研究実績
2026
9.
Xiaohui Gao, Chaebeen Ko, Yuanchao Dong, Takeru Fujii, Satoshi Uchino, Yoshiaki Kobayashi, Akihito Harada, Hiroaki Ohishi, Yasuyuki Ohkawa, Hiroshi Kimura, Hiroshi Ochiai
Minute-scale coupling of chromatin marks and transcriptional bursts Journal Article
In: bioRxiv, 2026.
Abstract | Links | タグ: Kimura G, Ochiai G, Ohkawa G
@article{Gao2026.02.08.704500,
title = {Minute-scale coupling of chromatin marks and transcriptional bursts},
author = {Xiaohui Gao and Chaebeen Ko and Yuanchao Dong and Takeru Fujii and Satoshi Uchino and Yoshiaki Kobayashi and Akihito Harada and Hiroaki Ohishi and Yasuyuki Ohkawa and Hiroshi Kimura and Hiroshi Ochiai},
url = {https://www.biorxiv.org/content/early/2026/02/10/2026.02.08.704500},
doi = {10.64898/2026.02.08.704500},
year = {2026},
date = {2026-02-10},
urldate = {2026-01-01},
journal = {bioRxiv},
publisher = {Cold Spring Harbor Laboratory},
abstract = {Histone modifications are often described as stable epigenetic marks that contribute to maintaining gene-expression programs during development and environmental responses. However, transcription of many genes is intermittent, switching between transcriptionally active and inactive episodes within minutes. Whether chromatin marks around individual genes change on these rapid timescales remains unclear. Here we show that local chromatin modification signals around endogenous genes in mouse embryonic stem cells fluctuate reversibly with transcriptional state, using live imaging of individual genes together with fluorescent probes that report histone modifications. Activation-associated acetylation and methylation marks increased in association with transcriptional activation and decreased with inactivation, whereas a Polycomb-associated repressive mark behaved oppositely. Transcriptional coactivators and both histone acetyltransferase and deacetylase complexes were enriched during transcriptionally active state, consistent with opposing enzymatic activities shaping local acetylation levels. Inhibiting histone deacetylases altered the durations of active and inactive events, supporting a role for deacetylation in regulating transcriptional state transitions. Thus, histone modifications undergo reversible, minute-scale changes coupled to transcriptional activity. This framework helps explain how stochastic transcriptional bursts can occur with stable gene regulation over longer timescales.},
keywords = {Kimura G, Ochiai G, Ohkawa G},
pubstate = {published},
tppubtype = {article}
}
Histone modifications are often described as stable epigenetic marks that contribute to maintaining gene-expression programs during development and environmental responses. However, transcription of many genes is intermittent, switching between transcriptionally active and inactive episodes within minutes. Whether chromatin marks around individual genes change on these rapid timescales remains unclear. Here we show that local chromatin modification signals around endogenous genes in mouse embryonic stem cells fluctuate reversibly with transcriptional state, using live imaging of individual genes together with fluorescent probes that report histone modifications. Activation-associated acetylation and methylation marks increased in association with transcriptional activation and decreased with inactivation, whereas a Polycomb-associated repressive mark behaved oppositely. Transcriptional coactivators and both histone acetyltransferase and deacetylase complexes were enriched during transcriptionally active state, consistent with opposing enzymatic activities shaping local acetylation levels. Inhibiting histone deacetylases altered the durations of active and inactive events, supporting a role for deacetylation in regulating transcriptional state transitions. Thus, histone modifications undergo reversible, minute-scale changes coupled to transcriptional activity. This framework helps explain how stochastic transcriptional bursts can occur with stable gene regulation over longer timescales.
8.
Gabriel Galindo, Daiki Maejima, Jacob DeRoo, Scott R. Burlingham, Gretchen Fixen, Tatsuya Morisaki, Hallie P. Febvre, Ryan Hasbrook, Ning Zhao, Soham Ghosh, E. Handly Mayton, Christopher D. Snow, Brian J. Geiss, Yasuyuki Ohkawa, Yuko Sato, Hiroshi Kimura, Timothy J. Stasevich
AI-assisted protein design to rapidly convert antibody sequences to intrabodies targeting diverse peptides and histone modifications Journal Article
In: Sci. Adv., vol. 12, no. 1, 2026, ISSN: 2375-2548.
Abstract | Links | タグ: Kimura G, Ohkawa G
@article{Galindo2026,
title = {AI-assisted protein design to rapidly convert antibody sequences to intrabodies targeting diverse peptides and histone modifications},
author = {Gabriel Galindo and Daiki Maejima and Jacob DeRoo and Scott R. Burlingham and Gretchen Fixen and Tatsuya Morisaki and Hallie P. Febvre and Ryan Hasbrook and Ning Zhao and Soham Ghosh and E. Handly Mayton and Christopher D. Snow and Brian J. Geiss and Yasuyuki Ohkawa and Yuko Sato and Hiroshi Kimura and Timothy J. Stasevich},
doi = {10.1126/sciadv.adx8352},
issn = {2375-2548},
year = {2026},
date = {2026-01-02},
urldate = {2026-01-02},
journal = {Sci. Adv.},
volume = {12},
number = {1},
publisher = {American Association for the Advancement of Science (AAAS)},
abstract = {Intrabodies are engineered antibodies that function inside living cells, enabling therapeutic, diagnostic, and imaging applications. While powerful, their development has been hindered by challenges associated with their folding, solubility, and stability in the reduced intracellular environment. Here, we present an artificial intelligence-driven pipeline integrating AlphaFold2, ProteinMPNN, and live-cell screening to optimize antibody framework regions while preserving epitope-binding complementarity-determining regions. Using this approach, we successfully converted 19 of 26 antibody sequences into functional single-chain variable fragment intrabodies, including a panel targeting diverse histone modifications for real-time imaging of chromatin dynamics and gene regulation. Notably, 18 of these 19 sequences had failed to convert using the standard approach, demonstrating the unique effectiveness of our method. As antibody sequence databases expand, our method will accelerate intrabody design, making their development easier, more cost effective, and broadly accessible for biological research.},
keywords = {Kimura G, Ohkawa G},
pubstate = {published},
tppubtype = {article}
}
Intrabodies are engineered antibodies that function inside living cells, enabling therapeutic, diagnostic, and imaging applications. While powerful, their development has been hindered by challenges associated with their folding, solubility, and stability in the reduced intracellular environment. Here, we present an artificial intelligence-driven pipeline integrating AlphaFold2, ProteinMPNN, and live-cell screening to optimize antibody framework regions while preserving epitope-binding complementarity-determining regions. Using this approach, we successfully converted 19 of 26 antibody sequences into functional single-chain variable fragment intrabodies, including a panel targeting diverse histone modifications for real-time imaging of chromatin dynamics and gene regulation. Notably, 18 of these 19 sequences had failed to convert using the standard approach, demonstrating the unique effectiveness of our method. As antibody sequence databases expand, our method will accelerate intrabody design, making their development easier, more cost effective, and broadly accessible for biological research.
2025
7.
Kazumitsu Maehara, Yasuyuki Ohkawa
Geometry-preserving vector field reconstruction of high-dimensional cell-state dynamics using ddHodge Journal Article
In: Nat Commun, vol. 16, no. 1, 2025, ISSN: 2041-1723.
Abstract | Links | タグ: Ohkawa G
@article{Maehara2025,
title = {Geometry-preserving vector field reconstruction of high-dimensional cell-state dynamics using ddHodge},
author = {Kazumitsu Maehara and Yasuyuki Ohkawa},
doi = {10.1038/s41467-025-67782-6},
issn = {2041-1723},
year = {2025},
date = {2025-12-29},
journal = {Nat Commun},
volume = {16},
number = {1},
publisher = {Springer Science and Business Media LLC},
abstract = {The differentiation potency of cells is governed by dynamic changes in gene expression, which can be inferred from single-cell RNA sequencing (scRNA-seq) data. While velocity-based approaches have been used to analyze cell state changes as vector fields, extracting acceleration (change of change) information remains challenging because of the sparsity and high-dimensionality of the data. Here, we develop ddHodge, a framework based on Hodge decomposition for precise vector-field reconstruction. ddHodge accurately recovers all basic components of the vector field, namely, the gradient, curl, and divergence, including the acceleration of the cell state, as second-order derivatives, even from biased and sparse samples. Furthermore, we extend the method to approximate high-dimensional gene expression dynamics on lower-dimensional data manifolds. By applying ddHodge to scRNA-seq data from mouse embryogenesis, we reveal that the gene expression dynamics during development follow a gradient system shaped by potential landscapes, which has not previously been validated with real data. Furthermore, we quantify differentiation potency as cell state stability on the basis of the divergence and identify key genes that drive potency. Our general computational framework for analyzing complex biological systems can elucidate cell fate decisions in developmental processes.},
keywords = {Ohkawa G},
pubstate = {published},
tppubtype = {article}
}
The differentiation potency of cells is governed by dynamic changes in gene expression, which can be inferred from single-cell RNA sequencing (scRNA-seq) data. While velocity-based approaches have been used to analyze cell state changes as vector fields, extracting acceleration (change of change) information remains challenging because of the sparsity and high-dimensionality of the data. Here, we develop ddHodge, a framework based on Hodge decomposition for precise vector-field reconstruction. ddHodge accurately recovers all basic components of the vector field, namely, the gradient, curl, and divergence, including the acceleration of the cell state, as second-order derivatives, even from biased and sparse samples. Furthermore, we extend the method to approximate high-dimensional gene expression dynamics on lower-dimensional data manifolds. By applying ddHodge to scRNA-seq data from mouse embryogenesis, we reveal that the gene expression dynamics during development follow a gradient system shaped by potential landscapes, which has not previously been validated with real data. Furthermore, we quantify differentiation potency as cell state stability on the basis of the divergence and identify key genes that drive potency. Our general computational framework for analyzing complex biological systems can elucidate cell fate decisions in developmental processes.
6.
Takeru Fujii, Kosuke Tomimatsu, Michiko Kato, Miho Ito, Shoko Sato, Hitoshi Kurumizaka, Yuko Sato, Kazumitsu Maehara, Hiroshi Kimura, Akihito Harada, Yasuyuki Ohkawa
Reconstructing epigenomic dynamics through a single-cell multi-epigenome data integration framework Journal Article
In: Nat Commun, vol. 16, no. 1, 2025, ISSN: 2041-1723.
Abstract | Links | タグ: Kimura G, Kurumizaka G, Ohkawa G
@article{Fujii2025,
title = {Reconstructing epigenomic dynamics through a single-cell multi-epigenome data integration framework},
author = {Takeru Fujii and Kosuke Tomimatsu and Michiko Kato and Miho Ito and Shoko Sato and Hitoshi Kurumizaka and Yuko Sato and Kazumitsu Maehara and Hiroshi Kimura and Akihito Harada and Yasuyuki Ohkawa},
doi = {10.1038/s41467-025-67016-9},
issn = {2041-1723},
year = {2025},
date = {2025-12-17},
journal = {Nat Commun},
volume = {16},
number = {1},
publisher = {Springer Science and Business Media LLC},
abstract = {Transcriptional regulation arises from the dynamic and combinatorial actions of multiple regulatory factors on genomic DNA. Although many epigenomic regulators have been identified, the precise order in which these factors accumulate at individual gene loci to activate transcription remains unclear. Here we show a single-cell data integration framework that infers the binding order of multiple chromatin factors at single-cell resolution. Central to this framework is sci-mtChIL-seq, a scalable single-cell method that simultaneously profiles genome-wide binding of RNA polymerase II (RNAPII) and diverse epigenomic regulators. By defining transcriptional states through RNAPII occupancy and integrating multiple sci-mtChIL-seq datasets, we systematically link the combinatorial patterns of transcription factor binding, histone modifications and chromatin remodeling. This framework reveals the temporal coordination among chromatin factors during transcriptional activation, providing a powerful approach to uncover context-dependent epigenomic dynamics and the principles of gene regulation in complex cellular systems.},
keywords = {Kimura G, Kurumizaka G, Ohkawa G},
pubstate = {published},
tppubtype = {article}
}
Transcriptional regulation arises from the dynamic and combinatorial actions of multiple regulatory factors on genomic DNA. Although many epigenomic regulators have been identified, the precise order in which these factors accumulate at individual gene loci to activate transcription remains unclear. Here we show a single-cell data integration framework that infers the binding order of multiple chromatin factors at single-cell resolution. Central to this framework is sci-mtChIL-seq, a scalable single-cell method that simultaneously profiles genome-wide binding of RNA polymerase II (RNAPII) and diverse epigenomic regulators. By defining transcriptional states through RNAPII occupancy and integrating multiple sci-mtChIL-seq datasets, we systematically link the combinatorial patterns of transcription factor binding, histone modifications and chromatin remodeling. This framework reveals the temporal coordination among chromatin factors during transcriptional activation, providing a powerful approach to uncover context-dependent epigenomic dynamics and the principles of gene regulation in complex cellular systems.
5.
Chihiro Matsuda, Akane Ichiki, Yuko Sato, Yukino Kudo, Mika Saotome, Chihiro Takayama, Khoa Minh Le, Satoshi Uchino, Ryota Higuchi, Kazuhiko Kawata, Kosuke Tomimatsu, Manabu Ozawa, Masahito Ikawa, Yasuyuki Ohkawa, Yoshihiro Baba, Hiroshi Kimura
Organization and Dynamics of Transcription Elongation Foci in Mouse Tissues Journal Article
In: Journal of Molecular Biology, 2025, ISSN: 0022-2836.
Abstract | Links | タグ: Kimura G, Ohkawa G
@article{Matsuda2025,
title = {Organization and Dynamics of Transcription Elongation Foci in Mouse Tissues},
author = {Chihiro Matsuda and Akane Ichiki and Yuko Sato and Yukino Kudo and Mika Saotome and Chihiro Takayama and Khoa Minh Le and Satoshi Uchino and Ryota Higuchi and Kazuhiko Kawata and Kosuke Tomimatsu and Manabu Ozawa and Masahito Ikawa and Yasuyuki Ohkawa and Yoshihiro Baba and Hiroshi Kimura},
doi = {10.1016/j.jmb.2025.169395},
issn = {0022-2836},
year = {2025},
date = {2025-08-13},
journal = {Journal of Molecular Biology},
publisher = {Elsevier BV},
abstract = {RNA polymerase II (RNAP2) transcribes most genes in eukaryotic nuclei. During the transition from transcription initiation to productive elongation, and throughout the elongation phase, RNAP2 becomes phosphorylated at the Ser2 residue within the heptapeptide repeats of the carboxyl-terminal domain of its largest subunit. Antibodies specific to RNAP2 Ser2 phosphorylation (Ser2ph) have enabled visualization of active transcription sites in fixed cells and tissues. Here, we report the generation and characterization of knock-in mice ubiquitously expressing a fluorescent protein-tagged, modification-specific intracellular antibody (mintbody) targeting RNAP2 Ser2ph. Using these mice, we successfully visualized transcription elongation foci in mouse tissues and characterized their distribution and dynamics across diverse cell types. RNAP2 Ser2ph-mintbody formed hundreds to thousands of nuclear foci, which were excluded from heterochromatin and transcriptionally repressed domains, such as the XY body in pachytene spermatocytes. Quantitative analysis revealed tissue- and cell type-specific variation in both the number and mobility of transcription elongation foci. The mobility of transcription foci was more restricted in differentiated cells compared to differentiating and proliferating cells, likely reflecting a reduced number of actively transcribed genes and more limited open chromatin regions upon differentiation. These findings suggest that the spatial organization and dynamics of transcription elongation are closely associated with cell identity and differentiation status. The RNAP2 Ser2ph-mintbody knock-in mice provide a valuable tool for future studies of transcription organization and dynamics at the tissue level.},
keywords = {Kimura G, Ohkawa G},
pubstate = {published},
tppubtype = {article}
}
RNA polymerase II (RNAP2) transcribes most genes in eukaryotic nuclei. During the transition from transcription initiation to productive elongation, and throughout the elongation phase, RNAP2 becomes phosphorylated at the Ser2 residue within the heptapeptide repeats of the carboxyl-terminal domain of its largest subunit. Antibodies specific to RNAP2 Ser2 phosphorylation (Ser2ph) have enabled visualization of active transcription sites in fixed cells and tissues. Here, we report the generation and characterization of knock-in mice ubiquitously expressing a fluorescent protein-tagged, modification-specific intracellular antibody (mintbody) targeting RNAP2 Ser2ph. Using these mice, we successfully visualized transcription elongation foci in mouse tissues and characterized their distribution and dynamics across diverse cell types. RNAP2 Ser2ph-mintbody formed hundreds to thousands of nuclear foci, which were excluded from heterochromatin and transcriptionally repressed domains, such as the XY body in pachytene spermatocytes. Quantitative analysis revealed tissue- and cell type-specific variation in both the number and mobility of transcription elongation foci. The mobility of transcription foci was more restricted in differentiated cells compared to differentiating and proliferating cells, likely reflecting a reduced number of actively transcribed genes and more limited open chromatin regions upon differentiation. These findings suggest that the spatial organization and dynamics of transcription elongation are closely associated with cell identity and differentiation status. The RNAP2 Ser2ph-mintbody knock-in mice provide a valuable tool for future studies of transcription organization and dynamics at the tissue level.
4.
Gabriel Galindo, Daiki Maejima, Jacob DeRoo, Scott R. Burlingham, Gretchen Fixen, Tatsuya Morisaki, Hallie P. Febvre, Ryan Hasbrook, Ning Zhao, Soham Ghosh, E. Handly Mayton, Christopher D. Snow, Brian J. Geiss, Yasuyuki Ohkawa, Yuko Sato, Hiroshi Kimura, Timothy J. Stasevich
bioRxiv, 2025.
Abstract | Links | タグ: Kimura G, Ohkawa G
@unpublished{Galindo2025,
title = {AI-assisted protein design to rapidly convert antibody sequences to intrabodies targeting diverse peptides and histone modifications},
author = {Gabriel Galindo and Daiki Maejima and Jacob DeRoo and Scott R. Burlingham and Gretchen Fixen and Tatsuya Morisaki and Hallie P. Febvre and Ryan Hasbrook and Ning Zhao and Soham Ghosh and E. Handly Mayton and Christopher D. Snow and Brian J. Geiss and Yasuyuki Ohkawa and Yuko Sato and Hiroshi Kimura and Timothy J. Stasevich},
url = {http://biorxiv.org/lookup/doi/10.1101/2025.02.06.636921},
doi = {10.1101/2025.02.06.636921},
year = {2025},
date = {2025-02-08},
urldate = {2025-02-08},
publisher = {Cold Spring Harbor Laboratory},
abstract = {<jats:title>ABSTRACT</jats:title><jats:p>Intrabodies are engineered antibodies that function inside living cells, enabling therapeutic, diagnostic, and imaging applications. While powerful, their development has been hindered by challenges associated with their folding, solubility, and stability in the reduced intracellular environment. Here, we present an AI-driven pipeline integrating AlphaFold2, ProteinMPNN, and live-cell screening to optimize antibody framework regions while preserving epitope-binding complementarity-determining regions. Using this approach, we successfully converted 19 out of 26 antibody sequences into functional single-chain variable fragment (scFv) intrabodies, including a panel targeting diverse histone modifications for real-time imaging of chromatin dynamics and gene regulation. Notably, 18 of these 19 sequences had failed to convert using the standard approach, demonstrating the unique effectiveness of our method. As antibody sequence databases expand, our method will accelerate intrabody design, making their development easier, more cost-effective, and broadly accessible for biological research.</jats:p>},
howpublished = {bioRxiv},
keywords = {Kimura G, Ohkawa G},
pubstate = {published},
tppubtype = {unpublished}
}
<jats:title>ABSTRACT</jats:title><jats:p>Intrabodies are engineered antibodies that function inside living cells, enabling therapeutic, diagnostic, and imaging applications. While powerful, their development has been hindered by challenges associated with their folding, solubility, and stability in the reduced intracellular environment. Here, we present an AI-driven pipeline integrating AlphaFold2, ProteinMPNN, and live-cell screening to optimize antibody framework regions while preserving epitope-binding complementarity-determining regions. Using this approach, we successfully converted 19 out of 26 antibody sequences into functional single-chain variable fragment (scFv) intrabodies, including a panel targeting diverse histone modifications for real-time imaging of chromatin dynamics and gene regulation. Notably, 18 of these 19 sequences had failed to convert using the standard approach, demonstrating the unique effectiveness of our method. As antibody sequence databases expand, our method will accelerate intrabody design, making their development easier, more cost-effective, and broadly accessible for biological research.</jats:p>
2024
3.
Hiroaki Ohishi, Soya Shinkai, Hitoshi Owada, Takeru Fujii, Kazufumi Hosoda, Shuichi Onami, Takashi Yamamoto, Yasuyuki Ohkawa, Hiroshi Ochiai
Transcription-coupled changes in genomic region proximities during transcriptional bursting Journal Article
In: Sci. Adv., vol. 10, no. 49, 2024, ISSN: 2375-2548.
Abstract | Links | タグ: Ochiai G, Ohkawa G
@article{Ohishi2024,
title = {Transcription-coupled changes in genomic region proximities during transcriptional bursting},
author = {Hiroaki Ohishi and Soya Shinkai and Hitoshi Owada and Takeru Fujii and Kazufumi Hosoda and Shuichi Onami and Takashi Yamamoto and Yasuyuki Ohkawa and Hiroshi Ochiai},
doi = {10.1126/sciadv.adn0020},
issn = {2375-2548},
year = {2024},
date = {2024-12-06},
urldate = {2024-12-06},
journal = {Sci. Adv.},
volume = {10},
number = {49},
publisher = {American Association for the Advancement of Science (AAAS)},
abstract = {<jats:p>The orchestration of our genes heavily relies on coordinated communication between enhancers and promoters, yet the mechanisms behind this dynamic interplay during active transcription remain unclear. Here, we investigated enhancer-promoter (E-P) interactions in relation to transcriptional bursting in mouse embryonic stem cells using sequential DNA/RNA/immunofluorescence–fluorescence in situ hybridization analyses. Our data reveal that the active state of specific genes is characterized by specific proximities between different genomic regions and the accumulation of transcriptional regulatory factors. Mathematical simulations suggest that an increase in local viscosity could potentially contribute to stabilizing the duration of these E-P proximities. Our study provides insights into the association among E-P proximity, protein accumulation, and transcriptional dynamics, paving the way for a more nuanced understanding of gene-specific regulatory mechanisms.</jats:p>},
keywords = {Ochiai G, Ohkawa G},
pubstate = {published},
tppubtype = {article}
}
<jats:p>The orchestration of our genes heavily relies on coordinated communication between enhancers and promoters, yet the mechanisms behind this dynamic interplay during active transcription remain unclear. Here, we investigated enhancer-promoter (E-P) interactions in relation to transcriptional bursting in mouse embryonic stem cells using sequential DNA/RNA/immunofluorescence–fluorescence in situ hybridization analyses. Our data reveal that the active state of specific genes is characterized by specific proximities between different genomic regions and the accumulation of transcriptional regulatory factors. Mathematical simulations suggest that an increase in local viscosity could potentially contribute to stabilizing the duration of these E-P proximities. Our study provides insights into the association among E-P proximity, protein accumulation, and transcriptional dynamics, paving the way for a more nuanced understanding of gene-specific regulatory mechanisms.</jats:p>
2.
Yuichi Saito, Akihito Harada, Miho Ushijima, Kaori Tanaka, Ryota Higuchi, Akemi Baba, Daisuke Murakami, Stephen L Nutt, Takashi Nakagawa, Yasuyuki Ohkawa, Yoshihiro Baba
Plasma cell differentiation is regulated by the expression of histone variant H3.3 Journal Article
In: Nat Commun, vol. 15, no. 1, pp. 5004, 2024, ISSN: 2041-1723.
Abstract | Links | タグ: Ohkawa G
@article{pmid38902223,
title = {Plasma cell differentiation is regulated by the expression of histone variant H3.3},
author = {Yuichi Saito and Akihito Harada and Miho Ushijima and Kaori Tanaka and Ryota Higuchi and Akemi Baba and Daisuke Murakami and Stephen L Nutt and Takashi Nakagawa and Yasuyuki Ohkawa and Yoshihiro Baba},
doi = {10.1038/s41467-024-49375-x},
issn = {2041-1723},
year = {2024},
date = {2024-06-01},
urldate = {2024-06-01},
journal = {Nat Commun},
volume = {15},
number = {1},
pages = {5004},
abstract = {The differentiation of B cells into plasma cells is associated with substantial transcriptional and epigenetic remodeling. H3.3 histone variant marks active chromatin via replication-independent nucleosome assembly. However, its role in plasma cell development remains elusive. Herein, we show that during plasma cell differentiation, H3.3 is downregulated, and the deposition of H3.3 and chromatin accessibility are dynamically changed. Blockade of H3.3 downregulation by enforced H3.3 expression impairs plasma cell differentiation in an H3.3-specific sequence-dependent manner. Mechanistically, enforced H3.3 expression inhibits the upregulation of plasma cell-associated genes such as Irf4, Prdm1, and Xbp1 and maintains the expression of B cell-associated genes, Pax5, Bach2, and Bcl6. Concomitantly, sustained H3.3 expression prevents the structure of chromatin accessibility characteristic for plasma cells. Our findings suggest that appropriate H3.3 expression and deposition control plasma cell differentiation.},
keywords = {Ohkawa G},
pubstate = {published},
tppubtype = {article}
}
The differentiation of B cells into plasma cells is associated with substantial transcriptional and epigenetic remodeling. H3.3 histone variant marks active chromatin via replication-independent nucleosome assembly. However, its role in plasma cell development remains elusive. Herein, we show that during plasma cell differentiation, H3.3 is downregulated, and the deposition of H3.3 and chromatin accessibility are dynamically changed. Blockade of H3.3 downregulation by enforced H3.3 expression impairs plasma cell differentiation in an H3.3-specific sequence-dependent manner. Mechanistically, enforced H3.3 expression inhibits the upregulation of plasma cell-associated genes such as Irf4, Prdm1, and Xbp1 and maintains the expression of B cell-associated genes, Pax5, Bach2, and Bcl6. Concomitantly, sustained H3.3 expression prevents the structure of chromatin accessibility characteristic for plasma cells. Our findings suggest that appropriate H3.3 expression and deposition control plasma cell differentiation.
1.
Kosuke Tomimatsu, Takeru Fujii, Ryoma Bise, Kazufumi Hosoda, Yosuke Taniguchi, Hiroshi Ochiai, Hiroaki Ohishi, Kanta Ando, Ryoma Minami, Kaori Tanaka, Taro Tachibana, Seiichi Mori, Akihito Harada, Kazumitsu Maehara, Masao Nagasaki, Seiichi Uchida, Hiroshi Kimura, Masashi Narita, Yasuyuki Ohkawa
Precise immunofluorescence canceling for highly multiplexed imaging to capture specific cell states Journal Article
In: Nat Commun, vol. 15, no. 1, pp. 3657, 2024.
Abstract | Links | タグ: Kimura G, Ochiai G, Ohkawa G
@article{10.1038/s41467-024-47989-9,
title = {Precise immunofluorescence canceling for highly multiplexed imaging to capture specific cell states},
author = {Kosuke Tomimatsu and Takeru Fujii and Ryoma Bise and Kazufumi Hosoda and Yosuke Taniguchi and Hiroshi Ochiai and Hiroaki Ohishi and Kanta Ando and Ryoma Minami and Kaori Tanaka and Taro Tachibana and Seiichi Mori and Akihito Harada and Kazumitsu Maehara and Masao Nagasaki and Seiichi Uchida and Hiroshi Kimura and Masashi Narita and Yasuyuki Ohkawa},
doi = {10.1038/s41467-024-47989-9},
year = {2024},
date = {2024-05-08},
urldate = {2024-05-08},
journal = {Nat Commun},
volume = {15},
number = {1},
pages = {3657},
abstract = {Cell states are regulated by the response of signaling pathways to receptor ligand-binding and intercellular interactions. High-resolution imaging has been attempted to explore the dynamics of these processes and, recently, multiplexed imaging has profiled cell states by achieving a comprehensive acquisition of spatial protein information from cells. However, the specificity of antibodies is still compromised when visualizing activated signals. Here, we develop Precise Emission Canceling Antibodies (PECAbs) that have cleavable fluorescent labeling. PECAbs enable high-specificity sequential imaging using hundreds of antibodies, allowing for reconstruction of the spatiotemporal dynamics of signaling pathways. Additionally, combining this approach with seq-smFISH can effectively classify cells and identify their signal activation states in human tissue. Overall, the PECAb system can serve as a comprehensive platform for analyzing complex cell processes. Multiplexed imaging to study cellular pathways can be hampered by lack of antibody specificity, especially when assessing signal activation. Here, the authors present Precise Emission Canceling Antibodies (PECAbs), which enable high-specificity sequential imaging and the study of signaling pathways.},
keywords = {Kimura G, Ochiai G, Ohkawa G},
pubstate = {published},
tppubtype = {article}
}
Cell states are regulated by the response of signaling pathways to receptor ligand-binding and intercellular interactions. High-resolution imaging has been attempted to explore the dynamics of these processes and, recently, multiplexed imaging has profiled cell states by achieving a comprehensive acquisition of spatial protein information from cells. However, the specificity of antibodies is still compromised when visualizing activated signals. Here, we develop Precise Emission Canceling Antibodies (PECAbs) that have cleavable fluorescent labeling. PECAbs enable high-specificity sequential imaging using hundreds of antibodies, allowing for reconstruction of the spatiotemporal dynamics of signaling pathways. Additionally, combining this approach with seq-smFISH can effectively classify cells and identify their signal activation states in human tissue. Overall, the PECAb system can serve as a comprehensive platform for analyzing complex cell processes. Multiplexed imaging to study cellular pathways can be hampered by lack of antibody specificity, especially when assessing signal activation. Here, the authors present Precise Emission Canceling Antibodies (PECAbs), which enable high-specificity sequential imaging and the study of signaling pathways.
