CpG Methylation Altered the Stability and Structure of the i-Motifs Located in the CpG Islands
Cytosine methylation within the 5′-C-phosphate-G-3′ sequence of nucleotides (called CpG methylation) is a well-known epigenetic modification of genomic DNA that plays an important role in gene expression and development. CpG methylation is likely to be altered in the CpG islands. CpG islands are ric...
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MDPI AG
2022-06-01
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| Series: | International Journal of Molecular Sciences |
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| author | Daiki Oshikawa Shintaro Inaba Yudai Kitagawa Kaori Tsukakoshi Kazunori Ikebukuro |
| author_facet | Daiki Oshikawa Shintaro Inaba Yudai Kitagawa Kaori Tsukakoshi Kazunori Ikebukuro |
| author_sort | Daiki Oshikawa |
| collection | DOAJ |
| description | Cytosine methylation within the 5′-C-phosphate-G-3′ sequence of nucleotides (called CpG methylation) is a well-known epigenetic modification of genomic DNA that plays an important role in gene expression and development. CpG methylation is likely to be altered in the CpG islands. CpG islands are rich in cytosine, forming a structure called the i-motif via cytosine-cytosine hydrogen bonding. However, little is known about the effect of CpG methylation on the i-motif. In this study, The CpG methylation-induced structural changes on the i-motif was examined by thermal stability, circular dichroism (CD) spectroscopy, and native-polyacrylamide gel electrophoresis (Native-PAGE) evaluation of five i-motif-forming DNAs from four cancer-related genes (<i>VEGF</i>, <i>C-KIT</i>, <i>BCL2</i>, and <i>HRAS</i>). This research shows that CpG methylation increased the transitional pH of several i-motif-forming DNAs and their thermal stability. When examining the effect of CpG methylation on the i-motif in the presence of opposite G4-forming DNAs, CpG methylation influenced the proportion of G4 and i-motif formation. This study showed that CpG methylation altered the stability and structure of the i-motif in CpG islands. |
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| format | Article |
| id | doaj.art-01e000f9981e4899adbe911eb57b5727 |
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| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T23:35:39Z |
| publishDate | 2022-06-01 |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-01e000f9981e4899adbe911eb57b57272023-11-23T17:01:18ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-06-012312646710.3390/ijms23126467CpG Methylation Altered the Stability and Structure of the i-Motifs Located in the CpG IslandsDaiki Oshikawa0Shintaro Inaba1Yudai Kitagawa2Kaori Tsukakoshi3Kazunori Ikebukuro4Graduate School of Management of Technology, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, JapanDepartment of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, JapanDepartment of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, JapanDepartment of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, JapanDepartment of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, JapanCytosine methylation within the 5′-C-phosphate-G-3′ sequence of nucleotides (called CpG methylation) is a well-known epigenetic modification of genomic DNA that plays an important role in gene expression and development. CpG methylation is likely to be altered in the CpG islands. CpG islands are rich in cytosine, forming a structure called the i-motif via cytosine-cytosine hydrogen bonding. However, little is known about the effect of CpG methylation on the i-motif. In this study, The CpG methylation-induced structural changes on the i-motif was examined by thermal stability, circular dichroism (CD) spectroscopy, and native-polyacrylamide gel electrophoresis (Native-PAGE) evaluation of five i-motif-forming DNAs from four cancer-related genes (<i>VEGF</i>, <i>C-KIT</i>, <i>BCL2</i>, and <i>HRAS</i>). This research shows that CpG methylation increased the transitional pH of several i-motif-forming DNAs and their thermal stability. When examining the effect of CpG methylation on the i-motif in the presence of opposite G4-forming DNAs, CpG methylation influenced the proportion of G4 and i-motif formation. This study showed that CpG methylation altered the stability and structure of the i-motif in CpG islands.https://www.mdpi.com/1422-0067/23/12/6467CpG methylationepigeneticsCpG islandsi-motifG-quadruplexpH dependance |
| spellingShingle | Daiki Oshikawa Shintaro Inaba Yudai Kitagawa Kaori Tsukakoshi Kazunori Ikebukuro CpG Methylation Altered the Stability and Structure of the i-Motifs Located in the CpG Islands International Journal of Molecular Sciences CpG methylation epigenetics CpG islands i-motif G-quadruplex pH dependance |
| title | CpG Methylation Altered the Stability and Structure of the i-Motifs Located in the CpG Islands |
| title_full | CpG Methylation Altered the Stability and Structure of the i-Motifs Located in the CpG Islands |
| title_fullStr | CpG Methylation Altered the Stability and Structure of the i-Motifs Located in the CpG Islands |
| title_full_unstemmed | CpG Methylation Altered the Stability and Structure of the i-Motifs Located in the CpG Islands |
| title_short | CpG Methylation Altered the Stability and Structure of the i-Motifs Located in the CpG Islands |
| title_sort | cpg methylation altered the stability and structure of the i motifs located in the cpg islands |
| topic | CpG methylation epigenetics CpG islands i-motif G-quadruplex pH dependance |
| url | https://www.mdpi.com/1422-0067/23/12/6467 |
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