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Biochemical and Biophysical Research Communications 08/2012; 425(3):556-9. · 2.48 Impact Factor
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Shoko Kawamoto,
Junji Yoshii,
Katsuya Mizuno,
Kouichi Ito,
Yasuhide Miyamoto,
Tadashi Ohnishi,
Ryo Matoba,
Naohiro Hori,
Yuhiko Matsumoto,
Toshiyuki Okumura, [......],
Masahiro Yokoyama,
Atsushi Fukushima,
Teruyoshi Hishiki,
Akihiko Nakaya,
Jun Sese,
Norikazu Monma,
Hitoshi Nikaido,
Shinichi Morishita, Kenichi Matsubara,
Kousaku Okubo
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ABSTRACT: BodyMap is a collection of site-directed 3′ expressed sequence tags (ESTs) (gene signatures, GSs) that contains the transcript compositions of various human tissues and was the first systematic effort to acquire gene expression data. For the construction of BodyMap, cDNA libraries were made, preserving abundance information and histologic resolutions of tissue mRNAs. By sequencing 164,000 randomly selected clones, 88,587 GSs that represent chromosomally coded transcripts have been collected from 51 human organs and tissues. They were clustered into 18,722 independent 3′ termini from transcripts, and more than 3000 of these were not found among ESTs assembled in UniGene (Build 75). Assessment of the prevalence of polyadenylation signals and comparison with GenBank cDNAs indicated that there was no significant contamination by internally primed cDNAs or genomic fragments but that there was a relatively high incidence (12%) of alternative polyadenylation sites. We evaluated the sensitivity and resolution of expression information in BodyMap by in silico Northern hybridization and selection of tissue-specific gene probes. BodyMap is a unique resource for estimation of the absolute abundance of transcripts and selection of gene probes for efficient hybridization-based gene expression profiling. [BodyMap data are available at http://bodymap.ims.u-tokyo.ac.jp.]
Genome Research 12/2000; · 13.61 Impact Factor
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ABSTRACT: Through analyses of HBV DNA integratns in human cellular DNA, we identified three different integrant types, each of which
may reflect the process of primary integrant formation by the viral DNA. The first type, which we call “simple type” consists
of integrants found in some hepatocellular carcinomas (HCC’s). The structure of the viral genome is simple, and part of it
is deleted. The viral cohesive end sequence appears at one of the viral-cellular DNA junctions, and integration has elicited
a microdeletion in the target cellular DNA sequence. This structure suggests viral DNA replication intermediates as substrates
for integration. Judging from its frequency in HCC, this type may represent the most preferred one, if not all, among the
primary integration products. The second type, which we call “complex type” is essentially the same as the first type, except
tht the viral genome structure is complex. We considered the possibility that they may have been produced via the same process,
using preformed complex viral genomes such as “novel form DNA’s” (Rogler and Summers, 1982) as substrates. In cultured fetal
hepatocytes, integration of HBV DNA can occur only a few days after infection. Among such integrants, we found a third type
integrant, having a simple viral genome, but having a larger cellular DNA deletion. We propose that different forms of viral
DNA may be used a ssubstrates in the integration process, and the process is characterized by its eliciting of deletions of
different size in the target cellular DNA. The most preferred substrate may be the one producing the simple type integrants,
and the most frequently occurring deletion in the target DNA may be the microdeletion. The structure of one of the early integrants
is different from any of the above, and its formation seems to have a deleterious effect on the chromosome in which the integration
occurs, and hence to the host cell.
Journal of Gastroenterology 01/1990; 25:23-30. · 4.16 Impact Factor
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ABSTRACT: We have isolated a human cDNA clone representing a novel human gene. The predicted 683-amino-acid protein, designated FPM315, contains nine C2H2-type zinc finger motifs and two regions homologous to the LeR domain, a finger-associated structural domain, and the A element of the Kruppel-associated box (KRAB) domain involved in transcriptional repression. The FPM315 mRNAs were expressed in all human tissues so far examined. A cross-species genomic hybridization indicates that the FPM315 gene is highly conserved among eukaryotes. These data suggest that FPM315 might play an important role in basic cellular processes.
Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression.
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ABSTRACT: An expression profile of active genes in the human liver was obtained by collecting sequences with a 3′-directed cDNA library that faithfully represents composition of the mRNA population. The results show the relative activity of ca. 600 genes in maintaining the hepatocytes and sustaining their liver-specific phenotypes. The most active group of genes are those for the production of plasma proteins, followed by the genes for the synthesis of lipoproteins, protease inhibitors, coagulation factors, and complements. This balance of gene activity was maintained for four independently obtained expression profiles from human livers, including those of adult and fetus. The expression profiling was extended to the liver of adult mouse, used as a model for the molecular etiology of hepatocytes and for examining the effects of drugs. Subtle biological differences between the human and mouse livers are reflected in the global expression profiles of active genes, especially with regard to the synthesis of plasma proteins, lipoproteins and complements. This comparative analysis using expression profiling should find a wide application in comparative biology.
Gene.
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ABSTRACT: Increasing evidence suggests that in addition to storing excess energy as fat, adipose tissue acts as an endocrine organ secreting various factors into the blood stream. Every time a new factor is found in adipose tissue, however, its implication is discussed independently, and a systematic analyses based upon a global view of gene expression of this tissue has not been performed. To describe the function of this tissue in terms of gene expression, and to find new factors, we performed random complementary DNA (cDNA) sequencing using a 3'-directed cDNA library that faithfully represents the composition of the messenger RNA (mRNA). Various well-known but unexpected genes, including those for gelsolin, plasma glutathione peroxidase (GPX-3) and carboxypeptidase E (CPE) were shown to be very active. By comparing the expression profile of active genes in the adipose with those of other tissues and with data in dbEST, we identified seven new genes that are specifically expressed in adipose tissue. Among these, one encoded a protein with collagen-like repeats and a putative secretion signal. These data can be used as new tools for analyses of the physiology of this tissue, as well as the etiology and complications of obesity.
Gene.
