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Research: Enduring epigenetic landmarks define the cancer microenvironment
- Ruth Pidsley,
- Mitchell G. Lawrence,
- Elena Zotenko,
- Birunthi Niranjan,
- Aaron Statham,
- Jenny Song,
- Roman M. Chabanon,
- Wenjia Qu,
- Hong Wang,
- Michelle Richards,
- Shalima S. Nair,
- Nicola J. Armstrong,
- Hieu T. Nim,
- Melissa Papargiris,
- Preetika Balanathan,
- Hugh French,
- Timothy Peters,
- Sam Norden,
- Andrew Ryan,
- John Pedersen,
- James Kench,
- Roger J. Daly,
- Lisa G. Horvath,
- Phillip Stricker,
- Mark Frydenberg,
- Renea A. Taylor,
- Clare Stirzaker,
- Gail P. Risbridger,
- and Susan J. Clark
Genome Res. May 2018 28: 625-638; Published in Advance April 12, 2018, doi:10.1101/gr.229070.117
.... Oncogene 33: 4924–4931. ↵Berman BP, Weisenberger DJ, Aman JF, Hinoue T, Ramjan Z, Liu Y, Noushmehr H, Lange CP, van Dijk CM, Tollenaar RA, et al. 2012. Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina-associated domains. Nat Genet 44: 40...
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Method: Defining the separation landscape of topological domains for decoding consensus domain organization of the 3D genome
- Dachang Dang,
- Shao-Wu Zhang,
- Ran Duan,
- and Shihua Zhang
Genome Res. March 2023 33: 386-400; Published in Advance March 9, 2023, doi:10.1101/gr.277187.122
...al. 2006; Lieberman-Aiden et al. 2009; Rao et al. 2014) provide unprecedented opportunities to decipher the mysteries of three-dimensional (3D) genomic organizations in the nucleus of eukaryotes. The folds into a hierarchical configuration consisting of multiscale chromatin structures...
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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
....g., losses of heterozygosity), cancer cells show epigenetic alterations involving the misregulation of a single gene (e.g., expression silencing by hypermethylation of the promoter CpG island) ( Esteller 2007 ; Jones 2012 ) or large chromosomal regions (i.e., long-range epigenetic silencing) ( Frigola et al...
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Research: Estrogen-induced chromatin looping changes identify a subset of functional regulatory elements
- Hosiana Abewe,
- Alexandra Richey,
- Jeffery M. Vahrenkamp,
- Matthew Ginley-Hidinger,
- Craig M. Rush,
- Noel Kitchen,
- Xiaoyang Zhang,
- and Jason Gertz
Genome Res. March 2025 35: 393-403; Published in Advance March 3, 2025, doi:10.1101/gr.279699.124
...of Utah, Salt Lake City, Utah 84112, USA; 3Department of Biomedical Engineering, University of Utah, Salt Lake City, Utah 84112, USA Corresponding author: jay.gertz@hci.utah.eduAbstractTranscriptional enhancers can regulate individual or multiple genes through long-range three-dimensional (3D...
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Research: Characterization and dynamics of pericentromere-associated domains in mice
- Patrick J. Wijchers,
- Geert Geeven,
- Michael Eyres,
- Atze J. Bergsma,
- Mark Janssen,
- Marjon Verstegen,
- Yun Zhu,
- Yori Schell,
- Carlo Vermeulen,
- Elzo de Wit,
- and Wouter de Laat
Genome Res. July 2015 25: 958-969; Published in Advance April 16, 2015, doi:10.1101/gr.186643.114
...expression patterns of genes in different cell types. It is well established that higher-order organization of chromatinwithin the three-dimensional space of the nucleus is an important contributor to regulation of gene expression. In particular, long-range physical interactions of genomic elements...
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Method: FIND: difFerential chromatin INteractions Detection using a spatial Poisson process
- Mohamed Nadhir Djekidel,
- Yang Chen,
- and Michael Q. Zhang
Genome Res. March 2018 28: 412-422; Published in Advance February 12, 2018, doi:10.1101/gr.212241.116
..., Zotenko E, Bert SA, Giles KA, Bauer DC, et al. 2016. Three-dimensional disorganization of the cancer occurs coincident with long-range genetic and epigenetic alterations. Genome Res 26: 719–731. ↵Tang Z, Luo OJ, Li X, Zheng M, Zhu JJ, Szalaj P, Trzaskoma P, Magalska A, Wlodarczyk J, Ruszczycki B, et al...
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