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; Stephan Beck

doi:10.1101/gr.077479.108

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, Stephan Beck

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330 Citations (Scopus)

Abstract

We report a novel resource (methylation profiles of DNA, or mPod) for human genome-wide tissue-specific DNA methylation profiles. mPod consists of three fully integrated parts, genome-wide DNA methylation reference profiles of 13 normal somatic tissues, placenta, sperm, and an immortalized cell line, a visualization tool that has been integrated with the Ensembl genome browser and a new algorithm for the analysis of immunoprecipitation-based DNA methylation profiles. We demonstrate the utility of our resource by identifying the first comprehensive genome-wide set of tissue-specific differentially methylated regions (tDMRs) that may play a role in cellular identity and the regulation of tissue-specific genome function. We also discuss the implications of our findings with respect to the regulatory potential of regions with varied CpG density, gene expression, transcription factor motifs, gene ontology, and correlation with other epigenetic marks such as histone modifications.

Original language	English
Pages (from-to)	1518-1529
Number of pages	12
Journal	Genome Research
Volume	18
Issue number	9
DOIs	https://doi.org/10.1101/gr.077479.108
Publication status	Published - Sept 2008
Externally published	Yes

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Rakyan, V. K., Down, T. A., Thorne, N. P., Flicek, P., Kulesha, E., Gräf, S., Tomazou, E. M., Bäckdahl, L., Johnson, N., Herberth, M., Howe, K. L., Jackson, D. K., Miretti, M. M., Fiegler, H., Marioni, J. C., Birney, E., Hubbard, T. J. P., Carter, N. P., Tavaré, S., & Beck, S. (2008). An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs). Genome Research, 18(9), 1518-1529. https://doi.org/10.1101/gr.077479.108

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title = "An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)",

abstract = "We report a novel resource (methylation profiles of DNA, or mPod) for human genome-wide tissue-specific DNA methylation profiles. mPod consists of three fully integrated parts, genome-wide DNA methylation reference profiles of 13 normal somatic tissues, placenta, sperm, and an immortalized cell line, a visualization tool that has been integrated with the Ensembl genome browser and a new algorithm for the analysis of immunoprecipitation-based DNA methylation profiles. We demonstrate the utility of our resource by identifying the first comprehensive genome-wide set of tissue-specific differentially methylated regions (tDMRs) that may play a role in cellular identity and the regulation of tissue-specific genome function. We also discuss the implications of our findings with respect to the regulatory potential of regions with varied CpG density, gene expression, transcription factor motifs, gene ontology, and correlation with other epigenetic marks such as histone modifications.",

author = "Rakyan, {Vardhman K.} and Down, {Thomas A.} and Thorne, {Natalie P.} and Paul Flicek and Eugene Kulesha and Stefan Gr{\"a}f and Tomazou, {Eleni M.} and Liselotte B{\"a}ckdahl and Nathan Johnson and Marlis Herberth and Howe, {Kevin L.} and Jackson, {David K.} and Miretti, {Marcos M.} and Heike Fiegler and Marioni, {John C.} and Ewan Birney and Hubbard, {Tim J.P.} and Carter, {Nigel P.} and Simon Tavar{\'e} and Stephan Beck",

year = "2008",

month = sep,

doi = "10.1101/gr.077479.108",

language = "English",

volume = "18",

pages = "1518--1529",

journal = "Genome Research",

issn = "1088-9051",

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Rakyan, VK, Down, TA, Thorne, NP, Flicek, P, Kulesha, E, Gräf, S, Tomazou, EM, Bäckdahl, L, Johnson, N, Herberth, M, Howe, KL, Jackson, DK, Miretti, MM, Fiegler, H, Marioni, JC, Birney, E, Hubbard, TJP, Carter, NP, Tavaré, S & Beck, S 2008, 'An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)', Genome Research, vol. 18, no. 9, pp. 1518-1529. https://doi.org/10.1101/gr.077479.108

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T1 - An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)

AU - Rakyan, Vardhman K.

AU - Down, Thomas A.

AU - Thorne, Natalie P.

AU - Flicek, Paul

AU - Kulesha, Eugene

AU - Gräf, Stefan

AU - Tomazou, Eleni M.

AU - Bäckdahl, Liselotte

AU - Johnson, Nathan

AU - Herberth, Marlis

AU - Howe, Kevin L.

AU - Jackson, David K.

AU - Miretti, Marcos M.

AU - Fiegler, Heike

AU - Marioni, John C.

AU - Birney, Ewan

AU - Hubbard, Tim J.P.

AU - Carter, Nigel P.

AU - Tavaré, Simon

AU - Beck, Stephan

PY - 2008/9

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AB - We report a novel resource (methylation profiles of DNA, or mPod) for human genome-wide tissue-specific DNA methylation profiles. mPod consists of three fully integrated parts, genome-wide DNA methylation reference profiles of 13 normal somatic tissues, placenta, sperm, and an immortalized cell line, a visualization tool that has been integrated with the Ensembl genome browser and a new algorithm for the analysis of immunoprecipitation-based DNA methylation profiles. We demonstrate the utility of our resource by identifying the first comprehensive genome-wide set of tissue-specific differentially methylated regions (tDMRs) that may play a role in cellular identity and the regulation of tissue-specific genome function. We also discuss the implications of our findings with respect to the regulatory potential of regions with varied CpG density, gene expression, transcription factor motifs, gene ontology, and correlation with other epigenetic marks such as histone modifications.

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JF - Genome Research

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An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)

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