2019 Fiscal Year Annual Research Report
Role of retrotransposon in genome plasticity and diseases
Project/Area Number |
18F18721
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Research Institution | Institute of Physical and Chemical Research |
Principal Investigator |
Carninci Piero 国立研究開発法人理化学研究所, 生命医科学研究センター, 副センター長 (10333296)
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Co-Investigator(Kenkyū-buntansha) |
ROBBE PAULINE 国立研究開発法人理化学研究所, 生命医科学研究センター, 外国人特別研究員
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Project Period (FY) |
2018-07-25 – 2021-03-31
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Keywords | Transcriptomics / Genomics / cancer / Non-coding RNA / Non-coding mutations |
Outline of Annual Research Achievements |
The project planned in the beginning of the fellowship on hepatocellular carcinoma has been continued. The focus was made in learning bioinformatics techniques in order to analyse the biological data.
By combining information from public databases and data from hepatocellular carcinoma primary samples, a list of non-coding regulatory elements, specifically named enhancers was prepared. Several of these enhancers were found with many DNA alterations, or mutations which are absent in the normal liver tissues, and more than expected by chance by applying multiple statistical approaches to uncover them. Next, the region of interest were investigated by transcriptomics techniques. Additional experimental validation are also being planned.
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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 completed Aim 1: I have constructed a bioinformatics pipeline to analyze CAGE data and defined a robust and permissive maps of HCC specific enhancers. The results need discussion and revision.
I have partially completed Aim 2: I have finalized the list of non-coding regions potentially altered in HCC using whole genome sequencing. I have processed the RNA-seq data in order to validate some of the non-coding regions. I need to acquire additional skills in bioinformatics to finalise the work.
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Strategy for Future Research Activity |
To finalise the study, co-expression analysis will be conducted in order to link enhancers and target genes. Finally, experimental validated of selected targets should be performed in the lab.
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