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 un-changed 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.

Keywords:

• 5hmC
• gene expression
• ischemia reperfusion
• mouse kidney

Acknowledgements

We thank Li Tan, Lijun Xiong, Feizhen Wu, Ruitu Lv, and Wenqi Xu for their help in next generation sequencing and data analysis.

Disclosure statement

The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.

Funding information

This work was supported by National Natural Scientific Foundation of China [81301615] and Shanghai Natural Scientific Foundation [14ZR1406900].