Researchers elucidate new mechanism for controlling DNA methylation in cells

Reviewed by James Ives, M.Psych. (Editor)Mar 17 2020

Why normal cells turn into cancer cells One of the factors is deeply related to the failure of the cell differentiation mechanism called DNA methylation. The joint research groups of The Institute of Medical Science, the University of Tokyo, Yokohama City University, and Center for Integrated Protein Science Munich (CIPSM) have clarified new mechanism for controlling DNA methylation in cells.

Ubiquitination of a protein called PAF15 is an important factor for the inheritance of DNA methylation, according to the new research. The group also successfully demonstrated a molecular mechanism by which PAF15 is ubiquitinated. In this way, the group revealed the mechanism underlying how cellular memory is inherited when cells proliferate.

The research was published in Nature Communications (online version, March 6, 2020). The results are expected to greatly contribute to applications in this field, such as the development of new inhibitors of DNA methyltransferase that specifically target cancer cells.

The primary mechanism of this DNA methylation has not been fully elucidated

There are two factors that transform normal cells into cancer cells. One is a genetic mutation that alters the DNA sequence, and the other is an epigenetic mutation that changes how genes are used. An epigenetic mutation is defined as an aberrant pattern of "DNA methylation" and "histone modification". When cells proliferate, both genetic and epigenetic mutations are transmitted to new cells.

The research team decided to investigate the mechanism of faithful "DNA methylation inheritance" which is critical for cancer suppression and has not been sufficiently investigated.

As one of the lead researchers, associate professor Atsuya Nishiyama of the University of Tokyo, explains as follows:

Every cell has the same genetic information. Each cell has very different characteristics. It is DNA methylation that determines the characteristics of each cell. Until now, the correlation between the failure of the mechanism of DNA methylation and cancer of cells was known, but how DNA methylation controls disease was not. That's why we conducted research to understand the basic mechanisms of DNA methylation."

PAF15 is a factor guaranteeing the maintenance of DNA methylation

The research group conducted experiments using a cell-free system derived from Xenopus laevis eggs to analyze the DNMT1 protein complex. Their work resulted in the new discovery of PAF15 as a factor that specifically binds to DNMT1.

Further analysis revealed that PAF15 binds to chromosomes via PCNA during DNA replication, The research group also showed that two lysine residues of PAF15 undergo monoubiquitination by UHRF1 to facilitate DNMT1 chromatin localization. These results indicate that PAF15 is an important regulator of DNMT1.

During unperturbed S-phase, most of the DNMT1 on the chromosome was bound to ubiquitinated PAF15. Elevated histone H3 ubiquitination levels and the interaction between DNMT1 and ubiquitinated H3 were observed in conjunction with the inhibition of PAF15 function.

This finding suggests that PAF15 ubiquitination is the primary pathway controlling DNMT1 localization to DNA methylation sites, and that histone H3 ubiquitination may serve as a backup system. The team also introduced mutations to amino acids at the ubiquitination site of PAF15 in mouse ES cells, and found that the level of DNA methylation in the whole genome was greatly reduced, thus making it clear that PAF15 was a factor guaranteeing the maintenance of DNA methylation.

Potential to greatly contribute to the development of DNA methylase inhibitors

DNA methylase is also attracting attention as a material for anticancer drugs. The results of this study have shown not only the scientific significance of clarifying the new mechanism of DNA methylation inheritance, but also the potential to greatly contribute to the development of DNA methyltransferase inhibitors.

In addition, it has been reported that PAF15 is over-expressed in various cancer cells. It will be important to clarify the effect of PAF15 on DNA methylation control in the future.