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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
...cis-regulatory elements. Here, CTCF binds in tandem with beta-catenin and TCF/LEF to increase cohesin stalling and induce the formation of chromatin loops that contribute to the upregulation of a subset of Wnt target genes (Fig. 7). This, to our knowledge, represents a previously unknown mechanism...
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Method: A universal framework for detecting cis-regulatory diversity in DNA regions
- Anushua Biswas and
- Leelavati Narlikar
Genome Res. September 2021 31: 1646-1662; Published in Advance July 19, 2021, doi:10.1101/gr.274563.120
...DIVERSITY does not take into account the spatial distribution of the motifs in its model. However, in over two-thirds of the sequences, the distance between the two copies is <50 bp, suggesting cooperative binding.Unlike vertebrates, there is no evidence to support cohesin-CTCF-mediated chromatin loop formations...
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Research: Genome-wide and parental allele-specific analysis of CTCF and cohesin DNA binding in mouse brain reveals a tissue-specific binding pattern and an association with imprinted differentially methylated regions
- Adam R. Prickett,
- Nikolaos Barkas,
- Ruth B. McCole,
- Siobhan Hughes,
- Samuele M. Amante,
- Reiner Schulz,
- and Rebecca J. Oakey
Genome Res. October 2013 23: 1624-1635; Published in Advance June 26, 2013, doi:10.1101/gr.150136.112
...occupied than liver and brain, consistent with a ground-state pattern of CTCF binding that is elaborated during differentiation. CTCF binding sites without the canonical consensus motif were highly tissue specific. In brain, a third of CTCF and cohesin binding sites coincide, consistent with the potential...
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Research: Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin
- Elizabeth Ing-Simmons,
- Vlad C. Seitan,
- Andre J. Faure,
- Paul Flicek,
- Thomas Carroll,
- Job Dekker,
- Amanda G. Fisher,
- Boris Lenhard,
- and Matthias Merkenschlager
Genome Res. April 2015 25: 504-513; Published in Advance February 12, 2015, doi:10.1101/gr.184986.114
..., Schuijers J, Lee TI, Zhao K, et al. 2014. Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes. Cell 159: 374–387. Faure AJ, Schmidt D, Watt S, Schwalie PC, Wilson MD, Xu H, Ramsay RG, Odom DT, Flicek P. 2012. Cohesin regulates tissue-specific expression by stabilizing...
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Research: The genomic landscape of cohesin-associated chromatin interactions
- Laura E. DeMare,
- Jing Leng,
- Justin Cotney,
- Steven K. Reilly,
- Jun Yin,
- Richard Sarro,
- and James P. Noonan
Genome Res. August 2013 23: 1224-1234; Published in Advance May 23, 2013, doi:10.1101/gr.156570.113
...characterized on a -wide scale. Here we performed chromatin interaction analysis with paired-end tag sequencing (ChIA-PET) of the cohesin subunit SMC1A in developing mouse limb. We identified 2264 SMC1A interactions, of which 1491 (65%) involved sites co-occupied by CTCF. SMC1A participates in tissue-specific...
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Research: Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments
- Vlad C. Seitan,
- Andre J. Faure,
- Ye Zhan,
- Rachel Patton McCord,
- Bryan R. Lajoie,
- Elizabeth Ing-Simmons,
- Boris Lenhard,
- Luca Giorgetti,
- Edith Heard,
- Amanda G. Fisher,
- Paul Flicek,
- Job Dekker,
- and Matthias Merkenschlager
Genome Res. December 2013 23: 2066-2077; Published in Advance September 3, 2013, doi:10.1101/gr.161620.113
...Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments Vlad C. Seitan 1 , 7 , Andre J. Faure 2 , 7 , Ye Zhan 3 , Rachel Patton McCord 3 , Bryan R. Lajoie 3 , Elizabeth Ing...
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Resource: Allele-specific transcription factor binding across human brain regions offers mechanistic insight into eQTLs
- Ashlyn G. Anderson,
- Belle A. Moyers,
- Jacob M. Loupe,
- Ivan Rodriguez-Nunez,
- Stephanie A. Felker,
- James M.J. Lawlor,
- William E. Bunney,
- Blynn G. Bunney,
- Preston M. Cartagena,
- Adolfo Sequeira,
- Stanley J. Watson,
- Huda Akil,
- Eric M. Mendenhall,
- Gregory M. Cooper,
- and Richard M. Myers
Genome Res. August 2024 34: 1224-1234; Published in Advance August 16, 2024, doi:10.1101/gr.278601.123
...that predominantly bind at highly occupied “HOT” sites (Fig. 2B). ASB variants affecting cohesin complex members also had a higher degree of overlap with eQTLs (Fig. 4B) and were significantly enriched for mammalian sequence conservation (Fig. 3E). This suggests that genetic variants that alter three...
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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: Polycomb-dependent differential chromatin compartmentalization determines gene coregulation in Arabidopsis
- Ying Huang,
- Sanchari Sicar,
- Juan S. Ramirez-Prado,
- Deborah Manza-Mianza,
- Javier Antunez-Sanchez,
- Rim Brik-Chaouche,
- Natalia Y. Rodriguez-Granados,
- Jing An,
- Catherine Bergounioux,
- Magdy M. Mahfouz,
- Heribert Hirt,
- Martin Crespi,
- Lorenzo Concia,
- Fredy Barneche,
- Simon Amiard,
- Aline V. Probst,
- Jose Gutierrez-Marcos,
- Federico Ariel,
- Cécile Raynaud,
- David Latrasse,
- and Moussa Benhamed
Genome Res. July 2021 31: 1230-1244; Published in Advance June 3, 2021, doi:10.1101/gr.273771.120
...acts directly or indirectly to regulate chromatin interactions, although how this histone modification modulates 3D chromatin architecture remains elusive. To decipher the impact of the dynamic deposition of H3K27me3 on the Arabidopsis thaliana nuclear interactome, we combined genetics, transcriptomics...
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Research: Pou5f3, SoxB1, and Nanog remodel chromatin on high nucleosome affinity regions at zygotic genome activation
- Marina Veil,
- Lev Y. Yampolsky,
- Björn Grüning,
- and Daria Onichtchouk
Genome Res. March 2019 29: 383-395; Published in Advance January 23, 2019, doi:10.1101/gr.240572.118
...of HNARs, acting synergistically. Nanog binds to the HNAR center, whereas the Pou5f3 stabilizes the flanks. The HNAR model will provide a useful tool for regulatory studies in a variety of biological systems.The development of multicellular organisms is first driven by maternal products and occurs...

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