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[LIFE SCIENCE] Ikebukuro Team

Development of analytical method for CpG methylation of genomic DNA based on its structural change  

Team Head

Kazunori Ikebukuro

Affiliation Institute of Engineering
Division / Department Division of Biotechnology and Life Science
Position Professor
URL http://web.tuat.ac.jp/~tanpaku/

Foreign Researcher(s)

Richard J. Simpson

Affiliation La Trobe University(Australia)
Division / Department Department of Biochemistry and Genetics
Position Professor
URL https://scholars.latrobe.edu.au/display/r2simpson

Koji Sode

Affiliation University of North Carolina at Chapel Hill (U.S.A.)
Division / Department Joint Department of Biomedical Engineering
Position Professor
URL https://www.bme.unc.edu/people/koji-sode/

Man Bock Gu

Affiliation Korea University (Korea)
Division / Department Department of Biotechnology
Position Professor
URL https://koreauniv.pure.elsevier.com/en/persons/man-bock-gu

Members

Kazunori Ikebukuro (Institute of Engineering / Professor), Hiroki Oguri(Institute of Engineering / Professor), Jun-ichi Shirakashi(Institute of Engineering / Professor), Makoto Shibutani(Institute of Agriculture / Professor), Hiroko Tabunoki (Institute of Agriculture / Associate Professor), Yue Ma(Institute of Global Innovation / Assistant Professor)

Overview

The pattern of DNA methylations of human genomic DNA (mainly cytosine methylation of CG sequence, so it is called as CpG methylation) is the promising onset marker because it changes in daily life depending on the lifestyle habits of the individuals. Therefore the development of its quick analytical method is urgently required for the establishment of the prevention medicine or preemptive medical care. We made a first remark on the relationship between CpG methylation of human genomic DNA and G-quadruplex structure formation and determined to develop the analytical method of CpG methylation pattern of human genomic DNA by detecting the structural change of the G-quadruplex formed in the target regions of human genomic DNA.

Approaches

Analysis of CpG methylation pattern would be promising for the presymptomatic diagnosis and the development of its quick analytical method is urgently required for the promotion of the prevention medicine or preemptive medical care.
Bisulfite sequencing is the golden standard and very powerful tools for analysis of CpG methylation of human genomic DNA but it is not suitable for quick presymptomatic diagnosis because it requires many steps and severe chemical reactions.
PCR is also the golden standard for genetic analysis and the most of the quick analytical methods for genetic information is designed with the use of PCR, but it is currently difficult to amplify the CpG methylation with enzymatic reactions. Therefore, the method for useful quick analysis of CpG patterns of human genomic DNA, based on total different from the conventional genetic analysis method is strongly required.
We focused on the G-quadruplex (G4) structures formed in the CpG methylation site of human genomic DNA and try to develop analytical method of CpG methylation based on the structural change of G4 in the target region.

Plan

To develop the analytical method for the CpG methylation of the target region of the human genomic DNA based on the change of G-quadruplex (G4), we will perform the following four researches.
1) Analysis of the relationship between the G4 structures and its CpG methylation of the oligonucleotides with various sequences.
2) The screening of the small molecule ligands against the CpG methylated G4 structures.
3) The screening of the proteins against the CpG methylated G4 structures.
4) Development of the detection method or devise for the structural change of G4, binding of the small ligand against the methylated G4, or binding of the protein against the methylated G4.
We have already found and reported approximately 2000 of target regions from the CpG islands of human genomic DNA and we will use some of them as the target sequences.

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