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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
...that the different patterns of PTM enrichment between the three LAD clusters could affect their three-dimensional organization within the nucleus. We performed 3D DNA FISH to test whether the association with the nuclear lamina varies between clusters, using Lamin A/C staining to visualize the nuclear periphery (Fig...
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Research: The dynamics of DNA methylation fidelity during mouse embryonic stem cell self-renewal and differentiation
- Lei Zhao,
- Ming-an Sun,
- Zejuan Li,
- Xue Bai,
- Miao Yu,
- Min Wang,
- Liji Liang,
- Xiaojian Shao,
- Stephen Arnovitz,
- Qianfei Wang,
- Chuan He,
- Xuemei Lu,
- Jianjun Chen,
- and Hehuang Xie
Genome Res. August 2014 24: 1296-1307; Published in Advance May 16, 2014, doi:10.1101/gr.163147.113
...V, et al. 2012. In vivo control of CpG and non-CpG DNA methylation by DNA methyltransferases. PLoS Genet 8: e1002750. Bell AC, Felsenfeld G. 2000. Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene. Nature 405: 482–485. Bird A. 2002. DNAmethylation patterns...
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Method: Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk
- Arie B. Brinkman,
- Hongcang Gu,
- Stefanie J.J. Bartels,
- Yingying Zhang,
- Filomena Matarese,
- Femke Simmer,
- Hendrik Marks,
- Christoph Bock,
- Andreas Gnirke,
- Alexander Meissner,
- and Hendrik G. Stunnenberg
Genome Res. June 2012 22: 1128-1138; Published in Advance March 30, 2012, doi:10.1101/gr.133728.111
...-interacting proteins regulated by DNA and histone methylation. Cell 143: 470–484. Bell AC, Felsenfeld G. 2000. Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene.Nature 405: 482–485. Bock C...
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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
.... 2000. Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene. Nature 405: 482–485. Butcher DT, Mancini-DiNardo DN, Archer TK, Rodenhiser DI. 2004. DNA binding sites for putative methylation boundaries in the unmethylated region of the BRCA1 promoter. Int J Cancer 111...
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Letter: Lineage-specific DNA methylation in T cells correlates with histone methylation and enhancer activity
- Christian Schmidl,
- Maja Klug,
- Tina J. Boeld,
- Reinhard Andreesen,
- Petra Hoffmann,
- Matthias Edinger,
- and Michael Rehli
Genome Res. July 2009 19: 1165-1174; Published in Advance June 3, 2009, doi:10.1101/gr.091470.109
...of CD40LG (Supplemental Fig. S4), and the downstream DMR of LRRC32 (Supplemental Fig. S6). Correlation between DNA methylation, chromatin boundaries, and histone methylation Themajority of the detected DMRs were located at promoter-distal sites. To characterize the potential functions of these regions...
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Next-Generation DNA Sequencing/Review: Finding the fifth base: Genome-wide sequencing of cytosine methylation
- Ryan Lister and
- Joseph R. Ecker
Genome Res. June 2009 19: 959-966; Published in Advance March 9, 2009, doi:10.1101/gr.083451.108
..., S. , Rakyan, V. ( 2008 ) The methylome: Approaches for global DNA methylation profiling . Trends Genet. 24 : 231 – 237 . ↵ Bell, A.C. , Felsenfeld, G. ( 2000 ) Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene . Nature 405 : 482 – 485 . ↵ Bernstein, B...
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Review: The superpowers of imprinting control regions
- Bertille Montibus,
- Franck Court,
- and Philippe Arnaud
Genome Res. January 2026 36: 1-19; Published in Advance December 10, 2025, doi:10.1101/gr.281215.125
....ICR: a multifaceted cis-regulatory regionAllelic DNA methylation at ICRs, although constitutive, orchestrates the complex spatiotemporal expression patterns of imprinted genes by modulating a combination of regulatory mechanisms. In embryonic stem (ES) cells, allelic expression is initially confined to genes in close...
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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
...binding to DNA in mouse brain, wide and in an allele-specific manner with high read-depth ChIP-seq. By comparing our results with existing data for mouse liver and embryonic stem (ES) cells, we investigated the tissue specificity of CTCF binding sites. ES cells have fewer unique CTCF binding sites...
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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
...of local changes of nucleosome occupancy showed that DNA methylation correlated with more stably bound nucleosomes, whereas nucleosomes that shifted their position in CLL were at less methylated sites (Fig. 2A,B). This relation was also observed in our previous studies in mouse embryonic stem cells (Teif...
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Research: The aberrant epigenome of DNMT3B-mutated ICF1 patient iPSCs is amenable to correction, with the exception of a subset of regions with H3K4me3- and/or CTCF-based epigenetic memory
- Varsha Poondi Krishnan,
- Barbara Morone,
- Shir Toubiana,
- Monika Krzak,
- Salvatore Fioriniello,
- Floriana Della Ragione,
- Maria Strazzullo,
- Claudia Angelini,
- Sara Selig,
- and Maria R. Matarazzo
Genome Res. February 2023 33: 169-183; Published in Advance February 24, 2023, doi:10.1101/gr.276986.122
...perturbations of the epigenetic landscape induced by the primary DNA methylation changes.ICF1 patient-derived induced pluripotent stem cells (ICF1 iPSCs) provide a powerful model for studying the earliest pathogenic events in ICF1 syndrome and for identifying the genomic regions prone to DNA methylation...

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