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Diverse splicing patterns of exonized Alu elements in human tissues.

Lin L, Shen S, Tye A, Cai JJ, Jiang P, Davidson BL, Xing Y - PLoS Genet. (2008)

Bottom Line: Most of such exons are derived from ancient Alu elements in the genome.Realtime qPCR analysis of this SEPN1 exon in macaque and chimpanzee tissues indicates human-specific increase in its transcript inclusion level and muscle specificity 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Internal Medicine, University of Iowa, Iowa City, Iowa, USA.

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 Alu-derived 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 Alu-derived exons in 11 human tissues and detailed RT-PCR analyses of 38 exons, we show that some Alu-derived exons are constitutively spliced in a broad range of human tissues, and some display strong tissue-specific 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 muscle-specific inclusion of an Alu-derived exon may be important for regulating SEPN1 activity in muscle. Realtime qPCR analysis of this SEPN1 exon in macaque and chimpanzee tissues indicates human-specific increase in its transcript inclusion level and muscle specificity 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.

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Related in: MedlinePlus

Evolution of SEPN1 Alu-exon splicing in primates.A. The splicing pattern of SEPN1 Alu-derived exon. B. RT-PCR analysis of the SEPN1 Alu-derived exon in human, chimpanzee and macaque tissues. The RT-PCR primer was designed from the upstream and downstream constitutive exon on the human gene and matched perfectly to chimpanzee and macaque transcripts. C. Realtime qPCR primers that specifically amplify exon inclusion and skipping forms. The reverse PCR primer for the skipping form was designed from the junction of upstream and downstream constitutive exons. These PCR primers perfectly matched both human and chimpanzee transcripts. D. The ratio of exon inclusion/skipping in human tissues and tissues of two chimpanzees estimated by realtime qPCR. The SEPN1 exon showed strong exon inclusion in human muscle but not in chimpanzee muscle. C, cerebellum; K, kidney; L, liver; M, muscle.
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pgen-1000225-g003: Evolution of SEPN1 Alu-exon splicing in primates.A. The splicing pattern of SEPN1 Alu-derived exon. B. RT-PCR analysis of the SEPN1 Alu-derived exon in human, chimpanzee and macaque tissues. The RT-PCR primer was designed from the upstream and downstream constitutive exon on the human gene and matched perfectly to chimpanzee and macaque transcripts. C. Realtime qPCR primers that specifically amplify exon inclusion and skipping forms. The reverse PCR primer for the skipping form was designed from the junction of upstream and downstream constitutive exons. These PCR primers perfectly matched both human and chimpanzee transcripts. D. The ratio of exon inclusion/skipping in human tissues and tissues of two chimpanzees estimated by realtime qPCR. The SEPN1 exon showed strong exon inclusion in human muscle but not in chimpanzee muscle. C, cerebellum; K, kidney; L, liver; M, muscle.

Mentions: To further elucidate the evolution of this muscle-specific Alu exon in SEPN1, we obtained matching macaque and chimpanzee tissues and analyzed the splicing pattern of this exon in primate tissues using semi-quantitative RT-PCR as well as realtime quantitative PCR (see Materials and Methods). RT-PCR analysis of this exon in macaque tissues showed no exon inclusion (see Figure 3B), consistent with the fact that this Alu exon was absent from the corresponding SEPN1 region in the rhesus macaque genome. In chimpanzees, both exon inclusion and skipping forms were produced, but the exon inclusion levels were significantly lower compared to human tissues based on the RT-PCR gel pictures (Figure 3B). The splicing difference of this SEPN1 exon between humans and chimpanzees was further confirmed by realtime qPCR using isoform-specific primers (Figure 3C–D). These data depict the evolutionary history during the creation of an Alu-derived primate-specific exon and the establishment of its tissue-specific splicing pattern. Our results suggest that the strong transcript inclusion and muscle-specificity of the human SEPN1 exon was acquired after the divergence of humans and chimpanzees.


Diverse splicing patterns of exonized Alu elements in human tissues.

Lin L, Shen S, Tye A, Cai JJ, Jiang P, Davidson BL, Xing Y - PLoS Genet. (2008)

Evolution of SEPN1 Alu-exon splicing in primates.A. The splicing pattern of SEPN1 Alu-derived exon. B. RT-PCR analysis of the SEPN1 Alu-derived exon in human, chimpanzee and macaque tissues. The RT-PCR primer was designed from the upstream and downstream constitutive exon on the human gene and matched perfectly to chimpanzee and macaque transcripts. C. Realtime qPCR primers that specifically amplify exon inclusion and skipping forms. The reverse PCR primer for the skipping form was designed from the junction of upstream and downstream constitutive exons. These PCR primers perfectly matched both human and chimpanzee transcripts. D. The ratio of exon inclusion/skipping in human tissues and tissues of two chimpanzees estimated by realtime qPCR. The SEPN1 exon showed strong exon inclusion in human muscle but not in chimpanzee muscle. C, cerebellum; K, kidney; L, liver; M, muscle.
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Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2562518&req=5

pgen-1000225-g003: Evolution of SEPN1 Alu-exon splicing in primates.A. The splicing pattern of SEPN1 Alu-derived exon. B. RT-PCR analysis of the SEPN1 Alu-derived exon in human, chimpanzee and macaque tissues. The RT-PCR primer was designed from the upstream and downstream constitutive exon on the human gene and matched perfectly to chimpanzee and macaque transcripts. C. Realtime qPCR primers that specifically amplify exon inclusion and skipping forms. The reverse PCR primer for the skipping form was designed from the junction of upstream and downstream constitutive exons. These PCR primers perfectly matched both human and chimpanzee transcripts. D. The ratio of exon inclusion/skipping in human tissues and tissues of two chimpanzees estimated by realtime qPCR. The SEPN1 exon showed strong exon inclusion in human muscle but not in chimpanzee muscle. C, cerebellum; K, kidney; L, liver; M, muscle.
Mentions: To further elucidate the evolution of this muscle-specific Alu exon in SEPN1, we obtained matching macaque and chimpanzee tissues and analyzed the splicing pattern of this exon in primate tissues using semi-quantitative RT-PCR as well as realtime quantitative PCR (see Materials and Methods). RT-PCR analysis of this exon in macaque tissues showed no exon inclusion (see Figure 3B), consistent with the fact that this Alu exon was absent from the corresponding SEPN1 region in the rhesus macaque genome. In chimpanzees, both exon inclusion and skipping forms were produced, but the exon inclusion levels were significantly lower compared to human tissues based on the RT-PCR gel pictures (Figure 3B). The splicing difference of this SEPN1 exon between humans and chimpanzees was further confirmed by realtime qPCR using isoform-specific primers (Figure 3C–D). These data depict the evolutionary history during the creation of an Alu-derived primate-specific exon and the establishment of its tissue-specific splicing pattern. Our results suggest that the strong transcript inclusion and muscle-specificity of the human SEPN1 exon was acquired after the divergence of humans and chimpanzees.

Bottom Line: Most of such exons are derived from ancient Alu elements in the genome.Realtime qPCR analysis of this SEPN1 exon in macaque and chimpanzee tissues indicates human-specific increase in its transcript inclusion level and muscle specificity 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Internal Medicine, University of Iowa, Iowa City, Iowa, USA.

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 Alu-derived 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 Alu-derived exons in 11 human tissues and detailed RT-PCR analyses of 38 exons, we show that some Alu-derived exons are constitutively spliced in a broad range of human tissues, and some display strong tissue-specific 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 muscle-specific inclusion of an Alu-derived exon may be important for regulating SEPN1 activity in muscle. Realtime qPCR analysis of this SEPN1 exon in macaque and chimpanzee tissues indicates human-specific increase in its transcript inclusion level and muscle specificity 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.

Show MeSH
Related in: MedlinePlus