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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The inositol 1,4,5-trisphosphate receptor (IP3R) exists as a tetrameric complex to form a functional inositol 1,4,5-trisphosphate-gated Ca2+ channel. Molecular cloning studies have shown that there are at least three types of IP3R subunits, designated type 1, type 2, and type 3. The levels of expression of IP3R subunits in various cell lines were investigated by Western blot analysis using type-specific antibodies against 15 C-terminal amino acids of each IP3R subunit. We found that all the three types of IP3R subunits were expressed in each cell line examined, but their levels of expression varied. To determine whether IP3Rs form heterotetramers, we employed immunoprecipitation experiments using Chinese hamster ovary cells (CHO-K1 cells), in which all three types are abundantly expressed. Each type-specific antibody immunoprecipitated not only the respective cognate type but also the other two types. This result suggests that distinct types of IP3R subunits assemble to form heterotetramers in CHO-K1 cells. We also detected heterotetramers in rat liver, in which IP3R type 1 and type 2 are expressed abundantly. Previous studies have shown some functional differences among IP3R types, suggesting the possibility that various compositions of subunits show distinct channel properties. The diversity of IP3R channels may be further increased by the co-assembly of different IP3R subunits to form homo- or heterotetramers.

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Monoclonal antibodies were raised that specifically recognize the COOH-terminal sequences and the loop sequences between the fifth and the sixth transmembrane spanning regions of human inositol1,4,5-trisphosphate receptor (IP,R) type 1,2 and 3. Western blot analysis using Jurkat cells, mouse cerebellum, COS-7 expressing IP,R type 3 cDNA showed that those monoclonal antibodies reacted specifically with each of these three IP,R subtypes and that they do not cross-react. These antibodies could be used for the specific immunoprecipitation of IP,Rs. Using these monoclonal antibodies, the expression profiles of IP,R-subtype proteins were found to be different among inflammatory cells such as macrophages, polymorphonuclear cells, mast cells, eosinophils, splenocytes, thymocytes and megakaryocytic cells. Usually, more than one type of IP,R were expressed in a cell simultaneously. The observation of CMK cells under immunofluorescence confocal microscopy revealed that IP,R type 1 and type 2 are located at different subcellular fractions.

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Inositol I ,4,Qrisphosphate (IP,)-mediated Ca2+ signaling plays important roles in cellular responses to extracellular stimuli. We recently succeeded in cloning human counterparts of the three subtypes derived from separate genes. Using the cDNA sequences type-specific to these subtype receptors, we here analyzed the expression profile of IP,R subtypes in stimulated and unstimulated human hematopoietic cell lines representing T cells, B cells, neutrophils, macrophages, erythrocytes and megakaryocytes. Northern and dot blot analysis showed that each IP,R subtype is expressed differently in these cells and that the expression profile in each cell is dynamically changed upon stimuli which induce differentiation. Moreover, most of these cells were found to simultaneously express at least two different subtype receptors.