RIKEN Center for Integrative Medical Sciences Laboratory for Comprehensive Genomic Analysis

Team Leader: Yasushi Okazaki (M.D., Ph.D.)

Japanese Page

Research Summary

This facility will implement and standardize next generation sequencing applications, with particular focus on analysis of transcriptome, gene regulation network, ncRNA. The platform will provide highly standardized technological and analytical services to the users, in order to minimize the time from sample to data and to deliver high quality data.

Main Research Fields

Medicine, Dentistry & Pharmacy

Related Research Fields

Informatics
Biology

Keywords

Mitochondrial Disease
Bioinformatics
Inherited Disease

Selected Publications

1. Yuuri Yasuoka.
"Tissue-specific expression of carbohydrate sulfotransferases drives keratan sulfate biosynthesis in the notochord and otic vesicles of Xenopus embryos."
Front. Cell Dev. Biol. 11, 957805 (2023)
2. Imai-Okazaki A, Nitta KR, Yatsuka Y, Sugiura A, Arao M, Shimura M, Ebihara T, Onuki T, Ichimoto K, Ohtake A, Murayama K, Okazaki Y.
"Impact of measuring heteroplasmy of a pathogenic mitochondrial DNA variant at the single-cell level in individuals with mitochondrial disease."
J Inherit Metab Dis 45, 1143-1150 (2022)
3. Yip CW, Hon CC, Yasuzawa K, Sivaraman DM, Ramilowski JA, Shibayama Y, Agrawal S, Prabhu AV, Parr C, Severin J, Lan YJ, Dostie J, Petri A, Nishiyori-Sueki H, Tagami M, Itoh M, López-Redondo F, Kouno T, Chang JC, Luginbühl J, Kato M, Murata M, Yip WH, Shu X, Abugessaisa I, Hasegawa A, Suzuki H, Kauppinen S, Yagi K, Okazaki Y, Kasukawa T, de Hoon M, Carninci P, Shin JW.
"Uncovering the mesendoderm gene regulatory network through multi-omic data integration."
Cell Rep 38, 110364 (2022)
4. de Hoon M, Bonetti A, Plessy C, Ando Y, Hon CC, Ishizu Y, Itoh M, Kato S, Lin D, Maekawa S, Murata M, Nishiyori H, Shin JW, Stolte J, Suzuki AM, Tagami M, Takahashi H, Thongjuea S, Forrest ARR, Hayashizaki Y, Kere J, Carninci P.
"Deep sequencing of short capped RNAs reveals novel families of noncoding RNAs."
Genome Res 32, 1727-35 (2022)
5. Jansen C, Paraiso KD, Zhou JJ, Blitz IL, Fish MB, Charney RM, Cho JS, Yasuoka Y, Sudou N, Bright AR, Wlizla M, Veenstra GJC, Taira M, Zorn AM, Mortazavi A, Cho KWY.
"Uncovering the mesendoderm gene regulatory network through multi-omic data" integration.
Cell Rep 38, 110364 (2022)
6. Kato T, Manabe RI, Igarashi H, Kametani F, Hirokawa S, Sekine Y, Fujita N, Saito S, Kawashima Y, Hatano Y, Ando S, Nozaki H, Sugai A, Uemura M, Fukunaga M, Sato T, Koyama A, Saito R, Sugie A, Toyoshima Y, Kawata H, Murayama S, Matsumoto M, Kakita A, Hasegawa M, Ihara M, Kanazawa M, Nishizawa M, Tsuji S, Onodera O.
"Candesartan prevents arteriopathy progression in cerebral autosomal recessive arteriopathy with subcortical infarcts and leukoencephalopathy model."
J Clin Invest 131, e140555 (2021)
7. Ozaki K, Irioka T, Uchihara T, Yamada A,Nakamura A,Majima T,Igarashi S, Shintaku H,Yakeishi M, Tsuura Y, Okazaki Y,Ishikawa K, Yokota T.
"Neuropathology of SCA34 showing widespread oligodendroglial pathology with vacuolar white matter degeneration: a case study"
Acta Neuropathol Commun. 9(1)172(2021)
8. Inaba A, Arinaga A, Tanaka K, Endo T, Hayatsu N, Okazaki Y, Yamane T, Oishi Y, Imai H, Iwatsuki K.
"Interleukin-4 Promotes Tuft Cell Differentiation and Acetylcholine Production in Intestinal Organoids of Non-Human Primate"
Int J Mol Sci. 22(15)7921(2021)
9. Hashimoto M, Saito Y, Nakagawa R, Ogahara I, Takagi S, Takata S, Amitani H, Endo M, Yuki H, Ramilowski JA, Severin J, Manabe RI, Watanabe T, Ozaki K, Kaneko A, Kajita H, Fujiki S, Sato K, Honma T, Uchida N, Fukami T, Okazaki Y, Ohara O, Shultz LD, Yamada M, Taniguchi S, Vyas P, de Hoon M, Momozawa Y, Ishikawa F.
"Combined inhibition of XIAP and BCL2 drives maximal therapeutic efficacy in genetically diverse aggressive acute myeloid leukemia."
Nat Cancer 2, 340-356 (2021)
10. Kishita Y, Shimura M, Kohda M, Fushimi T, Nitta KR, Yatsuka Y, Hirose S, Ideguchi H, Ohtake A, Murayama K, Okazaki Y.
"Genome sequencing and RNA-seq analyses of mitochondrial complex I deficiency revealed Alu insertion-mediated deletion in NDUFV2."
Hum Mutat 42, 1422-1428 (2021)

Lab Members

Principal investigator

Yasushi Okazaki: Team Leader

Core members

Yuuri Yasuoka: Research Scientist
Norihito Hayatsu: Research Scientist
Tomoko Hirata: Technical Scientist
Yumiko Yamamoto: Technical Scientist
Michihira Tagami: Expert Technician
Shohei Noma: Senior Technical Staff
Chitose Takahashi: Technical Staff I
Yuki Yasuoka: Technical Staff II
Kayuri Kadoya: Technical Staff II

Contact Information

West Research Building 4F W403
1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama, Kanagawa,
230-0045, Japan
Tel: +81-(0)45-503-9237
Fax: +81-(0)45-503-9216
Email: LSA-support [at] riken.jp