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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
...), or hybridization capture (Mahmoud et al. 2024) has been used to isolate and analyze specific genomic regions of interest at higher coverage depth, akin to deep high-throughput sequencing panels. While standard methylation detection resolution is limited to 1/coverage levels (∼5% for an average 30× sequencing run...
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Resource: A DNA methylation fingerprint of 1628 human samples
- Agustin F. Fernandez,
- Yassen Assenov,
- Jose Ignacio Martin-Subero,
- Balazs Balint,
- Reiner Siebert,
- Hiroaki Taniguchi,
- Hiroyuki Yamamoto,
- Manuel Hidalgo,
- Aik-Choon Tan,
- Oliver Galm,
- Isidre Ferrer,
- Montse Sanchez-Cespedes,
- Alberto Villanueva,
- Javier Carmona,
- Jose V. Sanchez-Mut,
- Maria Berdasco,
- Victor Moreno,
- Gabriel Capella,
- David Monk,
- Esteban Ballestar,
- Santiago Ropero,
- Ramon Martinez,
- Marta Sanchez-Carbayo,
- Felipe Prosper,
- Xabier Agirre,
- Mario F. Fraga,
- Osvaldo Graña,
- Luis Perez-Jurado,
- Jaume Mora,
- Susana Puig,
- Jaime Prat,
- Lina Badimon,
- Annibale A. Puca,
- Stephen J. Meltzer,
- Thomas Lengauer,
- John Bridgewater,
- Christoph Bock,
- and Manel Esteller
Genome Res. February 2012 22: 407-419; Published in Advance May 25, 2011, doi:10.1101/gr.119867.110
..., Spain AbstractMost of the studies characterizing DNA methylation patterns have been restricted to particular genomic loci in a limited number of human samples and pathological conditions. Herein, we present a compromise between an extremely comprehensive study of a human sample population...
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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
..., Wen B, Feinberg AP. 2008. Comprehensive high-throughput arrays for relative methylation (CHARM). Genome Res 18: 780–790. Irizarry RA, Ladd-Acosta C, Wen B, Wu Z, Montano C, Onyango P, Cui H, Gabo K, Rongione M, Webster M, et al. 2009. The human colon cancer methylome shows similar hypo...
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Research: Large-scale methylation domains mark a functional subset of neuronally expressed genes
- Diane I. Schroeder,
- Paul Lott,
- Ian Korf,
- and Janine M. LaSalle
Genome Res. October 2011 21: 1583-1591; Published in Advance July 22, 2011, doi:10.1101/gr.119131.110
..., Carvalho B,WuH, Brandenburg SA, Jeddeloh JA, Wen B, Feinberg AP. 2008. Comprehensive high-throughput arrays for relative methylation (CHARM). Genome Res 18: 780–790. Jin S-G, Kadam S, Pfeifer GP. 2010. Examination of the specificity of DNA methylation profiling techniques towards 5-methylcytosine and 5...
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Next-Generation DNA Sequencing/Review: Finding the fifth base: Genome-wide sequencing of cytosine methylation
- Ryan Lister and
- Joseph R. Ecker
Genome Res. June 2009 19: 959-966; Published in Advance March 9, 2009, doi:10.1101/gr.083451.108
.... , Feinberg, A.P. ( 2008 ) Comprehensive high-throughput arrays for relative methylation (CHARM) Genome Res. 18 : 780 – 790 . ↵ Jackson, J.P. , Lindroth, A.M. , Cao, X. , Jacobsen, S.E. ( 2002 ) Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase . Nature 416 : 556 – 560...
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Method: Evaluation of affinity-based genome-wide DNA methylation data: Effects of CpG density, amplification bias, and copy number variation
- Mark D. Robinson,
- Clare Stirzaker,
- Aaron L. Statham,
- Marcel W. Coolen,
- Jenny Z. Song,
- Shalima S. Nair,
- Dario Strbenac,
- Terence P. Speed,
- and Susan J. Clark
Genome Res. December 2010 20: 1719-1729; Published in Advance November 2, 2010, doi:10.1101/gr.110601.110
...representation approaches that are based on methylation-sensitive (e.g., HELP) (Oda et al. 2009) or specific (e.g., CHARM) (Irizarry et al. 2008) restriction digestion (for review, see Jeddeloh et al. 2008), affinity-based methods such as methyl-DNA immunoprecipitation (MeDIP) (Weber et al. 2005, 2007; Novak et...
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Method: Chromatin and sequence features that define the fine and gross structure of genomic methylation patterns
- John R. Edwards,
- Anne H. O'Donnell,
- Robert A. Rollins,
- Heather E. Peckham,
- Clarence Lee,
- Maria H. Milekic,
- Benjamin Chanrion,
- Yutao Fu,
- Tao Su,
- Hanina Hibshoosh,
- Jay A. Gingrich,
- Fatemeh Haghighi,
- Robert Nutter,
- and Timothy H. Bestor
Genome Res. July 2010 20: 972-980; Published in Advance May 20, 2010, doi:10.1101/gr.101535.109
..., Stuart RK, Ching CW, et al. 2009. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459: 108–112. Irizarry RA, Ladd-Acosta C, Carvalho B, Wu H, Brandenburg SA. 2008. Comprehensive high-throughput arrays for relative methylation (CHARM). Genome Res 18: 780...
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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
...of variable methylation frequencies requires high sampling of individual molecules. High-throughput, single-molecule sequencing instruments have facilitated the -wide application of this approach. For example, direct shotgun bisulfite sequencing provided adequate coverage depth and proved cost...
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Methods: MEDME: An experimental and analytical methodology for the estimation of DNA methylation levels based on microarray derived MeDIP-enrichment
- Mattia Pelizzola,
- Yasuo Koga,
- Alexander Eckehart Urban,
- Michael Krauthammer,
- Sherman Weissman,
- Ruth Halaban,
- and Annette M. Molinaro
Genome Res. October 2008 18: 1652-1659; Published in Advance September 2, 2008, doi:10.1101/gr.080721.108
.... , Gentleman, R. ( 1996 ) R: A language for data analysis and graphics . J. Comput. Graph. Stat. 3 : 299 – 314 . ↵ Irizarry, R.A. , Ladd-Acosta, C. , Carvalho, B. , Wu, H. , Brandenburg, S.A. , Wen, B. , Feinberg, A.P. ( 2008 ) Comprehensive high-throughput arrays for relative methylation (CHARM) Genome Res...
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Research: Transcriptome dynamics through alternative polyadenylation in developmental and environmental responses in plants revealed by deep sequencing
- Yingjia Shen,
- R.C. Venu,
- Kan Nobuta,
- Xiaohui Wu,
- Varun Notibala,
- Caghan Demirci,
- Blake C. Meyers,
- Guo-Liang Wang,
- Guoli Ji,
- and Qingshun Q. Li
Genome Res. September 2011 21: 1478-1486; Published in Advance August 3, 2011, doi:10.1101/gr.114744.110
.... BMC Genomics 9: 220. doi: 10.1186/14712164-9-220. Irizarry RA, Ladd-Acosta C, Carvalho B,WuH, Brandenburg SA, Jeddeloh JA, Wen B, Feinberg AP. 2008. Comprehensive high-throughput arrays for relative methylation (CHARM). Genome Res 18: 780–790. Ji Z, Tian B. 2009. Reprogramming of 39 untranslated...

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