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Research: The mutational spectrum of non-CpG DNA varies with CpG content
- Jean-Claude Walser and
- Anthony V. Furano
Genome Res. July 2010 20: 875-882; Published in Advance May 24, 2010, doi:10.1101/gr.103283.109
...The mutational spectrum of non-CpG DNA varies with CpG content Jean-Claude Walser 1 and Anthony V. Furano 2 Section on Genomic Structure and Function, Laboratory of Molecular and Cellular Biology, National Institute of Diabetes and Digestive and Kidney...
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Research: Impact of replication timing on non-CpG and CpG substitution rates in mammalian genomes
- Chun-Long Chen,
- Aurélien Rappailles,
- Lauranne Duquenne,
- Maxime Huvet,
- Guillaume Guilbaud,
- Laurent Farinelli,
- Benjamin Audit,
- Yves d'Aubenton-Carafa,
- Alain Arneodo,
- Olivier Hyrien,
- and Claude Thermes
Genome Res. April 2010 20: 447-457; Published in Advance January 26, 2010, doi:10.1101/gr.098947.109
...increase in late-replicating regions (Watanabe et al. 2002; Stamatoyannopoulos et al. 2009). It was proposed that the increase in mutation rates in non-CpG and CpG sites results from a single mechanism, namely, an increase of DNA damage during replication (Stamatoyannopoulos et al. 2009). However...
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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: ZFX acts as a transcriptional activator in multiple types of human tumors by binding downstream from transcription start sites at the majority of CpG island promoters
- Suhn Kyong Rhie,
- Lijun Yao,
- Zhifei Luo,
- Heather Witt,
- Shannon Schreiner,
- Yu Guo,
- Andrew A. Perez,
- and Peggy J. Farnham
Genome Res. March 2018 28: 310-320; Published in Advance February 2, 2018, doi:10.1101/gr.228809.117
...step of the method is based on the treatment of chromatin with the M.CviPI methyltransferase. This enzyme methylates Cs in the context of GpC dinucleotides. GpCm does not occur in the human (the vast majority of DNA methylation in the human is at CpG dinucleotides, not GpC dinucleotides) and therefore...
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Research: DNA methylation epitypes highlight underlying developmental and disease pathways in acute myeloid leukemia
- Brian Giacopelli,
- Min Wang,
- Ada Cleary,
- Yue-Zhong Wu,
- Anna Reister Schultz,
- Maximilian Schmutz,
- James S. Blachly,
- Ann-Kathrin Eisfeld,
- Bethany Mundy-Bosse,
- Sebastian Vosberg,
- Philipp A. Greif,
- Rainer Claus,
- Lars Bullinger,
- Ramiro Garzon,
- Kevin R. Coombes,
- Clara D. Bloomfield,
- Brian J. Druker,
- Jeffrey W. Tyner,
- John C. Byrd,
- and Christopher C. Oakes
Genome Res. May 2021 31: 747-761; Published in Advance March 11, 2021, doi:10.1101/gr.269233.120
...methylation arrays, which provide the DNA methylation levels of CpG dinucleotides primarily in promoter and regulatory regions (Bibikova et al. 2011). We reduced the data based on overall variance using the 500 most variable probes for cluster analysis and performed unsupervised k-medoids-based clustering...
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Research: Combinatorial DNA methylation codes at repetitive elements
- Christophe Papin,
- Abdulkhaleg Ibrahim,
- Stéphanie Le Gras,
- Amandine Velt,
- Isabelle Stoll,
- Bernard Jost,
- Hervé Menoni,
- Christian Bronner,
- Stefan Dimitrov,
- and Ali Hamiche
Genome Res. June 2017 27: 934-946; Published in Advance March 27, 2017, doi:10.1101/gr.213983.116
...a major role in cell differentiation. [Supplemental material is available for this article.] DNA methylation is an epigenetic modification essential for mammalian development (Okano et al. 1999). In mammals, the cytosine bases at position 5 in CpG dinucleotides are modified -wide by dedicatedmethyl...
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Method: Detection and characterization of jagged ends of double-stranded DNA in plasma
- Peiyong Jiang,
- Tingting Xie,
- Spencer C. Ding,
- Ze Zhou,
- Suk Hang Cheng,
- Rebecca W.Y. Chan,
- Wing-Shan Lee,
- Wenlei Peng,
- John Wong,
- Vincent W.S. Wong,
- Henry L.Y. Chan,
- Stephen L. Chan,
- Liona C.Y. Poon,
- Tak Y. Leung,
- K.C. Allen Chan,
- Rossa W.K. Chiu,
- and Y.M. Dennis Lo
Genome Res. August 2020 30: 1144-1153; Published in Advance August 14, 2020, doi:10.1101/gr.261396.120
...as to how the 5′ jagged ends could be detected by introducing unmethylated cytosines (together with three other unmodified nucleotides) for DNA polymerase-mediated extension. All cytosines present in the CpG dinucleotides of a newly synthesized strand would be completely unmethylated. On the other hand...
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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
...epigenomic change in mammalian sperm methylomes and point to a divergence in trans-epigenetic mechanisms that govern the organization of epigenetic states at gene promoters.Mammalian DNA methylation is an epigenetic modification that occurs primarily on cytosines in the context of CpG dinucleotide and has...
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Research: The strand-biased mitochondrial DNA methylome and its regulation by DNMT3A
- Xiaoyang Dou,
- Jerome D. Boyd-Kirkup,
- Joseph McDermott,
- Xiaoli Zhang,
- Fang Li,
- Bowen Rong,
- Rui Zhang,
- Bisi Miao,
- Peilin Chen,
- Hao Cheng,
- Jianhuang Xue,
- David Bennett,
- Jiemin Wong,
- Fei Lan,
- and Jing-Dong J. Han
Genome Res. October 2019 29: 1622-1634; Published in Advance September 19, 2019, doi:10.1101/gr.234021.117
.... 2014; Devall et al. 2017), both CpG and non-CpG methylation were observed on mtDNA, and they are in a strand-biased pattern (Bellizzi et al. 2013). Conversely, by focusing only on the CpG or the average methylation level of all Cs of mtDNA, some studies showed the absence of mtDNA methylation...
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Methods: Multiplex padlock targeted sequencing reveals human hypermutable CpG variations
- Jin Billy Li,
- Yuan Gao,
- John Aach,
- Kun Zhang,
- Gregory V. Kryukov,
- Bin Xie,
- Annika Ahlford,
- Jung-Ki Yoon,
- Abraham M. Rosenbaum,
- Alexander Wait Zaranek,
- Emily LeProust,
- Shamil R. Sunyaev,
- and George M. Church
Genome Res. September 2009 19: 1606-1615; Published in Advance June 12, 2009, doi:10.1101/gr.092213.109
...with non-CpG divergence in the chimpanzee lineage in our data set (Fig. 4D,E). This correlationwould reflect the influence ofmutation rate components common to CpG and nonCpG mutations, such as exposure of DNA to damage and the efficiency of the BER system (Stamatoyannopoulos et al. 2009). It may also...

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