The Yachie Laboratory1,2,3,4,5,6,7

1University of Tokyo RCAST
2University of Tokyo Department of Biological Science
3University of Tokyo AIS
4University of Tokyo GPES
5University of Tokyo PEAK
6Keio University IAB
7Keio University SFC

Research Projects

The Yachie Laboratory is a Synthetic and Systems Biology laboratory at the University of Tokyo°«s Research Center for Advanced Science and Technology (RCAST). By utilizing technology and methods from Genetics, Synthetic Biology, and Computational Biology, we aim to develop novel experiments and technologies to measure the dynamics of molecules, cells, and cellular development in order to unveil new biological phenomena.

Our research topics include:

Development of new genome editing technologies
Development of technologies to trace cell lineages of cell development and cancer cell progression
High-throughput screening of protein interactions
Bioinformatics

Genome Editing Projects

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The recent understanding of CRISPR systems has triggered the dramatic development of genome editing technologies. In addition to double-stranded DNA cleavage and nicking, catalytically inactivated Cas9 mutants anchored to functional protein and RNA domains have enabled flexible regulation of gene transcriptions and epigenetic modifications at nearly any sequence complementary to the designed guide RNA. Notably, targeted DNA deamination strategies coupled with CRISPR systems enable targeted C•G to T•A and A•T to G•C modifications. This base editing approach allows direct genomic programming to create more stringent and complex cellular circuits compared to the conventional transcriptional induction systems. As basic techniques continue to enhance various research projects in our group, we are developing new base editors and new frameworks for genetics.

Cell Lineage Tracing Projects

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Development of any multicellular organism starts from a single fertilized egg. Individuals and organs are formed through cell divisions and differentiation where a large number of cells and their cellular pathways crosstalk. Based on a belief that a complete information of the cell lineaging pathways to organs and functional cells could be a strong backbone for developmental biology, we are developing a high resolution cell lineage tracing method using DNA barcodes, genome editing, and single cell technologies, aiming to capture the whole body cell lineage of mammalian development (mammalian reference cell lineage) at nearly single cell division resolution.

Interactome Projects

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Cancers and many other human diseases are not the product of defects in a few genes, proteins or simple pathways. Instead, they involve a complex web of molecular interactions that are dynamically regulated. Recent studies have demonstrated that the projection of genomic mutations to a reference cellular regulatory network could enhance the performance of disease phenotype prediction and that disease mutations alter more functional protein interactions than the other mutations. Therefore, conditional protein interactome information for different proteoforms (splicing variants and modifications), mutations, individuals and environments would deepen our understanding of collapses in functional networks and enable high precision prediction of disease phenotypes. However, such screening is difficult due to the combinatorial explosion in a number of experiments. Using DNA barcodes, barcode fusion concatenating different information and next-generation DNA sequencing, we are developing experimental frameworks that enable high-throughput screening methods of conditional protein interactions.

Bioinformatics Projects

Our group has various bioinformatics projects which range from supporting experimental projects by producing new types of experimental datasets, establishing new data analysis methods as well as other independent studies in bioinformatics. Our topics include data analysis of DNA barcodes and genome editing spectra, development of a parallel distributed computing method to reconstruct large cell and evolutionary lineages and discovery and analysis of structured and patterned DNA sequence elements in large genomic resources.


Other research topics in our group include laboratory automation, DNA data storage and in vitro DNA computing using genome editing.

Positions Available

We are seeking creative and talented postdocs and students.
Please see here if you are interested in joining us.