Performance information

• Genetic evidence: zebrafish hoxba and hoxbb clusters are essential for the anterior-posterior positioning of pectoral fins　　　　　　　　　　　　　　　
  Morimichi Kikuchi; Renka Fujii; Daiki Kobayashi; Yuki Kawabe; Haruna Kanno; Sohju Toyama; Farah Tawakkal; Kazuya Yamada; Akinori Kawamura
  Feb. 2025, [Last, Corresponding]
  DOI：https://doi.org/10.1101/2025.02.03.636262
  DOI ID：10.1101/2025.02.03.636262, ORCID：177282484
• Zebrafish hoxb7a mutants exhibit no apparent morphological abnormalities despite being the only paralogous group 7　　　　　　　　　　　　　　　
  Daiki Kobayashi; Akiteru Maeno; Renka Fujii; Akinori Kawamura
  Gene Reports, Jan. 2025, [Reviewed], [Last, Corresponding]
  Scientific journal
• Live Visualization of Calcified Bones in Zebrafish and Medaka Larvae and Juveniles Using Calcein and Alizarin Red S　　　　　　　　　　　　　　　
  Rina Koita; Sae Oikawa; Taisei Tani; Masaru Matsuda; Akinori Kawamura
  BIO-PROTOCOL, Volume：14, Number：1361, Dec. 2024, [Reviewed], [Last, Corresponding]
  Bio-Protocol, LLC, Scientific journal
  DOI：https://doi.org/10.21769/bioprotoc.5142
  DOI ID：10.21769/bioprotoc.5142, ISSN：2331-8325
• Physical constraints on the positions and dimensions of the zebrafish swim bladder by surrounding bones
  Koumi Satoh; Akiteru Maeno; Urara Adachi; Mizuki Ishizaka; Kazuya Yamada; Rina Koita; Hidemichi Nakazawa; Sae Oikawa; Renka Fujii; Hiroyuki Furudate; Akinori Kawamura
  Journal of Anatomy, Nov. 2024, [Reviewed], [Last, Corresponding]
  Abstract
  
  Precise regulation of organ size and position is crucial for optimal organ function. Since the swim bladder is primarily responsible for buoyancy in teleosts, early development and subsequent inflation of the swim bladder should be appropriately controlled with the body growth. However, the underlying mechanism remains unclear. In this study, we show that the size and position of the swim bladder are physically constrained by the surrounding bones in zebrafish. Non‐invasive micro‐CT scanning revealed that the anterior edge of the swim bladder is largely attached to the os suspensorium, which is an ossicle extending medioventrally from the 4th centrum. Additionally, we observed that hoxc6a mutants, which lack the os suspensorium, exhibited an anterior projection of the swim bladder beyond the 4th vertebra. During the swim bladder development, we found that the counterclockwise rotation of the os suspensorium correlates with posterior regression of the swim bladder, suggesting that the os suspensorium pushes the swim bladder posteriorly into its proper position. Furthermore, our results revealed a close association between the posterior region of the swim bladder and the pleural ribs. In hoxaa cluster mutants with additional ribs, the swim bladder expanded posteriorly, accompanied by an enlarged body cavity. Taken together, our results demonstrate the importance of the surrounding bones in the robust regulation of swim bladder size and position in zebrafish.
  Wiley, Scientific journal
  DOI：https://doi.org/10.1111/joa.14179
  DOI ID：10.1111/joa.14179, ISSN：0021-8782, eISSN：1469-7580
• The functional roles of zebrafish HoxA- and HoxD-related clusters in the pectoral fin development
  Mizuki Ishizaka; Akiteru Maeno; Hidemichi Nakazawa; Renka Fujii; Sae Oikawa; Taisei Tani; Haruna Kanno; Rina Koita; Akinori Kawamura
  Scientific Reports, Volume：14, Number：1, Oct. 2024, [Reviewed], [Last, Corresponding]
  Abstract
  
  The paralogs 9–13 Hox genes in mouse HoxA and HoxD clusters are critical for limb development. When both HoxA and HoxD clusters are deleted in mice, significant limb truncation is observed compared to the phenotypes of single and compound mutants of Hox9-13 genes in these clusters. In zebrafish, mutations in hox13 genes in HoxA- and HoxD-related clusters result in abnormal morphology of pectoral fins, homologous to forelimbs. However, the effect of the simultaneous deletions of entire HoxA- and HoxD-related clusters on pectoral fin development remains unknown. Here, we generated mutants with several combinations of hoxaa, hoxab, and hoxda cluster deletions and analyzed the pectoral fin development. In hoxaa^−/−;hoxab^−/−;hoxda^−/− larvae, the endoskeletal disc and the fin-fold are significantly shortened in developing pectoral fins. In addition, we show that this anomaly is due to defects in the pectoral fin growth after the fin bud formation. Furthermore, in the surviving adult mutants, micro-CT scanning reveals defects in the posterior portion of the pectoral fin which is thought to represent latent regions of the limb. Our results further support that the functional role of HoxA and HoxD clusters is conserved in the paired appendage formation in bony fishes.
  Springer Science and Business Media LLC, Scientific journal
  DOI：https://doi.org/10.1038/s41598-024-74134-9
  DOI ID：10.1038/s41598-024-74134-9, eISSN：2045-2322, ORCID：163082463
• The Hox code responsible for the pattering of the anterior vertebrae in zebrafish
  Akiteru Maeno; Rina Koita; Hidemichi Nakazawa; Renka Fujii; Kazuya Yamada; Sae Oikawa; Taisei Tani; Mizuki Ishizaka; Koumi Satoh; Atsuki Ishizu; Takumi Sugawara; Urara Adachi; Morimichi Kikuchi; Norimasa Iwanami; Masaru Matsuda; Akinori Kawamura
  Development (Cambridge, England), Jun. 2024, [Reviewed], [Last, Corresponding]
  The vertebral column is a characteristic structure of vertebrates. Genetic studies in mice have shown that Hox-mediated patterning plays a key role in specifying discrete anatomical regions of the vertebral column. Expression pattern analyses in several vertebrate embryos provided correlative evidence that the anterior boundaries of Hox expression coincide with distinct anatomical vertebrae. However, because functional analyses have been limited to mice, it remains unclear which Hox genes actually function in vertebral patterning in other vertebrates. In this study, various zebrafish hox mutants were generated for loss-of-function phenotypic analysis to functionally decipher the Hox code responsible for the zebrafish anterior vertebrae between the occipital and thoracic vertebrae. We found that hox genes in HoxB- and HoxC-related clusters participate in regulating the morphology of the zebrafish anterior vertebrae. In addition, medaka hoxc6a was found to be responsible for anterior vertebral identity as in zebrafish. Based on phenotypic similarities with Hoxc6 knockout mice, our results suggest that the Hox patterning system, including at least Hoxc6, may have been functionally established in the vertebral patterning of the common ancestor of ray-finned and lobe-finned fishes.
  The Company of Biologists, Scientific journal
  DOI：https://doi.org/10.1242/dev.202854
  DOI ID：10.1242/dev.202854, ISSN：0950-1991, eISSN：1477-9129
• Teleost Hox code defines regional identities competent for the formation of dorsal and anal fins.　　　　　　　　　　　　　　　
  Urara Adachi; Rina Koita; Akira Seto; Akiteru Maeno; Atsuki Ishizu; Sae Oikawa; Taisei Tani; Mizuki Ishizaka; Kazuya Yamada; Koumi Satoh; Hidemichi Nakazawa; Hiroyuki Furudate; Koichi Kawakami; Norimasa Iwanami; Masaru Matsuda; Akinori Kawamura
  Proceedings of the National Academy of Sciences of the United States of America, Volume：121, Number：25, First page：e2403809121, Jun. 2024, [Reviewed], [Last, Corresponding], ［International magazine］
  The dorsal and anal fins can vary widely in position and length along the anterior-posterior axis in teleost fishes. However, the molecular mechanisms underlying the diversification of these fins remain unknown. Here, we used genetic approaches in zebrafish and medaka, in which the relative positions of the dorsal and anal fins are opposite, to demonstrate the crucial role of hox genes in the patterning of the teleost posterior body, including the dorsal and anal fins. By the CRISPR-Cas9-induced frameshift mutations and positional cloning of spontaneous dorsalfinless medaka, we show that various hox mutants exhibit the absence of dorsal or anal fins, or a stepwise posterior extension of these fins, with vertebral abnormalities. Our results indicate that multiple hox genes, primarily from hoxc-related clusters, encompass the regions responsible for the dorsal and anal fin formation along the anterior-posterior axis. These results further suggest that shifts in the anterior boundaries of hox expression which vary among fish species, lead to diversification in the position and size of the dorsal and anal fins, similar to how modulations in Hox expression can alter the number of anatomically distinct vertebrae in tetrapods. Furthermore, we show that hox genes responsible for dorsal fin formation are different between zebrafish and medaka. Our results suggest that a novel mechanism has occurred during teleost evolution, in which the gene network responsible for fin formation might have switched to the regulation downstream of other hox genes, leading to the remarkable diversity in the dorsal fin position.
  English, Scientific journal
  DOI：https://doi.org/10.1073/pnas.2403809121
  DOI ID：10.1073/pnas.2403809121, PubMed ID：38861596
• An atlas of seven zebrafish hox cluster mutants provides insights into sub/neofunctionalization of vertebrate Hox clusters.　　　　　　　　　　　　　　　
  Kazuya Yamada; Akiteru Maeno; Soh Araki; Morimichi Kikuchi; Masato Suzuki; Mizuki Ishizaka; Koumi Satoh; Kagari Akama; Yuki Kawabe; Kenya Suzuki; Daiki Kobayashi; Nanami Hamano; Akinori Kawamura
  Development (Cambridge, England), Volume：148, Number：11, Jun. 2021, [Reviewed], [Last, Corresponding], ［International magazine］
  Vertebrate Hox clusters are comprised of multiple Hox genes that control morphology and developmental timing along multiple body axes. Although results of genetic analyses using Hox-knockout mice have been accumulating, genetic studies in other vertebrates have not been sufficient for functional comparisons of vertebrate Hox genes. In this study, we isolated all of the seven hox cluster loss-of-function alleles in zebrafish using the CRISPR-Cas9 system. Comprehensive analysis of the embryonic phenotype and X-ray micro-computed tomography scan analysis of adult fish revealed several species-specific functional contributions of homologous Hox clusters along the appendicular axis, whereas important shared general principles were also confirmed, as exemplified by serial anterior vertebral transformations along the main body axis, observed in fish for the first time. Our results provide insights into discrete sub/neofunctionalization of vertebrate Hox clusters after quadruplication of the ancient Hox cluster. This set of seven complete hox cluster loss-of-function alleles provide a formidable resource for future developmental genetic analysis of the Hox patterning system in zebrafish.
  English, Scientific journal
  DOI：https://doi.org/10.1242/dev.198325
  DOI ID：10.1242/dev.198325, PubMed ID：34096572
• A globin-family protein, Cytoglobin 1, is involved in the development of neural crest-derived tissues and organs in zebrafish.　　　　　　　　　　　　　　　
  Kazuki Takahashi; Yuki Ito; Mami Yoshimura; Masataka Nikaido; Tatsuya Yuikawa; Akinori Kawamura; Sachiko Tsuda; Daichi Kage; Kyo Yamasu
  Developmental biology, Volume：472, First page：1, Last page：17, Apr. 2021, [Reviewed], ［International magazine］
  The zebrafish is an excellent model animal that is amenable to forward genetics approaches. To uncover unknown developmental regulatory mechanisms in vertebrates, we conducted chemical mutagenesis screening and identified a novel mutation, kanazutsi (kzt). This mutation is recessive, and its homozygotes are embryonic lethal. Mutant embryos suffered from a variety of morphological defects, such as head flattening, pericardial edema, circulation defects, disrupted patterns of melanophore distribution, dwarf eyes, a defective jaw, and extensive apoptosis in the head, which indicates that the main affected tissues are derived from neural crest cells (NCCs). The expression of tissue-specific markers in kzt mutants showed that the early specification of NCCs was normal, but their later differentiation was severely affected. The mutation was mapped to chromosome 3 by linkage analyses, near cytoglobin 1 (cygb1), the product of which is a globin-family respiratory protein. cygb1 expression was activated during somitogenesis in somites and cranial NCCs in wild-type embryos but was significantly downregulated in mutant embryos, despite the normal primary structure of the gene product. The kzt mutation was phenocopied by cygb1 knockdown with low-dose morpholino oligos and was partially rescued by cygb1 overexpression. Both severe knockdown and null mutation of cygb1, established by the CRISPR/Cas9 technique, resulted in far more severe defects at early stages. Thus, it is highly likely that the downregulation of cygb1 is responsible for many, if not all, of the phenotypes of the kzt mutation. These results reveal a requirement for globin family proteins in vertebrate embryos, particularly in the differentiation and subsequent development of NCCs.
  English, Scientific journal
  DOI：https://doi.org/10.1016/j.ydbio.2020.12.016
  DOI ID：10.1016/j.ydbio.2020.12.016, PubMed ID：33358912
• Role of somite patterning in the formation of Weberian apparatus and pleural rib in zebrafish.　　　　　　　　　　　　　　　
  Kagari Akama; Kanami Ebata; Akiteru Maeno; Tomohito Taminato; Shiori Otosaka; Keiko Gengyo-Ando; Junichi Nakai; Kyo Yamasu; Akinori Kawamura
  Journal of anatomy, Volume：236, Number：4, First page：622, Last page：629, Apr. 2020, [Reviewed], [Last, Corresponding], ［International magazine］
  In the vertebrate body, a metameric structure is present along the anterior-posterior axis. Zebrafish tbx6-/- larvae, in which somite boundaries do not form during embryogenesis, were shown to exhibit abnormal skeletal morphology such as rib, neural arch and hemal arch. In this study, we investigated the role of somite patterning in the formation of anterior vertebrae and ribs in more detail. Using three-dimensional computed tomography scans, we found that anterior vertebrae including the Weberian apparatus were severely affected in tbx6-/- larvae. In addition, pleural ribs of tbx6 mutants exhibited severe defects in the initial ossification, extension of ossification, and formation of parapophyses. Two-colour staining revealed that bifurcation of ribs was caused by fusion or branching of ribs in tbx6-/- . The parapophyses in tbx6-/- juvenile fish showed irregular positioning to centra and abnormal attachment to ribs. Furthermore, we found that the ossification of the distal portion of ribs proceeded along myotome boundaries even in irregularly positioned myotome boundaries. These results provide evidence of the contribution of somite patterning to the formation of the Weberian apparatus and rib in zebrafish.
  English, Scientific journal
  DOI：https://doi.org/10.1111/joa.13135
  DOI ID：10.1111/joa.13135, PubMed ID：31840255, PubMed Central ID：PMC7083572, 共同研究・競争的資金等ID：30059329
• Transcriptional autoregulation of zebrafish tbx6 is required for somite segmentation.　　　　　　　　　　　　　　　
  Hiroyuki Ban; Daisuke Yokota; Shiori Otosaka; Morimichi Kikuchi; Hirofumi Kinoshita; Yuuri Fujino; Taijiro Yabe; Hiroki Ovara; Ayaka Izuka; Kagari Akama; Kyo Yamasu; Shinji Takada; Akinori Kawamura
  Development (Cambridge, England), Volume：146, Number：18, Sep. 2019, [Reviewed], [Last, Corresponding], ［International magazine］
  The presumptive somite boundary in the presomitic mesoderm (PSM) is defined by the anterior border of the expression domain of Tbx6 protein. During somite segmentation, the expression domain of Tbx6 is regressed by Ripply-meditated degradation of Tbx6 protein. Although the expression of zebrafish tbx6 remains restricted to the PSM, the transcriptional regulation of tbx6 remains poorly understood. Here, we show that the expression of zebrafish tbx6 is maintained by transcriptional autoregulation. We find that a proximal-located cis-regulatory module, TR1, which contains two putative T-box sites, is required for somite segmentation in the intermediate body and for proper expression of segmentation genes. Embryos with deletion of TR1 exhibit significant reduction of tbx6 expression at the 12-somite stage, although its expression is initially observed. Additionally, Tbx6 is associated with TR1 and activates its own expression in the anterior PSM. Furthermore, the anterior expansion of tbx6 expression in ripply gene mutants is suppressed in a TR1-dependent manner. The results suggest that the autoregulatory loop of zebrafish tbx6 facilitates immediate removal of Tbx6 protein through termination of its own transcription at the anterior PSM.
  English, Scientific journal
  DOI：https://doi.org/10.1242/dev.177063
  DOI ID：10.1242/dev.177063, PubMed ID：31444219, 共同研究・競争的資金等ID：30059129
• Deadenylation by the CCR4-NOT complex contributes to the turnover of hairy-related mRNAs in the zebrafish segmentation clock.　　　　　　　　　　　　　　　
  Yuuri Fujino; Kazuya Yamada; Chihiro Sugaya; Yuko Ooka; Hiroki Ovara; Hiroyuki Ban; Kagari Akama; Shiori Otosaka; Hirofumi Kinoshita; Kyo Yamasu; Yuichiro Mishima; Akinori Kawamura
  FEBS letters, Volume：592, Number：20, First page：3388, Last page：3398, Oct. 2018, [Reviewed], [Last, Corresponding], ［International magazine］
  In the zebrafish segmentation clock, hairy/enhancer of split-related genes her1, her7, and hes6 encodes components of core oscillators. Since the expression of cyclic genes proceeds rapidly in the presomitic mesoderm (PSM), these hairy-related mRNAs are subject to strict post-transcriptional regulation. In this study, we demonstrate that inhibition of the CCR4-NOT deadenylase complex lengthens poly(A) tails of hairy-related mRNAs and increases the amount of these mRNAs, which is accompanied by defective somite segmentation. In transgenic embryos, we show that EGFP mRNAs with 3'UTRs of hairy-related genes exhibit turnover similar to endogenous mRNAs. Our results suggest that turnover rates of her1, her7, and hes6 mRNAs are differently regulated by the CCR4-NOT deadenylase complex possibly through their 3'UTRs in the zebrafish PSM.
  English, Scientific journal
  DOI：https://doi.org/10.1002/1873-3468.13261
  DOI ID：10.1002/1873-3468.13261, PubMed ID：30281784
• Functional roles of the Ripply-mediated suppression of segmentation gene expression at the anterior presomitic mesoderm in zebrafish.　　　　　　　　　　　　　　　
  Hirofumi Kinoshita; Nanae Ohgane; Yuuri Fujino; Taijiro Yabe; Hiroki Ovara; Daisuke Yokota; Ayaka Izuka; Daichi Kage; Kyo Yamasu; Shinji Takada; Akinori Kawamura
  Mechanisms of development, Volume：152, First page：21, Last page：31, Aug. 2018, [Reviewed], [Last, Corresponding], ［International magazine］
  Somites sequentially form with a regular interval by the segmentation from the anterior region of the presomitic mesoderm (PSM). The expression of several genes involved in the somite segmentation is switched off at the transition from the anterior PSM to somites. Zebrafish Ripply1, which down-regulates a T-box transcription factor Tbx6, is required for the suppression of segmentation gene expression. However, the functional roles of the Ripply-mediated suppression of segmentation gene expression at the anterior PSM remain elusive. In this study, we generated ripply1 mutants and examined genetic interaction between ripply1/2 and tbx6. Zebrafish ripply1-/- embryos failed to form the somite boundaries as was observed in knockdown embryos. We found that somite segmentation defects in ripply1 mutants were suppressed by heterozygous mutation of tbx6 or partial translational inhibition of tbx6 by antisense morpholino. We further showed that somite boundaries that were recovered in tbx6+/-; ripply1-/- embryos were dependent on the function of ripply2, indicating that relative gene dosage between ripply1/2 and tbx6 plays a critical role in the somite formation. Interestingly, the expression of segmentation genes such mesp as was still not fully suppressed at the anterior PSM of tbx6+/-; ripply1-/- embryos although the somite formation and rostral-caudal polarity of somites were properly established. Furthermore, impaired myogenesis was observed in the segmented somites in tbx6+/-; ripply1-/- embryos. These results revealed that partial suppression of the segmentation gene expression by Ripply is sufficient to establish the rostral-caudal polarity of somites, and that stronger suppression of the segmentation gene expression by Ripply is required for proper myogenesis in zebrafish embryos.
  English, Scientific journal
  DOI：https://doi.org/10.1016/j.mod.2018.06.001
  DOI ID：10.1016/j.mod.2018.06.001, PubMed ID：29879477
• Enhancer activity-based identification of functional enhancers using zebrafish embryos.　　　　　　　　　　　　　　　
  Tomohito Taminato; Daisuke Yokota; Soh Araki; Hiroki Ovara; Kyo Yamasu; Akinori Kawamura
  Genomics, Volume：108, Number：2, First page：102, Last page：7, Aug. 2016, [Reviewed], [Last, Corresponding], ［International magazine］
  Chromatin immunoprecipitation (ChIP) against enhancer-associated marks with massive sequencing is a powerful approach to identify genome-wide distributions of putative enhancers. However, functional in vivo analysis is required to elucidate the activities of predicted enhancers. Using zebrafish embryos, we established a ChIP-Injection method that enables identification of functional enhancers based on their enhancer activities in embryos. Each reporter gene possessing the enhancer-associated genomic region enriched by ChIP was injected into zebrafish embryos to analyze the activity of putative enhancers. By using the ChIP-Injection, we identified 32 distinct putative enhancers that drove specific expression. Additionally, we generated transgenic lines that exhibit distributions of the EGFP signal as was observed in the screening. Furthermore, the expression pattern driven by the identified somite-specific enhancer resembled that of the gene acta2. The results indicate that ChIP-Injection provides an efficient approach for identification of active enhancers in a potentially wide variety of developmental tissues and stages.
  ACADEMIC PRESS INC ELSEVIER SCIENCE, English, Scientific journal
  DOI：https://doi.org/10.1016/j.ygeno.2016.05.005
  DOI ID：10.1016/j.ygeno.2016.05.005, ISSN：0888-7543, eISSN：1089-8646, PubMed ID：27256877, Web of Science ID：WOS:000381477700007, 共同研究・競争的資金等ID：30059129
• Posterior-anterior gradient of zebrafish hes6 expression in the presomitic mesoderm is established by the combinatorial functions of the downstream enhancer and 3'UTR.　　　　　　　　　　　　　　　
  Akinori Kawamura; Hiroki Ovara; Yuko Ooka; Hirofumi Kinoshita; Miki Hoshikawa; Kenji Nakajo; Daisuke Yokota; Yuuri Fujino; Shin-ichi Higashijima; Shinji Takada; Kyo Yamasu
  Developmental biology, Volume：409, Number：2, First page：543, Last page：54, Jan. 2016, [Reviewed], [Lead, Corresponding], ［International magazine］
  In vertebrates, the periodic formation of somites from the presomitic mesoderm (PSM) is driven by the molecular oscillator known as the segmentation clock. The hairy-related gene, hes6/her13.2, functions as a hub by dimerizing with other oscillators of the segmentation clock in zebrafish embryos. Although hes6 exhibits a posterior-anterior expression gradient in the posterior PSM with a peak at the tailbud, the detailed mechanisms underlying this unique expression pattern have not yet been clarified. By establishing several transgenic lines, we found that the transcriptional regulatory region downstream of hes6 in combination with the hes6 3'UTR recapitulates the endogenous gradient of hes6 mRNA expression. This downstream region, which we termed the PT enhancer, possessed several putative binding sites for the T-box and Ets transcription factors that were required for the regulatory activity. Indeed, the T-box transcription factor (Tbx16) and Ets transcription factor (Pea3) bound specifically to the putative binding sites and regulated the enhancer activity in zebrafish embryos. In addition, the 3'UTR of hes6 is required for recapitulation of the endogenous mRNA expression. Furthermore, the PT enhancer with the 3'UTR of hes6 responded to the inhibition of retinoic acid synthesis and fibroblast growth factor signaling in a manner similar to endogenous hes6. The results showed that transcriptional regulation by the T-box and Ets transcription factors, combined with the mRNA stability given by the 3'UTR, is responsible for the unique expression gradient of hes6 mRNA in the posterior PSM of zebrafish embryos.
  ACADEMIC PRESS INC ELSEVIER SCIENCE, English, Scientific journal
  DOI：https://doi.org/10.1016/j.ydbio.2015.11.010
  DOI ID：10.1016/j.ydbio.2015.11.010, ISSN：0012-1606, eISSN：1095-564X, ORCID：46524491, PubMed ID：26596999, SCOPUS ID：84947982899, Web of Science ID：WOS:000369122300019
• Gbx2 functions as a transcriptional repressor to regulate the specification and morphogenesis of the mid-hindbrain junction in a dosage- and stage-dependent manner　　　　　　　　　　　　　　　
  Yukiko Nakayama; Hiroshi Kikuta; Maiko Kanai; Kimihito Yoshikawa; Akinori Kawamura; Kana Kobayashi; Zhe Wang; Alam Khan; Koichi Kawakami; Kyo Yamasu
  MECHANISMS OF DEVELOPMENT, Volume：130, Number：11-12, First page：532, Last page：552, Nov. 2013, [Reviewed]
  The Gbx subfamily of homeodomain transcription factors is involved in the positioning of the isthmus, which patterns the midbrain and cerebellum in vertebrates. To uncover the details of Gbx functions, we first examined the dose dependency of its effects on brain formation in zebrafish and found that high-dose gbx2 mRNA injection affected the entire forebrain and midbrain, whereas low-dose mRNA specifically disrupted the isthmic folding at the midbrain-hindbrain boundary (MHB) but only weakly affected the expression of genes involved in MHB specification. Thus, isthmus morphogenesis, and not its early specification, is highly sensitive to gbx2. Transient induction of heat-inducible gbx2 using transgenic fish showed that MHB specification is most sensitive to gbx2 at the end of epiboly and further suggested that otx2 is the direct target gene. These together demonstrate that gbx2 regulates both specification and morphogenesis of the MHB/isthmus region. Deletion analyses showed that both the N- and C-terminal regions contribute to the suppressive activity of Gbx2 against the anterior brain and that the N-terminal core region, including the Eh1 and proline-rich sequences, is required for this Gbx2 activity. Comparison of the effects of activated and repressive forms with wild-type Gbx2 suggested that Gbx2 functions as a transcriptional repressor, which was further evidenced by a luciferase assay in which gbx2 repressed the MHB enhancer of fgf8a in mouse P19 cells. (C) 2013 Elsevier Ireland Ltd. All rights reserved.
  ELSEVIER SCIENCE BV, English, Scientific journal
  DOI：https://doi.org/10.1016/j.mod.2013.07.004
  DOI ID：10.1016/j.mod.2013.07.004, ISSN：0925-4773, eISSN：1872-6356, PubMed ID：23933069, Web of Science ID：WOS:000326983200002
• Mesendoderm specification depends on the function of Pou2, the class V POU-type transcription factor, during zebrafish embryogenesis.　　　　　　　　　　　　　　　
  Alam Khan; Andrew Nakamoto; Miyako Tai; Shinji Saito; Yukiko Nakayama; Akinori Kawamura; Hiroyuki Takeda; Kyo Yamasu
  Development, growth & differentiation, Volume：54, Number：7, First page：686, Last page：701, Sep. 2012, [Reviewed], ［Domestic magazine］
  Zebrafish pou2, encoding the class V POU transcription factor orthologous to mouse Oct-3/4, has been implicated in different aspects of development, such as dorsoventral patterning, endoderm formation, and brain regionalization, by analyzing pou2 mutant embryos. In the present study, we first conducted overexpression of pou2-modified genes by mRNA injection, and found that pou2 and its active form (vp-pou2) augmented mesoderm formation and suppressed endoderm specification, whereas repressive pou2 (en-pou2) affected the formation of the mesoderm and endoderm in a different manner. To avoid complications that might arise from different pou2 functions during the course of development, we used a transgenic line harboring inducible en-pou2 (HEP), which could function in a dominant-negative manner. We found that suppressing endogenous pou2 by HEP induction at the mid-blastula stage enhanced endoderm development at the expense of mesoderm, whereas the same treatment in the late blastulae promoted mesoderm formation and suppressed the endoderm specification. Further analyses using HEP induction revealed that, from late epiboly to early somitogenesis, pou2 regulated additional developmental aspects, such as brain regionalization, heart development, and tail formation. Our findings suggest that Pou2 functions in multiple aspects of vertebrate development, especially in the binary decision of the mesendoderm to mesoderm and endoderm in different ways depending on the developmental stage.
  English, Scientific journal
  DOI：https://doi.org/10.1111/j.1440-169X.2012.01369.x
  DOI ID：10.1111/j.1440-169X.2012.01369.x, ISSN：0012-1592, PubMed ID：22913532, Web of Science ID：WOS:000309060800002
• Pou2, a class V POU-type transcription factor in zebrafish, regulates dorsoventral patterning and convergent extension movement at different blastula stages　　　　　　　　　　　　　　　
  Khan Alam; Nakamoto Andrew; Okamoto Shun; Tai Miyako; Nakayama Yukiko; Kobayashi Kana; Kawamura Akinori; Takeda Hiroyuki; Yamasu Kyo
  MECHANISMS OF DEVELOPMENT, Volume：129, Number：9-12, First page：219, Last page：235, Sep. 2012, [Reviewed]
  DOI：https://doi.org/10.1016/j.mod.2012.07.007
  DOI ID：10.1016/j.mod.2012.07.007, ISSN：0925-4773, PubMed ID：22921661, Web of Science ID：WOS:000310355900003
• Ripply3, a Tbx1 repressor, is required for development of the pharyngeal apparatus and its derivatives in mice.　　　　　　　　　　　　　　　
  Tadashi Okubo; Akinori Kawamura; Jun Takahashi; Hisato Yagi; Masae Morishima; Rumiko Matsuoka; Shinji Takada
  Development (Cambridge, England), Volume：138, Number：2, First page：339, Last page：48, Jan. 2011, [Reviewed], ［International magazine］
  The pharyngeal apparatus is a transient structure that gives rise to the thymus and the parathyroid glands and also contributes to the development of arteries and the cardiac outflow tract. A typical developmental disorder of the pharyngeal apparatus is the 22q11 deletion syndrome (22q11DS), for which Tbx1 is responsible. Here, we show that Ripply3 can modulate Tbx1 activity and plays a role in the development of the pharyngeal apparatus. Ripply3 expression is observed in the pharyngeal ectoderm and endoderm and overlaps with strong expression of Tbx1 in the caudal pharyngeal endoderm. Ripply3 suppresses transcriptional activation by Tbx1 in luciferase assays in vitro. Ripply3-deficient mice exhibit abnormal development of pharyngeal derivatives, including ectopic formation of the thymus and the parathyroid gland, as well as cardiovascular malformation. Corresponding with these defects, Ripply3-deficient embryos show hypotrophy of the caudal pharyngeal apparatus. Ripply3 represses Tbx1-induced expression of Pax9 in luciferase assays in vitro, and Ripply3-deficient embryos exhibit upregulated Pax9 expression. Together, our results show that Ripply3 plays a role in pharyngeal development, probably by regulating Tbx1 activity.
  English, Scientific journal
  DOI：https://doi.org/10.1242/dev.054056
  DOI ID：10.1242/dev.054056, PubMed ID：21177346
• FGF receptor gene expression and its regulation by FGF signaling during early zebrafish development.　　　　　　　　　　　　　　　
  Satoshi Ota; Noriko Tonou-Fujimori; Noriko Tonou-Fujimori; Yukiko Nakayama; Yuki Ito; Akinori Kawamura; Kyo Yamasu
  Genesis (New York, N.Y. : 2000), Volume：48, Number：12, First page：707, Last page：16, Dec. 2010, [Reviewed], ［International magazine］
  The expression of all four fgfr genes was extensively examined throughout early embryogenesis of the zebrafish (Danio rerio). fgfr1 alone was expressed maternally throughout the blastoderm, and then zygotically in the anterior neural plate and presomitic mesoderm. fgfr4 expression was first detected in late blastulae and was gradually restricted to the brain. fgfr2 and fgfr3 expression were initiated in early and late gastrulae, respectively; fgfr2 was expressed in the anterior neural plate and somitic mesoderm, whereas fgfr3 was activated in the axial mesoderm and then in the midbrain and somitic mesoderm. During somitogenesis, each of these fgfr genes was expressed in a characteristic manner in the brain. Using an FGF signal inhibitor, dominant-negative FGF receptors and fgf8.1/fgf8a mutants, we found that fgfr expression is directly or indirectly regulated by FGF signaling during epiboly and at the end of somitogenesis, revealing the presence of an autoregulatory mechanism.
  WILEY-LISS, English, Scientific journal
  DOI：https://doi.org/10.1002/dvg.20682
  DOI ID：10.1002/dvg.20682, ISSN：1526-954X, PubMed ID：20960516, Web of Science ID：WOS:000285397300004
• Activator-to-repressor conversion of T-box transcription factors by the Ripply family of Groucho/TLE-associated mediators.　　　　　　　　　　　　　　　
  Akinori Kawamura; Sumito Koshida; Shinji Takada
  Molecular and cellular biology, Volume：28, Number：10, First page：3236, Last page：44, May 2008, [Reviewed], [Lead], ［International magazine］
  The T-box family of transcription factors, defined by a conserved DNA binding domain called the T-box, regulate various aspects of embryogenesis by activating and/or repressing downstream genes. In spite of the biological significance of the T-box proteins, how they regulate transcription remains to be elucidated. Here we show that the Groucho/TLE-associated protein Ripply converts T-box proteins from activators to repressors. In cultured cells, zebrafish Ripply1, an essential component in somite segmentation, and its structural relatives, Ripply2 and -3, suppress the transcriptional activation mediated by the T-box protein Tbx24, which is coexpressed with ripply1 during segmentation. Ripply1 associates with Tbx24 and converts it to a repressor. Ripply1 also antagonizes the transcriptional activation of another T-box protein, No tail (Ntl), the zebrafish ortholog of Brachyury. Furthermore, injection of a high dosage of ripply1 mRNA into zebrafish eggs causes defective development of the posterior trunk, similar to the phenotype observed in homozygous mutants of ntl. A mutant form of Ripply1 defective in association with Tbx24 also lacks activity in zebrafish embryos. These results indicate that the intrinsic transcriptional property of T-box proteins is controlled by Ripply family proteins, which act as specific adaptors that recruit the global corepressor Groucho/TLE to T-box proteins.
  English, Scientific journal
  DOI：https://doi.org/10.1128/MCB.01754-07
  DOI ID：10.1128/MCB.01754-07, PubMed ID：18332117, PubMed Central ID：PMC2423164
• Paf1 complex homologues are required for Notch-regulated transcription during somite segmentation.　　　　　　　　　　　　　　　
  Takashi Akanuma; Sumito Koshida; Akinori Kawamura; Yasuyuki Kishimoto; Shinji Takada
  EMBO reports, Volume：8, Number：9, First page：858, Last page：63, Sep. 2007, [Reviewed], ［International magazine］
  Members of the yeast polymerase-associated factor 1 (Paf1) complex, which is composed of at least five components (Paf1, Rtf1, Cdc73, Leo1 and Ctr9), are conserved from yeast to humans. Although these proteins have been implicated in RNA polymerase II-mediated transcription, their roles in vertebrate development have not been explained. Here, we show that a zebrafish mutant with a somite segmentation defect is deficient in rtf1. In addition, embryos deficient in rtf1 or ctr9 show abnormal development of the heart, ears and neural crest cells. rtf1 is required for correct RNA levels of the Notch-regulated genes her1, her7 and deltaC, and also for Notch-induced her1 expression in the presomitic mesoderm. Furthermore, the phenotype observed in rtf1-deficient mutants is enhanced by an additional deficiency in mind bomb, which encodes an effector of Notch signalling. Therefore, zebrafish homologues of the yeast Paf1 complex seem to preferentially affect a subset of genes, including Notch-regulated genes, during embryogenesis.
  English, Scientific journal
  ISSN：1469-221X, PubMed ID：17721442, PubMed Central ID：PMC1973952
• Cellular responses of the ciliate, Tetrahymena thermophila, to far infrared irradiation.　　　　　　　　　　　　　　　
  Robert Shiurba; Tatsuo Hirabayashi; Masaru Masuda; Akinori Kawamura; Yuta Komoike; William Klitz; Keiichi Kinowaki; Takashi Funatsu; Shunzo Kondo; Shin Kiyokawa; Toshiro Sugai; Kosuke Kawamura; Hideo Namiki; Toru Higashinakagawa
  Photochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology, Volume：5, Number：9, First page：799, Last page：807, Sep. 2006, [Reviewed], ［International magazine］
  Infrared rays from sunlight permeate the earth's atmosphere, yet little is known about their interactions with living organisms. To learn whether they affect cell structure and function, we tested the ciliated protozoan, Tetrahymena thermophila. These unicellular eukaryotes aggregate in swarms near the surface of freshwater habitats, where direct and diffuse solar radiation impinge upon the water-air interface. We report that populations irradiated in laboratory cultures grew and mated normally, but major changes occurred in cell physiology during the stationary phase. Early on, there were significant reductions in chromatin body size and the antibody reactivity of methyl groups on lysine residues 4 and 9 in histone H3. Later, when cells began to starve, messenger RNAs for key proteins related to chromatin structure, intermediary metabolism and cellular motility increased from two- to nearly nine-fold. Metabolic activity, swimming speed and linearity of motion also increased, and spindle shaped cells with a caudal cilium appeared. Our findings suggest that infrared radiation enhances differentiation towards a dispersal cell-like phenotype in saturated populations of Tetrahymena thermophila.
  English, Scientific journal
  ISSN：1474-905X, PubMed ID：17047831
• Groucho-associated transcriptional repressor ripply1 is required for proper transition from the presomitic mesoderm to somites.　　　　　　　　　　　　　　　
  Akinori Kawamura; Sumito Koshida; Hiroko Hijikata; Akiko Ohbayashi; Hisato Kondoh; Shinji Takada
  Developmental cell, Volume：9, Number：6, First page：735, Last page：44, Dec. 2005, [Reviewed], [Lead], ［International magazine］
  Concomitant with the transition from the presomitic mesoderm (PSM) to somites, the periodical gene expression characteristic of the PSM is drastically changed and translated into the segmental structure. However, the molecular mechanism underlying this transition has remained obscure. Here, we show that ripply1, encoding a nuclear protein associated with the transcriptional corepressor Groucho, is required for this transition. Zebrafish ripply1 is expressed in the anterior PSM and in several newly formed somites. Ripply1 represses mesp-b expression in the PSM through a Groucho-interacting motif. In ripply1-deficient embryos, somite boundaries do not form, the characteristic gene expression in the PSM is not properly terminated, and the initially established rostrocaudal polarity in the segmental unit is not maintained, whereas paraxial mesoderm cells become differentiated. Thus, ripply1 plays dual roles in the transition from the PSM to somites: termination of the segmentation program in the PSM and maintenance of the rostrocaudal polarity.
  English, Scientific journal
  ISSN：1534-5807, PubMed ID：16326386, 共同研究・競争的資金等ID：30059135
• Zebrafish hairy/enhancer of split protein links FGF signaling to cyclic gene expression in the periodic segmentation of somites.　　　　　　　　　　　　　　　
  Akinori Kawamura; Sumito Koshida; Hiroko Hijikata; Takuya Sakaguchi; Hisato Kondoh; Shinji Takada
  Genes & development, Volume：19, Number：10, First page：1156, Last page：61, May 2005, [Reviewed], [Lead], ［International magazine］
  Notch and fibroblast growth factor (FGF) signaling pathways have been implicated in the establishment of proper periodicity of vertebrate somites. Here, we show evidence that a Hes6-related hairy/Enhancer of split-related gene, her13.2, links FGF signaling to the Notch-regulated oscillation machinery in zebrafish. Expression of her13.2 is induced by FGF-soaked beads and decreased by an FGF signaling inhibitor. her13.2 is required for periodic repression of the Notch-regulated genes her1 and her7, and for proper somite segmentation. Furthermore, Her13.2 augments autorepression of her1 in association with Her1 protein. Therefore, FGF signaling appears to maintain the oscillation machinery by supplying a binding partner, Her13.2, for Her1.
  English, Scientific journal
  ISSN：0890-9369, PubMed ID：15905406, PubMed Central ID：PMC1132002, 共同研究・競争的資金等ID：30059135
• Zebrafish Polycomb group gene ph2alpha is required for epiboly and tailbud formation acting downstream of FGF signaling.　　　　　　　　　　　　　　　
  Yuta Komoike; Akinori Kawamura; Norihisa Shindo; Chie Sato; Junichi Satoh; Robert Shiurba; Toru Higashinakagawa
  Biochemical and biophysical research communications, Volume：328, Number：4, First page：858, Last page：66, Mar. 2005, [Reviewed], ［International magazine］
  We analyzed Polycomb group gene ph2alpha functionally in zebrafish embryos by a gene knock-down procedure using morpholino antisense oligos. Inhibition of ph2alpha message translation resulted in abnormal epibolic movements as well as a thick tailbud or incomplete covering of the yolk plug. At the 24hpf stage, morphants had short trunks and tails, phenotypes similar to those with disturbances in FGF signaling. Accordingly, we looked at the effects of ph2alpha expression upstream and downstream of the FGF pathway. Treatment with SU5402, an inhibitor of Fgfrs, or injection of dominant-negative Fgfr1 DNA markedly reduced ph2alpha expression in the tailbud. In addition, cells expressing mRNAs for no tail, spadetail, myoD, and papc, which are involved in FGF-related development of posterior mesoderm, were distributed abnormally. Collectively, the data argue that ph2alpha is required for epiboly and tailbud formation, acting downstream of the FGF signaling pathway.
  English, Scientific journal
  ISSN：0006-291X, PubMed ID：15707958
• pc1 and psc1, zebrafish homologs of Drosophila Polycomb and Posterior sex combs, encode nuclear proteins capable of complex interactions.　　　　　　　　　　　　　　　
  Akinori Kawamura; Shin'ichiro Yokota; Kouji Yamada; Hitoshi Inoue; Keiji Inohaya; Ken Yamazaki; Ikuo Yasumasu; Toru Higashinakagawa
  Biochemical and biophysical research communications, Volume：294, Number：2, First page：456, Last page：63, Jun. 2002, [Reviewed], [Lead], ［International magazine］
  Drosophila Polycomb group proteins are thought to form multimeric nuclear complexes that are responsible for stable transmission of repressed states of gene expression during the proliferation of differentiating embryos. In this study, we cloned, sequenced, and characterized two Polycomb group homologs, designated pc1 and psc1, in zebrafish. Amino acid sequence analyses determined that pc1 is a structural homolog of Drosophila Polycomb and that psc1 is a homolog of Drosophila Posterior sex combs. Northern blots and whole-mount in situ hybridization revealed that pc1 and psc1 had overlapping expression patterns at successive stages of embryogenesis. Immunocytochemistry localized both Pc1 and Psc1 protein in blastomere nuclei. Pull-down assays and two-hybrid system deletion analyses showed that these proteins were capable of homotypic and heterotypic interactions and identified the regions required for these interactions. The evidence supports the idea that zebrafish Polycomb group proteins, like those of other species, form nuclear complexes with compositions that may vary in a spatio-temporal manner during development.
  English, Scientific journal
  ISSN：0006-291X, PubMed ID：12051733
• Alternative transcripts of a polyhomeotic gene homolog are expressed in distinct regions of somites during segmentation of zebrafish embryos.　　　　　　　　　　　　　　　
  Akinori Kawamura; Kouji Yamada; Ken'ichi Fujimori; Toru Higashinakagawa
  Biochemical and biophysical research communications, Volume：291, Number：2, First page：245, Last page：54, Feb. 2002, [Reviewed], [Lead], ［International magazine］
  Here we describe isolation and characterization of two zebrafish cDNAs, designated ph2alpha and ph2beta, which were identified as structural homologs of the Drosophila polyhomeotic, mouse Mph2, and human HPH2 genes, collectively termed the Polycomb group. The alpha and beta transcripts shared a 1.9-kb sequence at their 3'-termini. Alpha had an additional 1.6-kb sequence extending toward its 5'-terminus. Only a short 0.1-kb segment was unique to beta. Sequencing of a genomic clone corresponding to the two cDNAs indicated that the mRNAs were transcribed from a single gene locus by alternative promoters. Northern blots revealed expression of alpha transcripts during the segmentation period, while beta expression occurred at all developmental stages examined. Whole-mount in situ hybridizations with an alpha-specific probe and a probe recognizing both transcripts revealed distinct spatio-temporal expression patterns along developing somites. Alpha transcripts were detected initially at the 7-8 somite stage; beta transcripts appeared in the first somites. As segmentation proceeded, alpha and beta expression shifted position toward the tailbud in parallel with the formation of each somite. Within individual somites, the signal corresponding to alpha was strongest at the posterior border and weakest in the anterior region. Conversely, that corresponding to beta was strongest at the anterior border and weakest in the posterior region. The data support the idea that Ph2alpha and Ph2beta are involved in spatio-temporal generation of somites as well as in specification of antero-posterior regional differences within individual somites.
  English, Scientific journal
  ISSN：0006-291X, PubMed ID：11846397

• 魚の背ビレやしりビレを作る位置はどのように決まるのか？ ～Hox遺伝子と改良メダカ～　　　　　　　　　　　　　　　
  松田 勝; 川村哲規, [Contributor]
  Oct. 2024
• 分子生物学15講　　　　　　　　　　　　　　　
  東中川, 徹; 桑山, 秀一; 川村, 哲規, [Joint editor]
  Oct. 2024
  Japanese, Total pages：xiv, 377p
  CiNii Books：http://ci.nii.ac.jp/ncid/BD08964852
  ISBN：9784274228094, CiNii Books ID：BD08964852
• 動物の事典　　　　　　　　　　　　　　　
  [Contributor]
  Nov. 2020
  ISBN：4254171668
• Groucho結合因子Ripply1による分節プログラム　　　　　　　　　　　　　　　
  川村 哲規; 越田 澄人; 高田 慎治, [Contributor]
  Feb. 2006

• 多様な形態を示すヒレの形成を司るHox遺伝子群　　　　　　　　　　　　　　　
  川村哲規
  Sep. 2022
  Public symposium
• Functional analysis of hox clusters by using zebrafish genetics　　　　　　　　　　　　　　　
  Akinori Kawamura
  Sep. 2020
  Sep. 2020 - Sep. 2020, Public symposium
  共同研究・競争的資金等ID：30059127
• 成長に伴うゼブラフィッシュの体節間血管の再配置に関する研究　　　　　　　　　　　　　　　
  松野由美香; 乙坂栞里; 鈴木聖人; 川村哲規
  Mar. 2020
  Poster presentation
• Chemical Screeningを用いたゼブラフィッシュ肋骨形成の解析　　　　　　　　　　　　　　　
  佐藤こうみ; 川村哲規
  Mar. 2020
  Poster presentation
• ゼブラフィッシュ成魚の全身骨格および軟組織形成におけるhoxクラスターの機能解析　　　　　　　　　　　　　　　
  鈴木聖人; 山田一哉; 前野哲輝; 菊地守道; 荒木 颯; 石坂瑞樹; 赤間 燿; 川村 哲規
  Mar. 2020
  Poster presentation
  共同研究・競争的資金等ID：30059127
• ゼブラフィッシュ胚発生におけるhoxクラスターの機能解析　　　　　　　　　　　　　　　
  菊地守道; 山田一哉; 前野哲輝; 荒木 颯; 鈴木聖人; 石坂瑞樹; 赤間 燿; 川村哲規
  Mar. 2020
  Poster presentation
  共同研究・競争的資金等ID：30059127
• Transcriptional autoregulation oftbx6 is required for the somite segmentation in zebrafish embryos　　　　　　　　　　　　　　　
  Ban H; Yokota D; Otosaka S; Kikuchi M; Kinoshita H; Fujino Y; Yabe T; Ovara H; Izuka A; Akama K; Yamasu K; Takada S; Kawamura A
  Sep. 2019
  Poster presentation
  共同研究・競争的資金等ID：30059129
• Different functional roles of hox clusters in zebrafish development　　　　　　　　　　　　　　　
  Yamada K; Kikuchi M; Maeno A; Araki S; Akama K; Suzuki M; Ishizaka M; Kawamura A
  Sep. 2019
  Poster presentation
  共同研究・競争的資金等ID：30059127
• ゼブラフィッシュ変異体を用いた肋骨形成機構の解析　　　　　　　　　　　　　　　
  江幡 奏美; 赤間 燿; 田港 朝仁; 弥益 恭; 川村 哲規
  Mar. 2018
  Poster presentation
• ゼブラフィッシュ未分節中胚葉におけるtbx6遺伝子の転写制御機構の解析　　　　　　　　　　　　　　　
  伴 博之; 横田 大佑; 乙坂 栞里; 木下 宏史; 藤野 友梨; 矢部 泰二郎; 小原 弘幹; 猪塚 彩花; 赤間 燿; 鹿毛 大地; 弥益 恭; 高田 慎治; 川村 哲規
  Mar. 2018
  Poster presentation
  共同研究・競争的資金等ID：30059129
• ゼブラフィッシュを用いたhoxクラスター変異体の作製と解析　　　　　　　　　　　　　　　
  荒木 颯; 赤間 燿; 弥益 恭; 川村 哲規
  Dec. 2017
  Poster presentation
• ゼブラフィッシュ分節時計におけるhairy関連遺伝子のmRNA不安定性に関する解析　　　　　　　　　　　　　　　
  藤野友梨; 菅谷千尋; 大岡優子; 木下宏史; 小原弘幹; 弥益 恭; 三嶋雄一郎; 川村哲規
  Dec. 2017
  Poster presentation
• ゼブラフィッシュ未分節中胚葉におけるtbx6遺伝子の発現は positive autoregulatory loopによって維持される　　　　　　　　　　　　　　　
  伴 博之; 横田大佑; 木下宏史; 藤野友梨; 矢部泰二郎; 小原弘幹; 猪塚彩花; 赤間 耀; 鹿毛大地; 弥益 恭; 高田慎治; 川村哲規
  Dec. 2017
  Poster presentation
• Somite patterning provides positional cues for the segmental ossification of the vertebral column in teleosts　　　　　　　　　　　　　　　
  Akama K; Inohaya K; Taminato T; Ebata K; Fujino Y; Kinoshita H; Yamasu K; Kawamura A
  Aug. 2017
  Poster presentation
• Distinct mRNA turnover rate mediated by 3’UTR of hairy-related genes in the segmentation clock of zebrafish embryos　　　　　　　　　　　　　　　
  Fujino Y; Sugaya C; Ooka Y; Kinoshita H; Ovara H; Yamasu K; Mishima Y; Kawamura A
  Aug. 2017
  Poster presentation
• Transcriptional autoregulatory loop maintains the expression of tbx6 in the zebrafish presomitic mesoderm　　　　　　　　　　　　　　　
  Ban H; Yokota D; Kinoshita H; Fujino Y; Yabe T; Ovara H; Izuka A; Akama K; Kage D; Yamasu K; Takada S; Kawamura A
  Aug. 2017
  Poster presentation
• Genetic interactions between Ripply and Tbx6 in the somite segmentation and myogenesis in zebrafish embryos　　　　　　　　　　　　　　　
  Kinoshita H; Fujino Y; Ohgane N; Yabe T; Yokota D; Ovara H; Izuka A; Ban H; Kage D; Yamasu K; Takada S; Kawamura A
  50th Annual Meeting of the Japanese Society of Developmental Biologists, May 2017
  Poster presentation

• 2017 - Present
  分子発生制御学特論, Saitama University, Graduate School of Science and Engineering
• 2013 - Present
  基礎生物学演習Ⅰ,Ⅱ, Saitama University
• 2013 - Present
  発生生物学輪講ⅠＡ,Ｂ, Saitama University, Graduate School of Science and Engineering
• 2013 - Present
  発生生物学特論Ⅰ, Saitama University, Graduate School of Science and Engineering
• 2013 - Present
  発生生物学Ⅱ, Saitama University
• 2008 - Present
  生体制御学実験/生物学実験Ｂ
• 2007 - Present
  生体制御学実験Ⅲ（旧：発生情報学実験）, Saitama University
• 2007 - Present
  発生情報学演習, Saitama University

• Present, The Molecular Biology Society of Japan
• Present, The Zoological Society of Japan
• Present, Japanese Society of Developmental Biologists

• マイクロ CT スキャンを用いた魚の形態多様性をもたらす分子機構の解析　　　　　　　　　　　　　　　
  Apr. 2025 - Mar. 2026
  Principal investigator
• ゼブラフィッシュHoxコードの発生遺伝学解析　　　　　　　　　　　　　　　
  Apr. 2023 - Mar. 2026
  Grant amount(Total)：4550000, Direct funding：3500000, Indirect funding：1050000
  Grant number：23K05790
• ゼブラフィッシュを用いたHox遺伝子群の機能解析　　　　　　　　　　　　　　　
  Dec. 2023 - Mar. 2025
• マイクロCTスキャンを用いたゼブラフィッシュHox変異体の解析　　　　　　　　　　　　　　　
  Apr. 2021 - Mar. 2025
• Functional analysis of Hox gene clusters using zebrafish　　　　　　　　　　　　　　　
  Japan Society for the Promotion of Science, Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (C), Grant-in-Aid for Scientific Research (C), Apr. 2018 - Mar. 2022
  Akinori Kawamura, Saitama University, Principal investigator
  Grant amount(Total)：4290000, Direct funding：3300000, Indirect funding：990000
  Hox clusters, in which multiple Hox genes are arranged, and play a fundamental role in the development of animal body. Due to whole genome duplication that occurred during vertebrate evolution, Hox clusters diverged into four in mouse and human, and into seven in zebrafish. Until now, most of functional studies have been performed in mice, which have revealed the functions of the Hox genes, however it remained unclear whether the functional roles revealed in mice are conserved among vertebrates. In this study, we generated seven zebrafish Hox cluster mutants and compared their functions. Our results revealed many functional differences of Hox genes between zebrafish and mice, suggesting that the vertebrate Hox cluster has acquired different sub/neofunctinalization after the quadruplication of Hox clusters.
  Grant number：18K06177
  講演・口頭発表等ID：30059323
• ゼブラフィッシュ最前部椎骨を司るHox遺伝子の解析　　　　　　　　　　　　　　　
  Oct. 2021
• Micro-CT scan analysis for the formation of the vertebrate body　　　　　　　　　　　　　　　
  NIG-JOINT(A), Apr. 2019 - Mar. 2021
  Principal investigator
  論文ID：30059067
• ChIP-Injection: Identification of functional enhancers using zebrafish embryos　　　　　　　　　　　　　　　
  Japan Society for the Promotion of Science, Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (C), Grant-in-Aid for Scientific Research (C), Apr. 2014 - Mar. 2018
  Akinori Kawamura, Saitama University, Principal investigator
  Grant amount(Total)：5070000, Direct funding：3900000, Indirect funding：1170000
  Using zebrafish embryos, we established a ChIP-Injection method that enables identification of functional enhancers based on their enhancer activities in embryos. Each reporter gene possessing the enhancer-associated genomic region enriched by ChIP was injected into zebrafish embryos to analyze the activity of putative enhancers. By using the ChIP-Injection, we identified 32 distinct putative enhancers that drove specific expression. Additionally, we generated transgenic lines that exhibit distributions of the EGFP signal as was observed in the screening. Furthermore, the expression pattern driven by the identified somite-specific enhancer resembled that of the gene acta2. The results indicate that ChIP-Injection provides an efficient approach for identification of active enhancers in a potentially wide variety of developmental tissues and stages.
  Grant number：26430182
  論文ID：30059068, 講演・口頭発表等ID：30059645
• Studies on the genetic network allowing the integrated regulation of brain regionalization and neurogenesis in vertebrate embryos　　　　　　　　　　　　　　　
  Japan Society for the Promotion of Science, Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (C), Grant-in-Aid for Scientific Research (C), Apr. 2014 - Mar. 2017
  YAMASU Kyo, Saitama University, Coinvestigator
  Grant amount(Total)：5070000, Direct funding：3900000, Indirect funding：1170000
  We sought to integratively understand the regulation of brain regionalization and neurogenesis, which undergo in parallel in the neural tube of vertebrate embryos, using zebrafish as a model. We first showed that the expression of the two brain regionalization genes, pou2 and gbx2, is closely associated with the neural precursor regions, and these two genes were indeed functionally implicated in the regulation of various neurogenesis genes. Furthermore, we identified the genes whose expression in embryos had been altered by inhibiting pou2 function by the microarray method, showing that pou2 regulates many neurogenesis-related genes. Furthermore, the transcriptional regulation of pou2 and bHLH-O (her3 and her5) was examined in cultured cells, revealing the interaction among neurogenesis genes. We also found that pou2 is involved in neural differentiation in the caudal neural tube from tailbud stem cells.These findings confirmed the integrated regulation of neural development.
  Grant number：26440114
• Mechanism of the development of local organizers in the brain primordium using zebrafish as a model system　　　　　　　　　　　　　　　
  Japan Society for the Promotion of Science, Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (C), Grant-in-Aid for Scientific Research (C), 2011 - 2013
  YAMASU Kyo; KAWAMURA Akinori, Saitama University, Coinvestigator
  Grant amount(Total)：5200000, Direct funding：4000000, Indirect funding：1200000
  We studied the regulatory mechanism of vertebrate brain formation in zebrafish. We revealed the details of the function of two isthmus-forming genes, gbx2 and pou2, suggesting that both are involved in neurogenesis. We also extended the analysis on the transcriptional regulation of an ANB-forming gene, emx3, and two isthmus-forming genes, pax2a and pou2. Meanwhile, it was shown that the development of the neural crest and somite is affected in a novel mutation, kanazutsi, and its causative gene encodes a globin-family protein. In addition, we succeeded in introducing two novel experimental techniques, the GAL4/UAS system and TALEN.
  Grant number：23570247
• Molecular analysis of specification along anteiroposterior axis in body of vertebrates　　　　　　　　　　　　　　　
  Japan Society for the Promotion of Science, Grants-in-Aid for Scientific Research Grant-in-Aid for Young Scientists (B), Grant-in-Aid for Young Scientists (B), 2010 - 2012
  KAWAMURA Akinori, Saitama University, Principal investigator
  Grant amount(Total)：4290000, Direct funding：3300000, Indirect funding：990000
  During embryogenesis of vertebrates, the repeated and segmental structure, somites, are formed, and subsequently specification along the anteroposterior axis is established in vertebrates, Hox genes have been known to play roles in the specification of identity along the anteroposterior axis. However, the molecular mechanisms underlying this ordered expression patterns of Hox genes remains poorly understood. In this study, we analyzed the zebrafish mutant and identified candidate genes by genetic analyses. In addition, we analyzed the transcriptional regulation of hairy-related gene, which play important roles in the somite patterning. The DNA region downstream of hairy-related gene shows enhancer activity, consistent with the endogenous gene expression. At present, we further proceed toanalyze this DNA region.
  Grant number：22770208
• ゼブラフィッシュを用いた細胞移動の制御機構の解析　　　　　　　　　　　　　　　
  Apr. 2010 - Mar. 2011
  Principal investigator
• Regulatory mechanism of the formation of the signaling center for regionalization of the brain primordium in vertebrate embryos.　　　　　　　　　　　　　　　
  Japan Society for the Promotion of Science, Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (C), Grant-in-Aid for Scientific Research (C), 2008 - 2010
  YAMASU Kyo; KAWAMURA Akinori, Saitama University
  Grant amount(Total)：4810000, Direct funding：3700000, Indirect funding：1110000
  The enhancers of the regulatory genes for the two signaling centers, anterior neural boundary (ANB) and midbrain-hindbrain boundary (MHB), were identified in zebrafish, and their regulation was analyzed by binding assays and reporter assays. In addition, the role of pou2 in MHB formation was examined by using heat-inducible repressive Pou2, showing the stages of pou2 function and the downstream genes. Furthermore, the phenotypes of a novel developmental mutant was analyzed and its causative gene was explored, resulting in identifying a limited number of candidate genes.
  Grant number：20570197
• Molecular mechanism underlying metameric morphogenesis　　　　　　　　　　　　　　　
  Japan Society for the Promotion of Science, Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (S), Grant-in-Aid for Scientific Research (S), 2006 - 2010
  TAKADA Shinji; KOSHIDA Sumito; OHKUBO Tadashi; YABE Taijiro; AKANUMA Takashi; KAWAMURA Akinori; TAKADA Ritsuko; UTSUMI Hideko; CHEN Quihong; TAKAHASHI Jun; TSUNOKUNI Hiroyuki; WANGLAR Chimwar, National Institutes of Natural Sciences Okazaki Research Facilities
  Grant amount(Total)：111020000, Direct funding：85400000, Indirect funding：25620000
  To understand the molecular mechanism underlying the development of metameric structures, we identified several genes required for somite segmentation. One of these genes, Ripply1, represses the function of T-box transcription factors through several ways, resulting in proper positioning of the segmentation boundary. Furthermore, the interaction between Ripply and T-box factors also appears to be required for the segmentation of another metameric structure, the pharyngeal arch, suggesting that a common machinery is involved in segmentation of different tissues.
  Grant number：18107006
• Screening for the zebrafish mutants that exhibit the abnormal expression patterns of Hox genes.　　　　　　　　　　　　　　　
  Japan Society for the Promotion of Science, Grants-in-Aid for Scientific Research Grant-in-Aid for Young Scientists (B), Grant-in-Aid for Young Scientists (B), 2008 - 2009
  KAWAMURA Akinori, Saitama University
  Grant amount(Total)：4290000, Direct funding：3300000, Indirect funding：990000
  In vertebrates, the characteristic features such as limbs and ribs were observed along the anteroposterior axis. These morphological differences along the anteroposterior axis are specified during early embryogenesis. Genetic studies in Drosophila have shown that Hox genes play a central role in this process. Several lines of accumulating evidence indicate that the identity along the anteroposterior axis is specified by the ordered expression patterns of Hox genes in Drosophila as well as vertebrates. However, the molecular mechanism how the ordered expression patterns of Hox genes along the anteroposterior axis remains poorly understood in vertebrates. In this study to isolate the mutant that exhibits the abnormal expression patterns of Hox genes. I have performed the F2 mutant screening by using zebrafish treated with ENU mutagen. So far, I identified at least 13 mutants which exhibit the abnormal development in zebrafsih. At present, I have investigated the expression patterns of several genes including Hox genes by whole-mount in situ hybridization. In addition, I proceed to perform the F2 screening for further identification of mutants.
  Grant number：20770172
• 脊椎動物の体節における領域形成と特異化をつかさどる分子機構　　　　　　　　　　　　　　　
  2005 - 2007
  Principal investigator
  Grant amount(Total)：3300000, Direct funding：3300000
  Grant number：05J04326
  論文ID：30059073

• CTスキャンで生物研究 筋肉・内臓も360度観察、レプリカ作成も　　　　　　　　　　　　　　　
  11 Dec. 2024, [Internet]
• 生物の体内 CTで360度観察　　　　　　　　　　　　　　　
  29 Nov. 2024, [Paper]
• 魚にもあった !? 「首の骨」　　　　　　　　　　　　　　　
  26 Aug. 2024, [Paper]
• Do fish have neck bones? Saitama University led group finds high probability of only one bone being present　　　　　　　　　　　　　　　
  21 Aug. 2024, [Internet]
• Saitama University clarifies the role of Hox gene in formation of fish fins　　　　　　　　　　　　　　　
  13 Aug. 2024, [Internet]
• 魚のひれの形を決める「Hox遺伝子」とは 埼玉大などがゲノム編集技術で初めて解明　　　　　　　　　　　　　　　
  04 Aug. 2024, [Internet]
• 魚のひれの形を決める「Hox遺伝子」とは 埼玉大などがゲノム編集技術で初めて解明　　　　　　　　　　　　　　　
  04 Aug. 2024, [Internet]
• 魚のひれの形を決める「Hox遺伝子」とは 埼玉大などがゲノム編集技術で初めて解明　　　　　　　　　　　　　　　
  04 Aug. 2024, [Internet]
• 魚のひれの形を決める「Hox遺伝子」とは 埼玉大などがゲノム編集技術で初めて解明　　　　　　　　　　　　　　　
  04 Aug. 2024, [Internet]
• 魚のひれの形を決める「Hox遺伝子」とは 埼玉大などがゲノム編集技術で初めて解明　　　　　　　　　　　　　　　
  04 Aug. 2024, [Internet]
• 魚のひれの形を決める「Hox遺伝子」とは　　　　　　　　　　　　　　　
  04 Aug. 2024, [Internet]
• 魚のひれの形を決める「Hox遺伝子」とは 埼玉大などがゲノム編集技術で初めて解明　　　　　　　　　　　　　　　
  04 Aug. 2024, [Internet]
• 魚のひれの形を決める「Hox遺伝子」とは 埼玉大などがゲノム編集技術で初めて解明　　　　　　　　　　　　　　　
  04 Aug. 2024, [Internet]
• 魚のひれの形を決める「Hox遺伝子」とは 埼玉大などがゲノム編集技術で初めて解明　　　　　　　　　　　　　　　
  04 Aug. 2024, [Paper]
• 魚のひれの形を決める「Hox遺伝子」とは 埼玉大などがゲノム編集技術で初めて解明　　　　　　　　　　　　　　　
  04 Aug. 2024, [Internet]
• 哺乳類の首の骨は7個…では魚は何個？ 埼玉大などが解明　　　　　　　　　　　　　　　
  03 Aug. 2024, [Internet]
• 哺乳類の首の骨は7個…では魚は何個？ 埼玉大などが解明　　　　　　　　　　　　　　　
  03 Aug. 2024, [Internet]
• 哺乳類の首の骨は7個…では魚は何個？ 埼玉大などが解明　　　　　　　　　　　　　　　
  03 Aug. 2024, [Internet]
• 哺乳類の首の骨は7個…では魚は何個？ 埼玉大などが解明　　　　　　　　　　　　　　　
  03 Aug. 2024, [Internet]
• 哺乳類の首の骨は7個…では魚は何個？ 埼玉大などが解明　　　　　　　　　　　　　　　
  03 Aug. 2024, [Paper]
• 哺乳類の首の骨は7個…では魚は何個？ 埼玉大などが解明　　　　　　　　　　　　　　　
  03 Aug. 2024, [Internet]
• 鱼类有颈骨（颈椎）吗？”埼玉大学等发现可能“有一块　　　　　　　　　　　　　　　
  30 Jul. 2024, [Internet]
• ひれの多様な「設計図」、埼玉大など発表　　　　　　　　　　　　　　　
  24 Jul. 2024
• 魚に首の骨（頸椎）があるのか？ ―脊椎動物の共有形質「背骨」の進化を探る　　　　　　　　　　　　　　　
  19 Jul. 2024, [Paper]
• ひれの多様な「設計図」、埼玉大など発表　　　　　　　　　　　　　　　
  16 Jul. 2024, [Paper]
• ひれの多様な「設計図」、埼玉大など発表　　　　　　　　　　　　　　　
  15 Jul. 2024, [Paper]
• 魚に首の骨はあるのか？意外な結果が判明　　　　　　　　　　　　　　　
  12 Jul. 2024, [Internet]
• 魚のひれ「設計図」解明、埼玉大などが遺伝子研究　　　　　　　　　　　　　　　
  10 Jul. 2024, [Paper]
• 魚に首の骨は存在するのか？1つだけある可能性 脊椎動物は陸で首を発達 埼玉大など　　　　　　　　　　　　　　　
  09 Jul. 2024, [Internet]
• 魚に首の骨（頸椎）があるのか？ ―脊椎動物の共有形質「背骨」の進化を探る　　　　　　　　　　　　　　　
  09 Jul. 2024, [Internet]
• 魚の頸椎の調査から脊椎動物の「背骨」の進化を探る―埼玉大など　　　　　　　　　　　　　　　
  09 Jul. 2024, [Internet]
• 魚のひれ決める遺伝子 埼玉大・宇都宮大が解明　　　　　　　　　　　　　　　
  08 Jul. 2024, [Paper]
• 魚のひれ決める遺伝子 埼玉大・宇都宮大が解明　　　　　　　　　　　　　　　
  08 Jul. 2024, [Paper]
• 魚のひれ決める遺伝子 埼玉大・宇都宮大が解明　　　　　　　　　　　　　　　
  08 Jul. 2024, [Paper]
• 魚のひれ決める遺伝子 埼玉大・宇都宮大が解明　　　　　　　　　　　　　　　
  08 Jul. 2024, [Paper]
• 魚のひれ決める遺伝子働き解明 埼玉・宇都宮グループ　　　　　　　　　　　　　　　
  07 Jul. 2024, [Paper]
• 魚の背ひれや尻びれ 形決める遺伝子解明 埼玉、宇都宮大グループ　　　　　　　　　　　　　　　
  07 Jul. 2024, [Paper]
• 魚のひれ設計の遺伝子 埼玉大・宇都宮大、機能を解明　　　　　　　　　　　　　　　
  06 Jul. 2024, [Paper]
• 魚のひれ設計の遺伝子 埼玉大・宇都宮大、機能を解明　　　　　　　　　　　　　　　
  06 Jul. 2024, [Paper]
• 魚のひれ決める遺伝子働き解明 埼玉・宇都宮グループ　　　　　　　　　　　　　　　
  06 Jul. 2024, [Paper]
• 魚のひれ設計の遺伝子 埼玉大・宇都宮大、機能を解明　　　　　　　　　　　　　　　
  06 Jul. 2024, [Paper]
• 魚のひれ設計の遺伝子 埼玉大・宇都宮大、機能を解明　　　　　　　　　　　　　　　
  06 Jul. 2024, [Paper]
• 魚のひれ設計の遺伝子 埼玉大・宇都宮大、機能を解明　　　　　　　　　　　　　　　
  06 Jul. 2024, [Paper]
• 魚のヒレ 形成位置を制御 埼玉大などHox遺伝子の仕組み解明 システム変更が多様性生み出す　　　　　　　　　　　　　　　
  05 Jul. 2024, [Paper]
• 「魚のヒレ」長かったり、短かったり!? 仕組みを解明 ヒレの多様性をもたらす単純なシステム・埼玉大学　　　　　　　　　　　　　　　
  14 Jun. 2024, [Internet]
• 魚のヒレは長かったり、短かったり、はなぜ？　　　　　　　　　　　　　　　
  14 Jun. 2024, [Internet]
• 魚のヒレの幅や長さはどのように決まるのか？ 観賞魚創造に貢献 埼玉大など　　　　　　　　　　　　　　　
  14 Jun. 2024, [Internet]
• サイ・テクこらむ 知と技の発信「【575】魚から探る脊椎動物の進化」　　　　　　　　　　　　　　　
  05 Jun. 2024, [Paper]
• サイ・テクこらむ 知と技の発信「【369】脊椎動物の規則的な体作り」　　　　　　　　　　　　　　　
  19 Sep. 2018
• サイ・テクこらむ 知と技の発信「【130】脊椎動物の形を決める時計」　　　　　　　　　　　　　　　
  04 Sep. 2013, [Paper]