ArticleProceedings of the National Academy of Sciences of the United States of America2006
Genomic fossils as a snapshot of the human transcriptome.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Complex Analysis of Retroposed Genes' Contribution to Human Genome, Proteome and Transcriptome.Genes · 2020Article
- The Genomic Impact of Gene Retrocopies: What Have We Learned from Comparative Genomics, Population Genomics, and Transcriptomic Analyses?Genome biology and evolution · 2017Article
- The life history of retrocopies illuminates the evolution of new mammalian genes.Genome research · 2016Article
- AnABlast: a new in silico strategy for the genome-wide search of novel genes and fossil regions.DNA research : an international journal for rapid publication of reports on genes and genomes · 2015Article
- The serine/threonine kinase 33 is present and expressed in palaeognath birds but has become a unitary pseudogene in neognaths about 100 million years ago.BMC genomics · 2015Article
- Why so many unknown genes? Partitioning orphans from a representative transcriptome of the lone star tick Amblyomma americanum.BMC genomics · 2013Article
- Follow the leader: preference for specific amino acids directly following the initial methionine in proteins of different organisms.Genomics, proteomics & bioinformatics · 2010Article
- Processed pseudogenes: the 'fossilized footprints' of past gene expression.Trends in genetics : TIG · 2009Article
- CNVVdb: a database of copy number variations across vertebrate genomes.Bioinformatics (Oxford, England) · 2009Article
- RNA-based gene duplication: mechanistic and evolutionary insights.Nature reviews. Genetics · 2009Review
- Identification and analysis of ancestral hominoid transcriptome inferred from cross-species transcript and processed pseudogene comparisons.Genome research · 2008Article
- Alternative splicing: a missing piece in the puzzle of intron gain.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
- Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution.Genome research · 2007Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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 cDNA sequences are usually no longer transcribed and are considered "dead on arrival." Here we show that PPGs can be used to generate a map of the transcriptome. By analyzing thousands of human PPGs, we were able to discover hundreds of transcript variants so far unidentified. An experimental verification of a subset of these variants by RT-PCR indicates that most of them are still active in the human transcriptome. Furthermore, we demonstrate that PPGs can enable the identification of ancient splice variants that were expressed ancestrally but are now extinct. Our results show that the genome itself carries a "virtual cDNA library" that can readily be used to analyze both present and ancestral transcripts. Our approach can be applied to sequenced metazoan genomes to computationally annotate splicing variation even when expressed sequences are unavailable.
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