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Yasuhiro Tomaru

Publications and source records attributed to Yasuhiro Tomaru.

15 recordsLinked to original sources
PubMed2006

Cancer research with non-coding RNA.

Cancer research is not limited to medical research; it expands over several disciplines, incorporating molecular bioscience at both the macro and micro levels. All stages and aspects of cells, from development and differentiation, apoptosis, cell adhesion and many more, are research fields with a connection to cancer. Cancer research in itself is the research of cancer cures. Recently, not only cancer but also bioscience research has surfed on the new wave of RNA knowledge. Most of those RNAs are non-protein-coding RNAs and are connected to cell development and differentiation, and thereby with cancer differentiation and treatment. Here we would like to introduce the latest in cancer research that has emerged from the field of molecular biology research.

Cell Differentiation↗
PubMed2005

Comparative analysis of expression of histone H2a genes in mouse.

BACKGROUND: At least 18 replication-dependent histone H2a genes are distributed in 3 Hist gene clusters on different chromosomes of the mouse genome. In this analysis we designed specific PCR primers for each histone H2a transcript and studied the expression levels and patterns using quantitative RT-PCR (qRT-PCR). In addition, we compared histone H3 K9 acetylation levels in the promoter regions of H2a genes by ChIP (chromatin immunoprecipitation)--quantitative PCR (qPCR) analysis. RESULTS: RT-PCR analysis indicated that all 20 histone H2a genes assessed in this study are expressed. The replication-dependent histone H2a genes have different expression levels but similar expression patterns. Among the 20 histone H2a genes, the expression-level of H2afz, a replication-independent gene, was highest, and that of Hist1h2aa, a replication-dependent gene, was lowest. Among 18 replication-dependent H2a genes, the expression level of Hist3h2a was highest. The ChIP-qPCR analysis showed that histone H3 K9 acetylation levels in promoter regions of both H2afz and Hist3h2a are clearly higher than that in the promoter region of Hist1h2aa. The H3 K9 acetylation level in the promoter of Hist1h2aa is similar to that in the gamma-satellite region. CONCLUSION: These results strongly suggest that histone H3 K9 acetylation plays a role in the expression of histone genes.

Acetylation↗
PubMed2005

Naturally occurring antisense RNA of histone H2a in mouse cultured cell lines.

BACKGROUND: An antisense transcript of histone H2a that has no significant protein-coding region has been cloned from a mouse full-length cDNA library. In the present study, we evaluated this transcript by using RT-PCR and compared the expression patterns of the sense and antisense transcripts by using quantitative RT-PCR (qRT-PCR). RESULTS: This antisense RNA was expressed in three mouse cell lines. We call it ASH2a. ASH2a includes not only the complementary sequence of the transcript of Hist2h2aa2 (a replication-dependent histone H2a gene), but also that of the promoter of Hist2h2aa2. The upstream genomic sequence of the transcription start site of the ASH2a-coding gene (ASH2a) lacks both CCAAT and TATA boxes. This absence suggests that the regulation of ASH2a is different from that of the replication-dependent histone H2a genes. Findings from qRT-PCR indicated that the expression pattern of ASH2a was different from that of Hist2h2aa2. Expression of Hist2h2aa2 peaked at 2 to 4 h during S-phase, but that of ASH2a peaked at 1 h. CONCLUSION: We showed the existence of ASH2a, a histone H2a antisense RNA, in mouse cultured cells. The expression pattern of ASH2a is different from that of the sense RNA.

Animals↗
PubMed2005

A novel replication-independent histone H2a gene in mouse.

BACKGROUND: An uncharacterized histone H2a-coding transcript (E130307C13) has been cloned from a mouse full-length cDNA library. This transcript is encoded on chromosome 6, approximately 4 kb upstream of a histone H4 gene, Hist4h4. The proteins encoded by this transcript and the human H2afj mRNA isoform-2 have the highest amino acid similarity. In this paper, we characterize it from the expression pattern given by quantitative RT-PCR. RESULTS: Quantitative RT-PCR indicated that the gene that encodes E130307C13 (E130307C13) is regulated in a replication-independent manner, and therefore it is H2afj. Certainly, H2afj transcript lacks a stem-loop structure at the 3'-UTR but contains a poly (A) signal. In addition, its promoter region has a different structure from those of the replication-dependent histone H2a genes. CONCLUSION: The bioinformatics imply that E130307C13 is a replication-independent H2a gene. In addition, quantitative RT-PCR analysis shows that it is replication-independent. Thus, it is H2afj, a novel replication-independent H2a gene in mouse.

Animals↗
PubMed2004

Comprehensive search for HNF-1beta-regulated genes in mouse hepatoma cells perturbed by transcription regulatory factor-targeted RNAi.

The identification of genes targeted by a specific transcription regulatory factor (TRF) is essential to our understanding of the regulatory mechanism of gene expression. We constructed a system for the comprehensive identification of genes directly regulated by a TRF. It includes a combination of perturbation of gene expression by RNA interference (RNAi) of the TRF, cDNA microarray analysis, computer searches for the putative TRF recognition sequences, and in vivo and in vitro TRF-DNA binding assays. Endogenous hepatocyte nuclear factor-1beta (HNF-1beta) mRNA was efficiently degraded by transfection of mouse hepatoma cells with short interfering RNAs. Expression profile analysis with 20 K mouse cDNA microarrays detected 243 genes whose expression levels were decreased by >50% upon RNAi of HNF-1beta. The upstream regions of the top 26 downregulated genes were searched for the HNF-1beta consensus recognition sequences leading to the extraction of 13 candidate genes. Finally, TRF-DNA binding assays identified five novel as well as three known HNF-1beta-regulated genes. In combination with quantitative real-time RT-PCR, the present system revealed the existence of a more expanded regulatory network among seven HNF family members, demonstrating its practicability to identify the TRF network as well as genes directly regulated by a specific TRF.

5' Flanking Region↗
PubMed2004

EICO (Expression-based Imprint Candidate Organizer): finding disease-related imprinted genes.

We have developed an integrated database that is specialized for the study of imprinted disease genes. The database contains novel candidate imprinted genes identified by the RIKEN full-length mouse cDNA microarray study, information on validated single nucleotide polymorphisms (SNPs) to confirm imprinting using reciprocal mouse crosses and the predicted physical position of imprinting-related disease loci in the mouse and human genomes. It has two user-friendly search interfaces: the SNP-central view (MuSCAT: MoUse SNP CATalog) and the candidate gene-central view (CITE: Candidate Imprinted Transcripts by Expression). The database, EICO (Expression-based Imprint Candidate Organizer), can be accessed via the World Wide Web (http://fantom2.gsc.riken.jp/EICODB/) and the DAS client software. These data and interfaces facilitate understanding of the mechanism of imprinting in mammalian inherited traits.

Animals↗
PubMed2003

A comprehensive search for HNF-3alpha-regulated genes in mouse hepatoma cells by 60K cDNA microarray and chromatin immunoprecipitation/PCR analysis.

To characterize the regulatory pattern by a specific transcription regulatory factor, we used a combination of expression analysis with the mouse cDNA microarray composed of 60,000 cDNA clones and cross-linking/chromatin immunoprecipitation (X-ChIP) followed by comparative PCR. Overexpression of mouse hepatocyte nuclear factor-3alpha (HNF-3alpha) in a mouse hepatoma cell line resulted in accompanied perturbed expression of more than 1500 genes. Search for HNF-3alpha consensus recognition sequences in the upstream regions of their coding sequences, which were mapped on the mouse genome, enabled us to mine 300 genes as the potential HNF-3alpha-regulated genes and classify 135 annotated ones into several functional categories. Further X-ChIP/PCR analysis demonstrated in vivo binding of HNF-3alpha to the 5(')-flanking sequences of 25 members selected out of these genes. Besides known HNF-3alpha-regulated genes such as albumin and alpha-fetoprotein genes, the genes newly identified as the HNF-3alpha-regulated ones include three encoding CDP-diacylglycerol-inositol 3-phosphatidyltransferase, phosphatidylserine decarboxylase, and phospholipase A2, which are located en suite in the lipid metabolic pathway in liver. The potential usefulness of the present approach to extensive characterization of gene expression framework directed by a specific transcription regulatory factor is discussed.

5' Flanking Region↗
PubMed2003

Systematic expression profiling of the mouse transcriptome using RIKEN cDNA microarrays.

The number of known mRNA transcripts in the mouse has been greatly expanded by the RIKEN Mouse Gene Encyclopedia project. Validation of their reproducible expression in a tissue is an important contribution to the study of functional genomics. In this report, we determine the expression profile of 57,931 clones on 20 mouse tissues using cDNA microarrays. Of these 57,931 clones, 22,928 clones correspond to the FANTOM2 clone set. The set represents 20,234 transcriptional units (TUs) out of 33,409 TUs in the FANTOM2 set. We identified 7206 separate clones that satisfied stringent criteria for tissue-specific expression. Gene Ontology terms were assigned for these 7206 clones, and the proportion of 'molecular function' ontology for each tissue-specific clone was examined. These data will provide insights into the function of each tissue. Tissue-specific gene expression profiles obtained using our cDNA microarrays were also compared with the data extracted from the GNF Expression Atlas based on Affymetrix microarrays. One major outcome of the RIKEN transcriptome analysis is the identification of numerous nonprotein-coding mRNAs. The expression profile was also used to obtain evidence of expression for putative noncoding RNAs. In addition, 1926 clones (70%) of 2768 clones that were categorized as "unknown EST," and 1969 (58%) clones of 3388 clones that were categorized as "unclassifiable" were also shown to be reproducibly expressed.

Animals↗
PubMed2002

Identification of genes regulating colorectal carcinogenesis by using the algorithm for diagnosing malignant state method.

We studied the expression profiles of various stages of colorectal tumors (adenoma (AD), seven samples; carcinoma (CA), 16 samples) by using cDNA microarrays and developed ADMS (algorithm for diagnosing malignant state) method, selecting 335 clones characteristic of CA state. We, then, applied ADMS to 12 additional samples (five from primary lesions with metastasis and seven metastases); all 16 CAs and 12 metastatic tumors were diagnosed correctly as cancerous states. Although three of the seven ADs were diagnosed as "cancerous," the large size of two of these tumors suggested their potential malignancy. Our strategy for selecting clones characteristic of the malignant state is widely applicable to diagnosis and for predicting the stage of progression during multistep carcinogenesis. Of the 335 clones we selected, 135 were known genes. Included in the 135 genes were tumor suppressor and growth factor-related genes and were consistent with the literature. ADMS is a reliable means for identifying genes useful for the diagnosis of cancer.

Adenoma↗
PubMed2002

Asb4, Ata3, and Dcn are novel imprinted genes identified by high-throughput screening using RIKEN cDNA microarray.

Genes differentially expressed between parthenogenetic and androgenetic embryos are candidates for the identification of imprinted genes, which are expressed specifically from the maternal or paternal allele. To search for genes differentially expressed between parthenogenetic and androgenetic embryos, we used the RIKEN full-length enriched mouse cDNA microarray. The 25 candidates obtained included 8 known imprinted genes (such as IgfII, Snrpn, and Neuronatin) and 3 new ones--Asb4 (ankyrin repeat and SOCS box-containing protein 4), Ata3 (amino acid transport system A3), and Decorin--which were confirmed by using normal diploid embryos from the reciprocal F1 crosses of B6 and JF1 mice. The 25 candidates also included genes that showed no imprinting-associated expression in normal diploid embryos. We describe a feasible high-throughput method of screening for novel imprinted genes by using the RIKEN cDNA microarray.

Amino Acid Transport System A↗
PubMed2002

Analysis of gene expression involved in brain metastasis from breast cancer using cDNA microarray.

BACKGROUND: Brain metastases occur in 15% to 30% of breast cancer patients, usually as a late event. The patterns of metastases to different organs are determined by the tumor cell phenotype and interactions between the tumor cells and the organ environment. METHODS: We investigated the gene expression profile occurring in brain metastases from a breast cancer cell line. We used cDNA microarrays to compare patterns of gene expression between the mouse breast cancer cell line Jyg MC (A) and a subline that often metastasis to brain, (B). RESULTS: By Microarray analysis about 350 of 21,000 genes were significantly up-regulated in Jyg MC (B). Many candidate genes that may be associated with the establishment of brain metastasis from breast cancer were included. Interestingly, we found that the expression of astrocyte derived cytokine receptors (IL-6 receptor, TGF-beta receptor and IGF receptor) were significantly increased in Jyg MC (B) cells. These results were confirmed by RT-PCR. CONCLUSIONS: These results suggest that cytokines produced by glial cells in vivo may contribute, in a paracrine manner, to the development of brain metastases from breast cancer cells.

Animals↗
PubMed2002

Identification of seven loci for static glucokinesis and dynamic glucokinesis in mice.

Non-insulin-dependent diabetes mellitus (NIDDM) is characterized by a breakdown of glucose homeostasis and is responsible for serious complications in various organs and vessels. Most of the genetic factors of NIDDM are yet unknown. Here, we identified two types of genetic factors that regulate homeostasis of blood glucose by measuring various pharmacokinetic parameters, some of which are used in the non-compartment analysis of drug metabolism in 340 F(2) progeny from the NIDDM model KK-A(y)/Ta Jcl mouse strain, and in non-diabetic PWK strain. We define "static glucokinesis" as the regulation of homeostasis that occurs during glucose deprivation, and "dynamic glucokinesis" as that during glucose stress; for instance, glucose tolerance test. Quantitative trait locus analysis revealed eight loci involved in the regulation of glucose homeostasis on chromosomes 7 ( Nidd1k), 2 ( Nidd2k), 1 ( Nidd3k, Nidd4k, and Nidd5k), 11 ( Nidd6k), 5 ( Nidd7k) (named Nidd1k through Nidd7k), and 4 ( Bwt1k). Nidd1k, Nidd4k, and Nidd7k were novel loci associated with NIDDM in mice. Nidd1k, Nidd2k, Nidd3k, and Nidd4k had linkage to factors characteristic of both static and dynamic glucokinesis. Nidd5k and Nidd6k showed linkage specific to markers of dynamic glucokinesis, and Nidd7k had linkage specific to static glucokinesis. Bwt1k was linked to obesity. Thus, the genetic factors for static glucokinesis and those for dynamic glucokinesis partially overlapped.

Animals↗
PubMed2002

Mechanism of postoperative liver failure after excessive hepatectomy investigated using a cDNA microarray.

BACKGROUND/PURPOSE: Excessive hepatectomy often causes fatal liver failure. We have reported that this is mainly mediated by apoptosis, characterized pathologically by terminal deoxynucleotidyl transferase-mediated dUTP-biotin nick end labelling (TUNEL) assay-positive hepatocytes and a ladder pattern in DNA fragmentation assays. METHODS: To investigate the mechanism, we used cDNA microarray analysis to compare clearly differentiated rat partial hepatectomy (PHx) models (90% PHx, and 95% PHx). All 90% PHx rats survived, but the 95% PHx animals died of hepatic failure within 96 h. Remnant liver was obtained at four time points (1, 3, 12, and 24 h after PHx). After RNA extraction, two samples were labeled with different fluorescent dyes and hybridized to the Institute of Physical and Chemical Research (RIKEN) set of 18 816 full-length enriched mouse cDNA arrays. Scanning for fluorescent dye signals was performed, and the mRNA expression ratio of the two models was examined. RESULTS: Genes of the p21 cyclin-dependent kinase (CDK) inhibitor, Fas, interleukin (IL)-18, and many caspases were upregulated at 1 h after PHx in the 95% PHx group. On the other hand, genes of Bcl-2, heat shock proteins, and glutathione-S-transferase were downregulated. CONCLUSIONS: We concluded that fatal hepatic failure after excessive hepatectomy was characterized by increased apoptosis and diminished liver regeneration.

Animals↗