As a base for human transcriptome and functional genomics, we created the "full-length long Japan" (FLJ) collection of sequenced human cDNAs. We determined the entire sequence of 21,243 selected clones and found that 14,490 cDNAs (10,897 clusters) were unique to the FLJ collection. About half of them (5,416) seemed to be protein-coding. Of those, 1,999 clusters had not been predicted by computational methods. The distribution of GC content of nonpredicted cDNAs had a peak at ∼58% compared with a peak at ∼42%for predicted cDNAs. Thus, there seems to be a slight bias against GC-rich transcripts in current gene prediction procedures. The rest of the cDNAs unique to the FLJ collection (5,481) contained no obvious open reading frames (ORFs) and thus are candidate noncoding RNAs. About one-fourth of them (1,378) showed a clear pattern of splicing. The distribution of GC content of noncoding cDNAs was narrow and had a peak at ∼42%, relatively low compared with that of protein-coding cDNAs.

By analyzing 1,780,295 5Ј-end sequences of human full-length cDNAs derived from 164 kinds of oligo-cap cDNA libraries, we identified 269,774 independent positions of transcriptional start sites (TSSs) for 14,628 human RefSeq genes. These TSSs were clustered into 30,964 clusters that were separated from each other by more than 500 bp and thus are very likely to constitute mutually distinct alternative promoters. To our surprise, at least 7674 (52%) human RefSeq genes were subject to regulation by putative alternative promoters (PAPs). On average, there were 3.1 PAPs per gene, with the composition of one CpG-island-containing promoter per 2.6 CpG-less promoters. In 17% of the PAP-containing loci, tissue-specific use of the PAPs was observed. The richest tissue sources of the tissue-specific PAPs were testis and brain. It was also intriguing that the PAP-containing promoters were enriched in the genes encoding signal transduction-related proteins and were rarer in the genes encoding extracellular proteins, possibly reflecting the varied functional requirement for and the restricted expression of those categories of genes, respectively. The patterns of the first exons were highly diverse as well. On average, there were 7.7 different splicing types of first exons per locus partly produced by the PAPs, suggesting that a wide variety of transcripts can be achieved by this mechanism. Our findings suggest that use of alternate promoters and consequent alternative use of first exons should play a pivotal role in generating the complexity required for the highly elaborated molecular systems in humans.[Supplemental material is available online at www.genome.org. The sequence data from this study have been submitted to DDBJ under accession nos. DA000001-DA999999, DB000001-DB294747, DB294748-DB384947, BP192706-BP383670, AU279383-AU280837, and AU116788-U160826.]One of the most striking findings revealed by the Human Genome Project is that the human genome contains only 20,000-25,000 kinds of protein-coding genes (International Human Genome Sequencing Consortium 2004). This number is unexpectedly small compared with the total gene numbers in yeast, fly, and worm genomes, which are estimated to be 6,000, 14,000, and 19,000, respectively (Goffeau et al. 1996;C. elegans Sequencing Consortium 1998;Adams et al. 2000). It is supposed that there must be other factors in addition to mere gene numbers to satisfy the prerequisites that enable the human genome to fabricate such highly elaborated systems as the brain and immune systems. To explain this, it has been hypothesized that multifaceted use of the genes should play a pivotal role in functional

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A novel reagent, FTY720 (2-amino-2-[2-(4-octylphenyl)ethyl]-1,3-propanediol hydrochloride), has been shown to induce a significant decrease of lymphocytes and lymphoma cells and is expected to be a potent immunosuppressant and anti-tumor drug. The decrease in lymphocytes and lymphoma cells is mainly the result of FTY720-induced apoptosis. FTY720 directly affects mitochondria and induces cell death. Moreover, FTY720 activates protein phosphatase (PP) 2A and affects anti-apoptotic intracellular signal transduction proteins to attenuate the anti-apoptotic effect. In this study, we examined the relationship between FTY720-induced apoptosis and cell cycle regulation. FTY720 induced apoptosis significantly at the G0/G1 phase and caused G0/G1 cell cycle arrest of the human lymphoma cell lines HL-60RG and Jurkat. Simultaneously, retinoblastoma protein (pRB) was dephosphorylated, suggesting that dephosphorylation of pRB was related to FTY720-induced G0/G1 cell cycle arrest. Because this dephosphorylation was completely blocked by a specific PP1/ 2A inhibitor, okadaic acid, it appears that FTY720-activated PP2A is essential for FTY720-induced cell cycle arrest. FTY720-induced apoptosis was inhibited by Bcl-2 overexpression in Jurkat cells, but this did not prevent FTY720-induced cell cycle arrest, suggesting that the mechanism of FTY720-induced cell cycle arrest is independent of the mechanism of FTY720-induced apoptosis. These two independent pathways strengthen the effect of FTY720.

Black-pigmented bacteria which produce cytotoxic metabolic end-products and cell membrane-associated proteases have been reported to play an important role in the pathogenesis of periodontal diseases. These bacterial virulence factors can be modified by the environmental conditions including nutrients supplied variously into the oral cavity. Although glucose is one of the most essential nutrients for oral bacteria, the exogenous supply of glucose may be discontinuous and the glucose concentration in a periodontal pocket may be influenced by the depth of the periodontal pocket. Therefore, effects of glucose as an environmental factor on the virulence factors of Prevotella intermedia, Prevotella nigrescens and Porphyromonas in the presence o glucose.,bo t P. intermedia and P. nigrescens markedly decreased the production of cytotoxic end-products including succinate.,isobutyrate,isovalerate and ammonia, although their growth was increased. Furthermore, the proteolytic activities such as immunoglobulin- albumin- and casein-degrading activities of these bacteria were decreased in the presence of glucose. On the other hand, no effect of glucose on the metabolic activity of P gingivalis was observed. These results suggest that pathogenicity of P. intermedia P. nigrescens may be decreased by the presence of glucose.