A5022765178- Genomics and Chromatin Dynamics
- Developmental Biology and Gene Regulation
- Genomics and Phylogenetic Studies
- RNA Research and Splicing
- Chromosomal and Genetic Variations
- Marine Ecology and Invasive Species
- Planarian Biology and Electrostimulation
- Congenital limb and hand anomalies
- Animal Genetics and Reproduction
- Congenital heart defects research
- Pluripotent Stem Cells Research
- Genetic diversity and population structure
- Physiological and biochemical adaptations
- Epigenetics and DNA Methylation
- Molecular Biology Techniques and Applications
- Histone Deacetylase Inhibitors Research
- Plant and Biological Electrophysiology Studies
- Cancer-related gene regulation
- Single-cell and spatial transcriptomics
- Heat shock proteins research
- Muscle Physiology and Disorders
- dental development and anomalies
- Renal and related cancers
- Connexins and lens biology
- Cephalopods and Marine Biology
Research Institute of Molecular Pathology
2018-2024
National Institute of Genetics
2022-2024
The Graduate University for Advanced Studies, SOKENDAI
2024
Nara Institute of Science and Technology
2010-2023
Vienna Biocenter
2018-2021
University of Tsukuba
2019
Nagahama Institute of Bio-Science and Technology
2014-2018
TU Dresden
2016
Abstract Lungfishes belong to lobe-fined fish (Sarcopterygii) that, in the Devonian period, ‘conquered’ land and ultimately gave rise all vertebrates, including humans 1–3 . Here we determine chromosome-quality genome of Australian lungfish ( Neoceratodus forsteri ), which is known have largest any animal. The vast size this genome, about 14× larger than that humans, attributable mostly huge intergenic regions introns with high repeat content (around 90%), components resemble those tetrapods...
Connective tissues—skeleton, dermis, pericytes, fascia—are a key cell source for regenerating the patterned skeleton during axolotl appendage regeneration. This complexity has made it difficult to identify cells that regenerate skeletal tissue. Inability these impeded mechanistic understanding of blastema formation. By tracing digit tip regeneration using brainbow transgenic axolotls, we show from each connective tissue compartment have distinct spatial and temporal profiles proliferation,...
Vertebrates harbor recognizably orthologous gene complements but vary 100-fold in genome size. How chromosomal organization scales with expansion is unclear, and how acute changes regulation, as during axolotl limb regeneration, occur the context of a vast has remained riddle. Here, we describe chromosome-scale assembly giant, 32 Gb genome. Hi-C contact data revealed scaling properties interphase mitotic chromosome organization. Analysis yielded understanding evolution large, syntenic...
The salamander limb correctly regenerates missing segments because connective tissue cells have segment-specific identities, termed "positional information". How positional information is molecularly encoded at the chromatin level has been unknown. Here, we performed genome-wide profiling in mature and regenerating axolotl cells. We find levels of histone H3K27me3 as major mark, especially homeoprotein gene loci but not their upstream regulators, constituting an intrinsic segment code....
Abstract Coleoid cephalopods (squid, cuttlefish, octopus) have the largest nervous system among invertebrates that together with many lineage-specific morphological traits enables complex behaviors. The genomic basis underlying these innovations remains unknown. Using comparative and functional genomics in model squid Euprymna scolopes , we reveal unique genomic, topological, regulatory organization of cephalopod genomes. We show coleoid genomes been extensively restructured compared to...
Recent studies underscore a role for the differential degeneration of enhancers in evolutionary diversification paralogue expression. However, no one has reported evidence involvement innovative cis-regulatory changes. Here we show that silencer innovation diversified expression vertebrate paralogues, pax2 and pax8. shows multi-tissue expression, as does ancestral amphioxus orthologue, pax2/5/8, whereas pax8 localizes to subset pax2-expressing tissues. We reveal both retain capable directing...
Planarians are non-parasitic Platyhelminthes (flatworms) famous for their regeneration ability and having a well-organized brain. Dugesia japonica is typical planarian species that widely distributed in the East Asia. Extensive cellular molecular experimental methods have been developed to identify functions of thousands genes this species, making good model biology neurobiology. However, no genome-level information available D. japonica, few gene regulatory networks identified thus far. To...
<ns4:p>The taxon Elasmobranchii (sharks and rays) contains one of the long-established evolutionary lineages vertebrates with a tantalizing collection species occupying critical aquatic habitats. To overcome current limitation in molecular resources, we launched Squalomix Consortium 2020 to promote genome-wide array approaches, specifically targeting shark ray species. Among various bottlenecks working elasmobranchs are their elusiveness low fecundity as well large highly repetitive genomes....
Many amphibians can regenerate limbs, even in adulthood. If a limb is amputated, the stump generates blastema that makes complete, new process similar to developmental morphogenesis. The thought inherit its limb-patterning properties from cells stump, and it retains information despite changes morphology, gene expression, differentiation states required by regeneration. We hypothesized these cellular are maintained as epigenetic memory through histone modifications. To test this hypothesis,...
Xenopus is one of the essential model systems for studying vertebrate development. However, drawback this system that, because opacity embryos, 3D imaging analysis limited to surface structures, explant cultures, and post-embryonic tadpoles. To develop a technique tissue/organ in whole we identified optimal conditions using placental alkaline phosphatase (PLAP) as transgenic reporter applied it correlative light microscopy block-face (CoMBI) method visualization PLAP-expressing...
Abstract Limb development in salamanders is unique among tetrapods significant ways. Not only can regenerate lost limbs repeatedly and throughout their lives, but also the preaxial zeugopodial element digits form before postaxial ones and, hence, with a reversed polarity compared to all other tetrapods. Moreover, free‐swimming larval stages, as exemplified by axolotl ( Ambystoma mexicanum ), each digit buds independently, instead of undergoing paddle stage. Here, we report gene expression...
Extant eukaryote ecology is primarily sustained by oxygenic photosynthesis, in which chlorophylls play essential roles. The exceptional photosensitivity of allows them to harvest solar energy for but on the other hand, they also generate cytotoxic reactive oxygen species. A risk such phototoxicity chlorophyll must become particularly prominent upon dynamic cellular interactions that potentially disrupt mechanisms are designed quench photoexcited phototrophic cells. Extensive examination a...
The regulated removal of the gene-silencing epigenetic mark, trimethylation lysine 27 histone H3 (H3K27me3), has been shown to be critical for tissue-specific activation developmental genes; however, extent embryonic expression its demethylases, JMJD3 and UTX, remained unclear. In this study, we investigated <I>jmjd3</I> <I>utx</I> genes in <I>Xenopus</I> embryos parallel with that H3K27 methylase gene, <I>ezh2</I>. At blastula stage, <I>jmjd3, utx</I> <I>ezh2</I> showed similar patterns...
Abstract The salamander limb regenerates only the missing portion. Each segment can form segments equivalent to- or more distal to their own identity, relying on a property termed “positional information”. How positional information is encoded in cells has been unknown. By cell-type-specific chromatin profiling of upper arm, lower and hand, we found segment-specific levels histone H3K27me3 at homeoprotein gene loci but not upstream regulators, constituting an intrinsic code. During...
Temporally controlled induction of gene expression is a useful technique for analyzing function. To make such possible in Ciona intestinalis embryos, we employed the cis-regulatory region heat-shock protein 70 (HSP70) Ci-HSPA1/6/7-like heat-inducible C. embryos. We showed that becomes heat shock-inducible by 32-cell stage during embryogenesis. The 5'-upstream Ci-HSPA1/6/7-like, which contains elements indispensable expression, induces shock-dependent reporter whole embryo from to middle...
Abstract In higher eukaryotic cells, a string of nucleosomes, where long genomic DNA is wrapped around core histones, are rather irregularly folded into number condensed chromatin domains, which have been revealed by super-resolution imaging and Hi-C technologies. Inside these nucleosomes fluctuate locally behave like liquid. The behavior may be highly related to transaction activities such as transcription repair, often upregulated in cancer cells. To investigate cells compare those...