研究実績
2026
7.
Kotaro Tomuro, Shiho Makino, Takanori Akaiwa, Akane Harada, Kenta Kobayashi, Nobuyuki Shiina, Takashi Fukaya, Kyogo Kawaguchi, Yuichi Shichino, Shintaro Iwasaki
Sequence features and dynamics of subcellular translation revealed by APEX-Ribo-Seq Unpublished
bioRxiv, 2026, (Preprint (not peer reviewed), version 3, posted September 3, 2026.).
Abstract | Links | タグ: Fukaya G
@unpublished{Tomuro2025,
title = {Sequence features and dynamics of subcellular translation revealed by APEX-Ribo-Seq},
author = {Kotaro Tomuro and Shiho Makino and Takanori Akaiwa and Akane Harada and Kenta Kobayashi and Nobuyuki Shiina and Takashi Fukaya and Kyogo Kawaguchi and Yuichi Shichino and Shintaro Iwasaki},
url = {https://www.biorxiv.org/content/10.1101/2025.05.26.656194v3},
doi = {10.1101/2025.05.26.656194},
year = {2026},
date = {2026-09-03},
urldate = {2026-09-03},
publisher = {openRxiv},
abstract = {Local translation at specific subcellular regions is proposed to define appropriate protein destinations and functions. However, our understanding of local translation still remains far from complete due to a lack of versatile analytical tools. Here, we developed a new method, termed “APEX-Ribo-Seq”, that integrates ribosome profiling (Ribo-Seq) with APEX2-based proximity labeling. We mapped local translation across 14 distinct organelles and identified over 3,000 genes undergoing localized translation, encoding components of complexes that function at these specific sites. RNA language-model predictors captured compartment-associated information beyond protein sequence, and model-derived attribution nominated sequence-sensitive transcript regions for mechanistic follow-up. Gene-set-level RBP enrichment and knockdown experiments separately identified RBPs associated with compartment-specific translation. The utility of APEX-Ribo-Seq was demonstrated in primary neurons, revealing compartment-specific translatomes in dendrites, axons, and presynapses. Extending this approach in vivo, we applied APEX-Ribo-Seq to germ granules in Drosophila embryos, profiling the temporal transition from translationally silent mRNA storage to localized translation during early embryogenesis. Our results provide a comprehensive view of the spatiotemporal translatome and its regulation.},
howpublished = {bioRxiv},
note = {Preprint (not peer reviewed), version 3, posted September 3, 2026.},
keywords = {Fukaya G},
pubstate = {published},
tppubtype = {unpublished}
}
Local translation at specific subcellular regions is proposed to define appropriate protein destinations and functions. However, our understanding of local translation still remains far from complete due to a lack of versatile analytical tools. Here, we developed a new method, termed “APEX-Ribo-Seq”, that integrates ribosome profiling (Ribo-Seq) with APEX2-based proximity labeling. We mapped local translation across 14 distinct organelles and identified over 3,000 genes undergoing localized translation, encoding components of complexes that function at these specific sites. RNA language-model predictors captured compartment-associated information beyond protein sequence, and model-derived attribution nominated sequence-sensitive transcript regions for mechanistic follow-up. Gene-set-level RBP enrichment and knockdown experiments separately identified RBPs associated with compartment-specific translation. The utility of APEX-Ribo-Seq was demonstrated in primary neurons, revealing compartment-specific translatomes in dendrites, axons, and presynapses. Extending this approach in vivo, we applied APEX-Ribo-Seq to germ granules in Drosophila embryos, profiling the temporal transition from translationally silent mRNA storage to localized translation during early embryogenesis. Our results provide a comprehensive view of the spatiotemporal translatome and its regulation.
6.
Tetsuya Yamamoto, Koji Kawasaki, Takashi Fukaya
Polymeric mechanism of enhancer-promoter cooperativity in transcriptional bursting Journal Article
In: bioRxiv, 2026.
Abstract | Links | タグ: Fukaya G
@article{YAMAMOTO2026.04.29.721797,
title = {Polymeric mechanism of enhancer-promoter cooperativity in transcriptional bursting},
author = {Tetsuya Yamamoto and Koji Kawasaki and Takashi Fukaya},
url = {https://www.biorxiv.org/content/early/2026/05/02/2026.04.29.721797},
doi = {10.64898/2026.04.29.721797},
year = {2026},
date = {2026-05-02},
urldate = {2026-05-02},
journal = {bioRxiv},
publisher = {Cold Spring Harbor Laboratory},
abstract = {Emerging evidence suggest that gene expression is controlled though the modulation of transcriptional bursting across species. However, the underlying regulatory mechanisms remain largely uncertain. Recent live-imaging studies have reported that transcription factors (TFs) form a cluster at enhancers just prior to gene activation, thereby locally concentrating the active transcription machinery. This process is thought to be mediated by multivalent interaction between Mediator recruited by TFs. Conversely, transcription itself is also suggested that to influence the assembly of the TF clustering, implicating the presence of a feedback mechanism. To understand the theoretical framework underlying the interplay between TF clustering and transcription, we here develop a polymer micelle model of transcriptional bursting. With this model, multiple RNA polymerase II (Pol II) molecules loaded to the promoter, together with enhancer-bound Mediator, assemble a micelle-like structure due to their connectivity via DNA when the chromatin fiber connecting enhancer and promoter adopts closed conformation, analogous to polysoap micelle. This assembly further recruits freely diffusing Pol II and Mediator in the nucleoplasm even at low concentration up to the optimal size. Our theoretical framework enables quantitative prediction of how dynamic transitions of enhancer-promoter conformation and the stability of the micelle impact the kinetics of transcriptional bursting.Competing Interest StatementThe authors have declared no competing interest.Japan Society for the Promotion of Science, https://ror.org/00hhkn466, 24K06969, 24K18090, 25H02301, 25H00967, 24H02327, 25H02441Japan Science and Technology Agency, https://ror.org/00097mb19, JPMJFR214W, JPMJCR25T2, JPMJAX2327},
keywords = {Fukaya G},
pubstate = {published},
tppubtype = {article}
}
Emerging evidence suggest that gene expression is controlled though the modulation of transcriptional bursting across species. However, the underlying regulatory mechanisms remain largely uncertain. Recent live-imaging studies have reported that transcription factors (TFs) form a cluster at enhancers just prior to gene activation, thereby locally concentrating the active transcription machinery. This process is thought to be mediated by multivalent interaction between Mediator recruited by TFs. Conversely, transcription itself is also suggested that to influence the assembly of the TF clustering, implicating the presence of a feedback mechanism. To understand the theoretical framework underlying the interplay between TF clustering and transcription, we here develop a polymer micelle model of transcriptional bursting. With this model, multiple RNA polymerase II (Pol II) molecules loaded to the promoter, together with enhancer-bound Mediator, assemble a micelle-like structure due to their connectivity via DNA when the chromatin fiber connecting enhancer and promoter adopts closed conformation, analogous to polysoap micelle. This assembly further recruits freely diffusing Pol II and Mediator in the nucleoplasm even at low concentration up to the optimal size. Our theoretical framework enables quantitative prediction of how dynamic transitions of enhancer-promoter conformation and the stability of the micelle impact the kinetics of transcriptional bursting.Competing Interest StatementThe authors have declared no competing interest.Japan Society for the Promotion of Science, https://ror.org/00hhkn466, 24K06969, 24K18090, 25H02301, 25H00967, 24H02327, 25H02441Japan Science and Technology Agency, https://ror.org/00097mb19, JPMJFR214W, JPMJCR25T2, JPMJAX2327
5.
Raku Saito, Yusuke Umemura, Shiho Makino, Takashi Fukaya
Decoding the molecular logic of rapidly evolving ZAD zinc finger proteins in Drosophila Journal Article
In: Sci. Adv., vol. 12, no. 9, 2026, ISSN: 2375-2548.
Abstract | Links | タグ: Fukaya G
@article{Saito2026,
title = {Decoding the molecular logic of rapidly evolving ZAD zinc finger proteins in \textit{Drosophila}},
author = {Raku Saito and Yusuke Umemura and Shiho Makino and Takashi Fukaya},
doi = {10.1126/sciadv.ady7568},
issn = {2375-2548},
year = {2026},
date = {2026-02-27},
urldate = {2026-02-27},
journal = {Sci. Adv.},
volume = {12},
number = {9},
publisher = {American Association for the Advancement of Science (AAAS)},
abstract = {The zinc finger–associated domain (ZAD)–containing C2H2 zinc finger proteins (ZAD-ZnFs) represent the most abundant class of transcription factors that emerged during insect evolution, yet their molecular diversity and biological functions remain largely unclear. Here, we established a systematic CRISPR-based protein-tagging approach that enables direct, unambiguous comparison of nuclear localization and genome-wide binding profiles of endogenous ZAD-ZnFs in developing Drosophila embryos. Evidence is provided that a subset of ZAD-ZnFs forms nuclear condensates through the stacking of the N-terminal ZAD dimerization surface. Disruption of condensation activity leads to misregulation of genome-wide binding profiles and lethality, underscoring its functional and physiological significance in development. Integrative chromatin immunoprecipitation sequencing and Micro-C analyses reveal that many ZAD-ZnFs colocalize with core insulator proteins such as CCCTC-binding factor and Centrosomal protein 190 kD to control the formation of topological boundaries. We suggest that the diverse molecular functions of ZAD-ZnFs have evolutionarily arisen from their ancestral role as insulator-binding proteins.},
keywords = {Fukaya G},
pubstate = {published},
tppubtype = {article}
}
The zinc finger–associated domain (ZAD)–containing C2H2 zinc finger proteins (ZAD-ZnFs) represent the most abundant class of transcription factors that emerged during insect evolution, yet their molecular diversity and biological functions remain largely unclear. Here, we established a systematic CRISPR-based protein-tagging approach that enables direct, unambiguous comparison of nuclear localization and genome-wide binding profiles of endogenous ZAD-ZnFs in developing Drosophila embryos. Evidence is provided that a subset of ZAD-ZnFs forms nuclear condensates through the stacking of the N-terminal ZAD dimerization surface. Disruption of condensation activity leads to misregulation of genome-wide binding profiles and lethality, underscoring its functional and physiological significance in development. Integrative chromatin immunoprecipitation sequencing and Micro-C analyses reveal that many ZAD-ZnFs colocalize with core insulator proteins such as CCCTC-binding factor and Centrosomal protein 190 kD to control the formation of topological boundaries. We suggest that the diverse molecular functions of ZAD-ZnFs have evolutionarily arisen from their ancestral role as insulator-binding proteins.
4.
Yusuke Umemura, Takashi Fukaya
The Drosophila ZAD zinc finger protein Mulberry shapes the organization of the regulatory genome in the early embryo Journal Article
In: bioRxiv, 2026.
Abstract | Links | タグ: Fukaya G
@article{Umemura2026.02.03.703437,
title = {The Drosophila ZAD zinc finger protein Mulberry shapes the organization of the regulatory genome in the early embryo},
author = {Yusuke Umemura and Takashi Fukaya},
url = {https://www.biorxiv.org/content/early/2026/02/05/2026.02.03.703437},
doi = {10.64898/2026.02.03.703437},
year = {2026},
date = {2026-02-05},
urldate = {2026-01-01},
journal = {bioRxiv},
publisher = {Cold Spring Harbor Laboratory},
abstract = {Long-range regulatory interactions play a fundamentally important role in the control of gene activity during animal development, yet the underlying mechanisms remain largely unclear. Here, we identified a zinc finger-associated domain (ZAD)-C2H2 zinc finger protein, CG31365/Mulberry, as a looping factor that mediates long-range tethering activity in the early Drosophila embryo. Evidence is provided that Mulberry is specifically recruited to a subset of loop anchors and topological boundaries at key developmental loci to shape genome organization and gene activity. Super-resolution imaging analysis revealed that Mulberry forms nuclear condensates that associate with its target loci through the structured N-terminal ZAD domain. Micro-C analysis further demonstrated that the formation of loops and boundaries is lost in the condensation-deficient Mulberry mutant in a locus-specific manner. We propose that Mulberry acts as a condensation-dependent structural regulator of genome topology, organizing "multi-way regulatory hubs" that mediate long-range gene activation during early embryogenesis.},
keywords = {Fukaya G},
pubstate = {published},
tppubtype = {article}
}
Long-range regulatory interactions play a fundamentally important role in the control of gene activity during animal development, yet the underlying mechanisms remain largely unclear. Here, we identified a zinc finger-associated domain (ZAD)-C2H2 zinc finger protein, CG31365/Mulberry, as a looping factor that mediates long-range tethering activity in the early Drosophila embryo. Evidence is provided that Mulberry is specifically recruited to a subset of loop anchors and topological boundaries at key developmental loci to shape genome organization and gene activity. Super-resolution imaging analysis revealed that Mulberry forms nuclear condensates that associate with its target loci through the structured N-terminal ZAD domain. Micro-C analysis further demonstrated that the formation of loops and boundaries is lost in the condensation-deficient Mulberry mutant in a locus-specific manner. We propose that Mulberry acts as a condensation-dependent structural regulator of genome topology, organizing "multi-way regulatory hubs" that mediate long-range gene activation during early embryogenesis.
2025
3.
Takashi Fukaya
Multilayered mechanisms for long-range regulatory interactions in eukaryotic transcription Journal Article
In: Journal of Molecular Biology, 2025, ISSN: 0022-2836.
Abstract | Links | タグ: Fukaya G
@article{Fukaya2025,
title = {Multilayered mechanisms for long-range regulatory interactions in eukaryotic transcription},
author = {Takashi Fukaya},
doi = {10.1016/j.jmb.2025.169311},
issn = {0022-2836},
year = {2025},
date = {2025-06-26},
journal = {Journal of Molecular Biology},
publisher = {Elsevier BV},
abstract = {Transcription is a fundamental biological reaction that underlies essentially all developmental and physiological processes across species. While substantial efforts have been made to decipher the basic mechanisms of transcriptional regulation over the decades, we are still far from a comprehensive understanding of this highly intricate biological reaction including the temporal and spatial dynamics of the process. In recent years, new concepts and models have been proposed based on novel insights obtained from the use of cutting-edge technologies such as genome editing, whole-genome assays, structural analysis, and quantitative live-imaging approaches. In this review, I summarize emerging models and concepts for the dynamic modulation of long-range regulatory interactions in the context of animal development. I suggest that the multilayered actions of enhancers and associating regulatory DNAs such as ”Facilitators” and “Range Extenders” dynamically modulate clustering of transcription machineries at specific genomic loci to flexibly control the temporal and spatial dynamics of gene expression during development.},
keywords = {Fukaya G},
pubstate = {published},
tppubtype = {article}
}
Transcription is a fundamental biological reaction that underlies essentially all developmental and physiological processes across species. While substantial efforts have been made to decipher the basic mechanisms of transcriptional regulation over the decades, we are still far from a comprehensive understanding of this highly intricate biological reaction including the temporal and spatial dynamics of the process. In recent years, new concepts and models have been proposed based on novel insights obtained from the use of cutting-edge technologies such as genome editing, whole-genome assays, structural analysis, and quantitative live-imaging approaches. In this review, I summarize emerging models and concepts for the dynamic modulation of long-range regulatory interactions in the context of animal development. I suggest that the multilayered actions of enhancers and associating regulatory DNAs such as ”Facilitators” and “Range Extenders” dynamically modulate clustering of transcription machineries at specific genomic loci to flexibly control the temporal and spatial dynamics of gene expression during development.
2.
Raku Saito, Yusuke Umemura, Shiho Makino, Takashi Fukaya
Decoding the molecular logic of rapidly evolving ZAD zinc-finger proteins inDrosophila Unpublished
bioRxiv, 2025.
Abstract | Links | タグ: Fukaya G
@unpublished{Saito2025,
title = {Decoding the molecular logic of rapidly evolving ZAD zinc-finger proteins in\textit{Drosophila}},
author = {Raku Saito and Yusuke Umemura and Shiho Makino and Takashi Fukaya},
url = {http://biorxiv.org/lookup/doi/10.1101/2025.05.21.655257},
doi = {10.1101/2025.05.21.655257},
year = {2025},
date = {2025-05-21},
urldate = {2025-05-21},
publisher = {Cold Spring Harbor Laboratory},
abstract = {<jats:title>Summary</jats:title><jats:p>The zinc-finger associated domain (ZAD)-containing C2H2 zinc-finger proteins (ZAD-ZnFs) represent the most abundant class of transcription factors that emerged during insect evolution, yet their molecular diversity and biological functions remain largely unclear. Here, we established a systematic CRISPR-based protein-tagging approach that enables direct, unambiguous comparison of nuclear localization and genome-wide binding profiles of endogenous ZAD-ZnFs in developing<jats:italic>Drosophila</jats:italic>embryos. Evidence is provided that a subset of ZAD-ZnFs forms nuclear condensates through the stacking of the N-terminal ZAD dimerization surface. Disruption of condensation activity leads to misregulation of genome-wide binding profiles and lethality, underscoring its functional and physiological significance in development. Importantly, integrative ChIP-seq and Micro-C data analyses reveal that many ZAD-ZnFs colocalize with core insulator proteins such as CTCF and CP190 to strengthen the formation of topological boundaries. We suggest that the diverse molecular functions of ZAD-ZnFs have evolutionally arisen from their ancestral role as insulator-binding proteins.</jats:p>},
howpublished = {bioRxiv},
keywords = {Fukaya G},
pubstate = {published},
tppubtype = {unpublished}
}
<jats:title>Summary</jats:title><jats:p>The zinc-finger associated domain (ZAD)-containing C2H2 zinc-finger proteins (ZAD-ZnFs) represent the most abundant class of transcription factors that emerged during insect evolution, yet their molecular diversity and biological functions remain largely unclear. Here, we established a systematic CRISPR-based protein-tagging approach that enables direct, unambiguous comparison of nuclear localization and genome-wide binding profiles of endogenous ZAD-ZnFs in developing<jats:italic>Drosophila</jats:italic>embryos. Evidence is provided that a subset of ZAD-ZnFs forms nuclear condensates through the stacking of the N-terminal ZAD dimerization surface. Disruption of condensation activity leads to misregulation of genome-wide binding profiles and lethality, underscoring its functional and physiological significance in development. Importantly, integrative ChIP-seq and Micro-C data analyses reveal that many ZAD-ZnFs colocalize with core insulator proteins such as CTCF and CP190 to strengthen the formation of topological boundaries. We suggest that the diverse molecular functions of ZAD-ZnFs have evolutionally arisen from their ancestral role as insulator-binding proteins.</jats:p>
2024
1.
Shiho Makino, Takashi Fukaya
Dynamic modulation of enhancer-promoter and promoter-promoter connectivity in gene regulation Journal Article
In: Bioessays, pp. e2400101, 2024, ISSN: 1521-1878.
Abstract | Links | タグ: Fukaya G
@article{pmid38922969,
title = {Dynamic modulation of enhancer-promoter and promoter-promoter connectivity in gene regulation},
author = {Shiho Makino and Takashi Fukaya},
doi = {10.1002/bies.202400101},
issn = {1521-1878},
year = {2024},
date = {2024-06-01},
urldate = {2024-06-01},
journal = {Bioessays},
pages = {e2400101},
abstract = {Enhancers are short segments of regulatory DNA that control when and in which cell-type genes should be turned on in response to a variety of extrinsic and intrinsic signals. At the molecular level, enhancers serve as a genomic scaffold that recruits sequence-specific transcription factors and co-activators to facilitate transcription from linked promoters. However, it remains largely unclear how enhancers communicate with appropriate target promoters in the context of higher-order genome topology. In this review, we discuss recent progress in our understanding of the functional interplay between enhancers, genome topology, and the molecular properties of transcription machineries in gene regulation. We suggest that the activities of transcription hubs are highly regulated through the dynamic rearrangement of enhancer-promoter and promoter-promoter connectivity during animal development.},
keywords = {Fukaya G},
pubstate = {published},
tppubtype = {article}
}
Enhancers are short segments of regulatory DNA that control when and in which cell-type genes should be turned on in response to a variety of extrinsic and intrinsic signals. At the molecular level, enhancers serve as a genomic scaffold that recruits sequence-specific transcription factors and co-activators to facilitate transcription from linked promoters. However, it remains largely unclear how enhancers communicate with appropriate target promoters in the context of higher-order genome topology. In this review, we discuss recent progress in our understanding of the functional interplay between enhancers, genome topology, and the molecular properties of transcription machineries in gene regulation. We suggest that the activities of transcription hubs are highly regulated through the dynamic rearrangement of enhancer-promoter and promoter-promoter connectivity during animal development.
