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Research: Distinct classes of lamina-associated domains are defined by differential patterns of repressive histone methylation
- Caden J. Martin,
- Elizabeth A. Oser,
- Prabakaran Nagarajan,
- Liudmila V. Popova,
- Benjamin D. Sunkel,
- Benjamin Z. Stanton,
- and Mark R. Parthun
Genome Res. September 2025 35: 1959-1974; Published in Advance August 5, 2025, doi:10.1101/gr.280380.124
...a lack of uniformity across LADs in their MNase accessibility, linker histone enrichment, lamin B1 occupancy, CTCF dependency, primary lamin interactor (B or A/C), histone PTM enrichment, and more (Bian et al. 2013; Lund et al. 2015; Zheng et al. 2015; Vertii et al. 2019; Kaczmarczyk et al. 2022; Alagna...
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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
.... 2009. Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains. Genome Res 19: 24–32. doi:10.1101/gr.082800.108 ↵Dans PD, Walther J, Gómez H, Orozco M. 2016. Multiscale simulation of DNA. Curr Opin Struct Biol 37: 29–45. doi...
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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
...indicate that CTCF gene and protein expression levels decrease in the transition from pluripotency tomultipotent neural progenitor cells in parallel with a global decrease in the number of -wide CTCF binding sites. CTCF occupancy in NPCs is largely preestablished in the pluripotent state To better...
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Research: Drosophila CTCF tandemly aligns with other insulator proteins at the borders of H3K27me3 domains
- Kevin Van Bortle,
- Edward Ramos,
- Naomi Takenaka,
- Jingping Yang,
- Jessica E. Wahi,
- and Victor G. Corces
Genome Res. November 2012 22: 2176-2187; Published in Advance June 21, 2012, doi:10.1101/gr.136788.111
...Maggert 2011), V(D)J recombination (Guo et al. 2011), and global chromatin organization (Kim et al. 2007; Handoko et al. 2011). The combinatorial use of its 11 zinc fingers in binding to discrete DNA target sequences, as well as the diverse, context-dependent protein-interaction networks of CTCF, have been...
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Resource: Chromatin accessibility dynamics reveal novel functional enhancers in C. elegans
- Aaron C. Daugherty,
- Robin W. Yeo,
- Jason D. Buenrostro,
- William J. Greenleaf,
- Anshul Kundaje,
- and Anne Brunet
Genome Res. December 2017 27: 2096-2107; Published in Advance November 15, 2017, doi:10.1101/gr.226233.117
...(Ftz-F1), mouse (Nr5a1), and human (NR5A1) exhibit a consistent signature of three-dimensional chromatin architecture downstream from the 3′ UTR (insulator class I in flies and CTCF-binding sites in mice and humans [Sharov et al. 2006; Rosenbloom et al. 2013; Attrill et al. 2016]). While C. elegans...
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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
...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 1 , Nikolaos Barkas 1 , Ruth B. Mc...
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Research: Nature and function of insulator protein binding sites in the Drosophila genome
- Yuri B. Schwartz,
- Daniela Linder-Basso,
- Peter V. Kharchenko,
- Michael Y. Tolstorukov,
- Maria Kim,
- Hua-Bing Li,
- Andrey A. Gorchakov,
- Aki Minoda,
- Gregory Shanower,
- Artyom A. Alekseyenko,
- Nicole C. Riddle,
- Youngsook L. Jung,
- Tingting Gu,
- Annette Plachetka,
- Sarah C.R. Elgin,
- Mitzi I. Kuroda,
- Peter J. Park,
- Mikhail Savitsky,
- Gary H. Karpen,
- and Vincenzo Pirrotta
Genome Res. November 2012 22: 2188-2198; Published in Advance July 5, 2012, doi:10.1101/gr.138156.112
...multiple insulator elements. Subsequent work has shown that CP190 also shares some of its chromatin binding sites with BEAF-32 and CTCF and can interact directly with the latter (Gerasimova et al. 2007; Mohan et al. 2007; Bushey et al. 2009; Nègre et al. 2010). The mechanistic interdependencies between CP...
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Research: Widespread plasticity in CTCF occupancy linked to DNA methylation
- Hao Wang,
- Matthew T. Maurano,
- Hongzhu Qu,
- Katherine E. Varley,
- Jason Gertz,
- Florencia Pauli,
- Kristen Lee,
- Theresa Canfield,
- Molly Weaver,
- Richard Sandstrom,
- Robert E. Thurman,
- Rajinder Kaul,
- Richard M. Myers,
- and John A. Stamatoyannopoulos
Genome Res. September 2012 22: 1680-1688; doi:10.1101/gr.136101.111
..., Mukhopadhyay R, Docquier F, Farrar D, et al. 2007. CTCF interacts with and recruits the largest subunit of RNA polymerase II to CTCF target sites -wide. Mol Cell Biol 27: 1631–1648. Cuddapah S, Jothi R, Schones DE, Roh TY, Cui K, Zhao K. 2008. Global analysis of the insulator binding protein CTCF in chromatin...
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Research: The BEAF-32 insulator coordinates genome organization and function during the evolution of Drosophila species
- Jingping Yang,
- Edward Ramos,
- and Victor G. Corces
Genome Res. November 2012 22: 2199-2207; Published in Advance August 15, 2012, doi:10.1101/gr.142125.112
..., allometries and sexual dimorphism. Heredity 102: 246–256. Cuddapah S, Jothi R, Schones DE, Roh T-Y, Cui K, Zhao K. 2009. Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains. Genome Res 19: 24–32. Yang et al. 2206 Genome...
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Research: Genome-wide profiling reveals functional interplay of DNA sequence composition, transcriptional activity, and nucleosome positioning in driving DNA supercoiling and helix destabilization in C. elegans
- Kristina Krassovsky,
- Rajarshi P. Ghosh,
- and Barbara J. Meyer
Genome Res. July 2021 31: 1187-1202; Published in Advance June 24, 2021, doi:10.1101/gr.270082.120
...correlated with the level of transcription by dividing genes into deciles of expression based on their global run-on sequencing (GRO-seq) level (Fig. 1D) and then plotted total BP signal in 100-bp regions around the TSSs (Fig. 1E). BP signal increased incrementally up to the fifth decile, beyond which...

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