title: 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.
authors.affiliation: Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, USA.
authors.forename: Zhaolei
authors.initials: Z
authors.lastname: Zhang
authors.forename: Paul M
authors.initials: PM
authors.lastname: Harrison
authors.forename: Yin
authors.initials: Y
authors.lastname: Liu
authors.forename: Mark
authors.initials: M
authors.lastname: Gerstein
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic; D019143:Evolution, Molecular; D015894:Genome, Human; D006801:Humans; D020407:Internet; D032085:Isochores / Q000235:genetics; D051379:Mice; D011506:Proteins / Q000235:genetics; D011544:Pseudogenes / Q000235:genetics*; D012323:RNA Processing, Post-Transcriptional; D017422:Sequence Analysis, DNA / Q000379:methods
chemical_list: D032085:Isochores; D011506:Proteins