Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome

Genome Res. 2003 Dec;13(12):2541-58. doi: 10.1101/gr.1429003.

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.

Publication types

  • Comparative Study
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Animals
  • Computational Biology / methods
  • Databases, Genetic
  • Evolution, Molecular*
  • Genome, Human*
  • Humans
  • Internet
  • Isochores / genetics
  • Mice
  • Proteins / genetics
  • Pseudogenes / genetics*
  • RNA Processing, Post-Transcriptional
  • Sequence Analysis, DNA / methods

Substances

  • Isochores
  • Proteins