Genomic distribution of 5-Hydroxymethylcytosine in mouse kidney and its relationship with gene expression

Abstract

Ten-Eleven Translocation (TET) proteins oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytonsie (5hmC). Our recent work found a decline in global 5hmC level in mouse kidney insulted by ischemia reperfusion (IR). However, the genomic distribution of 5hmC in mouse kidney and its relationship with gene expression remain elusive. Here, we profiled the DNA hydroxymethylome of mouse kidney by hMeDIP-seq and revealed that 5hmC is enriched in genic regions but depleted from intergenic regions. Correlation analyses showed that 5hmC enrichment in gene body is positively associated with gene expression level in mouse kidney. Moreover, IR injury-associated genes (both up-and down-regulated genes during renal IR injury) in mouse kidney exhibit significantly higher 5hmC enrichment in their gene body regions when compared to those unchanged genes. Collectively, our study not only provides the first DNA hydroxymethylome of kidney tissues but also suggests that DNA hyper-hydroxymethylation in gene body may be a novel epigenetic marker of IR injury-associated genes.ARTICLE HISTORY

Ten-eleven translocation methyl-cytosine dioxygenase 2 deficiency exacerbates renal ischemia-reperfusion injury

“…We have previously shown that Tet2 is dramatically downregulated in the IR-injured kidney, which is accompanied by a reduction of the global 5hmC level [7]. By performing hydroxymethylated DNA immunoprecipitation sequencing (hMeDIP-seq) analysis, we also revealed that 5hmC was enriched in the gene body regions of renal IR injuryassociated genes [8]. In addition, a few studies have shown that Tet3 confers protection against kidney fibrosis [9][10][11].…”

Distributive Processing by the Iron(II)/α-Ketoglutarate-Dependent Catalytic Domains of the TET Enzymes Is Consistent with Epigenetic Roles for Oxidized 5-Methylcytosine Bases

“…Mammalian ten-eleven translocation (TET) proteins are iron­(II)- and α-ketoglutarate-dependent (Fe/αKG) oxygenases that transform this methylated base ( 5m C) to 5-hydroxymethylcytosine ( 5hm C), 5-formylcytosine ( 5f C), and 5-carboxycytosine ( 5ca C) in three consecutive reactions. − In each step, substrate oxidation is coupled to conversion of αKG to succinate and CO 2 (Scheme ). , Results from studies such as those demonstrating in vitro recognition and excision of 5f C and 5ca C by thymine-DNA glycosidase (TDG) and increased levels of the two modifications in mouse embryonic stem cells lacking TDG supported the notion that the oxidized species might merely be intermediates in the active reversion of the 5m C marker. − However, recent data revealing the association of 5hm C, 5f C, and 5ca C with regulatory elements have led to the hypothesis that they might have their own roles in gene regulation. ,, This is supported by enrichment-based and single-base resolution sequencing studies, which show 5hm C, 5f C, and 5ca C to be enriched at various promoter, enhancer, and exon sites. ,− Two recent studies by Bachman and co-workers showed that 5hm C and 5f C are both stable modifications in mouse DNA and are most abundant in the adult brain. , Levels of 5m C-oxidized forms in various tissues did not correlate with the levels of their oxidation precursors. ,, Both sets of observations imply that the three-step oxidation of 5m C to 5ca C does not occur on a genome-wide level but is probably limited to specific sequences and directed by specific cellular signals. All in all, the above observations evoke a role for 5m C modifications in gene regulation.…”

The chromatin accessibility landscape in the dental pulp of mouse molars and incisors

“…To clarify the relationship between ATAC-seq enrichment and RNA expression, we used a previously published approach (Wang et al, 2016) where genes are separated into five groups (10-20%, 20-40%, 40-60%, 60-80% and 80-100%) based on their mRNA expression levels. Box plots of average ATAC-seq peak values were generated for each group of genes in promoter and gene bodies for studying both incisors and molars.…”

“…To analyze the correlation between gene expression and the ATAC-seq signals at the promoter and gene body regions, we used a previously published approach (Wang et al, 2016). Briefly, we separated genes into five groups according to their expression levels (from low to high: 0-20%, 20-40%, 40-60%, 60-80% and 80-100%) (A) ATAC-seq peaks are primarily enriched in the intergenic regions and gene bodies of both the incisor and molar genomes.…”