Epigenetic profiling of somatic tissues from human autopsy specimens identifies tissue- and individual-specific DNA methylation patterns.
DNA methylation is known to be associated with cell differentiation, aging, disease and cancer. There exists an expanding base of knowledge regarding tissue-specific DNA methylation, but we have little information about person-specific DNA methylation. Here, we analyze the DNA methylation patterns of multiple tissues from multiple individuals using a high-throughput quantitative assay of genome-wide DNA methylation, namely the Illumina GoldenGate BeadArray. DNA methylation patterns were largely conserved across 11 different tissues (r = 0.852) and across six individuals (r = 0.829), and we found that DNA was highly methylated in non-CpG islands and/or CpG sites that are not occupied by either H3K4me3 or H3K27me3 (P < 0.05). Finally, we found that the Illumina GoldenGate assay features a large number of probes (265/1505 probes, 17.6%) that contain single-nucleotide polymorphisms, which may interfere with DNA methylation analyses in genome-wide studies.
Jane Anne Nohl Division of Hematology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.
Hyang-Min
HM
Byun
Kimberly D
KD
Siegmund
Fei
F
Pan
Daniel J
DJ
Weisenberger
Gary
G
Kanel
Peter W
PW
Laird
Allen S
AS
Yang
D001344:Autopsy; D018899:CpG Islands; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D055106:Genome-Wide Association Study / Q000379:methods; D006801:Humans; D020641:Polymorphism, Single Nucleotide