RIKEN Center for Life Science Technologies


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To let you know about our research, this area contains 4 types of information about CLST; “Article”, “Videos”, “Event” and “Study”.
At “Article”, you can read articles on interviews and lectures, and you can enjoy the videos about CLST at “Videos”. If you want to meet and talk directly with the researcher, “Visit” give you some information of such events. You can find more difficult contents to know about our research deeply at “Study”.
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Labs & Technologies

Cell Conversion Technology Team

Making sense of gene networks


* Due to the reorganization starting as new centers in April 2018, this laboratory is now belong to the Center for Integrative Medical Sciences. As for the latest information, please see the following URL below.
> The webpage of Laboratory for Advanced Genomics Circuit, Center for Integrative Medical Sciences

Team Leader
Jay W. Shin  D.Sci.

W 406 1-7-22 Suehiro-cho Tsurumi-ku Yokohama 230-0045 JAPAN
Tel: +81-(0)45-503-9111 (Ext. 8397)


Research Area

Human somatic cells have the ability to convert into another cell type by introducing a set of defined factors. These so called reprogrammed-cells are applicable in regenerative medicine, disease modeling, and drug discovery.  My unit focuses on the development of key technologies to achieve multitude of cell conversions using both high-throughput robotics and single-cell “multiplex” screening system. These systems integrate with Next Generation Sequencers (NGS) to map the network of mediators, such as transcription factors, noncoding RNAs and epigenetic factors, that are involved in the regulation of (direct) cellular reprogramming.

Research Topics

    Figure: Induction of neurons starting from either human fibroblasts or iPS cells, stained with neuron-markers (beta3-tublin and MAP2).

    Figure: Induction of neurons starting from either human fibroblasts or iPS cells,

    stained with neuron-markers (beta3-tublin and MAP2).

Main Publications List


A predictive computational framework for direct reprogramming between human cell types

Rackham OJ, Firas J, Fang H, Oates ME, Holmes ML, Knaupp AS,; FANTOM Consortium, Suzuki H, Nefzger CM, Daub CO, Shin JW, Petretto E, Forrest AR, Hayashizaki Y, Polo JM, Gough J.
Nat Genet, 48(3), 331-335 (2016).

Paradigm shifts in genomics through the FANTOM projects

De Hoon, M., Shin, J.W., Carninci, P.
Mammalian Genome, 26(9), 391-402 (2015).

A transient disruption of fibroblastic transcriptional regulatory network facilitates trans-differentiation.

Tomaru Y, Hasegawa R, Suzuki T, Sato T, Kubosaki A, Suzuki M, Kawaji H, Forrest AR, Hayashizaki Y; FANTOM Consortium, Shin JW, Suzuki H.
Nucleic Acids Research, 42(14), 8905-8913 (2014).

Comparison of CAGE and RNA-seq transcriptome profiling using clonally amplified and single-molecule next-generation sequencing

Kawaji, H., Lizio, M., Itoh, M., Kanamori-Katayama, M., Kaiho, A., Nishiyori-Sueki, H., Shin, JW., Kojima-Ishiyama, M., Kawano, M., Murata, M., Ninomiya-Fukuda, N., Ishikawa-Kato, S., Nagao-Sato, S., Noma, S., Hayashizaki, Y., Forrest, ARR., Carninci, P
Genome Res, 24(4), 708-717 (2014).

A promoter-level mammalian expression atlas

FANTOM Consortium and the RIKEN PMI and CLST (DGT)
Nature, 507(7493), 462-470 (2014).

Temporal dynamics and transcriptional control using single-cell gene expression analysis

Kouno T, de Hoon M, Mar JC, Tomaru Y, Kawano M, Carninci P, Suzuki H, Hayashizaki Y, Shin JW.
Genome Biol, 14(10), R118 (2013).

Identification of ZNF395 as a novel modulator of adipogenesis

Hasegawa R, Tomaru Y, de Hoon M, Suzuki H, Hayashizaki Y, Shin JW.
Exp Cell Res, 319(3), 68-76 (2013).

Establishment of single-cell screening system for the rapid identification of transcriptional modulators involved in direct cell reprogramming.

Shin JW, Suzuki T, Ninomiya N, Kishima M, Hasegawa Y, Kubosaki A, Yabukami H, Hayashizaki Y, Suzuki H.
Nucleic Acids Res, 40(21), e165 (2012).

Reconstruction of monocyte transcriptional regulatory network accompanies monocytic functions in human fibroblasts.

Suzuki T, Nakano-Ikegaya M, Yabukami-Okuda H, de Hoon M, Severin J, Saga-Hatano S, Shin JW, Kubosaki A, Simon C, Hasegawa Y, Hayashizaki Y, Suzuki H.
PLoS One, 7(3), e33474 (2012).

CC chemokine ligand 2 and leukemia inhibitory factor cooperatively promote pluripotency in mouse induced pluripotent cells.

Hasegawa Y, Takahashi N, Forrest AR, Shin JW, Kinoshita Y, Suzuki H, Hayashizaki Y.
Stem Cells, 29(8), 1196-1205 (2011).

Member  *concurrent

CLST was reorganized into three centers according to the RIKEN 4th Medium-Term Plan from April 1, 2018. For the latest information of Cell Conversion Technology Team, please visit the following websites.

> The webpage of Laboratory for Advanced Genomics Circuit, Center for Integrative Medical Sciences [http://www.ims.riken.jp/labo/66/index.html]