Evaluating the role of cis-regulatory tandem DNA repeats in human disease and evolution
| Project/Area Number |
21H02460
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| Research Category |
Grant-in-Aid for Scientific Research (B)
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| Allocation Type | Single-year Grants |
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| Section | 一般 |
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| Review Section |
Basic Section 43050:Genome biology-related
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| Research Institution | Kyoto University |
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Principal Investigator |
ウォルツェン クヌート 京都大学, iPS細胞研究所, 准教授 (50589489)
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| Co-Investigator(Kenkyū-buntansha) |
川路 英哉 公益財団法人東京都医学総合研究所, ゲノム医学研究センター, 副センター長 (20525406)
依馬 正次 滋賀医科大学, 動物生命科学研究センター, 教授 (60359578)
井上 詞貴 京都大学, 高等研究院, 特定准教授 (60525369)
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| Project Period (FY) |
2021-04-01 – 2024-03-31
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| Project Status |
Completed (Fiscal Year 2023)
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| Budget Amount *help |
¥17,420,000 (Direct Cost: ¥13,400,000、Indirect Cost: ¥4,020,000)
Fiscal Year 2023: ¥5,070,000 (Direct Cost: ¥3,900,000、Indirect Cost: ¥1,170,000)
Fiscal Year 2022: ¥5,850,000 (Direct Cost: ¥4,500,000、Indirect Cost: ¥1,350,000)
Fiscal Year 2021: ¥6,500,000 (Direct Cost: ¥5,000,000、Indirect Cost: ¥1,500,000)
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| Keywords | ゲノム編集 / ゲノム解析 / DNAリピート / ヒトiPS細胞 / CRISPR-Cas9 / iPS細胞 / レポーターアッセイ |
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| Outline of Research at the Start |
The expansion of genomic tandem repeats is coincident with the rapid evolutionary trajectory of hominid species. However, apart from a few rare examples, associations between repeat sequences and biological function remain statistical. How extensively have non-coding DNA repeat variants influenced primate brain evolution and human neurological disease? In this study we will develop a variant classification and genome editing framework in primate stem cells for defining the role of tandem repeats in primate gene regulation and their influence on disease and evolution.
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| Outline of Annual Research Achievements |
Variable Number Tandem Repeats (VNTRs) are repetitive DNA sequences that differ in number between individuals. VNTR copy number is shown to correlate with changes in gene expression, and are probable causes of human disease. To understand these relationships, we developed a new bioinformatic pipeline to identify, analyze, and design gene editing strategies for VNTRs. We characterized 5 VNTRs for copy-number polymorphisms across 22 human iPS cell lines. We designed CRISPR-Cas9 strategies that target and cut each repeats, which triggers cellular DNA repair and reduces the repeat number to one. We verified the repeat sequence with long-read nanopore technology. Moreover, we developed a new gene editing strategy to control VNTR copy-number reduction, which has never been previously achieved. We used this method to generate iPS cells with VNTRs of various copy numbers for disease modeling. With these novel tools, we have begun to study VNTRs more broadly across the human genome and in non-human primate models.
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| Research Progress Status |
令和5年度が最終年度であるため、記入しない。
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| Strategy for Future Research Activity |
令和5年度が最終年度であるため、記入しない。
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Report
(3 results)
Research Products
(14 results)
