Diverse splicing patterns of exonized Alu elements in human tissues
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abstract
Exonization of Alu elements is a major mechanism for birth of new exons in primate genomes. Prior analyses of expressed sequence tags show that almost all Aluderived exons are alternatively spliced, and the vast majority of these exons have low transcript inclusion levels. In this work, we provide genomic and experimental evidence for diverse splicing patterns of exonized Alu elements in human tissues. Using Exon array data of 330 Aluderived exons in 11 human tissues, and detailed RTPCR analyses of 38 exons, we show that some Aluderived exons are constitutively spliced in a broad range of human tissues, and some display strong tissuespecific switch in their transcript inclusion levels. Most of such exons are derived from ancient Alu elements in the genome. In SEPN1, mutations of which are linked to a form of congenital muscular dystrophy, the musclespecific inclusion of an Aluderived exon may be important for regulating SEPN1 activity in muscle. Realtime qPCR analysis of this SEPN1 exon in macaque and chimpanzee tissues indicates humanspecific increase in its transcript inclusion level and musclespecificity after the divergence of humans and chimpanzees. Our results imply that some Alu exonization events may have acquired adaptive benefits during the evolution of primate transcriptomes.Supported by the Hereditary Disease Foundation (to YX and BLD) and Roy J. Carver Trust (to BLD).
