Role of histone H3 lysine 36 methyltransferase WHSC1 in developmental and pathological gene regulation.
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Histones are the chief protein components of chromosome. A defect in histone methyltransferase WHSC1 causes a human disease, Wolf-Hirschhorn syndrome. In this study, I will elucidate the molecular function of WHSC1 during developmental gene regulation. I believe that this histone modifier will functionally link developmental transcription factors to nuclear architectures during the stepwise process of transcription. A new concept of transcriptional control will point to a new direction for the understanding and treatment of dysregulated transcription in human diseases.
Molecular basis of epigenetic regulation mediated by DNA methylation and demethylation
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This research project aims to understand the molecular basis of DNA demethylation, which is an essential process for the changes in DNA methylation patterns during development, differentiation, carcinogenesis and reprogramming. To gain biological new insight into the dynamic process involving chromatin structure modulation, structural and functional properties of key protein regulators to DNA demethylation are investigated using a combination of protein crystallography and NMR spectroscopy with reconstituted nucleosome. Based on the structural basis, we will attempt to develop a new approach for modulation of the DNA demethylation patterns in cells.
Analysis of the importance of histone modification during spermatogenesis
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As a part of stem cell research, this study attempts to reveal mechanisms of epigenetic regulation, especially histone modifications, in spermatogonial stem cells and mature sperm using systematic high-throughput methods. The outcome of this study is expected to provide knowledge, which can be utilized for developing reproductive engineering techniques and treatment of infertility.
Development of chemistry-based system for highly effective visualization of methylated DNA
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The new DNA methylation imaging technology is developed for efficient and quantitative analysis of the diseases caused by epigenetic aberrations. The effective reaction for sequence-selective visualization of methylated DNA is explored. The technology that developed based on our knowledge of chemistry will be applied to the fluorescent imaging assay of the target methylated region in vitro and in vivo, which would represent a breakthrough in epigenetics studies.
Analysis of the establishment mechanism of heterochromatin
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For clinical application of cellular epigenetic regulation, molecular mechanism of gene inactivation as well as activation must be fully understood. In particular, understanding of heterochromatin that inactivates specific loci and contributes to cellular identity is very important. Using the fission yeast as a model organism, this study aims to elucidate the molecular mechanism that establishes the silent state of specific chromatin loci.
Analysis of the epigenetic regulation mechanism of gene expression
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We found the new region where a genetic expression state changed into when yeast repeated division, in spite of the same DNA sequence. We inserted H2B-EGFP gene in this region to observe a change of the gene expression that was a phenotype in the single cell. As a result, the fluorescence disappears when yeast strain repeated division, and the fluorescence recovered again when it repeated division more. In this project,we aim to understand the molecular mechanism about this epigenetic phenomenon.
Epigenetics of cellular senescence and cancer
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When oncogenes are activated, cells fall into irreversible arrest as a barrier against unscheduled proliferation. This study is to clarify epigenetics during oncogene-induced senescence, and cancer epigenetics at the standpoint of escape from senescence through epigenetic aberration.
Dynamic regulation of heterochromatic modifications
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Transcriptionally silent genes are associated with heterochromatic modifications such as DNA methylation and histone H3 Lysine9 methylation. Although removal of such modifications is essential for gene de-repression, the molecular mechanisms underlying the removal of the heterochromatic modifications are poorly understood. Using model plant Arabidopsis, I investigate the dynamic regulation of heterochromatic modifications and try to identify novel factors involved in this process. Results of this study would have broad implications for epigenetic regulation of gene activities in a wide variety of organisms.
Discovery and application of compounds that control epigenetics
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Compounds that control epigenetics can be utilized as tools for elucidating life phenomena and as therapeutic agents. In this study, I will try to discover specific inhibitors of histone deacetylases and histone demethylases which play pivotal roles in epigenetic gene expression. Further, I will perform chemical genetics study using those specific inhibitors, which will lead to not only the understanding of the mechanism of diseases that are related to epigenetics but also presenting guideline for therapy.
Discovery and application of compounds that control epigenetics
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New techniques are making it easier to map DNA methylation patterns on a large scale and the results have provided surprises. In particular, the conventional view that DNA methylation functions predominantly to irreversibly silence transcription is being challenged. Many organisms including human seem to target DNA methylation specifically to the bodies of active genes. In this project, epigenetic function and molecular mechanism of the gene body methylation will be studied using an invertebrate chordate Ciona intestinalis as a model organism. It will reveal a novel role of DNA methylation in the basal gene transcription system.
Analysis of methylated epigenome for early mammalian development
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Histone methylation and DNA methylation are major epigenetic marks in higher eukaryotes. The function of DNA methylation for mammalian development has been studied extensively. However, the dynamism of histone methyation and its role on mammalian development remain to be determined. We analyze dynamic regulation of histone methylation during early murine embryo development and elucidate its biological importance.
Understanding the mechanisms underlying the chromatin demethylation
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Reprogramming of cell genome is an essential mechanism for the development and the regeneration of organisms. However, the reprogramming mechanisms remain unclear. The biggest question of genome reprogramming is how chromatin is demethylated. Through the identification and the analysis of molecules responsible for chromatin demethylation, we attempt to elucidate the molecular mechanism of chromatin demethylation that happens in the genome reprogramming.
Genetic Screening of Mammalian Polycomb Group and Trithorax Group
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In particular differentiation steps of a variety of stem cells, expressions of some tissue-specific master genes determine each cell fates. It has been shown that both Polycomb group of repressors and trithorax group of transcriptional regulators are the most prominent key-epigenetic regulators to maintain expressions of such master genes under determined states. Recent accumulative evidence suggests that these regulators are involved not only in stem cell biology, but also in cancer progression. In this project, by aid of a genetic screening using genome-wide siRNA library, we will identify new mammalian Polycomb group/trithorax group genes exhaustively. Further functional analyses of these genes are expected to contribute to many stem cell studies.
A Challenge for the Immortal DNA Strand Mechanism
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Non-random segregation of chromosomes bearing old parental DNA strands (immortal DNA strands) is proposed to contribute to self-renewal of adult stem cells during asymmetric cell divisions. However, the molecular basis of this epigenetic mechanism has rarely been studied. Using a yeast model system, this research project aims to develop technologies for identification of immortal DNA strands and elucidate the molecular mechanism of non-random chromosome segregation.
Switching mechanism in Polycomb-mediated gene regulations
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Polycomb group (PcG) proteins play central roles in regulations of developmental key genes, which are involved in cell fate decision-making. However, little is known about its underlying mechanisms. Here we would like to elucidate a mechanism of how PcG proteins repress genes and cancel its repression so that cells can properly differentiate.
Epigenetic analysis of neurodegenerative diseases
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During the development and ageing, human brain adapts dynamically to physical status and environment. This adaptation is certainly based on one’s genome information, which serves as a blue print; and epigenetics play an important role when utilizing the information at the optimal way when certain change is required from the original information in the genome. This research focuses on the possibility that neurodegenerative disease such as Alzheimer’s disease and Parkinson’s disease could be caused by the error in these epigenetic regulations.
Molecular mechanism of RNA-directed DNA methylation
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RNA-directed DNA methylation (RdDM), which is one of several RNAi-mediated pathways in the nucleus, appears to be highly elaborated in the plant kingdom. RdDM is characterized by de novo cytosine methylation that occurs in all sequence contexts based on ‘heterochromatic’ small interfering RNA-DNA complementarity. To date, a number of proteins of the RdDM machinery were identified by forward and reverse genetic approaches. However, the question of how the siRNA-protein complex can recognize the target region remains to be answered. In this work, a forward genetic screen will be carried out to identify proteins required for this recognition step.
Diversity and evoution of epigenetic regulations
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Phenotypic plasticity and sex chromosomal rearrangement
Epigenetic mechanism underlying tissue heterogeneity and associated plasticity as a novel therapeutic target for human neoplasia
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Functional and morphological heterogeneity characterizes aggressive neoplasia and contributes to invasion, metastasis and drug resistance. The molecular mechanisms underlying this heterogeneity are poorly understood. In this project, using glioblastoma (GBM) as a heterogeneous tumor model, we investigated the potential role of epigenetic machinery in aberrant differentiation of glioma initiating cell (GIC) during tumor progression. In addition, we will identify potent small molecules as a candidate drug for targeting this epigenetic mechanism. This study in heterogeneous GBM not only addresses molecular mechanisms attributed to tumor heterogeneity, but also provides supporting data for a potent drug against human GBMs.
Molecular basis for small RNA-mediated epigenome formation
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The genomes of multicellular organisms contain many transposable elements (TEs). The majority of TEs have the potential to increase their copy numbers in the genome by a 'copy and paste' mechanism. This could become a serious problem in terms of maintaining the genome integrity. Recent studies have revealed that small RNAs act as repressors of the transposable activity of TEs. However, the mechanism(s) involved remain unclear. Therefore, this study is to elucidate how small RNAs repress the transposable activity of TEs using Drosophila as a model organism.
in silico analysis of histone modification dynamics that regulate developmental processes
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DNA is compactly stored by being wrapped around histones, which are modified to regulate gene expressions. Recently, it has been reported that non-coding RNAs are involved in histone modification. This research project aims to reveal how the patterns of histone modification change during Drosophila development from embryo to adult, how non-coding RNAs are involved in these dynamics and how these dynamics regulate the developmental processes.
Study on mechanisms acting downstream of DNA mechanism
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DNA methylation is an important chromatin modifications found in mammalian and plant genomes and is associated with chromatin compaction and its transcription. However, the downstream mechanisms explaining how DNA methylation affects chromatin structure and regulates transcription are less clear. In this study, I will try to identify the factors acting downstream of DNA methylation by genetic approaches using plant mutants, and reveal their molecular actions.
Epigenetic regulation of the intestinal immune system by gut sybiotic microbiota
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The mammalian gastrointestinal tract harbors the vast majority of symbiotic microbiota. The gut microbioata shapes the intestinal immune system; however, the molecular machinery that mediate host-symbiotic interaction has long been unknwon. Our preliminary studies suggest that epigenetic regulation may be involved in this process. This study aims to clarify the epigenetic regulaiton of the gut immune system by symbiotic microbiota.
Identification of a new epigenetic marker that is involved in centromere specification.
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The centromere is essential for faithful chromosome segregation during cell division. Centromere is specified by a kind of epigenetic mechanism. However it remains to be determined which kind of epigenetic marker is involved in kinetochore formation. In this study, we try to identify a new epigenetic marker that define a centromere identity and to elucidate the mechanism of centromere formation.
Elucidation and medical applications of epigenetic regulation in amphibian regeneration
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Amphibian such as newts have a strong ability to regenerate most of their tissues. During regeneration, unique phenomena such as dedifferentiation and transdifferentiation are observed and those unique biological events are extremely crucial. In this study epigenetic regulation in amphibian regeneration will be investigated. Eventually, the elucidated knowledge will be applied to regenerative therapies.
Development of a new reverse-genetic strategy for studying histones in mammalian cells
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Histones are subject to various types of chemical modifications, which are supposed to convey epigenetic information. While enzymes responsible for these modifications have been identified and characterized in detail, not much progress has been made in our understanding of the functional role of each histone residue, largely due to technical difficulties. The objective of this study is to establish a new experimental system that allows us to elucidate the importance of each histone residue in mammalian cells and thereby promote epigenetic research.
Molecular Mechanism of Epigenetic regulation in Lymphocyte development
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T cells and B cells play pivotal roles in the protection against infection.These lymphocytes(Immune cells) are derived from hematopoietic stem cells in bone marrow. It remains unclear how the cell fate is determined and mainteined in the lymphocyte development. In this study, we try to unveil the mechanism how the cell fate is epigenetically regulated in this process.
Transposon and host genome response subjected to environmental change
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The purpose of the study is to understand the genetic and epigenetic change of transposons and the host genome subjected to an environmental stress. So far a progeny of heat-stressed plants gained some stress tolerance that may be caused by transposon activation. The genetic and epigenetic change of the stress-tolerant plant will be analyzed and the mechanism of transposition event will be understood by analyzing each plant tissue.
Analysis of cytosine modification status in the brains of patients with mood disorders
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Despite the extensive genetic studies, the cause of mood disorders such as major depression and bipolar disorder remains largely unknown. Recent studies suggest involvement of epigenetic factors for the pathophysiology of the mood disorders. In this project, cytosine modification status of postmortem brains of patients will be studied. Epigenetic biomarkers will be also explored.
Pathophysiological analysis of heart failure toward establishment of epigenetic therapy
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It has been clarified that "epigenetic alteration" plays an important role in the development of heart failure. The distributions of trimethylation marks of histone H3 on lysine-4 and lysine-9 between left ventricular cardiomyocytes of failed heart and those of normal heart are widely different. In this project, we focus on "heart failure-specific epigenetic alteration" and explore the possibility of the establishment of epigenetic therapy for heart failure (i) with inhibitor of histone modifying enzyme and (ii) by identification of noncoding RNA which regulates disease-specific histone modifications.
Stem cell research using live imaging of X chromosome reactivation
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In stem cell research, reactivation of X chromosomes is recognized as an indicator of the pluripotent grand state of stem cells. However, there is no report of the monitoring method on this phenomenon. Therefore, this applicant is planning to develop a novel method to monitor this phenomenon based on a live-imaging technique. He will utilize this method to understand the reprogramming process at the molecular level. This trial would contribute to the effective establishment of human iPS cells and to the evaluation of the safety of human iPS cells in regenerative therapy. The outcomes of this search will have considerable impact in medical care.
Dvelopment of Imaging System for Histone Modification Dynamics
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Post-translational histone modifications are thought to play a central role in epigenetic regulation. These modifications are dynamically and reversibly controlled. We will develop a series of genetically encoded fluorescent indicators to visualize the dynamic nature of histone modifications in living cells. The goal of this study is to reveal epigenetic dynamics during differentiation and reprogramming process.
Structural basis for the chromatin remodeling mechanism by FACT
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The final goal of this research is to obtain the structural information of chromatin remodeling in response to epigenetic regulation. In this study,I aim to reveal the molecular mechanism of the chromatin remodeling by FACT, which is related to both the chromatin structure at the boundary of euchromatin and heterochromatin and plays a critical role in the chromatin remodeling.
Structural basis for the chromatin remodeling mechanism by FACT
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The final goal of this research is to obtain the structural information of chromatin remodeling in response to epigenetic regulation. In this study,I aim to reveal the molecular mechanism of the chromatin remodeling by FACT, which is related to both the chromatin structure at the boundary of euchromatin and heterochromatin and plays a critical role in the chromatin remodeling.
Significance of facultative heterochromatin formation in early mouse development
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Analysis of in vitro models of mouse embryogenesis suggests that facultative heterochromatin formed during the early stages of development is stably maintained in virtually all downstream somatic cell types. This led me to hypothesize that such heterochromatin architecture might be involved in the maintenance of differentiated state in somatic cells. In this project, I will elucidate the molecular basis of this facultative heterochromatin formation and explore its significance in mouse development.
Study of epigenetics acting as a memory tag
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Analysis of in vitro models of mouse embryogenesis suggests that facultative heterochromatin formed during the early stages of development is stably maintained in virtually all downstream somatic cell types. This led me to hypothesize that such heterochromatin architecture might be involved in the maintenance of differentiated state in somatic cells. In this project, I will elucidate the molecular basis of this facultative heterochromatin formation and explore its significance in mouse development.
Visualization and understanding of cohesin-mediated chromatin structure
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Cohesin, which is essential for sister chromatid cohesion, has been recently realized as a regulator of gene expression, since mutations in cohesin complex cause human developmental disorders, so called "cohesinopathies." Although cohesin is thought to change chromatin structure in higher order and thereby modulate transcriptional activity, there is so far no direct evidence showing the changes of chromatin structure mediated by cohesin. By using simple in vitro model system, this study aims to visualize cohesin-mediated chromatin structure and understand how cohesin could regulate gene expression.
Role of histone glycosylations in epigenetic control
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Histone modifications play fundamental roles in epigenetics as well as DNA methylations. This research aims to understand a molecular function of the histone glycosylations by developping a seriese of their specific antibodies. To uncover cross-talks between histone glycosylations and other modifications on a nucleosome,we also attempt to introduce methodology, which determine unknown modifications of the enriched nucleosomes by chromatin immunoprecipitation and high-resolution mass spectorometry.
Epigenetic gene silencing by long non-coding RNA
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In higher eukaryotes, most part of the genome DNA produce RNA without any ORF, thus called non-coding RNAs. Although these non-coding RNAs are known to suppress transcription of surrounding genomic regions, molecular mechanism of the suppression is poorly understood. In this project, using Xist RNA as a model system, we will try to uncover the molecular mechanism of the transcriptional repression by long non-coding RNAs.
