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Research: Retrotransposition creates sloping shores: a graded influence of hypomethylated CpG islands on flanking CpG sites
- Fiorella C. Grandi,
- James M. Rosser,
- Simon J. Newkirk,
- Jun Yin,
- Xiaoling Jiang,
- Zhuo Xing,
- Leanne Whitmore,
- Sanum Bashir,
- Zoltán Ivics,
- Zsuzsanna Izsvák,
- Ping Ye,
- Y. Eugene Yu,
- and Wenfeng An
Genome Res. August 2015 25: 1135-1146; Published in Advance May 20, 2015, doi:10.1101/gr.185132.114
...elements and processed pseudogenes, have made an indelible impact on the structure and function of the human . One consequence is the creation of new CpG islands (CGIs). In fact, more than half of all CGIs in the are associated with repetitive DNA, three-quarters of which are derived from retrotransposons...
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Research: Distal CpG islands can serve as alternative promoters to transcribe genes with silenced proximal promoters
- Shrutii Sarda,
- Avinash Das,
- Charles Vinson,
- and Sridhar Hannenhalli
Genome Res. April 2017 27: 553-566; Published in Advance February 21, 2017, doi:10.1101/gr.212050.116
...for this article.] In mammalian DNA, cytosines within CpG dinucleotides are heavily methylated throughout the , yet there are several discrete “islands” that contain a high frequency of unmethylated CpG sites. These are called CpG islands (CGI), and their identification has long been considered important...
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Research: Evolutionary expansion of DNA hypomethylation in the mammalian germline genome
- Jianghan Qu,
- Emily Hodges,
- Antoine Molaro,
- Pascal Gagneux,
- Matthew D. Dean,
- Gregory J. Hannon,
- and Andrew D. Smith
Genome Res. February 2018 28: 145-158; Published in Advance December 19, 2017, doi:10.1101/gr.225896.117
...methylation has substantially impacted the large-scale evolution of mammalian s. Spontaneous deamination elevates the mutation rate at methylated cytosines (Bird 1980). Consequently, germline DNA methylation profiles have shaped the CpG landscape of mammalian s (Cohen et al. 2011), resulting in the CpG island...
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Letter: Dynamic changes in the human methylome during differentiation
- Louise Laurent,
- Eleanor Wong,
- Guoliang Li,
- Tien Huynh,
- Aristotelis Tsirigos,
- Chin Thing Ong,
- Hwee Meng Low,
- Ken Wing Kin Sung,
- Isidore Rigoutsos,
- Jeanne Loring,
- and Chia-Lin Wei
Genome Res. March 2010 20: 320-331; Published in Advance February 4, 2010, doi:10.1101/gr.101907.109
...in cancer cells, particularly down-regulation of genes with tumor suppressor functions by hypermethylation of their promoter regions (Ting et al. 2006). In mammals, the predominant form of DNA methylation occurs symmetrically on the cytosine residues on both strands of CpG dinucleotides, although...
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Research: Critical threshold levels of DNA methyltransferase 1 are required to maintain DNA methylation across the genome in human cancer cells
- Yi Cai,
- Hsing-Chen Tsai,
- Ray-Whay Chiu Yen,
- Yang W. Zhang,
- Xiangqian Kong,
- Wei Wang,
- Limin Xia,
- and Stephen B. Baylin
Genome Res. April 2017 27: 533-544; Published in Advance February 23, 2017, doi:10.1101/gr.208108.116
...maintenance. (A) The top bars represent the percentages of gene body probes with different basal DNA methylation values (β≥ 0.75) of intermediate (0.25 < β < 0.75) and low (β≤ 0.25) in genes with and without promoter CpG islands (CpGi) in HCT116 cells. The pie charts represent promoter methylation profiles...
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Research: Comparative methylome analysis of benign and malignant peripheral nerve sheath tumors
- Andrew Feber,
- Gareth A. Wilson,
- Lu Zhang,
- Nadege Presneau,
- Bernadine Idowu,
- Thomas A. Down,
- Vardhman K. Rakyan,
- Luke A. Noon,
- Alison C. Lloyd,
- Elia Stupka,
- Vassia Schiza,
- Andrew E. Teschendorff,
- Gary P. Schroth,
- Adrienne Flanagan,
- and Stephan Beck
Genome Res. April 2011 21: 515-524; Published in Advance February 1, 2011, doi:10.1101/gr.109678.110
...(http://www.bioinformatics.bbsrc.ac.uk/projects/seqmonk/). Concordance with the Batmanmethylation score was assessed for those CpG sites covered by at least 10 reads. Pyrosequencing One microgram each of pooled DNA from the MPNST, NF, and SC samples was bisulfite-treated using a EZ DNA methylation kit...
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Method: Guide Positioning Sequencing identifies aberrant DNA methylation patterns that alter cell identity and tumor-immune surveillance networks
- Jin Li,
- Yan Li,
- Wei Li,
- Huaibing Luo,
- Yanping Xi,
- Shihua Dong,
- Ming Gao,
- Peng Xu,
- Baolong Zhang,
- Ying Liang,
- Qingping Zou,
- Xin Hu,
- Lina Peng,
- Dan Zou,
- Ting Wang,
- Hongbo Yang,
- Cizhong Jiang,
- Shaoliang Peng,
- Feizhen Wu,
- and Wenqiang Yu
Genome Res. February 2019 29: 270-280; Published in Advance January 22, 2019, doi:10.1101/gr.240606.118
...DNA methylation coverage rate, at nearly 96% of the human liver and can also detect strand-specific whole- methylome. Compared with WGBS, the advantages of GPS include higher cytosine coverage, especially in CpG islands and repetitive elements, and higher accuracy in DNA methylation detection...
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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
...; Valouev et al. 2011; Portela et al. 2013). Epigenetic changes, in particular the aberrant DNA methylation and silencing of CpG island (CGI) promoters, are a common signature of cancer (Baylin and Jones 2011). This early observation, alongwith the fact that >60%of promoters are locatedwithin CGIs, has...
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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
...regulation (Kelly et al. 2010; Wolff et al. 2010; Andreu-Vieyra et al. 2011; Taberlay et al. 2011; You et al. 2011). To date, however, research has primarily focused on DNA methylation and loss of function of CpG island-containing promoters, which represent only a small proportion of the potential regulatory...
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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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