A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome

The functional complexity of the human transcriptome is not yet fully elucidated. We report a high- throughput sequence of the human transcriptome from a human embryonic kidney and a B cell line. We used shotgun sequencing of transcripts to generate randomly distributed reads. Of these, 50% mapped to unique genomic locations, of which 80% corresponded to known exons. We found that 66% of the polyadenylated transcriptome mapped to known genes and 34% to nonannotated genomic regions. On the basis of known transcripts, RNA- Seq can detect 25% more genes than can microarrays. A global survey of messenger RNA splicing events identified 94,241 splice junctions ( 4096 of which were previously unidentified) and showed that exon skipping is the most prevalent form of alternative splicing.