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Summary: We constructed a website for inferring a network by applying the graphical Gaussian model, from a large amount of data, including redundant information. The available tools on the website are based on a system, named ASIAN (Automatic System for Inferring A Network), in combination with the two methods in our previous papers, which were designed to analyze gene expression profiles on a genomic scale. One of the remarkable features of the website is its ability to infer a network, concomitant with hierarchical clustering and the following estimation of cluster boundaries. Availability: http://eureka.ims.u-tokyo.ac.jp/asian

We have characterized the genomic structure and expression of the mouse gene for Pur-1. The cloned Pur-1 gene spans a 5-kb region encompassing the promoter, five exons, four introns and the 3'-untranslated region. All exon-intron junction sequences conform to the GT/AG rule. The promoter region has typical features of a housekeeping gene: a high G + C content (77.5%); a high frequency of CpG dinucleotides, in particular within the region 0.5 kb upstream of the site of initiation of translation; and the absence of canonical TATA and CAAT boxes. S1 nuclease protection assay demonstrated the presence of multiple sites for initiation of transcription around a site 108 nucleotides upstream of the ATG codon. Comparison of Pur-1 with the human gene for MAZ (Myc-associated zinc finger protein) revealed a striking homology of both their nucleotide and deduced protein sequences, an identical genomic organization and high similarity in promoter architecture and mRNA expression pattern. Sequence analysis of the 5'-flanking region of Pur-1 revealed numerous potential binding sites for transcription factors Sp1, AP-2 and Pur-1/MAZ itself. An element required for basal Pur-1 expression was mapped from nucleotide -258 to +43. This region also mediated stimulation of basal transcription by ectopically expressed MAZ protein. We conclude that the Pur-1 gene is the murine homolog of human MAZ and, like it, belongs to the family of housekeeping genes.

KNSL4 (Kid; kinesin-like DNA-binding protein) is a member of the kinesin family that is involved in spindle formation and the movements of chromosomes during mitosis and meiosis. Myc-associated zinc finger protein (MAZ) participates in both the initiation and the termination of transcription of target genes. We isolated genomic DNA clones that encoded KNSL4 and MAZ from a human cosmid library. Sequence analysis revealed that the two genes were very close to one another. The distance between the two genes was only 1.2 kb, and this intervening 1.2-kb region was extremely GC-rich. The gene for KNSL4 spanned 16 kb and consisted of 14 exons and 13 introns, while the gene for MAZ spanned 6 kb and consisted of 5 exons and 4 introns. The two genes were mapped to chromosome 16p11.2 by fluorescence in situ hybridization.

We have cloned and characterized the genomic structure of the human gene for Myc-associated zinc finger protein (MAZ), which is located on chromosome 16p11.2. This gene is transcribed as an mRNA of 2.7 kilobases (kb) that encodes a 60-kDa MAZ protein. A 40-kb cosmid clone was isolated that includes the promoter, five exons, four introns, and one 3'-untranslated region. All exon-intron junction sequences conform to the GT/AG rule. The promoter region has features typical of a housekeeping gene: a high G + C content (88. 4%); a high frequency of CpG dinucleotides, in particular within the region 0.5 kb upstream of the site of initiation of translation; and the absence of canonical TATA and CAAT boxes. An S1 nuclease protection assay demonstrated the presence of multiple sites for initiation of transcription around a site 174 nucleotides (nt) upstream of the ATG codon and such expression was reflected by the promoter activity of a MAZ promoter/CAT (chloramphenicol acetyltransferase) reporter gene. Cis-acting positive and negative elements controlling basal transcription of the human MAZ gene were found from nucleotides (nt) -383 to -248 and nt -2500 to -948. Moreover, positive and negative autoregulatory elements were also identified in the regions from nt -248 to -189 and from nt -383 to -248 after co-transfection of HeLa cells with plasmids that carried the MAZ promoter/CAT construct and the MAZ-expression vector. Our results indicate that the 5'-end flanking sequences are responsible for the promoter activities of the MAZ gene.

The transcription factor KBF2 has been characterized as a factor that binds to the NFkB site of mouse major histocompatibility complex (MHC) class I genes and its amino acid sequence has been shwn to be identical to those of members of the recombination signal-sequence binding protein (RBP-Jk) family. Previous studies by Amakawa et al. (Genomics 17, 306-315, 1993) demonstrated that the functional gene is localized at human chromosome 3q25. However, in the present study we showed by in situ hybridization with the functional KBF2/RBPJk cosmid clone that the gene is localized at 9p12-13 and 9q13, namely, at the same loci as pseudogenes that were reported previously (Zhang et al, Jpn J Human Genet 39, 391-401, 1994).

Various types of repeat sequences are abundant in genomic sequences, and they are associated with the biological phenomena at distinct levels. In particular, comparative analyses of whole-genome-sized sequence data have revealed that repeat sequences cause segmental duplications, which are a type of chromosomal structural arrangement. In this study, we analyzed the relationships between segmental duplications and repeat sequences in human chromosome 7. For this purpose, three methods for detecting repeat sequences were applied to the genomic sequences of human chromosome 7: RepeatMasker for the dispersed repeats, TRF for the tandem repeats, and STEPSTONE for the inter-spread repeats. By plotting the detected repeat sequences against the locations on the chromosome, all three types of repeats were found to be concentrated around the regions of segmental duplications, as a macroscopic feature of their distributions. Furthermore, the latter two repeat sequences were classified in terms of their periods, and the distribution bias of the detected repeat sequences was statistically tested between the segmental duplication regions and the other regions. As a result, the periods of two repeats were biased, with less than a 5% level of significance probability by the chi(2) test, and the repeats with long periods, about 130bp and more than 400bp, were attributed to a bias with a 5% level of significance probability by the normalized residual test. The mechanism of segmental duplications is discussed based on the present results.

Three possible causes responsible for the large genome size of a cyanobacterium Anabaena sp. PCC7120 are investigated: 1) sequential tandem duplications of gene segments, genes or genomic segments, 2) horizontal gene transfers from other organisms, and 3) whole-genome duplication. We evaluated the frequency distribution of angles between paralog locations for the possibility 1), the fraction of genes deviated in GC content, GC skew, AT skew and codon adaptation index for the 2) and the gene-configuration comparison of paralogs for the 3). As a result, the possibility 3), the whole-genome duplication, was more reasonable as a molecular cause than the other causes for the large genome size in Anabaena sp. PCC7120. In addition, the whole-genome duplication was supported by the analysis of distribution pattern of protein genes with respect to functional categories.

Various types of periodic patterns in nucleotide sequences are known to be very abundant in a genomic DNA sequence, and to play important biological roles such as gene expression, genome structural stabilization, and recombination. We present a new method, named "STEPSTONE", to find a specific periodic pattern of repeat sequence, inter-spread repeat, in which the tandem repeats of the conserved and the not-conserved regions appear periodically. In our method, at first, the data on periods of short repeat sequences found in a target sequence are stored as a hash data, and then are selected by application of an auto-correlation test in time series analysis. Among the statistically selected sequences, the inter-spread repeats are obtained by usual alignment procedures through two steps. To test the performance of our method, we examined the inter-spread repeats in Mycobacterium tuberculosis and Zamia paucijuga genomic sequences. As a result, our method exactly detected the repeats in the two sequences, being useful for identifying systematically the inter-spread repeats in DNA sequence.