Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome
- PMID: 14656962
- PMCID: PMC403796
- DOI: 10.1101/gr.1429003
Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome
Abstract
Processed pseudogenes were created by reverse-transcription of mRNAs; they provide snapshots of ancient genes existing millions of years ago in the genome. To find them in the present-day human, we developed a pipeline using features such as intron-absence, frame-disruption, polyadenylation, and truncation. This has enabled us to identify in recent genome drafts approximately 8000 processed pseudogenes (distributed from http://pseudogene.org). Overall, processed pseudogenes are very similar to their closest corresponding human gene, being 94% complete in coding regions, with sequence similarity of 75% for amino acids and 86% for nucleotides. Their chromosomal distribution appears random and dispersed, with the numbers on chromosomes proportional to length, suggesting sustained "bombardment" over evolution. However, it does vary with GC-content: Processed pseudogenes occur mostly in intermediate GC-content regions. This is similar to Alus but contrasts with functional genes and L1-repeats. Pseudogenes, moreover, have age profiles similar to Alus. The number of pseudogenes associated with a given gene follows a power-law relationship, with a few genes giving rise to many pseudogenes and most giving rise to few. The prevalence of processed pseudogenes agrees well with germ-line gene expression. Highly expressed ribosomal proteins account for approximately 20% of the total. Other notables include cyclophilin-A, keratin, GAPDH, and cytochrome c.
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WEB SITE REFERENCES
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- http://bioinfo.mbb.yale.edu/genome/pseudogene; pseudogene database.
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- http://www.ebi.ac.uk/GOA/; GO annotation of SWISS-PROT/TrEmbl proteins.
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- http://www.ebi.ac.uk/proteome; EBI nonredundant human proteome.
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- http://www.ebi.ac.uk/swissprot/; SWISS-PROT human protein sequences.
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- http://www.ebi.ac.uk/trembl/; TrEMBL human protein sequences.
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