2015 Fiscal Year Annual Research Report
遺伝子発現に対するＲＮＡ分解および転写後制御の寄与
| Project/Area Number |
15J05075
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| Research Institution | The University of Tokyo |
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Principal Investigator |
前川 翔 東京大学, 新領域創成科学研究科, 特別研究員(DC1)
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| Project Period (FY) |
2015-04-24 – 2018-03-31
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| Keywords | トランスクリプトーム制御 / ゲノム制御 / RNA / RNA分解 / 転写制御 / 次世代シークエンサー |
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| Outline of Annual Research Achievements |
I have collected and conducted the next-generation sequencing on the bromo-uridine labelled and pulse-chased RNA for DLD-1 human cell line in hypoxia and normoxia. Following the sequencing, I have done primary analyses of the bromouridine labelled RNA and made an appropriate pipeline to obtain RNA half-life from the decay data. Data collection and creating the bioinformatic pipeline for the analysis of RNA decay is very important to understand the mechanisms behind RNA regulation, transcriptome-wide.
Characterisation of RNA half-lives
I have predominantly tried to generate RNA-seq library for BRIC-seq. I have conducted BRIC-seq in collaboration with Akimitsu Lab, using method previously published (Tani et. al. Genome Res. 2012) in DLD-1 adenocarcinoma cell-lines in Illumina Hi-seq 2000 for both hypoxia and normoxia. I sequenced and mapped on average of 27 million reads for hypoxia condition and 18.7 million for normoxia condition. I mapped the BRIC-seq reads to the human genome (GRCh37/hg19) and I quantified the sequence tag counts and tried to analyse the RNA decay by using three different decay models to fit the data.
Comparison with other data
By comparing our lab’s previous RNA-seq and epigenome data, I was able to make a list of genes where the half-life changes seems to be the causal reason behind the RNA expression change in hypoxia. I will be trying to verify some of these genes experimentally.
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| Current Status of Research Progress |
Current Status of Research Progress
2: Research has progressed on the whole more than it was originally planned.
Reason
I have managed to obtain and sequence the bromouridine pulse-chased RNA and I have managed to develop an primary bioinformatic pipelines to analyse the decay data that I have generated and I have been able to compare with previous data on transcriptome and epigenome to analyse the contribution of RNA decay in RNA genome-wide.
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| Strategy for Future Research Activity |
I have been trying to validate some of the claims through Western blot and qPCR, Luciferase assays, however it has not been successful yet. I am yet to find some of the regulatory motifs that are in RNA sequences and it is an effort that is still to be done next fiscal year and I will need to refine some of the computational simulations conducted in the last fiscal year.
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Research Products
(5 results)
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[Presentation] RNA decay factor mediated RNA stability contributions on RNA abundanc2015
Author(s)
Maekawa, S., Imamachi, N., Irie, T., Tani, H., Matsumoto, K., Mizutani, R., Imamura, K., Kakeda, M., Yada, T., Sugano, S., Suzuki, Y. and Akimitsu, N.
Organizer
The 11th International Workshop on Advanced Genomics
Place of Presentation
学術総合センター一橋講堂（東京都千代田区）
Year and Date
2015-05-20 – 2015-05-22
Int'l Joint Research
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[Presentation] RNA decay factor mediated RNA stability contributions on RNA abundance2015
Author(s)
Maekawa, S., Imamachi, N., Irie, T., Tani, H., Matsumoto, K., Mizutani, R., Imamura, K., Kakeda, M., Yada, T., Sugano, S., Suzuki, Y. and Akimitsu, N.
Organizer
Biology of Genomes
Place of Presentation
Cold Spring Habor, NY, USA
Year and Date
2015-05-06 – 2015-05-12
Int'l Joint Research
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