2020 Fiscal Year Annual Research Report

Role of retrotransposon in genome plasticity and diseases

Research Project

Project/Area Number	18F18721
Research Institution	Institute of Physical and Chemical Research
Host Researcher	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)
Foreign Research Fellow	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
Project Period (FY)	2018-07-25 – 2021-03-31
Keywords	Genomics / Cancer / Retrotransposons / Promoter / Enhancer
Outline of Annual Research Achievements	Dr. Robbe has engaged with exploring the function of the genome in cancer focusing on the non-protein-coding regions, which have been considered less important. She focused on the regulatory elements, promoters and enhancers, in liver cancer, capitalizing on the expertise of colleagues at RIKEN, in particular Dr. Hidewaki Nakagawa’s team. They conducted a broad computational analysis and identified regions involved in liver cancer. We broadened the search of regulatory elements beyond transposons, which was in the original plan, and refocused on a disease for which data became available, slight changes necessary for the success of the project. She used data collected in my laboratory in a project, Modhep (modelling hepatocellular carcinoma), constituted by Cap-Analysis Gene Expression (CAGE) data and mapped further DNA regulatory elements taking advantage of a second dataset, larger but based on a less sensitive technology to detect enhancers, RNA-sequencing. She developed strategies to filter the data and produced, based on their ability to produce RNAs, a map of liver specific enhancers. She further analyzed the relationships of the newly identified regulatory elements and the primary sequence of human cancers from the Cancer Genome Project by Prof. Nakagawa, identifying a list of regulatory elements altered/mutated in cancer. This broad exploration of the non-coding part of the genome is new in cancer. A manuscript is being prepared and Dr. Robbe will remain in my laboratory after the JSPS fellow. I am sure that this will be successfully published with a high impact.
Research Progress Status	令和2年度が最終年度であるため、記入しない。
Strategy for Future Research Activity	令和2年度が最終年度であるため、記入しない。