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Research: Dynamic barriers modulate cohesin positioning and genome folding at fixed occupancy
- Hadi Rahmaninejad,
- Yao Xiao,
- Maxime M.C. Tortora,
- and Geoffrey Fudenberg
Genome Res. August 2025 35: 1745-1757; Published in Advance July 8, 2025, doi:10.1101/gr.280108.124
...chromatin loops between convergent CTCF sites (van Ruiten and Rowland 2021). The genomic positions of boundaries and dots anchor all display enrichment for cohesin by ChIP-seq. Acute depletion of CTCF leads to -wide loss of TADs and dots in Hi-C contact maps as well as a loss of cohesin ChIP-seq enrichment...
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Method: Size-based expectation maximization for characterizing nucleosome positions and subtypes
- Jianyu Yang,
- Kuangyu Yen,
- and Shaun Mahony
Genome Res. September 2024 34: 1334-1343; Published in Advance June 17, 2024, doi:10.1101/gr.279138.124
...separates nucleosomes belonging to each subtype at TSSs and CTCF sites (Fig. 3E; Supplemental Fig. S1B). Specifically, short-fragment nucleosomes are enriched at the centers of TSSs and CTCF sites, whereas canonical nucleosomes are well positioned in the flanking regions (Fig. 3E; Supplemental Fig. S1B...
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Research: Nucleosome repositioning in chronic lymphocytic leukemia
- Kristan V. Piroeva,
- Charlotte McDonald,
- Charalampos Xanthopoulos,
- Chelsea Fox,
- Christopher T. Clarkson,
- Jan-Philipp Mallm,
- Yevhen Vainshtein,
- Luminita Ruje,
- Lara C. Klett,
- Stephan Stilgenbauer,
- Daniel Mertens,
- Efterpi Kostareli,
- Karsten Rippe,
- and Vladimir B. Teif
Genome Res. October 2023 33: 1649-1661; Published in Advance September 12, 2023, doi:10.1101/gr.277298.122
...). The profiles are averaged over all NBCs (black), M-CLL (red), and U-CLL (blue) samples. The number of regions (N) is indicated on the graphs. (F) Same as panel E but for the transcriptionally inactive B compartment.CLL-specific changes in nucleosome positioning, CTCF binding, and histone modifications...
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Research: Cohesin and CTCF do not assemble TADs in Xenopus sperm and male pronuclei
- Gregor Jessberger,
- Csilla Várnai,
- Roman R. Stocsits,
- Wen Tang,
- Georg Stary,
- and Jan-Michael Peters
Genome Res. December 2023 33: 2094-2107; Published in Advance December 21, 2023, doi:10.1101/gr.277865.123
...the position of cohesin on chromatin and not its levels, as is the case in mammalian cells (Busslinger et al. 2017). These results indicate that in Xenopus pronuclei, cohesin does normally not accumulate at CTCF sites because most of these are not bound by CTCF unless CTCF is exogenously added.In Xenopus...
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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
.... 2013) and lead to functionally important variations in the chromatin states (Kasowski et al. 2013). However, it remains unclear what drives the selection of sites within the many weak CTCF motifs throughout the . Here, we set out to dissect how nucleosome positioning, DNA (de)methylation and cell type...
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Research: Transcription factor activity and nucleosome organization in mitosis
- Nicola Festuccia,
- Nick Owens,
- Thaleia Papadopoulou,
- Inma Gonzalez,
- Alexandra Tachtsidi,
- Sandrine Vandoermel-Pournin,
- Elena Gallego,
- Nancy Gutierrez,
- Agnès Dubois,
- Michel Cohen-Tannoudji,
- and Pablo Navarro
Genome Res. February 2019 29: 250-260; Published in Advance January 17, 2019, doi:10.1101/gr.243048.118
...300, at regions losing ESRRB and/or POU5F1/SOX2 binding, as well as at CTCF binding sites (Oomen et al. 2019). At regions losing ESRRB in mitosis, a clear nucleosomal organization is only appreciated when regions are aligned relative to the ESRRB peak summit or the binding motifs for POU5F1/SOX2...
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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
...)methylation, nucleosome positioning, and chromatin binding of the architectural protein CTCF play an important role for establishing cell-type–specific chromatin states during differentiation. To elucidate molecular mechanisms that link these processes, we studied the perturbed DNA modification landscape in mouse...
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Method: Mapping nucleosome positions using DNase-seq
- Jianling Zhong,
- Kaixuan Luo,
- Peter S. Winter,
- Gregory E. Crawford,
- Edwin S. Iversen,
- and Alexander J. Hartemink
Genome Res. March 2016 26: 351-364; Published in Advance January 15, 2016, doi:10.1101/gr.195602.115
...significantly higher amplitude than random oscillations (Fig. 6 shows four examples: Abf1 and Reb1 in yeast, and CTCF and GABPA in human). This indicates that TF motif matches seem to locate preferentially with respect to the rotational phasing of the DNA along the nucleosome. We then placed these 26 TF motifs...
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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
...plots indicate that constitutive CTCF binding sites display markedly higher occupancy signal than sites that are dynamically altered upon changes in cellular state. These results confirm and extend recent reports suggesting that there is a larger class of dynamically occupied CTCF sites than previously...
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Method: Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules
- Theresa K. Kelly,
- Yaping Liu,
- Fides D. Lay,
- Gangning Liang,
- Benjamin P. Berman,
- and Peter A. Jones
Genome Res. December 2012 22: 2497-2506; Published in Advance September 7, 2012, doi:10.1101/gr.143008.112
...; Thorvaldsdottir et al. 2012). We compared the ability of NOMe-seq to accurately map the well-positioned nucleosomes flanking CTCF binding sites. We aligned reads to conserved CTCF binding motifs (Xie et al. 2007) located more than 2 kb away from TSSs that have been experimentally validated as bound in vivo...

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