Mammalian Genome Dynamics Team

RIKEN BioResource Research Center


Our lab has been established in 2002 at RIKEN BioResource Center, Tsukuba, Japan. We develop technologies to monitor and to analyze dynamic nature of mammalian cells. These technology will be useful tools for phenotyping biological resources collected at the BioResource Center. In order to achieve this goal, our team uses various approaches including genetics, genomics and transgenic/gene targeting technologies.
Using these approaches, we focus on early mouse developmental processes. In particular, we are interested in development and genomic reprogramming process of pluripotent embryonic cells and primordial germ cells.

Technology development

・ Visualization, purification and micro-scale analyses of specific cell lineage
(Lineage-specific reporter mouse strains,micro-cDNA cloning, micro-scale transcriptome analysis)

・ Analytical tools for epigenetic regulatory mechanisms operating during genomic reprogramming process ( new stem cell lines, novel techniques for DNA methylation analysis, non-coding RNA chip )

・ Development of resources and technologies for the analysis of wild-derived inbred mouse strains ( BAC libraries, cDNA libraries, BAC transgenic mice, SNP analytical techniques )

・ Analysis of functional processes in live animals by fluorescent in vivo imaging ( Fluorescent reporter transgenic mice, intravital microscope, non-invasive imaging of live mouse )

Research Projects

1. Studies of early mammalian development through the analysis of t-complex mutants.

2. Cell lineage-specific analysis of gene expression in pluripotent embryonic cells and germ cells.

3. Studies on dynamics of epigenetic changes during mammalian development.

4. Functional genomic analysis of wild-derived inbred mouse strains collected at BRC using novel research resources.

5. Phenotyping mouse mutants with in vivo imaging technology.

1. Study on developmental mutant showing defects in proliferation and differentiation of pluripotent embryonic cells.

tw5 mutant embryo at gastrulation stage(a; normal、b; mutant)

tclw5 is a t-complex recessive lethal mutation of the tw5-haplotype. Since tw5/tw5 embryos die soon after implantation, the tclw5 gene is thought to play an important role in early embryogenesis. tw5 homozygotes do not survive past the gastrulation stage due to extensive death of the embryonic ectoderm, a pluripotent cell type giving rise to all three germ layers at subsequent developmental stages. Using this mutant strain, molecular mechanism governing development of this pluripotent cell type will be sought.

2. Visualization of pluripotent embryonic stem cells, germ cells,
and genome wide analysis of gene expression in these cells.

Comprehensive analysis of cell lineage-specific gene expression

In developing mammalian embryos, there exist pluripotent stem cells, giving rise to all somatic cells as well as germ line cells. Primordial germ cell (PGC) is the cell-type appeared first in the germ cell lineage, sharing many features with the embryonic stem cells. We have established systematic methodologies to analyze PGCs and related embryonic cells: PGCs were purified from transgenic mouse embryos, in which the PGCs were marked by GFP-reporter expression. Transcriptomes of these cells were explored by EST analyses from PGC cDNA libraries and microarray.

3. Visualization of DNA methylation patterns in living ES cells; Dynamics of nuclear architecture reorganization during ES cell differentiation

Nuclear architecture is dynamically changed during cell differentiation

Changes in nuclear organization and the epigenetic state of the genome are important driving forces for developmental gene expression. However, a strategy that allows simultaneous visualization of the dynamics of the epigenomic state and nuclear structure has been lacking to date. The methylated DNA binding domain (MBD) and the nuclear localization signal (nls) sequence coding for human methyl CpG-binding domain protein 1 (MBD1) were fused to the enhanced green fluorescent protein (EGFP) reporter gene.The EGFP-MBD-nls protein was used to follow DNA methylation in situ under physiological conditions. We can also monitor the formation and rearrangement of methylated heterochromatin using EGFP-MBD-nls during cell differentiation.


  • MGD Logo. This picture shows our experimental materials, mouse and embryo ( egg cylinder stage ).


  • Life cycle and developmental processes of pluripotent embryonic cells and germ cells in mice.


Lab member

Team Leader Kuniya Abe, Ph.D.
Scientist Hiroki Ura, Ph.D.
Scientist Shinnosuke Suzuki, Ph.D.
Scientist Yuhki Tada, Ph.D.
Tech. staff Masayo Kondo, M.S.
Tech. staff Yumiko Koga, M.S.
IPA Maisarh Ab Samad
Assistant Miwako Kusayama


kuniya.abe at