Abstract
BackgroundMany groups, including our own, have proposed the use of DNA methylation profiles as biomarkers for various disease states. While much research has been done identifying DNA methylation signatures in cancer vs. normal etc., we still lack sufficient knowledge of the role that differential methylation plays during normal cellular differentiation and tissue specification. We also need thorough, genome level studies to determine the meaning of methylation of individual CpG dinucleotides in terms of gene expression.ResultsIn this study, we have used (insert statistical method here) to compile unique DNA methylation signatures from normal human heart, lung, and kidney using the Illumina Infinium 27 K methylation arraysand compared those to gene expression by RNA sequencing. We have identified unique signatures of global DNA methylation for human heart, kidney and liver, and showed that DNA methylation data can be used to correctly classify various tissues. It indicates that DNA methylation reflects tissue specificity and may play an important role in tissue differentiation. The integrative analysis of methylation and RNA-Seq data showed that gene methylation and its transcriptional levels were comprehensively correlated. The location of methylation markers in terms of distance to transcription start site and CpG island showed no effects on the regulation of gene expression by DNA methylation in normal tissues.ConclusionsThis study showed that an integrative analysis of methylation array and RNA-Seq data can be utilized to discover the global regulation of gene expression by DNA methylation and suggests that DNA methylation plays an important role in normal tissue differentiation via modulation of gene expression.
Highlights
Many groups, including our own, have proposed the use of DNA methylation profiles as biomarkers for various disease states
The methylation profiles were generated by Illumina HumanMethylation27 DNA Analysis BeadChip that contains 27,578 CpG loci located in either CpG islands or non-CpG islands of promoter regions
The DNA methylation profiles of human heart, kidney, and liver were integrated with RNA-Seq data for analysis
Summary
Many groups, including our own, have proposed the use of DNA methylation profiles as biomarkers for various disease states. Other studies have linked DNA methylation to tissuespecific gene expression by studying the promoter regions of a small number of imprinted genes and those involved in maintenance of pluripotency [13,14,15]. Both sexes use genomic imprinting to control the expression of approximately 100 imprinted genes and allowing monoallelic expression from either the maternal or paternal allele, and most imprinted genes regulate placental and fetal growth [16,17]. The inconsistent result may result from a limited number of genes being studied and differences in the CpG island content of their proximal promoter regions
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
