Quantitative analysis of human tissue-specific differences in methylation

Abstract

Tissue-specific differentially methylated regions (tDMRs) have been identified and implicated for their indispensable involvement in mammalian development and tissue differentiation. In this report, a quantitative DNA methylation analysis was performed for 13 human orthologous regions of recently confirmed mouse tDMRs by using Sequenom Mass Array, by which bisulfite-treated fragments are quantitatively detected using time of flight masspectroscopy analysis. Eight regions were shown as tDMRs in various tissues from three independent individuals. Testis DNA samples from eight individuals were also analyzed for methylation. Interestingly, there is evidence that the DNA methylation level is divergent among individuals. DNA methylation levels of five testisspecific DMRs were significantly inversely correlated with the number of spermatocytes. However, a positive correlation was seen at tDMRs located near the TRIM38 and CASZ1 genes. Our results indicate that tDMRs are conserved between mouse and human and may have an important role in regulating tissue function, differentiation and aging.

Potential forensic application of DNA methylation profiling to body fluid identification

“…DNA methylation patterns are susceptible to change in response to environmental stimuli such as diet or stress, and are most vulnerable to a change during early in utero development. Once DNA methylation patterns are established through cellular differentiation, however, they display a limited dynamic range in normal conditions, giving various cells and tissues a unique cell-or tissuespecific DNA methylation profile [17][18][19][20][21]. Genome-wide analysis of DNA methylation also indicates that numerous tissue-specific differentially methylated regions (tDMRs) exist in the mammalian genome [22][23][24].…”

Novel identification of biofluids using a multiplex methylation sensitive restriction enzyme-PCR system

“…Some CpG loci have been reported that are related to cell differentiation [11][12][13], allowing them to be used in identifying the specific cell or tissue types through their methylation status; this also provides opportunities for identification of biofluids for forensic purposes.…”

New clustering module in BDPC bisulfite sequencing data presentation and compilation web application for DNA methylation analyses

“…(D) Methylation map compiling all methylation data sorted manually by CpG observed/expected. (EG) Tissue clusterings showing the similarity between the methylation patterns of tissues obtained by reduced representation bisulfite sequencing from 17 mouse cell types compiled in 9114 regions of interest (14) (E) by quantitative MALDI-TOF methylation analysis (13) (F) or by meDIP (11) (G).…”

“…These data were analyzed with BiQ Analyzer and processed by BDPC. Additionally, to show the usability of the new BDPC module, we processed published DNA methylation data determined using the Sequenom Mass Array (13) and data generated by deep sequencing techniques (14). …”