title: Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes.
abstract: BACKGROUND
  The availability of genome sequences of numerous organisms allows comparative study of pseudogenes in syntenic regions. Conservation of pseudogenes suggests that they might have a functional role in some instances.
  
  
  RESULTS
  We report the first large-scale comparative analysis of ribosomal protein pseudogenes in four mammalian genomes (human, chimpanzee, mouse and rat). To this end, we have assigned these pseudogenes in the four organisms using an automated pipeline and make the results available online. Each organism has a large number of ribosomal protein pseudogenes (approximately 1,400 to 2,800). The majority of them are processed (generated by retrotransposition). However, we do not see a correlation between the number of pseudogenes associated with a ribosomal protein gene and its mRNA abundance. Analysis of pseudogenes in syntenic regions between species shows that most are conserved between human and chimpanzee, but very few are conserved between primates and rodents. Interestingly, syntenic pseudogenes have a lower rate of nucleotide substitution than their surrounding intergenic DNA. Moreover, evidence from expressed sequence tags indicates that two pseudogenes conserved between human and mouse are transcribed. Detailed analysis shows that one of them, the pseudogene of RPS27, is likely to be a protein-coding gene. This is significant as previous reports indicated there are exactly 80 ribosomal protein genes encoded by the human genome.
  
  
  CONCLUSIONS
  Our analysis indicates that processed ribosomal protein pseudogenes abound in mammalian genomes, but few of these are conserved between primates and rodents. This highlights the large amount of recent retrotranspositional activity in mammals and a relatively larger amount of it in the rodent lineage.
authors.affiliation: Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA. suganthi.bala@yale.edu
authors.forename: Suganthi
authors.initials: S
authors.lastname: Balasubramanian
authors.forename: Deyou
authors.initials: D
authors.lastname: Zheng
authors.forename: Yuen-Jong
authors.initials: YJ
authors.lastname: Liu
authors.forename: Gang
authors.initials: G
authors.lastname: Fang
authors.forename: Adam
authors.initials: A
authors.lastname: Frankish
authors.forename: Nicholas
authors.initials: N
authors.lastname: Carriero
authors.forename: Rebecca
authors.initials: R
authors.lastname: Robilotto
authors.forename: Philip
authors.initials: P
authors.lastname: Cayting
authors.forename: Mark
authors.initials: M
authors.lastname: Gerstein
mesh_terms: D000818:Animals; D020224:Expressed Sequence Tags; D016678:Genome / Q000235:genetics*; D006801:Humans; D020407:Internet; D008322:Mammals / Q000235:genetics; D051379:Mice; D002679:Pan troglodytes; D010802:Phylogeny; D011544:Pseudogenes; D012333:RNA, Messenger / Q000032:analysis; D051381:Rats; D018626:Retroelements / Q000235:genetics; D012269:Ribosomal Proteins / Q000235:genetics*; D026801:Synteny
chemical_list: D012333:RNA, Messenger; D018626:Retroelements; D012269:Ribosomal Proteins