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.
authors.affiliation: Institute of Cell and Molecular Science, Barts and the London, London E1 2AT, United Kingdom. v.rakyan@qmul.ac.uk
authors.forename: Vardhman K
authors.initials: VK
authors.lastname: Rakyan
authors.forename: Thomas A
authors.initials: TA
authors.lastname: Down
authors.forename: Natalie P
authors.initials: NP
authors.lastname: Thorne
authors.forename: Paul
authors.initials: P
authors.lastname: Flicek
authors.forename: Eugene
authors.initials: E
authors.lastname: Kulesha
authors.forename: Stefan
authors.initials: S
authors.lastname: Gräf
authors.forename: Eleni M
authors.initials: EM
authors.lastname: Tomazou
authors.forename: Liselotte
authors.initials: L
authors.lastname: Bäckdahl
authors.forename: Nathan
authors.initials: N
authors.lastname: Johnson
authors.forename: Marlis
authors.initials: M
authors.lastname: Herberth
authors.forename: Kevin L
authors.initials: KL
authors.lastname: Howe
authors.forename: David K
authors.initials: DK
authors.lastname: Jackson
authors.forename: Marcos M
authors.initials: MM
authors.lastname: Miretti
authors.forename: Heike
authors.initials: H
authors.lastname: Fiegler
authors.forename: John C
authors.initials: JC
authors.lastname: Marioni
authors.forename: Ewan
authors.initials: E
authors.lastname: Birney
authors.forename: Tim J P
authors.initials: TJ
authors.lastname: Hubbard
authors.forename: Nigel P
authors.initials: NP
authors.lastname: Carter
authors.forename: Simon
authors.initials: S
authors.lastname: Tavaré
authors.forename: Stephan
authors.initials: S
authors.lastname: Beck
mesh_terms: D000465:Algorithms; D018899:CpG Islands; D004247:DNA / Q000378:metabolism; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D020869:Gene Expression Profiling / Q000379:methods; D015894:Genome, Human; D006801:Humans; D012984:Software
chemical_list: D004247:DNA