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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
...around noncoding regions of the (Kerr et al. 2023). Though large-scale genomic studies will indeed include epigenetic data, this data will likely be confined to easily accessible sample types, e.g., blood and saliva.Tissue-specific methylation profiles are often the strongest epigenetic signature...
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Methods: DNA methylation profile of tissue-dependent and differentially methylated regions (T-DMRs) in mouse promoter regions demonstrating tissue-specific gene expression
- Shintaro Yagi,
- Keiji Hirabayashi,
- Shinya Sato,
- Wei Li,
- Yoko Takahashi,
- Tsutomu Hirakawa,
- Guoying Wu,
- Naoko Hattori,
- Naka Hattori,
- Jun Ohgane,
- Satoshi Tanaka,
- X. Shirley Liu,
- and Kunio Shiota
Genome Res. December 2008 18: 1969-1978; Published in Advance October 29, 2008, doi:10.1101/gr.074070.107
...DNA methylation profile of tissue-dependent and differentially methylated regions (T-DMRs) in mouse promoter regions demonstrating tissue-specific gene expression Shintaro Yagi 1 , Keiji Hirabayashi 1 , Shinya Sato 1 , Wei Li 2 , Yoko Takahashi 1...
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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
...by differentially methylated regions (DMRs) of DNA that confer parent of origin-specific transcription. We developed a new strategy to identify imprinted gene-associated DMRs. Using genome-wide methylation profiling of sodium bisulfite modified DNA from normal human tissues of biparental origin, candidate DMRs were...
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Method: Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage
- Lukas Chavez,
- Justyna Jozefczuk,
- Christina Grimm,
- Jörn Dietrich,
- Bernd Timmermann,
- Hans Lehrach,
- Ralf Herwig,
- and James Adjaye
Genome Res. October 2010 20: 1441-1450; Published in Advance August 27, 2010, doi:10.1101/gr.110114.110
...Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage Lukas Chavez 1 , 5 , Justyna Jozefczuk 1 , Christina Grimm 1 , Jörn Dietrich 1 , Bernd Timmermann 2...
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Research: A functional methylome map of ulcerative colitis
- Robert Häsler,
- Zhe Feng,
- Liselotte Bäckdahl,
- Martina E. Spehlmann,
- Andre Franke,
- Andrew Teschendorff,
- Vardhman K. Rakyan,
- Thomas A. Down,
- Gareth A. Wilson,
- Andrew Feber,
- Stephan Beck,
- Stefan Schreiber,
- and Philip Rosenstiel
Genome Res. November 2012 22: 2130-2137; Published in Advance July 23, 2012, doi:10.1101/gr.138347.112
.... An integrated resource for -wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs). Genome Res 18: 1518–1529. Rakyan VK, Beyan H, Down TA, Hawa MI, Maslau S, Aden D, Daunay A, Busato F, Mein CA, Manfras B, et al. 2011a. Identification of type 1 diabetes...
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Methods: Comparative isoschizomer profiling of cytosine methylation: The HELP assay
- Batbayar Khulan,
- Reid F. Thompson,
- Kenny Ye,
- Melissa J. Fazzari,
- Masako Suzuki,
- Edyta Stasiek,
- Maria E. Figueroa,
- Jacob L. Glass,
- Quan Chen,
- Cristina Montagna,
- Eli Hatchwell,
- Rebecca R. Selzer,
- Todd A. Richmond,
- Roland D. Green,
- Ari Melnick,
- and John M. Greally
Genome Res. August 2006 16: 1046-1055; Published in Advance June 29, 2006, doi:10.1101/gr.5273806
...of hypomethylated loci, usually but not exclusively at promoters and CpG islands. Intergenomic comparison found marked differences in cytosine methylation between spermatogenic and brain cells, identifying 223 new candidate tissue-specific differentially methylated regions (T-DMRs). Bisulfite pyrosequencing...
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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
..., and intragenic regions.CpG shores were discovered as hotbeds for cancer- and tissue-specific differentially methylated regions (cDMRs and tDMRs, respectively) (Irizarry et al. 2009). Although the average slope for low CGIs in somatic tissues was the same at the genomic level (Fig. 3C), by calculating...
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Letter: DNA methylation programming and reprogramming in primate embryonic stem cells
- Netta Mendelson Cohen,
- Vikas Dighe,
- Gilad Landan,
- Sigrún Reynisdóttir,
- Arnar Palsson,
- Shoukhrat Mitalipov,
- and Amos Tanay
Genome Res. December 2009 19: 2193-2201; Published in Advance November 3, 2009, doi:10.1101/gr.096685.109
.... An integrated resource for -wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs). Genome Res 18: 1518– 1529. Reik W. 2007. Stability and flexibility of epigenetic gene regulation in mammalian development. Nature 447: 425–432. Rollins RA, Haghighi F, Edwards JR, Das...
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Research: Comparative methylomics reveals gene-body H3K36me3 in Drosophila predicts DNA methylation and CpG landscapes in other invertebrates
- Lisa Nanty,
- Guillermo Carbajosa,
- Graham A. Heap,
- Francis Ratnieks,
- David A. van Heel,
- Thomas A. Down,
- and Vardhman K. Rakyan
Genome Res. November 2011 21: 1841-1850; Published in Advance September 22, 2011, doi:10.1101/gr.121640.111
..., Thorne NP, Flicek P, Kulesha E, Gra¨f S, Tomazou EM, Ba¨ckdahl L, Johnson N, Herberth M, et al. 2008. An integrated resource for -wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs). Genome Res 18: 1518–1529. Saxonov S, Berg P, Brutlag DL. 2006. A -wide...
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Letter: The presence of RNA polymerase II, active or stalled, predicts epigenetic fate of promoter CpG islands
- Hideyuki Takeshima,
- Satoshi Yamashita,
- Taichi Shimazu,
- Tohru Niwa,
- and Toshikazu Ushijima
Genome Res. November 2009 19: 1974-1982; Published in Advance August 3, 2009, doi:10.1101/gr.093310.109
...regions in human breast cancers (Supplemental Fig. S2). Between breast and prostate cancers, only 261 genes, 36% of the susceptible genes in breast cancers and 50% of those in prostate cancers, were commonly susceptible, showing the presence of tissue specificity. To explore possible selection bias...

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