Back to the roots of a new exon - The molecular archaeology of a SP100 splice variant

Retropseudogenes are intronless DNA sequences sharing a high degree of homo logy with the cDNA of their corresponding active genes. They are thought to have originated by reverse transcription of messenger RNA and reintegratio n of the cDNA into the genome. Usually considered a type of evolutionary wa ste, they melt into the background of their surrounding DNA by the loss of similarity to the active gene or disappear from the genome by the accumulat ion of deletions. On the other hand, in this paper we describe the evolutio nary recycling of this genomic waste. Recently, a splice variant of the gen e encoding the nuclear protein SP100 was identified in which the 3' part of the cDNA is replaced by an alternative exon apparently encoding an HMG1-DN A-binding domain. We were able to show that this HMG box is contributed by a new exon arising from an HMG1 retropseudogene that we have molecularly ch aracterized in detail. In addition to being found in human cells, correspon ding fusion transcripts were shown in Pan troglodytes, Gorilla gorilla, and Hylobates lar, but not in Macaca mulatta, Genomic DNA from M. mulatta enab led us to amplify by PCR the 5' part but not the 3' part of the HMG1 retrop seudogene. From our data we thus can date the underlying retrotransposition to more than 35 million years ago. Our findings offer a model as to how ne w exons may evolve during evolution. To our knowledge this is the first exa mple of a retropseudogene becoming part of an active gene in which both par ental parts are well characterized and remain in-frame with their cDNA. (C) 2000 Academic Press.