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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
...is also helpful in identifying and prioritizing previously missed SVs associated with methylation changes (Fig. 2D). In a large rare disease cohort, Cheung et al. (2023) discovered a hypermethylated region adjacent to a previously missed pathogenic repeat expansion in the DIP2B gene in a proband...
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Research: Late-replicating heterochromatin is characterized by decreased cytosine methylation in the human genome
- Masako Suzuki,
- Mayumi Oda,
- María-Paz Ramos,
- Marién Pascual,
- Kevin Lau,
- Edyta Stasiek,
- Frederick Agyiri,
- Reid F. Thompson,
- Jacob L. Glass,
- Qiang Jing,
- Richard Sandstrom,
- Melissa J. Fazzari,
- R. Scott Hansen,
- John A. Stamatoyannopoulos,
- Andrew S. McLellan,
- and John M. Greally
Genome Res. November 2011 21: 1833-1840; Published in Advance September 28, 2011, doi:10.1101/gr.116509.110
...E, Figueroa ME, Glass JL, Chen Q, Montagna C, et al. 2006. Comparative isoschizomer profiling of cytosine methylation: The HELP assay. Genome Res 16: 1046–1055. Kohonen T. 2001. Self Organizing Maps. Springer, Berlin, Germany. Krauss V. 2008. Glimpses of evolution: heterochromatic histone H3K9...
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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
...High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing Emily Hodges 1 , 2 , 6 , Andrew D. Smith 1 , 3 , 6 , Jude Kendall 1 , Zhenyu Xuan 1 , Kandasamy Ravi 1 , Michelle...
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Method: Multiplex mapping of chromatin accessibility and DNA methylation within targeted single molecules identifies epigenetic heterogeneity in neural stem cells and glioblastoma
- Nancy H. Nabilsi,
- Loic P. Deleyrolle,
- Russell P. Darst,
- Alberto Riva,
- Brent A. Reynolds,
- and Michael P. Kladde
Genome Res. February 2014 24: 329-339; Published in Advance October 8, 2013, doi:10.1101/gr.161737.113
...profiled DNA methylation and chromatin accessibility at 71 promoters and identified several classes of epigenetic heterogeneity as well as 29 promoters that were differentiallymethylated and/or differentially accessible between GBM and NSC. Strikingly, a subpopulation of cells exhibiting inaccessible...
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Method: Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm
- Bo Zhang,
- Yan Zhou,
- Nan Lin,
- Rebecca F. Lowdon,
- Chibo Hong,
- Raman P. Nagarajan,
- Jeffrey B. Cheng,
- Daofeng Li,
- Michael Stevens,
- Hyung Joo Lee,
- Xiaoyun Xing,
- Jia Zhou,
- Vasavi Sundaram,
- GiNell Elliott,
- Junchen Gu,
- Taoping Shi,
- Philippe Gascard,
- Mahvash Sigaroudinia,
- Thea D. Tlsty,
- Theresa Kadlecek,
- Arthur Weiss,
- Henriette O’Geen,
- Peggy J. Farnham,
- Cécile L. Maire,
- Keith L. Ligon,
- Pamela A.F. Madden,
- Angela Tam,
- Richard Moore,
- Martin Hirst,
- Marco A. Marra,
- Baoxue Zhang,
- Joseph F. Costello,
- and Ting Wang
Genome Res. September 2013 23: 1522-1540; Published in Advance June 26, 2013, doi:10.1101/gr.156539.113
...al. 2005, 2008), enrichment-based methods (MeDIPseq [Weber et al. 2005; Maunakea et al. 2010], MBD-seq [Serre et al. 2009]), and methylation-sensitive restriction enzyme based methods (HELP [Suzuki and Greally 2010], MRE-seq [Maunakea et al. 2010]). These methods yield largely concordant results...
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Methods: Comprehensive high-throughput arrays for relative methylation (CHARM)
- Rafael A. Irizarry,
- Christine Ladd-Acosta,
- Benilton Carvalho,
- Hao Wu,
- Sheri A. Brandenburg,
- Jeffrey A. Jeddeloh,
- Bo Wen,
- and Andrew P. Feinberg
Genome Res. May 2008 18: 780-790; Published in Advance March 3, 2008, doi:10.1101/gr.7301508
.... The paradigm of this method is the HELP (HpaII tiny fragment enrichment by ligation-mediated PCR) assay ( Khulan et al. 2006 ). DNA is digested in parallel with MspI (resistant to DNA methylation), and then the HpaII and MspI products are amplified by ligation-mediated PCR and hybridized using separate...
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Research: Phyloepigenomic comparison of great apes reveals a correlation between somatic and germline methylation states
- David I.K. Martin,
- Meromit Singer,
- Joseph Dhahbi,
- Guanxiong Mao,
- Lu Zhang,
- Gary P. Schroth,
- Lior Pachter,
- and Dario Boffelli
Genome Res. December 2011 21: 2049-2057; Published in Advance September 9, 2011, doi:10.1101/gr.122721.111
...component of the epi, cytosine methylation, a covalent modification of DNA that acts as a focal point in mechanisms that suppress transcription initiation (Klose and Bird 2006). We have compared the methylomes of human and chimpanzee in a homogeneous somatic cell type, the neutrophil, using the orangutan...
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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
...for an instructive mechanism of de novo methylation in cancer cells . Nat. Genet. 38 : 149 – 153 . ↵ Khulan, B. , Thompson, R. , Ye, K. , Fazzari, M. , Suzuki, M. , Stasiek, E. , Figueroa, M. , Glass, J. , Chen, Q. , Montagna, C. , et al. ( 2006 ) Comparative isoschizomer profiling of cytosine methylation: The HELP...
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Methods: Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver
- Alayne L. Brunner,
- David S. Johnson,
- Si Wan Kim,
- Anton Valouev,
- Timothy E. Reddy,
- Norma F. Neff,
- Elizabeth Anton,
- Catherine Medina,
- Loan Nguyen,
- Eric Chiao,
- Chuba B. Oyolu,
- Gary P. Schroth,
- Devin M. Absher,
- Julie C. Baker,
- and Richard M. Myers
Genome Res. June 2009 19: 1044-1056; Published in Advance March 9, 2009, doi:10.1101/gr.088773.108
...technology. It is based upon the historically most robust assay for DNA methylation—methyl-sensitive restriction enzymes ( Cedar et al. 1979 ). Here, we used the isoschizomers HpaII and MspI, which recognize the same cleavage site (5′-CCGG-3′); MspI digests at the site regardless of methylation status, while...
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RESOURCE: An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)
- Vardhman K. Rakyan,
- Thomas A. Down,
- Natalie P. Thorne,
- Paul Flicek,
- Eugene Kulesha,
- Stefan Gräf,
- Eleni M. Tomazou,
- Liselotte Bäckdahl,
- Nathan Johnson,
- Marlis Herberth,
- Kevin L. Howe,
- David K. Jackson,
- Marcos M. Miretti,
- Heike Fiegler,
- John C. Marioni,
- Ewan Birney,
- Tim J.P. Hubbard,
- Nigel P. Carter,
- Simon Tavaré,
- and Stephan Beck
Genome Res. September 2008 18: 1518-1529; Published in Advance June 24, 2008, doi:10.1101/gr.077479.108
.... 2006 ; Glass et al. 2007 ). The incorporation of experimental data, such as those presented here, will greatly assist in refining CGI definition and thereby help in understanding their function in the context of both promoter and nonpromoter regions of mammalian s. Association between DNA methylation...
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