Circadian E-boxes and surrounding CpG islands are free from methylation throughout the day

Abstract

Circadian E-boxes in the promoters of mPer1, mPer2, mCry1 and mDBP play a key role in regulating rhythmic gene expression by recruiting the BMAL1/CLOCK heterodimer. However, each of these circadian E-boxes seems different from one another. In the mouse liver, BMAL1/CLOCK binds to E-boxes in the mPer1 and mPer2 promoters constantly but binds with dynamic daily changes to mCry1 and mDBP promoters. It is unclear whether DNA methylation of these circadian E-boxes and the surrounding CpG islands would affect protein/DNA interactions and lead to distinct binding features. In the present study, bisulfite sequencing analysis indicated that all E-boxes and their surrounding CpG islands were free from methylation, suggesting that DNA methylation does not determine distinct binding features. The methylation status of the E-box in the MAP kinase phosphatase 1 (MKP1) promoter was also examined. Our results indicated that DNA methylation does not regulate the tissue-specific clock control of MKP1.

Keywords:

• clock gene
• circadian rhythm
• E-box
• CpG island
• methylation

Acknowledgements

The authors thank Jingyan Song for helpful discussion. Research support was provided by the National Natural Science Foundation of China (81071011, 30400148, 30430280), the National 973 Project Grant of China (2006CB500701, 2006CB943703, 2007CB947704), the National 863 Project Grant of China (2006AA02A408, 2006AA02A112, 2006AA02A114) and the Scientific Project of Beijing Municipal Science & Technology Commission (D07050701350703, D07050701350706).