Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes.
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.
Balasubramanian
Suganthi
S
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA. suganthi.bala@yale.edu
Zheng
Deyou
D
Liu
Yuen-Jong
YJ
Fang
Gang
G
Frankish
Adam
A
Carriero
Nicholas
N
Robilotto
Rebecca
R
Cayting
Philip
P
Gerstein
Mark
M
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
D012333:RNA, Messenger; D018626:Retroelements; D012269:Ribosomal Proteins