Genome-wide characterization of cytosine-specific 5-hydroxymethylation in normal breast tissue

Abstract

Despite recent evidence that 5-hydroxymethylcytosine (5hmC) possesses roles in gene regulation distinct from 5-methylcytosine (5mC), relatively little is known regarding the functions of 5hmC in mammalian tissues. To address this issue, we utilized an approach combining both paired bisulfite (BS) and oxidative bisulfite (oxBS) DNA treatment, to resolve genome-wide patterns of 5hmC and 5mC in normal breast tissue from disease-free women. Although less abundant than 5mC, 5hmC was differentially distributed, and consistently enriched among breast-specific enhancers and transcriptionally active chromatin. In contrast, regulatory regions associated with transcriptional inactivity, such as heterochromatin and repressed Polycomb regions, were relatively depleted of 5hmC. Gene regions containing abundant 5hmC were significantly associated with lactate oxidation, immune cell function, and prolactin signaling pathways. Furthermore, genes containing abundant 5hmC were enriched among those actively transcribed in normal breast tissue. Finally, in independent data sets, normal breast tissue 5hmC was significantly enriched among CpG loci demonstrated to have altered methylation in pre-invasive breast cancer and invasive breast tumors. Primarily, our findings identify genomic loci containing abundant 5hmC in breast tissues and provide a genome-wide map of nucleotide-level 5hmC in normal breast tissue. Additionally, these data suggest 5hmC may participate in gene regulatory programs that are dysregulated during breast-related carcinogenesis.

TET2 Inhibits PD-L1 Gene Expression in Breast Cancer Cells through Histone Deacetylation

“…Previous reports have showed that the downregulation of TET2 expression and 5hmC levels is an epigenetic hallmark of multiple types of cancers [ 21 , 40 , 41 , 42 ]. Dysregulation of the TET2/5hmC pathway promotes epithelial–mesenchymal transition (EMT), chemotherapy resistance, proliferation, invasion, and metastasis during breast cancer pathogenesis [ 43 , 44 , 45 ]. Based on the afore-mentioned regulatory mechanism, we speculate that TET2 loss may facilitate immune evasion by breast cancer cells through upregulating PD-L1 gene expression.…”

DNA 5-hydroxymethylcytosine in pediatric central nervous system tumors may impact tumor classification and is a positive prognostic marker

“…Unlike methylcytosine, 5hmC concentrates in gene bodies and enhancers and is associated with increased gene expression [ 13 – 15 ]. 5hmC tends to be depleted in promoter CpG islands and is instead observed in the flanking CpG shores and shelves [ 14 , 16 ].…”

Hydroxymethylation profile of cell free DNA is a biomarker for early colorectal cancer

“…5mC is oxidized to form hydroxymethylcytosine (5hmC), formylcytosine (5fC) and carboxylcytosine (5caC). 5mC and 5hmC have different functional roles: 5mC is present in heterochromatin and euchromatin and generally represses gene expression 17 whereas 5hmC is mainly present in euchromatin and is associated with the mostly highly transcribed gene bodies and their enhancers 18,19 , as well as with poised enhancers about to transition from inactive to active 20 . 5mC and 5hmC have differential a nity to epigenetic readers; for instance, methyl binding proteins (MBD) preferentially bind 5mC.…”