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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
...development. Despite much work, LAD structure and regulation are not fully understood, and a mounting number of studies have identified numerous genetic and epigenetic differences within LADs, demonstrating they are not a uniform group. Here, we profile lamin B1, CBX1 (also known as HP1B), H3K9me3, H3K9me2, H...
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Research: Comprehensive functional annotation of ESR1-driven enhancers in breast cancer reveals hierarchical activity independent of genomic and epigenomic contexts
- Yanis Zekri,
- Sebastian Gregoricchio,
- Elif Yapıcı,
- Chia-Chi Flora Huang,
- Tunç Morova,
- Umut Berkay Altıntaş,
- Gozde Korkmaz,
- Nathan A. Lack,
- and Wilbert Zwart
Genome Res. July 2025 35: 1530-1543; Published in Advance June 10, 2025, doi:10.1101/gr.280320.124
...of a similar model for ESR1. Supporting this, we found that 30% of ESR1-linked genes were associated with multiple ERBS classes, suggesting that all three enhancer types may participate in gene regulation in a context-dependent manner.Beyond validating our ERBS annotation through orthogonal in vitro data sets...
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Research: Epigenomic translocation of H3K4me3 broad domains over oncogenes following hijacking of super-enhancers
- Aneta Mikulasova,
- Daniel Kent,
- Marco Trevisan-Herraz,
- Nefeli Karataraki,
- Kent T.M. Fung,
- Cody Ashby,
- Agata Cieslak,
- Shmuel Yaccoby,
- Frits van Rhee,
- Maurizio Zangari,
- Sharmilan Thanendrarajan,
- Carolina Schinke,
- Gareth J. Morgan,
- Vahid Asnafi,
- Salvatore Spicuglia,
- Chris A. Brackley,
- Anne E. Corcoran,
- Sophie Hambleton,
- Brian A. Walker,
- Daniel Rico,
- and Lisa J. Russell
Genome Res. July 2022 32: 1343-1354; Published in Advance December 21, 2021, doi:10.1101/gr.276042.121
...of activity is reduced (class-switched memory B cells and plasma cells) (Fig. 1). A similar area of reduced activity was also observed in malignant samples derived from cells after class-switch recombination, including diffuse large B cell lymphoma (DLBCL), Burkitt lymphoma (BL), and multiple myeloma (MM...
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Research: KDM1A maintains genome-wide homeostasis of transcriptional enhancers
- Saurabh Agarwal,
- Katherine M. Bonefas,
- Patricia M. Garay,
- Emily Brookes,
- Yumie Murata-Nakamura,
- Robert S. Porter,
- Todd S. Macfarlan,
- Bing Ren,
- and Shigeki Iwase
Genome Res. February 2021 31: 186-197; Published in Advance January 7, 2021, doi:10.1101/gr.234559.118
...Corresponding authors: saurabhagarwal23@gmail.com, biren@ucsd.edu, siwase@umich.eduAbstractTranscriptional enhancers enable exquisite spatiotemporal control of gene expression in metazoans. Enrichment of monomethylation of histone H3 lysine 4 (H3K4me1) is a major chromatin signature of transcriptional enhancers...
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Research: Incomplete erasure of histone marks during epigenetic reprogramming in medaka early development
- Hiroto S. Fukushima,
- Hiroyuki Takeda,
- and Ryohei Nakamura
Genome Res. April 2023 33: 572-586; Published in Advance April 28, 2023, doi:10.1101/gr.277577.122
...Hiroto S. Fukushima, Hiroyuki Takeda and Ryohei Nakamura Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan Corresponding authors: htakeda@bs.s.u-tokyo.ac.jp, rynakamura@bs.s.u-tokyo.ac.jpAbstractEpigenetic modifications undergo drastic...
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Resource: A chromosome-scale epigenetic map of the Hydra genome reveals conserved regulators of cell state
- Jack F. Cazet,
- Stefan Siebert,
- Hannah Morris Little,
- Philip Bertemes,
- Abby S. Primack,
- Peter Ladurner,
- Matthias Achrainer,
- Mark T. Fredriksen,
- R. Travis Moreland,
- Sumeeta Singh,
- Suiyuan Zhang,
- Tyra G. Wolfsberg,
- Christine E. Schnitzler,
- Andreas D. Baxevanis,
- Oleg Simakov,
- Bert Hobmayer,
- and Celina E. Juliano
Genome Res. February 2023 33: 283-298; Published in Advance January 13, 2023, doi:10.1101/gr.277040.122
...A chromosome-scale epigenetic map of the Hydra reveals conserved regulators of cell state Jack F. Cazet1, Stefan Siebert1,2, Hannah Morris Little1, Philip Bertemes3, Abby S. Primack1, Peter Ladurner3, Matthias Achrainer3, Mark T. Fredriksen4, R. Travis Moreland4, Sumeeta Singh4, Suiyuan Zhang4...
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Research: Two contrasting classes of nucleolus-associated domains in mouse fibroblast heterochromatin
- Anastassiia Vertii,
- Jianhong Ou,
- Jun Yu,
- Aimin Yan,
- Hervé Pagès,
- Haibo Liu,
- Lihua Julie Zhu,
- and Paul D. Kaufman
Genome Res. August 2019 29: 1235-1249; Published in Advance June 14, 2019, doi:10.1101/gr.247072.118
...critical feature of chromosome-level local baseline correction. We detected two distinct classes of NADs. Type I NADs associate frequently with both the nucleolar periphery and the nuclear lamina, and generally display characteristics of constitutive heterochromatin, including late DNA replication...
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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
...accessibility directly in complex systems composed of multiple cell types could allow for high-throughput discovery of regulatory regions whose activities are restricted to rare or undefined subpopulations of cells. This is particularly relevant for enhancers, which are thought to be highly cell...
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Research: Multiple Pristionchus pacificus genomes reveal distinct evolutionary dynamics between de novo candidates and duplicated genes
- Neel Prabh and
- Christian Rödelsperger
Genome Res. July 2022 32: 1315-1327; Published in Advance May 26, 2022, doi:10.1101/gr.276431.121
..., show less expression, and are overrepresented on the sex chromosome. Although the contribution of de novo candidates increases toward young age classes, multiple comparisons within the same age class showed significantly higher attrition in de novo candidates than in known genes. Similarly, young genes...
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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
..., these results indicate that the corrected DNMT3B can fully restore the normal methylation signature only at CGI sites that display milder hypomethylation in patient iPSCs.We additionally observed that the percentage of hypomethylated GH promoters and enhancers reacquired proper DNA methylation at similar levels...

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