Remarkable progress has recently been made in molecular profiling tech-19nologies, including genome-wide technologies developed at RIKEN, and their effective use is one of the major interests in life science research, in partic-ular to solve medical problems. The RIKEN Preventive Medicine and Diagnosis Innovation Program (RIKEN PMI) coordinates translational studies that utilize RIKEN technologies to solve clinical problems, and our unit was established to conduct or support such studies with PMI funding, in particular from the per-spective of information sciences or computational genomics. Our projects are roughly classified into three categories: identification of cell markers required for regenerative medicine, exploration of diagnostic markers useful in patient treatment, and our own developments to assist in such translational as well as basic science research.Our collaborative research with RIKEN PMI led to the identification of biomarkers for iPSC induction to cardiac muscle (Ohashi F et al. Scientific Re-ports, 2019), a diagnostic biomarker of myeloproliferative neoplasms (Morishita S et al. Cancer Sci., 2020), and a prognostic biomarker of cholangiocarcinoma (Takahashi T et al., Eur J Surg Oncol., 2020). We also contributed to the field of oligonucleotide therapeutics in an assessment of off-target effects of gapmer antisense oligos (Yoshida et al. Genes to Cells, 2019). In collaborations within RIKEN IMS, we integrated epigenetic data into the FANTOM5 resource, the largest database of cis-regulatory regions based on transcriptome profiles, to as-sist translational researchers as well as basic scientists focusing on cis-regulatory regions (Lizio et al. Nucleic Acids Res. 2019; Figure) and contributed to its up-date (Abugessaisa I et al. Nucleic Acids Res. 2020). We further succeeded in dis-covering a substantial number of novel enhancers by development of a method called NET-CAGE, which can capture even RNAs that are subject to rapid deg-radation, such as enhancer RNAs (Hirabayashi et al. Nature Genet. 2019).Figure: Integrated view of transcriptome and epigenetic marks provided by the FANTOM5 web resourceGenomic view of the EGR-1 locus with the UCSC Genome browser database, which includes data provided by FANTOM5 and ChIP-Atlas (The figure is from Nucleic Acids Res. D752-758, 2019).Recent Major PublicationsHirabayashi S, Bhagat S, Matsuki Y, Takegami Y, Uehata T, Kanemaru A, Itoh M, Shirakawa K, Takaori-Kondo A, Takeuchi O, Carninci P, Katayama S, Hayashizaki Y, Kere J, Kawaji H, Murakawa Y. NET-CAGE characterizes the dynamics and topology of human transcribed cis-regulatory elements. Nat Genet 51, 1369-1379 (2019)Ohashi F, Miyagawa S, Yasuda S, Miura T, Kuroda T, Itoh M, Kawaji H, Ito E, Yoshida S, Saito A, Sameshima T, Kawai J, Sawa Y, Sato Y. CXCL4/PF4 is a predictive biomarker of cardiac differentiation potential of human induced pluripotent stem cells. Sci Rep 9, 4638 (2019)Lizio M, Abugessaisa I, Noguchi S, Kondo A, Hasegawa A, Hon CC, de Hoon M, Severin J, Oki S, Hayashizaki Y, Carn-inci P, Kasukawa T, Kawaji H. Update of the FANTOM web resource: expansion to provide additional transcriptome atlases. Nucleic Acids Res 47, D752-D758 (2019)Invited presentationsKawaji H, “Genomics resource of non human primates: recent updates and future perspective”, the 43rd annual meeting of the molecular biology society of Japan (On-line) December 2020Preventive Medicine and Applied Genomics UnitUnit Leader: Hideya Kawaji
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