Codon usage tabulated from the international DNA sequence databases.

Codon usage in 87 602 genes has been calculated using the nucleotide sequence data obtained from the GenBank Genetic Sequence Data Bank (Release 90.0; September 1995). The database is called the CUTG Database; the complete form of the database can be obtained by anonymous ftp from DDBJ and a part of the database, which lists the frequency of codon use in each organism, is made searchable through our World Wide Web server.     

Two-dimensional gel electrophoresis to separate large RNA molecules such as messenger RNAs

This paper describes a two-dimensional gel electrophoresis method for separating large RNA molecules such as messenger RNAs. RNAs were at first separated on a polyacrylamide plus agarose composite gel and subjected to a second dimension electrophoresis on a polyacrylamide gel containing urea. This method is illustrated by analyses of poly(A)+ yeast RNAs. About 80 discrete spots were detected on the gel, when RNAs from 1000 to 3500 nucleotides in size were examined.     

Bisulfite sequencing and dinucleotide content analysis of 15 imprinted mouse differentially methylated regions (DMRs): paternally methylated DMRs contain less CpGs than maternally methylated DMRs

Imprinted genes in mammals show monoallelic expression dependent on parental origin and are often associated with differentially methylated regions (DMRs). There are two classes of DMR: primary DMRs acquire gamete-specific methylation in either spermatogenesis or oogenesis and maintain the allelic methylation differences throughout development; secondary DMRs establish differential methylation patterns after fertilization. Targeted disruption of some primary DMRs showed that they dictate the allelic expression of nearby imprinted genes and the establishment of the allelic methylation of secondary DMRs. However, how primary DMRs are recognized by the imprinting machinery is unknown. As a step toward elucidating the sequence features of the primary DMRs, we have determined the extents and boundaries of 15 primary mouse DMRs (including 12 maternally methylated and three paternally methylated DMRs) in 12.5-dpc embryos by bisulfite sequencing. We found that the average size of the DMRs was 3.2 kb and that their average G+C content was 54%. Dinucleotide content analysis of the DMR sequences revealed that, although they are generally CpG rich, the paternally methylated DMRs contain less CpGs than the maternally methylated DMRs. Our findings provide a basis for the further characterization of DMRs.     

Antihypertensive effect of angiotensin I-converting enzyme inhibitory peptides from a sesame protein hydrolysate in spontaneously hypertensive rats

Sesame peptide powder (SPP) exhibited angiotensin I-converting enzyme (ACE) inhibitory activity, and significantly and temporarily decreased the systolic blood pressure (SBP) in spontaneously hypertensive rats (SHRs) by a single administration (1 and 10 mg/kg). Six peptide ACE inhibitors were isolated and identified from SPP. The representative peptides, Leu-Val-Tyr, Leu-Gln-Pro and Leu-Lys-Tyr, could competitively inhibit ACE activity at respective Ki values of 0.92 microM, 0.50 microM, and 0.48 microM. A reconstituted sesame peptide mixture of Leu-Ser-Ala, Leu-Gln-Pro, Leu-Lys-Tyr, Ile-Val-Tyr, Val-Ile-Tyr, Leu-Val-Tyr, and Met-Leu-Pro-Ala-Tyr according to their content ratio in SPP showed a strong antihypertensive effect on SHR at doses of 3.63 and 36.3 microg/kg, which accounted for more than 70% of the corresponding dosage for the SPP-induced hypotensive effect. Repeated oral administration of SPP also lowered both SBP and the aortic ACE activity in SHR. These results demonstrate that SPP would be a beneficial ingredient for preventing and providing therapy against hypertension and its related diseases.     

Replication timing of extremely large genes on human chromosomes 11q and 21q

Many human genes have been mapped precisely in the genome. These genes vary from a few kb to more than 1 Mb in length. Previously, we measured replication timing along the entire lengths of human chromosomes 11q and 21q at the sequence level. In the present study, we used the newest information for human chromosomes 11q and 21q to analyze the replication timing of 30 extremely large genes (>250 kb) in two human cell lines (THP-1 and Jurkat). The timing of replication differed between the 5'- and 3'-ends of each of extremely large genes on 11q and 21q, and the time interval between their replication varied among genes of different lengths. The large genes analyzed here included several tissue-specific genes associated with neural diseases and genes encoding cell adhesion molecules: some of these genes had different patterns of replication timing between the two cell lines. The amyloid precursor protein gene (APP), which is associated with familial Alzheimer's disease (AD1), showed the largest difference in timing of replication between its 5'- and 3'-ends in relation to gene length of all the large genes studied on 11q and 21q. These extremely large genes were concentrated in and around genomic regions in which replication timing switches from early to late on both 11q and 21q. The differences of replication timing between the 5'- and 3'-terminal regions of large genes may be related to the molecular mechanisms that underlie tissue-specific expression.     

Intranuclear arrangement of human chromosome 12 correlates to large-scale replication domains

The intranuclear arrangement of human chromosome 12 in G0(G1) nuclei from human myeloid leukemia HL60 cells was analyzed by multicolor fluorescence in situ hybridization (FISH) using band-specific cosmid clones as probes. Pairs of differently colored cosmids were detected on paraformaldehyde-fixed HL60 nuclei, and their relative positions, internal or peripheral, in individual nuclei were scored. Our results suggest that the intranuclear arrangement of human chromosome 12 is not random. Some chromosomal domains, including the centromere, were located in the periphery of the nucleus, while other domains, including the telomeres, were positioned in the internal areas of the nucleus in G0(G1) cells. Based on the replication banding patterns of metaphase spreads, human chromosome 12 was divided roughly into five large domains. Interestingly, the clones in late replicating domains were preferentially localized in the nuclear periphery, whereas clones in early replicating domains were arranged in the internal areas of the nuclei. The DNA replication timing of each cosmid determined by FISH-based assay did not reflect the replication bands, but an overall profile of the replication timing was relatively correlated with these domains on chromosome 12. These results suggest that the intranuclear arrangement of a human chromosome is correlated with the large-scale replication domains, even before DNA replication. Received: 23 January 1999; in revised form: 6 September 1999 / Accepted: 11 September 1999     

90Y-Labeled Anti-ROBO1 Monoclonal Antibody Exhibits Antitumor Activity against Small Cell Lung Cancer Xenografts

IntroductionROBO1 is a membrane protein that contributes to tumor metastasis and angiogenesis. We previously reported that ⁹⁰Y-labeled anti-ROBO1 monoclonal antibody (⁹⁰Y-anti-ROBO1 IgG) showed an antitumor effect against ROBO1-positive tumors. In this study, we performed a biodistribution study and radioimmunotherapy (RIT) against ROBO1-positive small cell lung cancer (SCLC) models.MethodsFor the biodistribution study, ¹¹¹In-labeled anti-ROBO1 monoclonal antibody (¹¹¹In-anti-ROBO1 IgG) was injected into ROBO1-positive SCLC xenograft mice via the tail vein. To evaluate antitumor effects, an RIT study was performed, and SCLC xenograft mice were treated with ⁹⁰Y-anti-ROBO1 IgG. Tumor volume and body weight were periodically measured throughout the experiments. The tumors and organs of mice were then collected, and a pathological analysis was carried out.ResultsAs a result of the biodistribution study, we observed tumor uptake of ¹¹¹In-anti-ROBO1 IgG. The liver, kidney, spleen, and lung showed comparably high accumulation of ¹¹¹In-labeled anti-ROBO1. In the RIT study, ⁹⁰Y-anti-ROBO1 IgG significantly reduced tumor volume compared with baseline. Pathological analyses of tumors revealed coagulation necrosis and fatal degeneration of tumor cells, significant reduction in the number of Ki-67-positive cells, and an increase in the number of apoptotic cells. A transient reduction of hematopoietic cells was observed in the spleen, sternum, and femur.ConclusionsThese results suggest that RIT with ⁹⁰Y-anti-ROBO1 IgG is a promising treatment for ROBO1-positive SCLC.