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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
...authors: Julie.zhu@umassmed.edu, paul.kaufman1@umassmed.eduAbstractIn interphase eukaryotic cells, almost all heterochromatin is located adjacent to the nucleolus or to the nuclear lamina, thus defining nucleolus-associated domains (NADs) and lamina-associated domains (LADs), respectively. Here, we...
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Research: The role of DNA methylation in directing the functional organization of the cancer epigenome
- Fides D. Lay,
- Yaping Liu,
- Theresa K. Kelly,
- Heather Witt,
- Peggy J. Farnham,
- Peter A. Jones,
- and Benjamin P. Berman
Genome Res. April 2015 25: 467-477; Published in Advance March 6, 2015, doi:10.1101/gr.183368.114
...largely devoid of all active, permissive, and repressive histone marks in HCT116. In HCT116 cells, these promoters were unexpressed (Fig. 2D) and associated with inactive promoter states (Supplemental Fig. 3B). Those that retained residual DNA methylation in DKO1 cells (the MM class) had relatively few...
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Research: Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer
- Phillippa C. Taberlay,
- Aaron L. Statham,
- Theresa K. Kelly,
- Susan J. Clark,
- and Peter A. Jones
Genome Res. September 2014 24: 1421-1432; Published in Advance June 10, 2014, doi:10.1101/gr.163485.113
...line (MCF7), as well as normal prostate epithelial cells (PrEC) and a prostate cancer cell line (PC3), to define the altered patterns of DNA methylation, histone modifications, and nucleosome occupancy that occur at distal regulatory elements in two different cell line models of cancer. First, we...
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Method: Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules
- Theresa K. Kelly,
- Yaping Liu,
- Fides D. Lay,
- Gangning Liang,
- Benjamin P. Berman,
- and Peter A. Jones
Genome Res. December 2012 22: 2497-2506; Published in Advance September 7, 2012, doi:10.1101/gr.143008.112
...expression. Active promoters have unmethylated DNA and lack nucleosomes just prior to the gene’s transcriptional start site (TSS), while inactive promoters have densely packed nucleosomes and can be unmethylated (poised or repressed) or methylated (silent). Due to this variety of chromatin structures, gene...
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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
...on the deposition of H3K27me3. It is possible that these regions and their boundaries are characterized by other (epi)genetic features such as overrepresentation of genomic elements like certain repeat classes, CpG islands, gene density, lamina-associated domains (Guelen et al. 2008), or transcriptional factor...
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Research: Genome-scale analysis of DNA methylation in lung adenocarcinoma and integration with mRNA expression
- Suhaida A. Selamat,
- Brian S. Chung,
- Luc Girard,
- Wei Zhang,
- Ying Zhang,
- Mihaela Campan,
- Kimberly D. Siegmund,
- Michael N. Koss,
- Jeffrey A. Hagen,
- Wan L. Lam,
- Stephen Lam,
- Adi F. Gazdar,
- and Ite A. Laird-Offringa
Genome Res. July 2012 22: 1197-1211; Published in Advance May 21, 2012, doi:10.1101/gr.132662.111
...that these genes are involved in cell differentiation, epithelial to mesenchymal transition, RAS and WNT signaling pathways, and cell cycle regulation, among others. Comparison of DNA methylation profiles between lung adenocarcinomas of current and never-smokers showed modest differences, identifying only LGALS4...
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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
...“switches” take place in NPCs to guide development toward neurogenesis, followed by gliogenesis; for review, see Gavin et al. (2017). These changes in differentiation path are directed by an interplay between DNA methylation and an increase in repressive histone modifications H3K9me3 and H3K27 methylation...
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Research: The loss of heterochromatin is associated with multiscale three-dimensional genome reorganization and aberrant transcription during cellular senescence
- Xianglin Zhang,
- Xuehui Liu,
- Zhenhai Du,
- Lei Wei,
- Huan Fang,
- Qiongye Dong,
- Jing Niu,
- Yanda Li,
- Juntao Gao,
- Michael Q. Zhang,
- Wei Xie,
- and Xiaowo Wang
Genome Res. July 2021 31: 1121-1135; Published in Advance June 17, 2021, doi:10.1101/gr.275235.121
...; Chojnowski et al. 2020), and the “global heterochromatin loss and redistribution” model has been summarized (Tsurumi and Li 2012; Sen et al. 2016; Sidler et al. 2017). In OIS, constitutive lamina-associated domains detach from the nuclear lamina and form highly condensed senescence-associated heterochromatin...
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Research: Suv39h-catalyzed H3K9me3 is critical for euchromatic genome organization and the maintenance of gene transcription
- Christine R. Keenan,
- Hannah D. Coughlan,
- Nadia Iannarella,
- Andres Tapia del Fierro,
- Andrew Keniry,
- Timothy M. Johanson,
- Wing Fuk Chan,
- Alexandra L. Garnham,
- Lachlan W. Whitehead,
- Marnie E. Blewitt,
- Gordon K. Smyth,
- and Rhys S. Allan
Genome Res. April 2024 34: 556-571; Published in Advance May 6, 2024, doi:10.1101/gr.279119.124
...(Fig. 2E,F). Of note, disrupted LADs showed higher levels of histone marks (both active and repressive) across LAD boundaries compared with nondisrupted LADs (Fig. 2E).View larger version: In this window In a new window Figure 2. Suv39DKO reduces lamina-associated domains (LADs) without inducing gene...
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Method: Identification of regulatory elements from nascent transcription using dREG
- Zhong Wang,
- Tinyi Chu,
- Lauren A. Choate,
- and Charles G. Danko
Genome Res. February 2019 29: 293-303; Published in Advance December 20, 2018, doi:10.1101/gr.238279.118
...the location of the majority of regulatory elements defined using orthogonal strategies at an estimated 5% false discovery rate: 81.3% or 96.1% of DNase I hypersensitive sites (DHSs) marked by transcription (using GRO-cap pairs) and 58.4%, 71.8%, or 84.9% of DHSs marked by the acetylation of histone 3 lysine...

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