DNA methylation is one of the earliest discovered epigenetic markers and plays an important role in regulating gene expression in eukaryotic cells. With the advancement of DNA methylation detection technology, research has found that DNA methylation has two states: complete methylation and semi methylation, as well as semi methylation modifications that can be stably inherited. There is still controversy over whether DNA semi methylation has unique biological functions, and therefore research on DNA semi methylation is needed. In addition, traditional methylation detection techniques based on base chemical transformation cause significant damage to DNA, therefore there is an urgent need to develop more mild and efficient semi methylation detection methods.
Xu Chenhuan's team from the Beijing Genome Research Institute (National Center for Biological Information) of the Chinese Academy of Sciences has developed a semi methylation measurement technology that does not rely on base transformation - MspJI assisted semi methylation sequencing, using the restriction endonuclease MspJI that specifically recognizes DNA single strand methylation. Compared to traditional DNA methylation detection techniques, Mhemi seq has two advantages: firstly, Mhemi seq does not rely on base conversion, avoiding damage to DNA, and therefore can more efficiently identify the methylation status of CpG in trace amounts of DNA; Secondly, Mhemi seq can directly identify the semi methylation status on a single CpG by analyzing the cleavage sites of MspJI.
Researchers applied Mhemi seq to the lymphoblastic cell line GM12878 and two types of human embryonic stem cells H1 and H9, and established methylation and semi methylation profiles for these three types of cells. The methylation pattern generated by Mhemi seq is basically consistent with the methylation pattern obtained by base chemical transformation methods, proving that Mhemi seq can accurately capture the DNA methylation state at a single CpG resolution. The study analyzed the results of Mhemi seq and found that semi methylated CpG can inhibit the binding of transcription factor CTCF and gene expression regulated by PCGF1, and its inhibition degree is similar to that of complete methylation, suggesting that semi methylation may achieve the regulatory effect of DNA methylation on gene expression. In addition, this study utilized Mhemi seq to identify a special type of DNA hemimethylation associated with Alu expression on the reversed transposon Alu precursor.
In summary, Mhemi seq can accurately and efficiently identify the methylation and semi methylation status of CpG in the genome, providing a new convenient tool for DNA methylation research.
On January 24th, the research findings were published in the journal Nucleic Acid Research, titled "Uncovering the roles of DNA hemi methylation in transcriptional regulation using MspJI assisted hemi methylation sequencing.". The research work has received support from the National Natural Science Foundation of China and the National Key Research and Development Program.
Paper link
Mhemi seq Experimental Principle (Part 1) and the Role of Hemimethylation in CTCF Binding and PCGF1 Regulated Gene Expression (Part 2)
