  Background: Gene duplication and exonization of intronic transposed elements
are two mechanisms that enhance genomic diversity. We examined whether there is
less selection against exonization of transposed elements in duplicated genes
than in single-copy genes. Results: Genome-wide analysis of exonization of
transposed elements revealed a higher rate of exonization within duplicated
genes relative to single-copy genes. The gene for TIF-IA, an RNA polymerase I
transcription initiation factor, underwent a humanoid-specific triplication,
all three copies of the gene are active transcriptionally, although only one
copy retains the ability to generate the TIF-IA protein. Prior to TIF-IA
triplication, an Alu element was inserted into the first intron. In one of the
non-protein coding copies, this Alu is exonized. We identified a single point
mutation leading to exonization in one of the gene duplicates. When this
mutation was introduced into the TIF-IA coding copy, exonization was activated
and the level of the protein-coding mRNA was reduced substantially. A very low
level of exonization was detected in normal human cells. However, this
exonization was abundant in most leukemia cell lines evaluated, although the
genomic sequence is unchanged in these cancerous cells compared to normal
cells. Conclusion: The definition of the Alu element within the TIF-IA gene as
an exon is restricted to certain types of cancers; the element is not exonized
in normal human cells. These results further our understanding of the delicate
interplay between gene duplication and alternative splicing and of the
molecular evolutionary mechanisms leading to genetic innovations. This implies
the existence of purifying selection against exonization in single copy genes,
with duplicate genes free from such constrains.
