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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
...consequential sites for LAD regulation (Briand and Collas 2020; Alagna et al. 2023). Besides the well-characterized enrichment of H3K27me3, previous studies have identified enrichment of factors such as CTCF, macro-H2A, and gene promoters in the vicinity of LAD borders (Guelen et al. 2008; Fu et al. 2015; Harr...
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Research: Genome-wide analysis of local chromatin packing in Arabidopsis thaliana
- Congmao Wang,
- Chang Liu,
- Damian Roqueiro,
- Dominik Grimm,
- Rebecca Schwab,
- Claude Becker,
- Christa Lanz,
- and Detlef Weigel
Genome Res. February 2015 25: 246-256; Published in Advance November 3, 2014, doi:10.1101/gr.170332.113
...is highly conserved between different cell types and across species (Dixon et al. 2012). Similar to the situation in Drosophila, sequence features such as insulator CTCF binding sites, housekeeping genes, tRNA genes, and SINE retrotransposons have been suggested to play roles in establishing mammalian...
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Research: Modest increase in the de novo single-nucleotide mutation rate in house mice born by assisted reproduction
- Laura Blanco-Berdugo,
- Alexis Garretson,
- and Beth L. Dumont
Genome Res. January 2026 36: 50-60; Published in Advance November 13, 2025, doi:10.1101/gr.281180.125
...G island” track from the UCSC Genome Browser. To compare GC content between cohorts, we calculated GC content within a 201 bp window centered on each dnSNV and contrasted the resulting cohort-specific distributions.BEDTools was used to intersect dnSNVs with CTCF binding sites and various histone...
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LETTER: Comparative analysis of human chromosome 7q21 and mouse proximal chromosome 6 reveals a placental-specific imprinted gene, TFPI2/Tfpi2, which requires EHMT2 and EED for allelic-silencing
- David Monk,
- Alexandre Wagschal,
- Philippe Arnaud,
- Pari-Sima Müller,
- Layla Parker-Katiraee,
- Déborah Bourc’his,
- Stephen W. Scherer,
- Robert Feil,
- Philip Stanier,
- and Gudrun E. Moore
Genome Res. August 2008 18: 1270-1281; Published in Advance May 14, 2008, doi:10.1101/gr.077115.108
...CTCF to form an insulator on the unmethylated allele. Here, downstream promoters are unable to interact with upstream enhancers through the formation of higher order chromatin structures, such as loops. This mechanism is known to control the expression of the reciprocally imprinted Igf2 and H19 genes...
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Research: Coassembly of REST and its cofactors at sites of gene repression in embryonic stem cells
- Hong-Bing Yu,
- Rory Johnson,
- Galih Kunarso,
- and Lawrence W. Stanton
Genome Res. August 2011 21: 1284-1293; Published in Advance June 1, 2011, doi:10.1101/gr.114488.110
..., subpopulations of SIN3A and SIN3B sites are recruited to the MYC cluster MTL—9.8% of MYC MTLs show evidence for binding of either SIN3A or SIN3B. In addition, 21% and 20% of RCOR2 and RCOR3, respectively, colocalize with CTCF, suggesting that these factors may play a role in boundary element specification...
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LETTER: A novel mode of enhancer evolution: The Tal1 stem cell enhancer recruited a MIR element to specifically boost its activity
- Aileen M. Smith,
- Maria-Jose Sanchez,
- George A. Follows,
- Sarah Kinston,
- Ian J. Donaldson,
- Anthony R. Green,
- and Berthold Göttgens
Genome Res. September 2008 18: 1422-1432; Published in Advance August 7, 2008, doi:10.1101/gr.077008.108
...by the presence of ubiquitous DNase I-hypersensitive sites and binding by the multi-zinc finger protein CTCF ( Xi et al. 2007 ). In contrast, the Tal1 +18 region is characterized by a tissue-specific hypersensitive site and not bound by CTCF (see Supplemental Fig. 5). Moreover, within our single-copy Hprt...
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