Searching journal content for articles similar to Jessberger et al. 33 (12): 2094.

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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
...to the formation and maintenance of TADs (Guo et al. 2015). Given that our CUT&RUN data revealed distinct losses and gains of CTCF and cohesin binding following Wnt activation, we wondered whether Wnt perturbation could induce 3D architectural alterations in the . Hence, we conducted HiChIP against CTCF for Wnt...
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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
...al. (2021) showed the collaborative role of MAZ and CTCF in controlling cohesin positioning and organization, and Clouaire et al. (2005) suggested that cellular THAP proteins may serve as zinc-dependent sequence-specific DNA-binding factors, playing crucial roles in chromosome segregation, chromatin...
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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: Revisiting chromatin packaging in mouse sperm
- Qiangzong Yin,
- Chih-Hsiang Yang,
- Olga S. Strelkova,
- Jingyi Wu,
- Yu Sun,
- Sneha Gopalan,
- Liyan Yang,
- Job Dekker,
- Thomas G. Fazzio,
- Xin Zhiguo Li,
- Johan Gibcus,
- and Oliver J. Rando
Genome Res. December 2023 33: 2079-2093; Published in Advance December 21, 2023, doi:10.1101/gr.277845.123
...IP-seq (Johnson et al. 2007) on formaldehyde-fixed sperm chromatin sheared via sonication (Methods) (Fig. 5; Supplemental Fig. S6). We focused on a sequence-specific DNA-binding protein, CTCF, and the histone modifications H3K4me3 and H3K27me3 (K4/27), as these epitopes were expected to show distinctive...
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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
...Jun Kim, Haoyu Wang and Sevinç Ercan Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York 10003, USA Corresponding author: sevinc@nyu.eduAbstractIn mammals, cohesin and CTCF organize the 3D into topologically associating domains (TADs) to regulate...
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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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Research: CTCF looping is established during gastrulation in medaka embryos
- Ryohei Nakamura,
- Yuichi Motai,
- Masahiko Kumagai,
- Candice L. Wike,
- Haruyo Nishiyama,
- Yoichiro Nakatani,
- Neva C. Durand,
- Kaori Kondo,
- Takashi Kondo,
- Tatsuya Tsukahara,
- Atsuko Shimada,
- Bradley R. Cairns,
- Erez Lieberman Aiden,
- Shinichi Morishita,
- and Hiroyuki Takeda
Genome Res. June 2021 31: 968-980; Published in Advance May 18, 2021, doi:10.1101/gr.269951.120
...enhanced contact frequency within themselves (Dixon et al. 2012; Nora et al. 2012; Rao et al. 2014). Loops often demarcate contact domains by physical tethering of a pair of loci, which are mediated by the insulator protein CTCF and the ring-shaped cohesin complex (Nora et al. 2017; Rao et al. 2017...
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Research: Active enhancers strengthen insulation by RNA-mediated CTCF binding at chromatin domain boundaries
- Zubairul Islam,
- Bharath Saravanan,
- Kaivalya Walavalkar,
- Umer Farooq,
- Anurag Kumar Singh,
- Sabarinathan Radhakrishnan,
- Jitendra Thakur,
- Awadhesh Pandit,
- Steven Henikoff,
- and Dimple Notani
Genome Res. January 2023 33: 1-17; Published in Advance January 17, 2023, doi:10.1101/gr.276643.122
...identifies both contact and loop domain TADs based on intra-domain interaction frequency. Both TADs and loops are thought to be formed by loop extrusion and to be dependent on CTCF and cohesin (Nora et al. 2017; Rao et al. 2017; Schwarzer et al. 2017; Wutz et al. 2017). HOMER identified 15,397 TAD boundaries...
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Research: Chromatin architecture transitions from zebrafish sperm through early embryogenesis
- Candice L. Wike,
- Yixuan Guo,
- Mengyao Tan,
- Ryohei Nakamura,
- Dana Klatt Shaw,
- Noelia Díaz,
- Aneasha F. Whittaker-Tademy,
- Neva C. Durand,
- Erez Lieberman Aiden,
- Juan M. Vaquerizas,
- David Grunwald,
- Hiroyuki Takeda,
- and Bradley R. Cairns
Genome Res. June 2021 31: 981-994; Published in Advance May 18, 2021, doi:10.1101/gr.269860.120
...their associations, which may involve both inter- and intra-enhancer interactions (Rao et al. 2017; Rosencrance et al. 2020). However, in normal cycling cells, these sub-TAD size interactions have been shown to have Med12/cohesin (lacking CTCF) (Phillips-Cremins et al. 2013). These observations in cultured mammalian...
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Research: Identification and characterization of centromeric sequences in Xenopus laevis
- Owen K. Smith,
- Charles Limouse,
- Kelsey A. Fryer,
- Nicole A. Teran,
- Kousik Sundararajan,
- Rebecca Heald,
- and Aaron F. Straight
Genome Res. June 2021 31: 958-967; Published in Advance April 19, 2021, doi:10.1101/gr.267781.120
.... Xenopus laevis egg extracts assemble centromeres in vitro, providing a system for studying centromeric DNA functions. However, centromeric sequences in Xenopus laevis have not been extensively characterized. In this study, we combine Cenpa ChIP-seq with a k-mer based analysis approach to identify...

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