contacts between cis-regulatory elements. Such a mechanism of folding could have strong regulatory implications for species that contain tissue-specific enhancers but lack CTCF...
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Method: Statistically rigorous and computationally efficient chromatin stripe detection with Quagga
- Fan Feng,
- Sean Moran,
- Anders S. Hansen,
- Xiaotian Zhang,
- and Jie Liu
Genome Res. January 2026 36: 159-168; Published in Advance November 12, 2025, doi:10.1101/gr.280132.124
...is reasonable, we consider that the median size for chromatin looping is 300 kb and that going beyond the median TAD boundary span of 500 kb would suggest a false positive (Hsieh et al. 2022). Quagga and Zebra's distributions of CTCF-occupied stripes align strongly with the expected spans, whereas Stripenn...
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Method: Early feature extraction drives model performance in high-resolution chromatin accessibility prediction
- Aayush Grover,
- Till Muser,
- Liine Kasak,
- Lin Zhang,
- Ekaterina Krymova,
- and Valentina Boeva
Genome Res. March 2026 36: 619-629; Published in Advance January 12, 2026, doi:10.1101/gr.281042.125
...of transcription factors such as SP1 and CTCF emerged prominently. The majorly identified transcription factors for each cell type were consistent with the findings of ChromBPNet (Pampari et al. 2024) (Supplemental Fig. S5). These findings indicate that the ConvNeXt V2 block effectively captures cell type...
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Research: MYC overexpression leads to increased chromatin interactions at super-enhancers and MYC binding sites
- Yi Xiang See,
- Kaijing Chen,
- and Melissa J. Fullwood
Genome Res. April 2022 32: 629-642; Published in Advance February 3, 2022, doi:10.1101/gr.276313.121
....1% (5624/11,929) of chromatin loops were lost (Supplemental Fig. S7C). TAD boundaries lost after CTCF siRNA knockdown showed a decrease in insulation, but insulation at the common and gained TAD boundaries remained mostly unchanged (Supplemental Fig. S7D). These results are similar to previous reports...
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Mini-Review: The chromatin tapestry as a framework for neurodevelopment
- Ben Nolan,
- Timothy E. Reznicek,
- Christopher T. Cummings,
- and M. Jordan Rowley
Genome Res. October 2024 34: 1477-1486; doi:10.1101/gr.278408.123
...chromatin interaction is also associated with a change in the local CTCF and H3K27ac landscape, indicative of coordinated changes to enhancer activity, CTCF looping, and E–P contacts (Fig. 2—NPC; Bonev et al. 2017; Chakraborty et al. 2023). As another example, while few, some CTCF-occupied sites do get...
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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
...CTCF sites can act as bifurcation points defining the differential methylation landscape. CTCF loss from such sites, for example, at promoters, boundaries of chromatin loops, and topologically associated domains (TADs), was correlated with DNA methylation/demethylation spreading and can be linked...
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Research: Estrogen-induced chromatin looping changes identify a subset of functional regulatory elements
- Hosiana Abewe,
- Alexandra Richey,
- Jeffery M. Vahrenkamp,
- Matthew Ginley-Hidinger,
- Craig M. Rush,
- Noel Kitchen,
- Xiaoyang Zhang,
- and Jason Gertz
Genome Res. March 2025 35: 393-403; Published in Advance March 3, 2025, doi:10.1101/gr.279699.124
...et al. 2015; Franke et al. 2016; Pinoli et al. 2020; Smits et al. 2023; Kim et al. 2024). In contrast, other studies have demonstrated that broad rewiring of 3D interactions, owing to acute depletion of topologically associating domain (TAD) boundaries or TAD architectural proteins (e.g., CTCF...

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