[HTML][HTML] Characterization of tissue-specific differential DNA methylation suggests distinct modes of positive and negative gene expression regulation

J Wan, VF Oliver, G Wang, H Zhu, DJ Zack, SL Merbs… - BMC genomics, 2015 - Springer
J Wan, VF Oliver, G Wang, H Zhu, DJ Zack, SL Merbs, J Qian
BMC genomics, 2015Springer
Background DNA methylation plays an important role in regulating gene expression during
many biological processes. However, the mechanism of DNA-methylation-dependent gene
regulation is not fully understood. Here, we explore two possible DNA methylation regulatory
mechanisms with opposite modes of gene expression regulation. Results By comparing the
genome-wide methylation and expression patterns in different tissues, we find that majority
of tissue-specific differentially methylated regions (T-DMRs) are negatively correlated with …
Background
DNA methylation plays an important role in regulating gene expression during many biological processes. However, the mechanism of DNA-methylation-dependent gene regulation is not fully understood. Here, we explore two possible DNA methylation regulatory mechanisms with opposite modes of gene expression regulation.
Results
By comparing the genome-wide methylation and expression patterns in different tissues, we find that majority of tissue-specific differentially methylated regions (T-DMRs) are negatively correlated with expression of their associated genes (negative T-DMRs), consistent with the classical dogma that DNA methylation suppresses gene expression; however, a significant portion of T-DMRs are positively correlated with gene expression (positive T-DMRs). We observe that the positive T-DMRs have similar genomic location as negative T-DMRs, except that the positive T-DMRs are more enriched in the promoter regions. Both positive and negative T-DMRs are enriched in DNase I hypersensitivity sites (DHSs), suggesting that both are likely to be functional. The CpG sites of both positive and negative T-DMRs are also more evolutionarily conserved than the genomic background. Interestingly, the putative target genes of the positive T-DMR are enriched for negative regulators such as transcriptional repressors, suggesting a novel mode of indirect DNA methylation inhibition of expression through transcriptional repressors. Likewise, two distinct sets of DNA sequence motifs exist for positive and negative T-DMRs, suggesting that two distinct sets of transcription factors (TFs) are involved in positive and negative regulation mediated by DNA methylation.
Conclusions
We find both negative and positive association between T-DMRs and gene expression, which implies the existence of two different mechanisms of DNA methylation-dependent gene regulation.
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