Bioinformatics methods for PacBio methylation data towards microbial differential epigenome analysis
| Project/Area Number |
19K20409
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| Research Category |
Grant-in-Aid for Early-Career Scientists
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| Allocation Type | Multi-year Fund |
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| Review Section |
Basic Section 62010:Life, health and medical informatics-related
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| Research Institution | National Institute of Advanced Industrial Science and Technology |
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Principal Investigator |
Saito Yutaka 国立研究開発法人産業技術総合研究所, 情報・人間工学領域, 主任研究員 (60721496)
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| Project Period (FY) |
2019-04-01 – 2022-03-31
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| Project Status |
Completed (Fiscal Year 2021)
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| Budget Amount *help |
¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000)
Fiscal Year 2021: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2020: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2019: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
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| Keywords | エピゲノム / DNAメチル化 / PacBio / 微生物 / バイオインフォマティクス / 機械学習 |
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| Outline of Research at the Start |
細菌や真核微生物のエピゲノム研究では、様々な種類のDNAメチル化（5mC、6mA、
4mC）を検出可能なPacBioシーケンサーが、Illuminaシーケンサーよりも広く使用されている。本研究では、PacBioデータからメチル化変化を高精度に検出する新しい解析技術を開発する。また、この手法を公開されている様々な微生物のPacBioデータに適用して、これまで見過ごされていた生育条件や発生段階によるメチル化変化の新たな発見を目指す。
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| Outline of Final Research Achievements |
In epigenome studies for bacteria and eukaryotic microorganisms, PacBio sequencers are widely used due to its ability to detect various types of DNA methylation including 6mA. When the polymerase encounters a methylated site during sequencing, it spends a longer time for incorporating the base, which is measured as a kinetics feature called inter pulse duration (IPD). In bioinformatics methods for PacBio methylation analysis, several machine learning (ML) models have been developed for using IPD for various downstream tasks e.g. methylation detection and methylation fraction estimation. In this study, we improved these ML models.
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| Academic Significance and Societal Importance of the Research Achievements |
本研究で開発した微生物エピゲノムデータ解析技術により、病原菌や環境細菌叢におけるエピゲノム研究を加速できる。これにより、人類の健康や環境問題の解決などに貢献できると期待される。
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Report
(4 results)
Research Products
(74 results)
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[Journal Article] Comprehensive epigenome characterization reveals diverse transcriptional regulation across human vascular endothelial cells2019
Author(s)
Nakato R, Wada Y, Nakaki R, Nagae G, Katou Y, Tsutsumi S, Nakajima N, Fukuhara H, Iguchi A, Kohro T, Kanki Y, Saito Y, Kobayashi M, Izumi-Taguchi A, Osato N, Tatsuno K, Kamio A, Hayashi-Takanaka Y, Wada H, Ohta S, Aikawa M, Nakajima H, Nakamura M, McGee RC, Heppner KW, Kawakatsu T, Genno M, Yanase H, Kume H, et al.
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Journal Title
Epigenetics & Chromatin
Volume: 12
Issue: 1
Pages: 77-77
DOI
Related Report
Peer Reviewed / Open Access / Int'l Joint Research
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