Yokohama City University Graduate School of Medicine & School of Medicine
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Epigenetics Chromatin and Histone DNA Architecture
Epigenetics & Stem Cell Fate

Elucidating epigenetic mechanisms controlling adult stem cell fate decisions

High-performance optical microscope objective lenses
Histological Imaging

High-resolution histological imaging of tissue architecture and cellular morphology

Super-resolution microscope observation
Advanced Bioimaging

Super-resolution laser microscopy (STED) for nanoscale nuclear chromatin structures

Next generation sequencer genomics data and bioinformatics analysis
Genomics & Bioinformatics

High-throughput next-generation sequencing for genome-wide epigenomics & transcriptomics

Ultra-microtome diamond knife sectioning
Ultra-Microtomy

Diamond knife ultramicrotomy for electron microscopy and histological analysis

Transmission electron microscope observation
Electron Microscopy

Transmission electron microscopy (TEM) for subcellular nanoscale ultrastructure

Stem cell cultures
Stem Cell Biology

Long-term in vitro culture of spermatogonial stem cells (GS cells) & stemness regulation

Molecular biology markers and antibodies
Molecular Markers

Germline-specific marker analysis and molecular functional screening

Making sample for sorting
Cell Purification

Purification of stem and progenitor cell fractions via fluorescence-activated sorting

Time lapse observation
Live Dynamics

Real-time live-cell imaging and dynamic tracking via high-sensitivity fluorescence microscopy

Research Topics

From unraveling the fundamental molecular basis of epigenetics to investigating germline development, infertility, and environmental influences.

Gene Expression Regulation through Epigenetic Modifications

In eukaryotic genomes, DNA is wrapped around histone octamers to form nucleosomes, the fundamental repeating units of chromatin architecture.

Chemical modifications to DNA and histones (such as DNA methylation and histone methylation or acetylation) precisely regulate gene expression ON/OFF states without altering the underlying nucleotide sequence. This phenomenon, known as epigenetics, constitutes an essential regulatory system that allows cells to differentiate and stably maintain lineage identity.

Our laboratory investigates the precise molecular mechanisms by which these epigenetic marks are deposited, recognized, and erased, and how they dictate higher-order chromatin dynamics and transcriptional control.

Chromatin higher-order dynamics regulated by DNA methylation and histone modifications
Transcriptional switching governed by epigenetic writers, readers, and erasers
Molecular basis of cell differentiation and fate commitment without DNA alterations
Gene Expression Regulation through Epigenetic Modifications Diagram
Model of chromatin condensation, relaxation, and histone/DNA modifications controlling transcription

Molecular Mechanisms of Infertility and Developmental Abnormalities

Disruption of epigenetic regulatory networks frequently leads to developmental arrest and various pathogenic disorders. In particular, germ cell development (sperm and oocytes) and early embryogenesis require extensive, genome-wide epigenetic reprogramming.

Aberrations in this reprogramming machinery cause severe phenotypes, including gametogenesis failure leading to infertility, or early embryonic arrest post-fertilization.

Utilizing animal models (e.g., mice) and germ cell lineages, we elucidate the molecular pathophysiology underlying why dysfunction in epigenetic regulators results in spermatogenic failure, gamete deficiency, and embryonic lethality.

Genome-wide epigenetic reprogramming during male and female gametogenesis
Spermatogenic arrest and gamete dysfunction caused by epigenetic regulator deficiencies
Identification of molecular cascades responsible for early embryonic failure and infertility
Molecular Mechanisms of Infertility and Developmental Abnormalities Diagram
Epigenomic reprogramming during gametogenesis and pathophysiology of developmental arrest

Environmental Changes Affect Cell Differentiation through the Epigenome

While the epigenome is robustly maintained, it is uniquely susceptible and responsive to environmental fluctuations, such as nutritional conditions, temperature, chemical exposure, and physiological stress.

Epigenetic aberrations induced by environmental stressors disrupt the delicate balance between stem cell self-renewal and lineage differentiation, thereby compromising tissue homeostasis. Furthermore, epigenetic alterations occurring in the germline can be transmitted across generations, impacting offspring health and phenotype.

We investigate how environmental cues are transduced through intracellular signaling pathways to alter the epigenome, driving aberrant differentiation and elevated disease susceptibility.

Epigenomic alterations in response to nutrition, chemicals, temperature, and stress
Disruption of stem cell self-renewal and differentiation leading to loss of tissue homeostasis
Transgenerational epigenetic inheritance mediated through the germline lineage
Environmental Changes Affect Cell Differentiation through the Epigenome Diagram
Signaling pathways connecting environmental stress to epigenomic remodeling and aberrant cell fate

Selected Publications

Key scientific papers and contributions published by our department.

2024 – 2025

Abstract Summary

Demonstrated that abnormal activation of H3K27me3 demethylases KDM6A/B triggers a localized loss of repressive H3K27me3 marks in cryptorchid spermatogonial stem cells, aberrantly derepressing developmental and pro-apoptotic genes and leading to stem cell degeneration.

✦ Identified aberrant H3K27me3 dynamics as the root epigenetic cause of cryptorchid germ cell loss
Development 2025
Development (2025)

Abnormal H3K27me3 underlies degenerative spermatogonial stem cells in cryptorchid testis.

Kazushige Kuroha, Ivana Dočkal, Uroš Radović, Kuniko Nakajima, Ikue Hoshi, Shion Matsuda, Noriko Kojitani, Kazuyuki Ohbo, Shin-ichi Tomizawa

Abstract Summary

Comprehensive spatio-temporal expression profiling of BMP signaling modifiers Smoc1 and Smoc2 throughout postnatal to adult testis development, identifying their distinct compartmentalization across somatic niche and germline lineages.

✦ First complete mapping of Smoc1 and Smoc2 during postnatal mammalian spermatogenesis
Cover Article Gene Expr Patterns 2024
Gene Expr Patterns (2024) 54, 119383

Spatial and temporal expression analysis of BMP signal modifiers, Smoc1 and Smoc2, from postnatal to adult developmental stages in the mouse testis.

M Ono, K Nakajima, S Tomizawa, T Shirakawa, I Okada, H Saitsu, N Matsumoto, K Ohbo

Abstract Summary

Demonstrated that non-canonical bivalent chromatin pre-programs Wfdc15a in spermatogonial stem cells, which acts downstream in late spermatids to control serine protease activity and testicular immune homeostasis, ensuring male fertility.

✦ Discovered stem-cell epigenetic pre-programming required for testicular immunity and fertility
Development 2024
Development (2024) 151(18): dev202834

A non-canonical bivalent gene Wfdc15a controls spermatogenic protease and immune homeostasis.

S. Tomizawa, R. Fellows, M. Ono, K. Kuroha, I. Dockal, Y. Kobayashi, K. Minamizawa, K. Natsume, K. Nakajima, I. Hoshi, S. Matsuda, M. Seki, Y. Suzuki, K. Aoto, H. Saitsu, K. Ohbo

Abstract Summary

Uncovered the vital niche role of Sertoli-derived brain-derived neurotrophic factor (BDNF) and its TrkB receptor in providing indispensable background survival signals and differentiation balance in mammalian spermatogonia.

✦ Elucidated the physiological significance of the testicular BDNF-TrkB signaling axis
Asian Journal of Andrology 2024
Asian J Androl (2024) 26, 1-7

A behind-the-scenes role of BDNF in the survival and differentiation of spermatogonia.

Shin-ichi Tomizawa*, Kazushige Kuroha*, Michio Ono, Kuniko Nakajima, Kazuyuki Ohbo

2019 – 2021

Abstract Summary

Demonstrated that oxygen concentration during in vitro follicle culture substantially alters de novo DNA methylation and transcriptomic fidelity in developing oocytes, establishing critical quality benchmarks for assisted reproduction.

✦ Revealed oxygen tension as a key determinant of female germline epigenomic integrity
Clinical Epigenetics 2021
Clinical Epigenetics (2021) 13: 132

Oxygen concentration affects de novo DNA methylation and transcription in in vitro cultured oocytes.

Florence Naillat, Heba Saadeh, Joanna Nowacka-Woszuk, Lenka Gahurova, Fatima Santos, Shin-ichi Tomizawa & Gavin Kelsey

Abstract Summary

Revealed that maintenance DNA methylation via Np95/Uhrf1 in pre-meiotic germ cells directly facilitates homologous chromosome pairing, establishing an essential epigenetic requirement for successful meiotic progression.

✦ Discovered that maintenance DNA methylation directly guides meiotic chromosome pairing
Development 2021
Development (2021) 148, dev194605

Maintenance DNA methylation in pre-meiotic germ cells regulates meiotic prophase by facilitating homologous chromosome pairing.

Takada Y, Yaman-Deveci R, Shirakawa T, Sharif J, Tomizawa S, Miura F, Ito T, Ono M, Nakajima K, Koseki Y, Shiotani F, Ishiguro K, Ohbo K, Koseki H.

Abstract Summary

Identified Tsga8 as an essential testis-specific structural gene required for sperm head shaping, flagellar assembly, and male fertility, establishing its role in mammalian spermiogenesis.

✦ Discovered Tsga8 as an essential genetic component for sperm morphogenesis and fertility
Development 2021
Development (2021) 148 (8): dev196212

Tsga8 is required for spermatid morphogenesis and male fertility in mice.

Kobayashi Y, Tomizawa S, Ono M, Kuroha K, Minamizawa K, Natsume K, Dizdarević S, Dočkal I, Tanaka H, Kawagoe T, Seki M, Suzuki Y, Ogonuki N, Inoue K, Matoba S, Anastassiadis K, Mizuki N, Ogura A, Ohbo K.

Abstract Summary

Generated WFDC2 (HE4) knockout mice, discovering that deficiency in this protease inhibitor leads to severe alveolar collapse, unregulated inflammation, and lethal neonatal respiratory failure.

✦ Characterized a vital clinical model for respiratory failure caused by WFDC2 deficiency
Dis Model Mech 2019
Dis Model Mech (2019) 12 (11): dmm040139

Lack of whey acidic protein four disulphide core (WFDC) 2 protease inhibitor causes neonatal death from respiratory failure in mice.

Nakajima K, Ono M, Radović U, Dizdarević S, Tomizawa SI, Kuroha K, Nagamatsu G, Hoshi I, Matsunaga R, Shirakawa T, Kurosawa T, Miyazaki Y, Seki M, Suzuki Y, Koseki H, Nakamura M, Suda T, Ohbo K.

Earlier Key Papers (2011 – 2018)

Abstract Summary

Revealed that histone methyltransferase Kmt2b deposits monovalent and bivalent H3K4me3 marks at germline and developmental gene promoters in spermatogonial stem cells, pre-programming future lineage fidelity.

✦ Discovered Kmt2b-dependent epigenetic pre-programming in male germline stem cells
Development (2018) 145: dev169102

Kmt2b conveys monovalent and bivalent H3K4me3 in spermatogonial stem cells at germline and embryonic promoters.

Tomizawa S, Kobayashi Y, Shirakawa T, Watanabe K, Mizoguchi K, Hoshi I, Nakajima K, Nakabayashi J, Singh S, Dahl A, Alexopoulou D, Seki M, Suzuki Y, Royo H, Peters AHFM, Anastassiadis K, Stewart AF, Ohbo K.

Abstract Summary

Demonstrated that the RNA-binding protein Nanos2 establishes a post-transcriptional buffering network that preserves stemness and prevents precocious differentiation in mouse spermatogonial stem cells.

✦ Discovered post-transcriptional buffering ensuring adult stem cell homeostasis
Dev Cell (2015) 34: 1-12

The RNA binding protein Nanos2 organizes a post-transcriptional buffering system to retain primitive state of mouse spermatogonial stem cells.

Zhou, Z., Shirakawa, T., Ohbo, K., Sada, A., Wu, Q., Hasegawa, K., Saba, R. and Saga, Y.

Abstract Summary

First report identifying an epigenetic checkpoint controlling the transition from a homogenous stem cell pool to progenitor states in mouse male germ cells, mediated by dynamic DNA methylation and histone changes.

✦ Introduced the seminal "Stem Cell Pool" and "Epigenetic Checkpoint" paradigms
Development (2013) 140: 3565-3576

An epigenetic checkpoint controls the transition from a stem cell pool to a progenitor cell state in mouse male germ cells.

Shirakawa T, Yaman-Deveci R, Tomizawa S, Kamizato Y, Nakajima K, et al., Ohbo K.

Abstract Summary

Demonstrated that piRNAs and long noncoding RNAs cooperate to direct target-specific de novo DNA methylation at imprinted loci (Rasgrf1) in the developing male germline.

✦ Proved the RNA-directed de novo DNA methylation paradigm at imprinted mammalian loci
Science (2011) 332: 848-852

Role for piRNAs and noncoding RNA in de novo DNA methylation of the imprinted mouse Rasgrf1 locus.

Watanabe T, Tomizawa S, Mitsuya K, Totoki Y, Yamamoto Y, et al., Sasaki H.

Laboratory Members

Faculty, technical staff, graduate students, and alumni.

Faculty

Dr. Shin-ichi Tomizawa

Shin-ichi Tomizawa

Ph.D. Lecturer researchmap
Dr. Michio Ono

Michio Ono

Ph.D. Assistant Professor researchmap
Dr. Kazushige Kuroha

Kazushige Kuroha

Ph.D. Assistant Professor researchmap

Technical Staff

Kuniko Nakajima

Kuniko Nakajima

Technician
Ikue Hoshi

Ikue Hoshi

Technician

Graduate Students

Noriko Kojitani

Noriko Kojitani

Doctoral Program
Nana Matsuda

Nana Matsuda

Master's Program (M2)
Yuga Kashiwagi

Yuga Kashiwagi

Master's Program (M2)

Current and Former Students (Alumni)

Retired Faculty Kazuyuki Ohbo (Retired in March 2026)
Doctoral Program Takayuki Shirakawa, Yuki Kobayashi
Other (Doctoral Program) Yusuke Minamisawa, Aki Hayashi
Master's Program Shion Matsuda, Monika Šafhauzer, Ivana Dočkal, Selma Dizdarević, Koji Natsume, Keita Mizoguchi, Uroš Radović
Graduate Students Yuki Maekawa, Watanabe, Sugiyama
Research Clerkship Ryo Kumagaya, Kentaro Fujisawa

Department Overview

Information regarding our location, laboratory overview, and contact details.

Overview

Department Department of Histology and Cell Biology, Yokohama City University School of Medicine
Address 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan (Fukuura Campus)
Principal Investigator -----
Study Areas Anatomy, Histology, Epigenetics, Germ cells, Cell biology
Key Technologies Super-resolution fluorescent microscopy (STED), Electron microscopy (TEM / SEM), High-throughput sequencing (ChIP-seq, RNA-seq, BS-seq, single-cell multiomics), Spermatogonial stem cell transplantation and ex-vivo culture
Personnel 3 Faculty instructors, 4 Technical staff, plus Graduate and Undergraduate students

Contact & Location

For inquiries regarding our research, collaborations, or prospective laboratory visits, please feel free to reach out to us.

Phone: +81-45-787-2567 / Fax: +81-45-787-2568
Access: 1-minute walk from "Shidai-Igakubu" Station (Kanazawa Seaside Line)

Prospective Students & Lab Visits

Please feel free to contact us anytime for prospective lab visits and graduate program admissions.

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