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Mini-Review: Evolution of genome-wide methylation profiling technologies
- Carolina Montano and
- Winston Timp
Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
...of the fifth carbon atom of cytosine, typically in mammals in a CG dinucleotide context. This dinucleotide is depleted largely across the and found predominantly in clusters known as “CpG islands” (Bird 1986). Cytosine methylation is catalyzed by methyltransferases (e.g., DNMT1, DNMT3A) that transfer a methyl...
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Research: H2A.B facilitates transcription elongation at methylated CpG loci
- Yibin Chen,
- Qiang Chen,
- Richard C. McEachin,
- James D. Cavalcoli,
- and Xiaochun Yu
Genome Res. April 2014 24: 570-579; Published in Advance January 8, 2014, doi:10.1101/gr.156877.113
...-specific expression of imprinted Kcnq1 was determined by different NlaIII digestion patterns based on the SNP between mus and cas. H2A.B and methylated CpG Genome Research 573 www..org Fig. S6E). Of note, the transcription of Kcnq1 was only from the maternal allele since Kcnq1ot1, transcribed from the paternal allele...
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Research: Genome-wide and parental allele-specific analysis of CTCF and cohesin DNA binding in mouse brain reveals a tissue-specific binding pattern and an association with imprinted differentially methylated regions
- Adam R. Prickett,
- Nikolaos Barkas,
- Ruth B. McCole,
- Siobhan Hughes,
- Samuele M. Amante,
- Reiner Schulz,
- and Rebecca J. Oakey
Genome Res. October 2013 23: 1624-1635; Published in Advance June 26, 2013, doi:10.1101/gr.150136.112
..., with the portion of the corresponding to regions of CTCF binding. We found that methylation at CpG dinucleotides appears to have a greater influence on CTCF binding than non-CpG methylation. Genome wide, 60.8% of CpGs are methylated in the mouse brain, in contrast to 51.9% of CpGs in regions of CTCF binding. NonCpG...
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Research: Pervasive polymorphic imprinted methylation in the human placenta
- Courtney W. Hanna,
- Maria S. Peñaherrera,
- Heba Saadeh,
- Simon Andrews,
- Deborah E. McFadden,
- Gavin Kelsey,
- and Wendy P. Robinson
Genome Res. June 2016 26: 756-767; Published in Advance January 14, 2016, doi:10.1101/gr.196139.115
...).Identification of novel imprinted placental DMRsWe sought to identify novel imprinted DMRs by identifying CpG islands (CGIs) that showed a profile consistent with imprinting in early human development: DMRs that were both differentially methylated in the germline and between triploid placental samples. First, CGIs...
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Methods: Genome-wide prediction of imprinted murine genes
- Philippe P. Luedi,
- Alexander J. Hartemink,
- and Randy L. Jirtle
Genome Res. June 2005 15: 875-884; doi:10.1101/gr.3303505
...and maternally expressed. Increased maternal transmission of male homosexuality has previously been observed ( Hamer et al. 1993 ), and it is proposed to result in part from imprinted genes ( Bocklandt and Hamer 2003 ). A -wide screen for methylated CpG islands found a germline differentially methylated region...
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Method: A novel approach identifies new differentially methylated regions (DMRs) associated with imprinted genes
- Sanaa Choufani,
- Jonathan S. Shapiro,
- Martha Susiarjo,
- Darci T. Butcher,
- Daria Grafodatskaya,
- Youliang Lou,
- Jose C. Ferreira,
- Dalila Pinto,
- Stephen W. Scherer,
- Lisa G. Shaffer,
- Philippe Coullin,
- Isabella Caniggia,
- Joseph Beyene,
- Rima Slim,
- Marisa S. Bartolomei,
- and Rosanna Weksberg
Genome Res. March 2011 21: 465-476; Published in Advance February 7, 2011, doi:10.1101/gr.111922.110
...for the utility of comparing -wide methylation profiles for genomic regions of uniparental versus biparental origin to identify new DMCpG sites associated with known imprinted genes as well as new candidate imprinted genes. To identify novel DMCpG sites, we screened the 26,486 autosomal CpG sites represented...
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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
...,165) and display the same pattern, while methylated CpG island promoters (781) are nucleosome-occupied and inaccessible to M.CviPI. (D) NonCpG island promoters are generally characterized by CpG methylation and inaccessibility to M.CviPI, indicating nucleosome occupancy. The few unmethylated non-CpG island...
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ARTICLE: Identification of Novel Imprinted Genes in a Genome-Wide Screen for Maternal Methylation
- Rachel J. Smith,
- Wendy Dean,
- Galia Konfortova,
- and Gavin Kelsey
Genome Res. April 1, 2003 13: 558-569; doi:10.1101/gr.781503
...) and CpG Island Clones Isolated in a Methylation-Sensitive Representational Difference Analysis (Me-RDA) Screen for Maternal Methylation Nap1l5 , a Novel Imprinted Gene on Chr 6 Encoding a Protein With Homology With NAPs We isolated DPC#24–1, a 449-bp fragment from the Hin 6I Me-RDA that maps to Chr 6...
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Methods: Genome-wide screen of promoter methylation identifies novel markers in melanoma
- Yasuo Koga,
- Mattia Pelizzola,
- Elaine Cheng,
- Michael Krauthammer,
- Mario Sznol,
- Stephan Ariyan,
- Deepak Narayan,
- Annette M. Molinaro,
- Ruth Halaban,
- and Sherman M. Weissman
Genome Res. August 2009 19: 1462-1470; Published in Advance June 2, 2009, doi:10.1101/gr.091447.109
...and the expression of imprinted genes (Feinberg 2004). Locus-specific hypermethylation occurs primarily in CpG islands that are often associated with gene regulatory regions. This, in turn, can lead to transcriptional inactivation of downstream gene(s), followed by changes in cellular functions. In cancer cells...
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Research: Genome-wide parent-of-origin DNA methylation analysis reveals the intricacies of human imprinting and suggests a germline methylation-independent mechanism of establishment
- Franck Court,
- Chiharu Tayama,
- Valeria Romanelli,
- Alex Martin-Trujillo,
- Isabel Iglesias-Platas,
- Kohji Okamura,
- Naoko Sugahara,
- Carlos Simón,
- Harry Moore,
- Julie V. Harness,
- Hans Keirstead,
- Jose Vicente Sanchez-Mut,
- Eisuke Kaneki,
- Pablo Lapunzina,
- Hidenobu Soejima,
- Norio Wake,
- Manel Esteller,
- Tsutomu Ogata,
- Kenichiro Hata,
- Kazuhiko Nakabayashi,
- and David Monk
Genome Res. April 2014 24: 554-569; Published in Advance January 8, 2014, doi:10.1101/gr.164913.113
...In addition to the known imprinted DMRs, the Infinium array screen of reciprocal UPDs and tissues samples uncovered several previously unidentified DMRs located within existing imprinted domains. We discovered four maternally methylated CpG islands located between the SNRPN and NDN genes on chromosome 15...

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