A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome

TLDR

The human transcriptome’s functional complexity remains incompletely understood. The authors generate a high‑throughput sequence of the human transcriptome from a human embryonic kidney and a B cell line. Shotgun sequencing of transcripts produced randomly distributed reads. RNA‑Seq mapped 50 % of reads to unique genomic loci, 80 % of which overlapped known exons, and revealed that 66 % of the polyadenylated transcriptome aligns to known genes while 34 % to novel regions; it detects 25 % more genes than microarrays and identified 94,241 splice junctions, including 4,096 novel sites, with exon skipping as the most common alternative splicing form.

Abstract

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.