This study describes comprehensive polling of transcription start and termination sites and analysis of previously unidentified full-length complementary DNAs derived from the mouse genome. We identify the 5' and 3' boundaries of 181,047 transcripts with extensive variation in transcripts arising from alternative promoter usage, splicing, and polyadenylation. There are 16,247 new mouse protein-coding transcripts, including 5154 encoding previously unidentified proteins. Genomic mapping of the transcriptome reveals transcriptional forests, with overlapping transcription on both strands, separated by deserts in which few transcripts are observed. The data provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development.

Only a small proportion of the mouse genome is transcribed into mature messenger RNA transcripts. There is an international collaborative effort to identify all full-length mRNA transcripts from the mouse, and to ensure that each is represented in a physical collection of clones. Here we report the manual annotation of 60,770 full-length mouse complementary DNA sequences. These are clustered into 33,409 'transcriptional units', contributing 90.1% of a newly established mouse transcriptome database. Of these transcriptional units, 4,258 are new protein-coding and 11,665 are new non-coding messages, indicating that non-coding RNA is a major component of the transcriptome. 41% of all transcriptional units showed evidence of alternative splicing. In protein-coding transcripts, 79% of splice variations altered the protein product. Whole-transcriptome analyses resulted in the identification of 2,431 sense-antisense pairs. The present work, completely supported by physical clones, provides the most comprehensive survey of a mammalian transcriptome so far, and is a valuable resource for functional genomics.

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We have previously described our systems for the high-throughput production of antibodies against mouse KIAA proteins and their validation (Proteomics 2004, 4, 1412-1416). Using our "libraries" of antibodies, we established a novel antibody microarray system in which surface plasmon resonance (SPR) technology is utilized for signal detection. Up to 400 real-time antibody-target bindings could be measured simultaneously within a single hour. This rapid detection was achieved by direct readout of the bindings using SPR technology. To evaluate our system, we assessed the reproducibility on crude protein samples and obtained satisfactorily reproducible results, exhibiting correlation values >0.92. Using this SPR-based antibody microarray system, we examined mKIAA protein expression in five different adult mouse tissues and identified the specific tissue expression patterns of several mKIAA proteins.