Ultra-discrete model and ChIP-Seq analysis for gene transcription
| Project/Area Number |
24500360
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| Research Category |
Grant-in-Aid for Scientific Research (C)
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| Allocation Type | Multi-year Fund |
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| Section | 一般 |
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| Research Field |
Bioinformatics/Life informatics
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| Research Institution | The University of Tokyo |
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Principal Investigator |
OHTA Yoshihiro 東京大学, 数理(科)学研究科(研究院), 特任教授 (80436592)
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| Co-Investigator(Kenkyū-buntansha) |
IHARA Sigeo 東京大学, 先端科学技術研究センター, 特任教授 (30345136)
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| Project Period (FY) |
2012-04-01 – 2015-03-31
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| Project Status |
Completed (Fiscal Year 2014)
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| Budget Amount *help |
¥4,940,000 (Direct Cost: ¥3,800,000、Indirect Cost: ¥1,140,000)
Fiscal Year 2014: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2013: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2012: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
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| Keywords | 超離散 / 配列解析 / 遺伝子転写 / 離散系 / シミュレーション / 数理モデル / 遺伝子 / 転写 / セルオートマトン / 超離散系 |
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| Outline of Final Research Achievements |
Previous models of traffic flow of RNA polymerase II (RNAPII) during transcription were restricted to one dimension along the DNA template. Here we modeled an application of traffic flow that allows preferential paths of different dimensions only restricted to visit some transit points. According to its position, an RNAPII protein molecule prefers paths obeying two types of time-evolution rules. One is an asymmetric simple exclusion process along DNA, and the other is a three-dimensional jump between transit points in DNA where RNAPIIs are staying. Simulations based on our model, and comparison experimental results, reveal how RNAPII molecules are distributed at the DNA-loop-formation-related protein binding sites as well as CTCF insulator proteins. As time passes after the stimulation, the RNAPII density at these sites becomes higher. Apparent far-distance jumps in one dimension are realized by short-range three-dimensional jumps between DNA loops.
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Report
(4 results)
Research Products
(11 results)
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[Journal Article] Direct Evidence for Pitavastatin Induced Chromatin Structure Change in the KLF4 Gene in Endothelial Cells.2014
Author(s)
Maejima T, Inoue T, Kanki Y, Kohro T, Li G, Ohta Y, Kimura H, Kobayashi M, Taguchi A, Tsutsumi S, Iwanari H, Yamamoto S, Aruga H, Dong S, Stevens JF, Poh HM, Yamamoto K, Kawamura T, Mimura I,
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Journal Title
PLoS One.
Volume: 9
Issue: 5
Pages: e96005-e96005
DOI
Related Report
Peer Reviewed / Open Access
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