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Shinya Oki Last modified date:2019.07.02





E-Mail
Homepage
http://www.dev.med.kyushu-u.ac.jp
Lab Home Page (Developmental Biology) .
https://researchmap.jp/okishinya/
Researchmap (Shinya Oki) .
http://chip-atlas.org
ChIP-Atlas (An integrative and comprehensive database for published ChIP-seq data) .
http://www.devbio.med.kyushu-u.ac.jp/sra_tailor/
SraTailor (A simple GUI software for processing ChIP-seq data) .
Academic Degree
Ph.D in Medicine
Field of Specialization
Developmental biology, Bioinformatics
Research
Research Interests
  • Development of the tools for analyzing and exploiting the ChIP-seq data.
    keyword : ChIP-seq, Data processing, Visualization
    2014.04~2017.04.
  • Dissection of the role of Nodal signaling in early mouse development
    keyword : Mouse, development, Nodal
    2011.04~2017.04.
  • Dissecting the Role of Fgf Signaling During Gastrulation and Left-Right Axis Formation in Mouse Embryos
    keyword : left-right asymmetry, nodal, node, lateral plate
    2009.04~2011.03Situs-specific organogenesis in the mouse results from leftward fluid flow in the node cavity and subsequent left-sided expression of Nodal in lateral plate mesoderm (LPM). Nodal expression at the node is essential for the subsequent asymmetric Nodal expression in left LPM, but the precise role of Nodal produced at the node has remained unknown. We have now investigated how the Nodal signal is transferred from the node to LPM. Externally supplied Nodal protein did not signal to LPM, suggesting that the Nodal signal is transferred to LPM via an internal route rather than an external one. Transgenic rescue experiments showed that the Nodal coreceptor Cryptic is required only in LPM, not at the node, for asymmetric Nodal expression in LPM, indicating that the Nodal signal is not relayed indirectly between the node and LPM. Nodal interacts in vitro with sulfated glycosaminoglycans (GAGs), which are specifically localized to the basement membrane–like structure between the node and LPM in the mouse embryo. Inhibition of sulfated GAG biosynthesis prevents Nodal expression in LPM. These data suggest that Nodal produced at the node may travel directly to LPM through interaction with sulfated GAGs..
Academic Activities
Papers
1. Oki, S*., Ohta, T., Shioi, G., Hatanaka, H., Ogasawara, O., Okuda, Y., Kawaji, H., Nakaki, R., Sese, J., and Meno, C* , ChIP-Atlas: a data-mining suite powered by full integration of public ChIP-seq data.
, EMBO Rep, 10.15252/embr.201846255, e46255, 2018.11.
2. Shinya Oki, Tazro Ohta, Go Shioi, Hideki Hatanaka, Osamu Ogasawara, Yoshihiro Okuda, Hideya Kawaji, Ryo Nakaki, Jun Sese & Chikara Meno, Integrative analysis of transcription factor occupancy at enhancers and disease risk loci in noncoding genomic regions, bioRxiv, 10.1101/262899, 2018.02, 論文などで報告されたほぼ全てのChIP-seqデータを統合解析することにより、組織特異性や遺伝性疾患の解明につながる発見を報告した。.
3. Shinya Oki, Kazumitsu Maehara, Yasuyuki Ohkawa, Chikara Meno, SraTailor: Graphical user interface software for processing and visualizing ChIP-seq data, Genes to Cells, 10.1111/gtc.12190, 19, 12, 919-926, 2014.12.
4. Shinya Oki, Keiko Kitajima, and Chikara Meno, Dissecting the Role of Fgf Signaling During Gastrulation and Left-Right Axis Formation in Mouse Embryos Using Chemical Inhibitors, Developmental Dynamics, 239, 6, 1768-1778, 2010.07.
5. Shinya Oki, Keiko Kitajima, Sara Marques, José António Belo, Takahiko Yokoyama, Hiroshi Hamada, and Chikara Meno, Reversal of left-right asymmetry induced by aberrant Nodal signaling in the node of mouse embryos, Development, in press, 2009.09.
6. Shinya Oki, Ryuju Hashimoto, Yuko Okui, Michael M. Shen, Eisuke Mekada, Hiroki Otani, Yukio Saijoh, and Hiroshi Hamada, Sulfated glycosaminoglycans are necessary for Nodal signal transmission from the node to the left lateral plate in the mouse embryo, Development, 134 (21) 3893-3904, 2007.11.
Works, Software and Database
1. An integrative and comprehensive database for visualizing and making use of public ChIP-seq data.
[URL].
2. .
Presentations
1. Shinya Oki, Tazro Ohta, Go Shioi, Hideki Hatanaka, Osamu Ogasawara, Yoshihiro Okuda, Hideya Kawaji, Ryo Nakaki, Jun Sese, Chikara Meno, Integrative analysis of transcription factor occupancy at enhancers and disease risk loci in noncoding genomic regions, Keystone Symposium; Gene Control in Development and Disease, 2018.03.
2. Shinya Oki, Tazro Ohta, Go Shioi, Hideki Hatanaka, Osamu Ogasawara, Yoshihiro Okuda, Hideya Kawaji, Ryo Nakaki, Jun Sese, Chikara Meno, Integrative analysis of transcription factor occupancy at enhancers and disease risk loci in noncoding genomic regions, 50th Annual Meeting of the Japanese Society of Developmental Biologists, 2017.05.
3. Shinya Oki, Tazro Ohta, Go Shioi, Hideki Hatanaka, Osamu Ogasawara, Yoshihiro Okuda, Hideya Kawaji, Ryo Nakaki, Jun Sese, Chikara Meno, The transcription factor landscape decodes the enhancers and risk variants in non-coding regions, Keystone Symposium; Epigenetics and Human Disease: Progress from Mechanisms to Therapeutics, 2017.01.
4. 沖 真弥, Comprehensive and integrative database and analysis of published ChIP-seq data, 横浜理研セミナー, 2016.04.
5. Shinya Oki, Tazro Ohta, Go Shioi, Ryo Nakaki, Osamu Ogasawara, Yoshihiro Okuda, Hideki Hatanaka, Chikara Meno, ChIP-Atlas: Comprehensive and integrative database for visualizing and mining all published ChIP-seq data., SYSTEMS BIOLOGY: GLOBAL REGULATION OF GENE EXPRESSION, 2016.03.
6. 沖 真弥, 大田 達郎, 塩井 剛, 仲木 竜, 目野 主税, Comprehensive database for visualizing all published ChIP-seq data, 48th Annual Meeting of JSDB, 2015.06.
7. 沖 真弥, How to visualize published ChIP-seq raw data.
, CDB seminar, 2014.07.
8. 沖 真弥, SraTailor: GUI software for visualizing high-throughput sequence read archives, 47th Annual Meeting for the Japanese Society of Developmental Biologists , 2014.05.
9. 沖 真弥, 目野 主税, Development of a Mac GUI Application to Visualize Published Raw ChIP-seq data, The 61st NIBB Conference Cellular Community in Mammalian Embryogenesis, 2013.07.
10. Dissecting the Role of Fgf Signaling During Gastrulation and Left-Right Axis Formation in Mouse Embryos Using Chemical Inhibitors.
11. Shinya Oki, Keiko Kitajima, Hiroshi Hamada, and Chikara Meno, Sulfated glycosaminoglycans are required for gastrulation, cell fate decision, and left-right axis formation in mouse embryo, 5th Global COE International Symposium, 2010.02.
12. The left-right axis of mammalian embryos is triggered by the nodal flow, a leftward fluid flow on the surface of the node. A secretory protein, Nodal, is then produced in the node and subsequently in the left side of the lateral plate mesoderm (LPM) depending on the nodal flow. At 1992, a recessive mutant, inv, was discovered, which displays complete situs inversus with reversed expression of Nodal in the LPM. It would be the simplest scenario if the nodal flow were ‘rightward’ in inv mutant. Mysteriously, however, the case is ‘leftward’. Why?
Here, we show that two Nodal inhibitors, Lefty and Cerl2, are aberrantly expressed in inv mutant and perturb Nodal signaling around the node, thereby resulting in reversed expression of Nodal in the LPM. Furthermore, we found that the leftward nodal flow is indispensable for the processes. With these results, we propose a reasonable mechanism that solves the longstanding mystery: “Why does inv mutant show the left-right reversal in spite of the normal direction of the nodal flow?”.
13. Sulfated glycosaminoglycans are necessary for Nodal signal transmission from the node to the left lateral plate in the mouse embryo.
14. Nodal produced in the node is essential for L-R axis determination of the lateral plate..
Membership in Academic Society
  • Japanese Association for Medical Artificial Intelligence