Hidemasa Bono

Hidemasa Bono
Hiroshima University | HU · Genome Editing Innovation Center

Professor
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About

309
Publications
22,205
Reads
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15,439
Citations
Introduction
Development of database technologies for genome editing and functional genomics by bioinformatic approach
Additional affiliations
April 2020 - April 2022
Hiroshima University
Position
  • Professor
Description
  • Laboratory of Genome Informatics. Development of database technologies for genome editing and functional genomics by bioinformatic approach
July 2007 - March 2020
Research Organization of Information and Systems (ROIS)
Position
  • Professor (Associate)
April 2003 - June 2007
Saitama Medical University
Position
  • Professor (Associate)
Education
April 1997 - March 2000
Kyoto University
Field of study
  • Bioinformatics
April 1995 - March 1997
Kyoto University
Field of study
  • Biophysics
April 1991 - March 1995
The University of Tokyo
Field of study
  • Pure and Applied Sciences

Publications

Publications (309)
Article
Full-text available
Data accumulation in public databases has resulted in extensive use of meta-analysis, a statistical analysis that combines the results of multiple studies. Oxidative stress occurs when there is an imbalance between free radical activity and antioxidant activity, which can be studied in insects by transcriptome analysis. This study aimed to apply a...
Article
Full-text available
Objective Insects are the most evolutionarily successful groups of organisms, and this success is largely due to their flight ability. Interestingly, some stick insects have lost their flight ability despite having wings. To elucidate the shift from wingless to flying forms during insect evolution, we compared the nutritional metabolism system amon...
Article
Full-text available
Hypoxia is a condition in which cells, tissues, or organisms are deprived of sufficient oxygen supply. Aerobic organisms have a hypoxic response system, represented by hypoxia-inducible factor 1-α (HIF1A), to adapt to this condition. Due to publication bias, there has been little focus on genes other than well-known signature hypoxia-inducible gene...
Preprint
Full-text available
Thanks to the dramatic progress in DNA sequencing technology, it is now possible to decipher sequences in a mixed state. Therefore, the subsequent data analysis has become important, and the demand for metagenomic analysis is very high. Existing metagenomic data analysis workflows for 16S amplicon sequences have been mainly focused on sequences fro...
Article
Full-text available
Next-generation sequencing has revolutionized entomological study, rendering it possible to analyze the genomes and transcriptomes of non-model insects. However, use of this technology is often limited to obtaining the nucleotide sequences of target or related genes, with many of the acquired sequences remaining unused because other available seque...
Article
Transposable elements (TEs) are grouped into several families with diverse sequences. Owing to their diversity, studies involving the detection, classification, and annotation of TEs are difficult tasks. Moreover, simple comparisons of TEs among different species with different methods can lead to misinterpretations. The genome data of several hone...
Article
Full-text available
Hypoxia is an abiotic stress in plants. Flooding resulting from climate change is a major crop threat that increases the risk of hypoxic stress. The molecular mechanisms underlying hypoxia in plants were elucidated in recent years, but new genes related to this stress remain to be discovered. Thus, we aimed to perform a meta-analysis of the RNA seq...
Preprint
Hypoxia is an abiotic stress in plants. Flooding resulting from climate change is a major crop threat that increases the risk of hypoxic stress. The molecular mechanisms underlying hypoxia have been elucidated in recent years, but genes related to this stress in plants remain to be discovered. Thus, we aimed to perform a meta-analysis of RNA sequen...
Preprint
Full-text available
Background Next generation sequencing has revolutionized entomological study, rendering it possible to analyze the genomes and transcriptomes of non-model insects. However, use of this technology is often limited to obtaining nucleotide sequences of target or related genes, with many of the acquired sequences remaining unused because other availabl...
Preprint
With increasing public data, a statistical analysis approach called meta-analysis, which combines transcriptome results obtained from multiple studies, has succeeded in providing novel insights into targeted biological processes. Locusts and aphids are representative of insect groups that exhibit density-dependent plasticity. Although the physiolog...
Preprint
Gene expression studies are intrinsically biased with many being influenced by concomitant information such as the gene-disease association. However, this can be overcome using a data-driven analysis approach, which can provide insights without relying on ancillary information. This is exemplified by the FANTOM CAGE Associated Transcriptome (FANTOM...
Article
Roxadustat and other hypoxia-inducible factor-prolyl hydroxylase inhibitors (HIF-PHIs) have recently been approved for the treatment of chronic renal anemia. In macrophages and monocytes, the activation of HIF-1 by pro-inflammatory cytokines induces iNOS expression and activity through the NF-κB pathway to produce nitric oxide (NO), which causes li...
Article
Full-text available
Naked mole-rats (NMRs) have a very low spontaneous carcinogenesis rate, which has prompted studies on the responsible mechanisms to provide clues for human cancer prevention. However, it remains unknown whether and how NMR tissues respond to experimental carcinogenesis induction. Here, we show that NMRs exhibit extraordinary resistance against pote...
Preprint
Avian sex is determined by various factors, such as the dosage of DMRT1 and cell-autonomous mechanisms. While the sex-determination mechanism in gonads is well analyzed, the mechanism in germ cells remains unclear. In this study, we explored the gene expression profiles of male and female primordial germ cells (PGCs) during embryogenesis in chicken...
Article
Full-text available
Analysis of RNA-sequencing (RNA-seq) data is an effective means to analyze the gene expression levels under specific conditions and discover new biological knowledge. More than 74,000 experimental series with RNA-seq have been stored in public databases as of 20 October 2021. Since this huge amount of expression data accumulated from past studies i...
Preprint
Full-text available
Analysis of RNA-sequencing (RNA-seq) data is an effective means to analyze the gene expression levels under specific conditions and discover new biological knowledge. More than 74000 ex-perimental series with RNA-seq have been stored in public databases as of October 20, 2021. Since this huge amount of expression data accumulated from past studies...
Preprint
Full-text available
Naked mole-rats (NMRs) have a very low spontaneous carcinogenesis rate, which has prompted scientists to study their cancer resistance mechanisms in order to provide clues for human cancer prevention. Although cancer resistance in NMRs has been intensively investigated at the cellular level, it is still unknown how strongly resistant NMR individual...
Article
Full-text available
Chrysanthemums are one of the most industrially important cut flowers worldwide. However, their segmental allopolyploidy and self-incompatibility have prevented the application of genetic analysis and modern breeding strategies. We thus developed a model strain, Gojo-0 (Chrysanthemum seticuspe), which is a diploid and self-compatible pure line. Her...
Preprint
We have recently identified neurosecretory protein GL (NPGL), a small secretory protein expressed in the vertebrate hypothalamus, as an orexigenic factor with remarkable fat accumulation by overexpression of the NPGL precursor gene (Npgl) for two months. In the present study, we analyzed the effects of short-term Npgl overexpression for 18 days as...
Article
Full-text available
Since understanding molecular mechanisms of SARS-CoV-2 infection is extremely important for developing effective therapies against COVID-19, we focused on the internalization mechanism of SARS-CoV-2 via ACE2. Although cigarette smoke is generally believed to be harmful to the pathogenesis of COVID-19, cigarette smoke extract (CSE) treatments were s...
Preprint
Chrysanthemums are one of the most industrially important cut flowers worldwide. However, their segmental allopolyploidy and self-incompatibility have prevented the application of genetic analysis and modern breeding strategies. We thus developed a model strain, Gojo-0 (Chrysanthemum seticuspe), which is a diploid and self-compatible pure line. Her...
Article
Full-text available
Herein, we performed RNA-seq analysis of ten major tissues/subparts of silkworm larvae. The sequences were mapped onto the reference genome assembly and the reference transcriptome data were successfully constructed. The reference data provided a nearly complete sequence for sericin-1, a major silk gene with a complex structure. We also markedly im...
Article
Full-text available
Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassig...
Article
In cellular signaling, the diverse physiological actions of biological gases, including O2, CO, NO, and H2S, have attracted much interest. Hypoxia-inducible factors (HIFs), including HIF-1 and HIF-2, are transcription factors that respond to reduced intracellular O2 availability. Polysulfides are substances containing varying numbers of sulfur atom...
Article
Naked mole-rats (Heterocephalus glaber) inhabit subterranean burrows in savannas and are thus unable to access free water. To identify their mechanism of osmoregulation in xeric environments, we molecularly cloned and analyzed the mineralocorticoid receptor (MR) gene, required for hormone-dependent regulation of genes contributing to body fluid hom...
Preprint
Full-text available
Hypoxia is a condition in which cells, tissues, or organisms are deprived of sufficient oxygen supply. Aerobic organisms have the hypoxic response system, represented by hypoxia-inducible factor 1-α (HIF1A), to avoid this condition. Because of publication bias, the genes other than well-known signature hypoxia-stimulating genes may not be focused....
Preprint
Full-text available
Since understanding molecular mechanisms of SARS-CoV-2 infection is extremely important for developing effective therapies against COVID-19, we focused on the internalization mechanism of SARS-CoV-2 via ACE2. Although cigarette smoke is generally believed to be harmful to the pathogenesis of COVID-19, cigarette smoke extract (CSE) treatments were s...
Preprint
Data accumulation in public databases has resulted in extensive use of meta-analysis, a statistical analysis that combines the results of multiple studies. Oxidative stress occurs when there is an imbalance between free radical activity and antioxidant activity, which can be studied in insects by transcriptome analysis. This study aimed to apply a...
Article
Full-text available
Background Species-level genetic characterization of complex bacterial communities has important clinical applications in both diagnosis and treatment. Amplicon sequencing of the 16S ribosomal RNA (rRNA) gene has proven to be a powerful strategy for the taxonomic classification of bacteria. This study aims to improve the method for full-length 16S...
Article
Full-text available
Cigarette smoking (CS) is a major contributing factor in the development of a large number of fatal and debilitating disorders, including degenerative diseases and cancers. Smoking and passive smoking also affect the establishment and maintenance of pregnancy. However, to the best of our knowledge, the effects of smoking on the human endometrium re...
Chapter
Reference Expression dataset (RefEx) is a web tool which allows users to search by the gene name, various types of IDs, chromosomal regions in genetic maps, gene family based on InterPro, gene expression patterns, or biological categories based on Gene Ontology. RefEx also provides information about genes with tissue-specific expression, and the re...
Article
The Functional ANnoTation Of the Mammalian genome (FANTOM) Consortium has continued to provide extensive resources in the pursuit of understanding the transcriptome, and transcriptional regulation , of mammalian genomes for the last 20 years. To share these resources with the research community , the FANTOM web-interfaces and databases are being re...
Article
Full-text available
Abstract The naked mole-rat (NMR) is a heterothermic mammal that forms eusocial colonies consisting of one reproductive female (queen), several reproductive males, and subordinates. Despite their heterothermy, NMRs possess brown adipose tissue (BAT), which generally induces thermogenesis in cold and some non-cold environments. Previous studies sugg...
Article
Full-text available
Phytophagous insect larvae feed on plants containing secondary metabolic products with biological activity against other predatory organisms. Phytophagous insects can use their specialised metabolic systems to covert these secondary metabolic products into compounds with therapeutic properties useful to mankind. Some Asians drink tea decoctions mad...
Article
Full-text available
Long noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes, and yet, their functions remain largely unknown. As part of the FANTOM6 project, we systematically knocked down the expression of 285 lncRNAs in human dermal fibroblasts and quantified cellular growth, morphological changes, and transcriptomic responses u...
Preprint
Full-text available
Report on the group 'TogoEx' in the BioHackathon Europe 2019.
Preprint
Full-text available
Naked mole-rats (NMRs) are the longest-lived rodents, showing minimal aging phenotypes. An unsolved paradox is that NMRs exhibit low intracellular anti-oxidant defence despite minimal aging. Here, we explained a link between these "contradicting" features by a phenomenon termed "senescent cell death (SCD)"—Senescence induced cell death in NMR cells...
Preprint
Full-text available
Background Species-level genetic characterization of complex bacterial communities has important clinical applications in both diagnosis and treatment. Amplicon sequencing of the 16S ribosomal RNA (rRNA) gene has proven to be a powerful strategy for the taxonomic classification of bacteria. This study aims to improve the method for full-length 16S...
Preprint
Full-text available
The naked mole-rat (NMR) is a poikilothermic mammal that forms eusocial colonies consisting of one breeding queen, several breeding kings, and subordinates. Despite their poikilothermic feature, NMRs possess brown adipose tissue (BAT), which in homeothermic mammals induces thermogenesis in cold environments. However, NMR-BAT thermogenic potential i...
Preprint
Full-text available
Background Mariner and mariner-like elements (MLEs) are distributed in various species and their sequences are highly diverse. In previous reports, a few transposable element in the genomes of Apis species mainly consist of mariner and MLE. For further insight of Apis MLEs, detailed classifications of Apis MLE and sequences analysis of long MLEs, w...
Article
Endometrial stromal cells differentiate into decidual cells through the process of decidualization. This differentiation is critical for embryo implantation and the successful establishment of pregnancy. Recent epidemiological studies have suggested that thyroid hormone is important in the endometrium during implantation, and it is commonly believe...
Preprint
Full-text available
We report on the activities of the 2015 edition of the BioHackathon, an annual event that brings together researchers and developers from around the world to develop tools and technologies that promote the reusability of biological data. We discuss issues surrounding the representation, publication, integration, mining and reuse of biological data...
Article
Full-text available
We previously demonstrated that expression of a Krüppel-like zinc finger transcription factor, GLIS1, dramatically increases under hypoxic conditions via a transcriptional mechanism induced by HIF-2α co-operating with AP-1 members. In this study, we focused on the functional roles of GLIS1 in breast cancer. To uncover its biological function, the e...
Article
Full-text available
Polyembryony is defined as the formation of several embryos from a single egg. This phenomenon can occur in humans, armadillo, and some endoparasitoid insects. However, the mechanism underlying polyembryogenesis in animals remains to be elucidated. The polyembryonic parasitoid wasp Copidosoma floridanum oviposits its egg into an egg of the host ins...
Preprint
Full-text available
Background: Polyembryony is defined as the formation of several embryos from a single egg. This phenomenon can occur in humans, armadillo, and some endoparasitoid insects. However, the mechanism underlying polyembryogenesis in animals remains to be elucidated. The polyembryonic parasitoid wasp Copidosoma floridanum oviposits its egg into an egg of...
Article
Full-text available
Gene expression data have been archived as microarray and RNA-seq datasets in two public databases, Gene Expression Omnibus (GEO) and ArrayExpress (AE). In 2018, the DNA DataBank of Japan started a similar repository called the Genomic Expression Archive (GEA). These databases are useful resources for the functional interpretation of genes, but hav...
Poster
Full-text available
In the integrated database project in Japan, Database Center for Life Science (DBCLS) has developed various computational tools for reuse of huge amount of data archived in the public repository (https://dbcls.rois.ac.jp/services-en.html). Meanwhile, DNA Data Bank of Japan (DDBJ) has archived and maintained data from the high-throughput sequencin...
Article
Full-text available
Hypoxia is the insufficiency of oxygen in the cell, and hypoxia-inducible factors (HIFs) are central regulators of oxygen homeostasis. In order to obtain functional insights into the hypoxic response in a data-driven way, we attempted a meta-analysis of the RNA-seq data from the hypoxic transcriptomes archived in public databases. In view of method...
Preprint
Background: Polyembryony is defined as the formation of several embryos from a single egg. This phenomenon can occur in humans, armadillo, and some endoparasitoid insects. However, the mechanism underlying polyembryogenesis in animals remains to be elucidated. The polyembryonic parasitoid wasp Copidosoma floridanum oviposits its egg into an egg of...
Preprint
Full-text available
Background The silkworm Bombyx mori is a lepidopteran model insect with biological and industrial importance. Its high-quality genome sequence has recently become available and the utilization of this information in combination with extensive transcriptomic analyses is expected to provide an elaborate gene model. It will also be possible to clarify...
Article
Full-text available
Perhaps, oxidative stress progresses pupation in some Lepidopteran insects; however, the reasons for this remain obscure. In our previous study, we clarified Bombyx mori SOD1 (BmSOD1) and B. mori SOD2 (BmSOD2) proteins respond in common to ultraviolet irradiation (UV) oxidative stress and metamorphosis. This result strongly suggested pupation initi...
Article
Full-text available
Publishing databases in the Resource Description Framework (RDF) model is becoming widely accepted to maximize the syntactic and semantic interoperability of open data in life sciences. Here we report advancements made in the 6th and 7th annual BioHackathons which were held in Tokyo and Miyagi respectively. This review consists of two major section...
Article
Copidosoma floridanum is a polyembryonic, caste-forming, wasp species. The ratio of investment in different castes changes with environmental stressors (e.g. multi-parasitism with competitors). The vasa gene was first identified in Drosophila melanogaster as a germ-cell-determining factor, and C. floridanum vasa (Cf-vas) gene positive cells have be...
Preprint
Long non-coding RNAs (lncRNAs) constitute the majority of transcripts in mammalian genomes and yet, their functions remain largely unknown. We systematically suppressed 285 lncRNAs in human dermal fibroblasts and quantified cellular growth, morphological changes, and transcriptomic responses using Capped Analysis of Gene Expression (CAGE). The resu...
Preprint
Background: Polyembryony, when several embryos are clonally produced from a single egg, is found in humans, armadillo, and some endoparasitoid insects. Thus, although polyembryony is conserved through insects to mammals, the polyembryogenesis progress remains obscure in these animals. The polyembryonic parasitoid wasp Copidosoma floridanum oviposit...
Poster
Full-text available
Gene expression data have been archived as microarray and RNA-seq data in two public databases, NCBI Gene Expression Omnibus (GEO) and EBI ArrayExpress. In 2018, DNA DataBank of Japan (DDBJ) recently started similar repository called Genomic Expression Archive (GEA; https://www.ddbj.nig.ac.jp/gea/ ) [1]. These databases are useful resource for the...
Preprint
Full-text available
Gene expression data have been archived as microarray and RNA-seq datasets in two public databases, Gene Expression Omnibus (GEO) and ArrayExpress (AE). In 2018, the DNA DataBank of Japan started a similar repository called the Genomic Expression Archive (GEA). These databases are useful resources for the functional interpretation of genes, but hav...
Article
Full-text available
The possibility that anesthesia during cancer surgery may affect cancer recurrence, metastasis, and patient prognosis has become one of the most important topics of interest in cancer treatment. For example, the volatile anesthetic isoflurane was reported in several studies to induce hypoxia-inducible factors, and thereby enhance malignant phenotyp...
Data
Direct effect of isoflurane on MTS and ATP assays. RCC4-EV cells were exposed to 0% or 4% isoflurane for 1 h. Cells were harvested and submitted to MTS [3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium] assay (A) and cellular ATP assay (B) Data represent the mean ± SD values (n = 3). P-values less than 0.05 i...
Data
Result of Data analysis of RNA-Seq. File is deposited at https://doi.org/10.6084/m9.figshare.6571730. (DOCX)
Data
Immunoblot before cropping. (A) HIF expression after 8 h at 20% and 1% O2, (B) after 8 h at 20% O2 with or without 2% isoflurane, (C) and after 8 h at 1% O2 with or without 2% isoflurane. Cells were harvested, and 35 μg whole-cell lysates were immunoblotted using primary antibodies to indicated proteins. (EPS)
Data
Dose-dependency of suppressive effect of isoflurane on cell migration. RCC4-EV (A) and RCC4-VHL (B) cells were allowed to migrate for 12 h with or without 1% or 2% isoflurane treatment for 2 h. Migration rate was assessed as described in Materials and Methods. (EPS)
Article
Full-text available
Insects are well adapted to changing environmental conditions. They have unique systems for eliminating reactive oxygen species (ROS). Superoxide dismutase (SOD) is a key enzyme that plays a primary role in removing ROS. Bombyx mori is a lepidopteran insect, whose body size is larger than the model insect Drosophila melanogaster, which enabled us t...