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Method: Statistically rigorous and computationally efficient chromatin stripe detection with Quagga
- Fan Feng,
- Sean Moran,
- Anders S. Hansen,
- Xiaotian Zhang,
- and Jie Liu
Genome Res. January 2026 36: 159-168; Published in Advance November 12, 2025, doi:10.1101/gr.280132.124
...of chromatin looping (Davidson et al. 2019; Gabriele et al. 2022). An integrated analysis of stripes with genomic and epigenomic features at a -wide scale also shows vast potential in understanding the cooperation between regulatory elements in 3D space (Barrington et al. 2019; Kraft et al. 2019; Zhang et al...
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Mini-Review: The chromatin tapestry as a framework for neurodevelopment
- Ben Nolan,
- Timothy E. Reznicek,
- Christopher T. Cummings,
- and M. Jordan Rowley
Genome Res. October 2024 34: 1477-1486; doi:10.1101/gr.278408.123
...contribution to neurodevelopment. We begin by defining several features of chromatin architecture, including the interplay between histone modifications, DNA methylation, and 3D organization. In the context of neurodevelopment, the dramatic alterations throughout normal neurodevelopment highlight...
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Research: Most chromatin interactions are not in linkage disequilibrium
- Sean Whalen and
- Katherine S. Pollard
Genome Res. March 2019 29: 334-343; Published in Advance January 7, 2019, doi:10.1101/gr.238022.118
...Francisco, San Francisco, California 94158, USA; 3Chan-Zuckerberg Biohub, San Francisco, California 94158, USA Corresponding author: kpollard@gladstone.ucsf.eduAbstractChromatin interactions and linkage disequilibrium (LD) are both pairwise measurements between genomic loci that show block patterns along...
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Method: The epigenetic landscape of Alu repeats delineates the structural and functional genomic architecture of colon cancer cells
- Mireia Jordà,
- Anna Díez-Villanueva,
- Izaskun Mallona,
- Berta Martín,
- Sergi Lois,
- Víctor Barrera,
- Manel Esteller,
- Tanya Vavouri,
- and Miguel A. Peinado
Genome Res. January 2017 27: 118-132; Published in Advance December 20, 2016, doi:10.1101/gr.207522.116
...-throughput genomic technologies to study DNA methylation profiles in cancer cells has demonstrated that DNA hypomethylation preferentially affects large chromatin blocks exhibiting gene expression variability and definite chromatin features ( Hansen et al. 2011 ; Berman et al. 2012 ; Hon et al. 2012 ; Timp et al...
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Resource: High-resolution mapping of open chromatin in the rice genome
- Wenli Zhang,
- Yufeng Wu,
- James C. Schnable,
- Zixian Zeng,
- Michael Freeling,
- Gregory E. Crawford,
- and Jiming Jiang
Genome Res. January 2012 22: 151-162; Published in Advance November 22, 2011, doi:10.1101/gr.131342.111
...associated with seedling tissue. (B) Seedling-specific and callus-specific DH sites within promoters showed higher levels of methylation than the average of all seedling DH sites within promoters. Randomly selected 3061 DH sites within promoters were used as a control. Open chromatin maps of rice Genome...
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Research: A heterozygous IDH1^R132H/WT mutation induces genome-wide alterations in DNA methylation
- Christopher G. Duncan,
- Benjamin G. Barwick,
- Genglin Jin,
- Carlo Rago,
- Priya Kapoor-Vazirani,
- Doris R. Powell,
- Jen-Tsan Chi,
- Darell D. Bigner,
- Paula M. Vertino,
- and Hai Yan
Genome Res. December 2012 22: 2339-2355; Published in Advance August 16, 2012, doi:10.1101/gr.132738.111
...more broadly distributed, with most occurring within CpG islands or CpG island ‘‘shores,’’ but many without (Supplemental Fig. 6), consistent with these loci having significant average preexisting methylation. Analysis of chromatin immunoprecipitation and massively parallel sequencing (ChIP-seq) data...
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Research: Late-replicating heterochromatin is characterized by decreased cytosine methylation in the human genome
- Masako Suzuki,
- Mayumi Oda,
- María-Paz Ramos,
- Marién Pascual,
- Kevin Lau,
- Edyta Stasiek,
- Frederick Agyiri,
- Reid F. Thompson,
- Jacob L. Glass,
- Qiang Jing,
- Richard Sandstrom,
- Melissa J. Fazzari,
- R. Scott Hansen,
- John A. Stamatoyannopoulos,
- Andrew S. McLellan,
- and John M. Greally
Genome Res. November 2011 21: 1833-1840; Published in Advance September 28, 2011, doi:10.1101/gr.116509.110
...chromatin organization and methylation, such relationships can be explored systematically. As well-defined surrogates for heterochromatin, we tested the relationship between DNA replication timing and DNase hypersensitivity with cytosine methylation in two human cell types, unexpectedly finding the later...
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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
...gene across multiple TADs (Schertzer et al. 2019). However, this deposition is not uniform along the domain, suggesting that genomic features contribute to the mechanism by which these lncRNAs silence their target genes. The observation that Airn expression is accompanied by changes in 3D chromatin...
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Research: Locus- and domain-dependent control of DNA methylation at mouse B1 retrotransposons during male germ cell development
- Kenji Ichiyanagi,
- Yungfeng Li,
- Toshiaki Watanabe,
- Tomoko Ichiyanagi,
- Kei Fukuda,
- Junko Kitayama,
- Yasuhiro Yamamoto,
- Satomi Kuramochi-Miyagawa,
- Toru Nakano,
- Yukihiro Yabuta,
- Yoshiyuki Seki,
- Mitinori Saitou,
- and Hiroyuki Sasaki
Genome Res. December 2011 21: 2058-2066; Published in Advance October 31, 2011, doi:10.1101/gr.123679.111
..., Fu Y, Su T, Hibshoosh H, et al. 2010. Chromatin and sequence features that define the fine and gross structure of genomic methylation patterns. Genome Res 20: 972–980. Elsik CG, Tellam RL, Worley KC, Gibbs RA, Muzny DM, Weinstock GM, Adelson DL, Eichler EE, Elnitski L, Guigo R, et al. 2009...
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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
...barriers across the . However, recent in vivo measurements present a puzzle: reported CTCF residence times on chromatin are in the range of a few minutes, whereas cohesin lifetimes are much longer. Can the observed features of folding result from relatively transient barriers? To address this question, we...
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