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Topical Review |
1 Sector of Neurobiology, International School for Advanced Studies (ISAS)-SISSA, AREA Science Park, SS 14, Km 163,5, Basovizza, 34012 Trieste, Italy
2 The Giovanni Armenise-Harvard Foundation Laboratory, ISAS-SISSA, AREA Science Park, SS 14, Km 163,5, Basovizza, 34012 Trieste, Italy
3 Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
4 Genome Science Laboratory, Discovery and Research Institute, RIKEN Wako Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
A comprehensive understanding of protein and regulatory networks is strictly dependent on the complete description of the transcriptome of cells. After the determination of the genome sequence of several mammalian species, gene identification is based on in silico predictions followed by evidence of transcription. Conservative estimates suggest that there are about 20 000 protein-encoding genes in the mammalian genome. In the last few years the combination of full-length cDNA cloning, cap-analysis gene expression (CAGE) tag sequencing and tiling arrays experiments have unveiled unexpected additional complexities in the transcriptome. Here we describe the current view of the mammalian transcriptome focusing on transcripts diversity, the growing non-coding RNA world, the organization of transcriptional units in the genome and promoter structures. In-depth analysis of the brain transcriptome has been challenging due to the cellular complexity of this organ. Here we present a computational analysis of CAGE data from different regions of the central nervous system, suggesting distinctive mechanisms of brain-specific transcription.
(Received 19 June 2006;
accepted after revision 13 July 2006;
first published online 20 July 2006)
P. Carninci: Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center, (GSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan. Email: carninci{at}riken.jp
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