From People - School of Science, The University of Tokyo
Genome Science, Functional Genomics
Comprehensive Analysis of Budding Yeast Transcriptome and Epigenome, Functional Analysis of Noncoding RNAs in Budding Yeast, Quantitative Analysis of Protein Interactions and Ubiquitination, Genome-wide High Resolution Analysis of DNA Methylation
Our lab is investigating the yeast transcriptome and proteome, as well as the mammalian epigenome. Budding yeast is an ideal model organism to use in understanding the eukaryotic cell as a molecular system. First, it has been studied extensively in biochemistry, genetics and molecular cell biology. Second, its genome can be modified easily and many elegant genetic techniques are available. Third, the recent advent of genome science has provided an unsurpassed wealth of functional and comparative genomics data, as well as useful resources for comprehensive experiments. Given these advantages, and making use of various functional genomics approaches, our aim is to reveal the universality and variation in cellular regulation in order to understand how regulatory systems have evolved. For epigenomic regulation, our approach includes a comprehensive analysis of DNA methylation in mammals.
We have performed a large-scale full length cDNA analysis of the budding yeast to uncover many novel noncoding RNAs (ncRNAs), thereby revealing the surprising complexity of the transcriptome. This finding indicates that pervasive transcription leading to a plethora of ncRNAs is not unique to higher eukaryotes but, rather, an intrinsic feature of eukaryotic genomes. Thus, the yeast would serve as a versatile model organism to examine this issue. We are curious as to what fractions of these ncDNAs are indeed functional. To address this issue, we can use next-generation sequencers to examine the transcription of a bacterial genome maintained as a yeast artificial chromosome (YAC). Since the YAC would have no function, its transcription can be regarded as a pure noise, from which we can estimate the frequency of neutral transcription and investigate the characteristics of transcription-prone regions. Such knowledge would, in turn, help us to discriminate between functional and neutral transcripts from the yeast genome. Through this and other approaches, we intend to identify functional ncRNAs to be integrated with gene regulatory networks.
We have conducted the first comprehensive two-hybrid analysis of yeast to become a pioneer of interactome analysis. The interactome data constitute a collection of simple binary relationships, such as "protein A binds protein B", and their integration provides a static protein-protein interaction network. To understand its dynamics, we need to know what fraction of protein A binds protein B and how static or dynamic the binding is. To this end, we have developed novel methods, based on stable isotope-labeling and mass spectrometry, to lay the foundation for quantitative interactome analysis. We also exploit quantitative proteomics approaches to analyze protein ubiquitination, an important post-translational modification that regulates various cellular processes. Much emphasis is placed on the identification of substrates for each enzyme involved in this modification as a first step to revealing the protein ubiquitination network.
DNA methylation is an important epigenetic modification that regulates mammalian genome function. It is essential to mammalian development and its defects are implicated in a variety of human diseases. However, genome-wide high resolution analysis of DNA methylation remains a challenge. We are developing a high performance method for whole-genome single-nucleotide resolution analysis by fully exploiting the next generation sequencing technologies. This method would enable us to analyze the dynamics and variations of DNA methylation with unsurpassed scale and accuracy, thereby improving significantly our understanding of epigenomic regulation.
In all of the above projects, we strive to develop novel methodologies and strategies that will lead to important contributions to the understanding of biological systems. We intend to educate students so that they can develop knowledge in biology as well as skills in omic measurements and bioinformatic analysis.
Epigenome, Transcriptome, Proteome, Interactome, Bioinformatics