BMC Genomics Research article Assessing the genomic evidence for conserved transcribed pseudogenes under selection Amit N Khachane and Paul M Harrison* BioMed Central Open Access Address: Department of Biology, McGill University, Stewart Biology Building, 1205 Docteur Penfield Ave., Montreal, QC, H3A 1B1 Canada Email: Amit N Khachane - amit.khachane@mcgill.ca; Paul M Harrison* - paul.harrison@mcgill.ca * Corresponding author Published: 15 September 2009 BMC Genomics 2009, 10:435 doi:10.1186/1471-2164-10-435 Received: 11 March 2009 Accepted: 15 September 2009 This article is available from: http://www.biomedcentral.com/1471-2164/10/435 © 2009 Khachane and Harrison; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Transcribed pseudogenes are copies of protein-coding genes that have accumulated indicators of coding-sequence decay (such as frameshifts and premature stop codons), but nonetheless remain transcribed. Recent experimental evidence indicates that transcribed pseudogenes may regulate the expression of homologous genes, through antisense interference, or generation of small interfering RNAs (siRNAs). Here, we assessed the genomic evidence for such transcribed pseudogenes of potential functional importance, in the human genome. The most obvious indicators of such functional importance are significant evidence of conservation and selection pressure. Results: A variety of pseudogene annotations from multiple sources were pooled and filtered to obtain a subset of sequences that have significant mid-sequence disablements (frameshifts and premature stop codons), and that have clear evidence of full-length mRNA transcription. We found 1750 such transcribed pseudogene annotations (TPAs) in the human genome (corresponding to ~11.5% of human pseudogene annotations). We checked for syntenic conservation of TPAs in other mammals (rhesus monkey, mouse, rat, dog and cow). About half of the human TPAs are conserved in rhesus monkey, but strikingly, very few in mouse (~3%). The TPAs conserved in rhesus monkey show evidence of selection pressure (relative to surrounding intergenic DNA) on: (i) their GC content, and (ii) their rate of nucleotide substitution. This is in spite of distributions of Ka/Ks (ratios of non-synonymous to synonymous substitution rates), congruent with a lack of protein-coding ability. Furthermore, we have identified 68 human TPAs that are syntenically conserved in at least two other mammals. Interestingly, we observe three TPA sequences conserved in dog that have intermediate character (i.e., evidence of both protein-coding ability and pseudogenicity), and discuss the implications of this. Conclusion: Through evolutionary analysis, we have identified candidate sequences for functional human transcribed pseudogenes, and have pinpointed 68 strong candidates for further investigation as potentially functional transcribed pseudogenes across multiple mammal species. Background Pseudogenes (derived from protein-coding genes) are gene copies that show signs diagnostic of protein-coding deficiency. Such signs commonly include premature stop codons and coding-sequence frameshifts, or neutral codon substitution patterns [1,2]. Pseudogenes can arise Page 1 of 14 (page number not for citation purposes)