A5041153024- Epigenetics and DNA Methylation
- Cancer-related gene regulation
- RNA modifications and cancer
- Esophageal Cancer Research and Treatment
- Cancer Genomics and Diagnostics
- Gastric Cancer Management and Outcomes
- Genomics and Chromatin Dynamics
- RNA and protein synthesis mechanisms
- CRISPR and Genetic Engineering
- Molecular Biology Techniques and Applications
- Pluripotent Stem Cells Research
- Birth, Development, and Health
- Genetic Syndromes and Imprinting
- Advanced biosensing and bioanalysis techniques
- Blood groups and transfusion
- Prenatal Screening and Diagnostics
- DNA and Nucleic Acid Chemistry
- Bacteriophages and microbial interactions
- Autophagy in Disease and Therapy
- Gene expression and cancer classification
- Immune Cell Function and Interaction
- Plant Molecular Biology Research
- Renal and related cancers
- Muscle Physiology and Disorders
- T-cell and B-cell Immunology
Kyushu University
2016-2025
The University of Tokyo
2004-2025
Japan Science and Technology Agency
2005-2019
Japan Agency for Medical Research and Development
2018
Nishikyushu University
2016
Tokyo University of Science
2001-2014
Kanazawa University
2001-2004
Hitachi (United Kingdom)
2001
DNA methylation plays a key role in epigenetic regulation of eukaryotic genomes. Hence the genome-wide distribution 5-methylcytosine, or methylome, has been attracting intense attention. In recent years, whole-genome bisulfite sequencing (WGBS) enabled methylome analysis at single-base resolution. However, WGBS typically requires microgram quantities as well global PCR amplification, thereby precluding its application to samples limited amounts. This is presumably because treatment...
DNA methylation is an epigenetic modification that plays a crucial role in normal mammalian development, retrotransposon silencing, and cellular reprogramming. Although mainly occurs on the cytosine CG site, non-CG prevalent pluripotent stem cells, brain, oocytes. We previously identified several CG-rich regions mouse germinal vesicle oocytes (GVOs), but overall distribution of enzymes responsible for this are unknown. Using amplification-free whole-genome bisulfite sequencing, which can be...
ChIP-Atlas (https://chip-atlas.org) is a web service providing both GUI- and API-based data-mining tools to reveal the architecture of transcription regulatory landscape. powered by comprehensively integrating all data sets from high-throughput ChIP-seq DNase-seq, method for profiling chromatin regions accessible DNase. In this update, we further collected ATAC-seq whole-genome bisulfite-seq six model organisms (human, mouse, rat, fruit fly, nematode, budding yeast) with latest genome...
Dynamic epigenetic reprogramming occurs during mammalian germ cell development, although the targets of this process, including DNA demethylation and de novo methylation, remain poorly understood. We performed genome-wide methylation analysis in male female mouse primordial cells at embryonic days 10.5, 13.5, 16.5 by whole-genome shotgun bisulfite sequencing. Our high-resolution methylome maps demonstrated gender-specific differences CpG gene-specific levels fetal germline progression. There...
We performed a large-scale cDNA analysis to explore the transcriptome of budding yeast Saccharomyces cerevisiae . sequenced two libraries, one from cells exponentially growing in minimal medium and other meiotic cells. Both libraries were generated by using vector-capping method that allows accurate mapping transcription start sites (TSSs). Consequently, we identified 11,575 TSSs associated with 3,638 annotated genomic features, including 3,599 ORFs, suggest most genes have or more TSSs. In...
Iron metabolism is closely associated with the pathogenesis of obesity. However, mechanism iron-dependent regulation adipocyte differentiation remains unclear. Here, we show that iron essential for rewriting epigenetic marks during differentiation. supply through lysosome-mediated ferritinophagy was found to be crucial early stage differentiation, and deficiency this period suppressed subsequent terminal This demethylation both repressive histone DNA in genomic regions...
Abstract DNA methylation is an essential epigenetic chromatin modification, and its maintenance in mammals requires the protein UHRF1. It yet unclear if UHRF1 functions solely by stimulating DNMT1, or it has important additional functions. Using degron alleles, we show that depletion causes a much greater loss of than DNMT1 depletion. This not caused passive demethylation as UHRF1-depleted cells proliferate more slowly DNMT1-depleted cells. Instead, bioinformatics, proteomics genetics...
Approximately half of all human genes have CpG islands (CGIs)around their promoter regions. Although CGIs usually escape methylation, those on Chromosome X in females and the vicinity imprinted are exceptions: They both methylated unmethylated alleles to display a "composite" pattern methylation analysis. In addition, aberrant is known often occur cancer cells. Here we developed simple HpaII-McrBC PCR method for discrimination full, null, incomplete, composite patterns, applied it...
Abstract Background An ideal format to describe transcriptome would be its composition measured on the scale of absolute numbers individual mRNAs per cell. It help not only precisely grasp structure but also accelerate data exchange and integration. Results We conceived an idea competitive PCR between genomic DNA cDNA. Since former contains every gene exactly at same copy number, it can serve as normalization standard for latter obtain stoichiometric transcriptome. This then easily converted...
Abstract The majority of histones are replaced by protamines during spermatogenesis, but small amounts retained in mammalian spermatozoa. Since nucleosomes spermatozoa influence epigenetic inheritance, it is important to know how distributed the sperm genome. Conflicting data, which may result from different conditions used for micrococcal nuclease (MNase) digestion, have been reported: retention at either gene promoter regions or within distal gene-poor regions. Here, we find that swim-up...
Hematopoietic stem cells (HSCs) exhibit functional alterations, such as reduced regenerative capacity and myeloid-biased differentiation, with age. The HSC niche, which is essential for the maintenance of HSCs, also undergoes marked changes aging. However, it has been technically challenging to directly evaluate contribution niche aging age-associated alterations without niche-damaging myeloablation in transplantation assays. We herein transplanted an excess aged HSCs into young mice...
Whole-genome bisulfite sequencing (WGBS) is the current gold standard of methylome analysis. Post-bisulfite adaptor tagging (PBAT) an increasingly popular WGBS protocol because high sensitivity and low bias. PBAT originally relied on two rounds random priming for adaptor-tagging single-stranded DNA (ssDNA) to attain efficiency but at a cost library insert length. To overcome this limitation, we developed terminal deoxyribonucleotidyl transferase (TdT)-assisted adenylate connector-mediated...
Abstract DNA methylation is an epigenetic modification that specifies the basic state of pluripotent stem cells and regulates developmental transition from to various cell types. In flowering plants, shoot apical meristem (SAM) contains a population which generates aerial part plants including germ cells. Under appropriate conditions, SAM undergoes leaf-forming vegetative inflorescence- flower-forming reproductive SAM. While characteristics are largely altered in this transition, complete...
Angioimmunoblastic T-cell lymphoma (AITL) is proposed to be initiated by age-related clonal hematopoiesis (ACH) with TET2 mutations, whereas the G17V RHOA mutation in immature cells mutations promotes development of T follicular helper (TFH)-like tumor cells. Here, we investigated mechanism which TET2-mutant immune enable AITL using mouse models and human samples. Among 2 models, mice lacking Tet2 all blood (Mx-Cre × Tet2flox/flox transgenic mice) spontaneously developed for approximately up...
Interleukin (IL)-17-producing T helper (Th17) cells are crucial for host defense against extracellular microbes and pathogenesis of autoimmune diseases. Here we show that the AP-1 transcription factor JunB is required Th17 cell development. Junb-deficient CD4+ able to develop in vitro into various subsets except Th17. The RNA-seq transcriptome analysis reveals Th17-specific gene expression program. mice completely resistant experimental encephalomyelitis, a Th17-mediated inflammatory...
The current gold standard method for methylome analysis is whole-genome bisulfite sequencing (WGBS), but its cost substantial, especially the purpose of multi-sample comparison large methylomes. Shotgun target-enriched DNA, or targeted (TMS), can be a flexible, cost-effective alternative to WGBS. However, TMS protocol requires considerable amount input DNA and hence hardly applicable samples limited quantity. Here we report overcome this limitation by using post-bisulfite adaptor tagging...
Abstract The accumulations of different types genetic alterations such as nucleotide substitutions, structural rearrangements and viral genome integrations epigenetic contribute to carcinogenesis. Here, we report correlation between the occurrence features aberrations by whole-genome bisulfite, shotgun, long-read, virus capture sequencing 373 liver cancers. Somatic substitutions rearrangement breakpoints are enriched in tumor-specific hypo-methylated regions with inactive chromatin marks...
Regulation of the epigenome during in vivo specification brain stem cells is still poorly understood. Here, we report DNA methylome analyses directly sampled cortical neural and progenitor (NS/PCs) at different development stages, as well those terminally differentiated neurons, astrocytes, oligodendrocytes. We found that sequential NS/PCs regulated by two successive waves demethylation early late which are responsible for establishment neuron- glia-specific low-methylated regions (LMRs),...
Adult muscles and their associated stem cells retain functional positional memory based on developmental origin.