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Research: Hydroxycarbamide effects on DNA methylation and gene expression in myeloproliferative neoplasms
- Stephania Contreras Castillo,
- Bertille Montibus,
- Azucena Rocha,
- Will Duke,
- Ferdinand von Meyenn,
- Donal McLornan,
- Claire Harrison,
- Ann Mullally,
- Reiner Schulz,
- and Rebecca J. Oakey
Genome Res. August 2021 31: 1381-1394; Published in Advance July 9, 2021, doi:10.1101/gr.270066.120
....oakey@kcl.ac.ukAbstractHydroxycarbamide (HC, hydroxyurea) is a cytoreductive drug inducing cell cycle blockade. However, emerging evidence suggests that HC plays a role in the modulation of transcription through the activity of transcription factors and DNA methylation. Examining the global mechanism of action of HC in the context...
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Research: Transcriptional alterations in glioma result primarily from DNA methylation–independent mechanisms
- Franck Court,
- Elisa Le Boiteux,
- Anne Fogli,
- Mélanie Müller-Barthélémy,
- Catherine Vaurs-Barrière,
- Emmanuel Chautard,
- Bruno Pereira,
- Julian Biau,
- Jean-Louis Kemeny,
- Toufic Khalil,
- Lucie Karayan-Tapon,
- Pierre Verrelle,
- and Philippe Arnaud
Genome Res. October 2019 29: 1605-1621; Published in Advance September 18, 2019, doi:10.1101/gr.249219.119
....arnaud@uca.frAbstractIn cancer cells, aberrant DNA methylation is commonly associated with transcriptional alterations, including silencing of tumor suppressor genes. However, multiple epigenetic mechanisms, including polycomb repressive marks, contribute to gene deregulation in cancer. To dissect the relative contribution...
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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
...Genome-scale analysis of DNA methylation in lung adenocarcinoma and integration with mRNA expression Suhaida A. Selamat 1 , Brian S. Chung 1 , Luc Girard 2 , Wei Zhang 2 , Ying Zhang 3 , Mihaela Campan 1 , Kimberly D. Siegmund...
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Resource: A DNA methylation fingerprint of 1628 human samples
- Agustin F. Fernandez,
- Yassen Assenov,
- Jose Ignacio Martin-Subero,
- Balazs Balint,
- Reiner Siebert,
- Hiroaki Taniguchi,
- Hiroyuki Yamamoto,
- Manuel Hidalgo,
- Aik-Choon Tan,
- Oliver Galm,
- Isidre Ferrer,
- Montse Sanchez-Cespedes,
- Alberto Villanueva,
- Javier Carmona,
- Jose V. Sanchez-Mut,
- Maria Berdasco,
- Victor Moreno,
- Gabriel Capella,
- David Monk,
- Esteban Ballestar,
- Santiago Ropero,
- Ramon Martinez,
- Marta Sanchez-Carbayo,
- Felipe Prosper,
- Xabier Agirre,
- Mario F. Fraga,
- Osvaldo Graña,
- Luis Perez-Jurado,
- Jaume Mora,
- Susana Puig,
- Jaime Prat,
- Lina Badimon,
- Annibale A. Puca,
- Stephen J. Meltzer,
- Thomas Lengauer,
- John Bridgewater,
- Christoph Bock,
- and Manel Esteller
Genome Res. February 2012 22: 407-419; Published in Advance May 25, 2011, doi:10.1101/gr.119867.110
...G methylation outside CpG islands in the different steps of tumorigenesis.First, unsupervised clustering of the DNA methylation profiles obtained from the 855 primary tumors demonstrated that each type of malignancy had its own aberrant DNA methylation landscape (Fig. 2A). From a quantitative standpoint, 1003...
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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
...-depleted regions, respectively. At higher-order genomic scales, we found that long, H3K9me3-marked domains had lower accessibility, consistent with a more compact chromatin structure. Taken together, our results demonstrate the nuanced and context-dependent role of DNA methylation in the functional, multiscale...
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Resource: Dynamic DNA methylation across diverse human cell lines and tissues
- Katherine E. Varley,
- Jason Gertz,
- Kevin M. Bowling,
- Stephanie L. Parker,
- Timothy E. Reddy,
- Florencia Pauli-Behn,
- Marie K. Cross,
- Brian A. Williams,
- John A. Stamatoyannopoulos,
- Gregory E. Crawford,
- Devin M. Absher,
- Barbara J. Wold,
- and Richard M. Myers
Genome Res. March 2013 23: 555-567; Published in Advance January 16, 2013, doi:10.1101/gr.147942.112
...display stable DNA methylation signatures, that comparingmethylation profiles between samples identifies methylation profiles relevant to the functional differences between cell types, and that these data provide a catalog of aberrant methylation found in cancer cell lines. We discovered that cancer...
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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
..., for PrEC and PC3 cells. Taberlay et al. 1426 Genome Research www..org that only certain regulatory factors play key roles in establishing nucleosome and DNA methylation phasing patterns. Discussion The critical events that underlie epigenetic aberrations at promoters have been largely deciphered (for...
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Research: Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer
- Gary C. Hon,
- R. David Hawkins,
- Otavia L. Caballero,
- Christine Lo,
- Ryan Lister,
- Mattia Pelizzola,
- Armand Valsesia,
- Zhen Ye,
- Samantha Kuan,
- Lee E. Edsall,
- Anamaria Aranha Camargo,
- Brian J. Stevenson,
- Joseph R. Ecker,
- Vineet Bafna,
- Robert L. Strausberg,
- Andrew J. Simpson,
- and Bing Ren
Genome Res. February 2012 22: 246-258; Published in Advance December 7, 2011, doi:10.1101/gr.125872.111
...such as the breast cancer susceptibility gene BRCA1 (Tapia et al. 2008) supports the notion that tumor suppressors are frequently inactivated by DNA methylation at CpG islands and promoters. Genome-scale methods including MeDIP-seq (Ruike et al. 2010) and CHARM (Irizarry et al. 2009) have confirmed global...
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Method: Bisulfite Patch PCR enables multiplexed sequencing of promoter methylation across cancer samples
- Katherine Elena Varley and
- Robi David Mitra
Genome Res. September 2010 20: 1279-1287; Published in Advance July 13, 2010, doi:10.1101/gr.101212.109
...63108, USA Abstract Aberrant DNA methylation frequently occurs at gene promoters during cancer progression. It is important to identify these loci because they are often misregulated and drive tumorigenesis. Bisulfite sequencing is the most direct and highest resolution assay for identifying...
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Methods: High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing
- Emily Hodges,
- Andrew D. Smith,
- Jude Kendall,
- Zhenyu Xuan,
- Kandasamy Ravi,
- Michelle Rooks,
- Michael Q. Zhang,
- Kenny Ye,
- Arindam Bhattacharjee,
- Leonardo Brizuela,
- W. Richard McCombie,
- Michael Wigler,
- Gregory J. Hannon,
- and James B. Hicks
Genome Res. September 2009 19: 1593-1605; Published in Advance July 6, 2009, doi:10.1101/gr.095190.109
...equally to this work. Abstract DNA methylation stabilizes developmentally programmed gene expression states. Aberrant methylation is associated with disease progression and is a common feature of cancer genomes. Presently, few methods enable quantitative, large-scale, single-base resolution...
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