Research

Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes

Suganthi Balasubramanian¹ , Deyou Zheng² , Yuen-Jong Liu¹ , Gang Fang¹ , Adam Frankish³ , Nicholas Carriero⁴ , Rebecca Robilotto⁵ , Philip Cayting¹ and Mark Gerstein^1,4,5

¹  Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA

²  The Saul R Korey Department of Neurology, Albert Einstein College of Medicine, NY 10461, USA

³  Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1HH, UK

⁴  Department of Computer Science, Yale University, New Haven, CT 06520, USA

⁵  Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA

author email corresponding author email

Genome Biology 2009, 10:R2doi:10.1186/gb-2009-10-1-r2

Published:	5 January 2009

Subject areas: Evolution, Genome studies, Molecular biology

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.