Biomedical subjects

Hidenori Kiyosawa

Publications and source records attributed to Hidenori Kiyosawa.

5 recordsLinked to original sources

PubMed2005

Disclosing hidden transcripts: mouse natural sense-antisense transcripts tend to be poly(A) negative and nuclear localized.

Genome-wide in silico analysis identified thousands of natural sense-antisense transcript (SAT) pairs in the mouse transcriptome. We investigated their expression using strand-specific oligo-microarray that distinguishes expression of sense and antisense RNA from 1947 SAT pairs. The majority of the predicted SATs are expressed at various steady-state levels in various tissues, and cluster analysis of the array data demonstrated that the ratio of sense and antisense expression for some of the SATs fluctuated markedly among these tissues, while the rest was unchanged. Surprisingly, further analyses indicated that vast amounts of multiple-sized transcripts are expressed from the SAT loci, which tended to be poly(A) negative, and nuclear localized. The tendency that the SATs are often not polyadenylated is conserved, even in the randomly chosen SAT genes in the plant Arabidopsis thaliana. Such common characteristics imply general roles of the SATs in regulation of gene expression.

Animals↗

PubMed2003

Antisense transcripts with FANTOM2 clone set and their implications for gene regulation.

We have used the FANTOM2 mouse cDNA set (60,770 clones), public mRNA data, and mouse genome sequence data to identify 2481 pairs of sense-antisense transcripts and 899 further pairs of nonantisense bidirectional transcription based upon genomic mapping. The analysis greatly expands the number of known examples of sense-antisense transcript and nonantisense bidirectional transcription pairs in mammals. The FANTOM2 cDNA set appears to contain substantially large numbers of noncoding transcripts suitable for antisense transcript analysis. The average proportion of loci encoding sense-antisense transcript and nonantisense bidirectional transcription pairs on autosomes was 15.1 and 5.4%, respectively. Those on the X chromosome were 6.3 and 4.2%, respectively. Sense-antisense transcript pairs, rather than nonantisense bidirectional transcription pairs, may be less prevalent on the X chromosome, possibly due to X chromosome inactivation. Sense and antisense transcripts tended to be isolated from the same libraries, where nonantisense bidirectional transcription pairs were not apparently coregulated. The existence of large numbers of natural antisense transcripts implies that the regulation of gene expression by antisense transcripts is more common that previously recognized. The viewer showing mapping patterns of sense-antisense transcript pairs and nonantisense bidirectional transcription pairs on the genome and other related statistical data is available on our Web site.

Animals↗

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

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

Mapping of 19032 mouse cDNAs on mouse chromosomes.

Finding genes by the positional candidate approach requires abundant cDNAs mapped to chromosomes. To provide such important information, we computationally mapped 19032 of our mouse cDNAs to mouse chromosomes by using data from public databases. We used 2 approaches. In the first, we integrated the mapping data of cDNAs on the human genome, known gene-related data, and comparative mapping data. From this, we calculated map positions on the mouse chromosomes. For this first approach, we developed a simple and powerful criterion to choose the correct map position from candidate positions in sequence homology searches. In the second approach, we related cDNAs to expressed sequence tags (EST) previously mapped in radiation hybrid experiments. We discuss improving the mapping by combining the 2 methods.

Animals↗