Genomic fossils as a snapshot of the human transcriptome

• DOI: 10.1073/pnas.0509330103
• Publication Date: 2006-01-24T01:53:41Z
• Authors: Ronen Shemesh; Amit Novik; Sarit Edelheit; Rotem Sorek
• Keywords: Pseudogene; Snapshot (computer storage)

Processed pseudogenes (PPGs) are cDNA sequences that were generated through reverse transcription of mature, spliced mRNAs and have subsequently been reinserted at a new genomic location. These usually no longer transcribed considered "dead on arrival." Here we show PPGs can be used to generate map the transcriptome. By analyzing thousands human PPGs, able discover hundreds transcript variants so far unidentified. An experimental verification subset these by RT-PCR indicates most them still active in Furthermore, demonstrate enable identification ancient splice expressed ancestrally but now extinct. Our results genome itself carries "virtual library" readily analyze both present ancestral transcripts. approach applied sequenced metazoan genomes computationally annotate splicing variation even when unavailable.