Diverse splicing patterns of exonized Alu elements in human tissues.
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...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2008-10-01
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| Series: | PLoS Genetics |
| Online Access: | http://europepmc.org/articles/PMC2562518?pdf=render |
| _version_ | 1818218920311521280 |
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| author | Lan Lin Shihao Shen Anne Tye James J Cai Peng Jiang Beverly L Davidson Yi Xing |
| author_facet | Lan Lin Shihao Shen Anne Tye James J Cai Peng Jiang Beverly L Davidson Yi Xing |
| author_sort | Lan Lin |
| collection | DOAJ |
| description | 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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| format | Article |
| id | doaj.art-3d11edab7e2744f88beaa6c4392bd4e5 |
| institution | Directory Open Access Journal |
| issn | 1553-7390 1553-7404 |
| language | English |
| last_indexed | 2024-12-12T07:31:25Z |
| publishDate | 2008-10-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Genetics |
| spelling | doaj.art-3d11edab7e2744f88beaa6c4392bd4e52022-12-22T00:33:01ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042008-10-01410e100022510.1371/journal.pgen.1000225Diverse splicing patterns of exonized Alu elements in human tissues.Lan LinShihao ShenAnne TyeJames J CaiPeng JiangBeverly L DavidsonYi XingExonization 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.http://europepmc.org/articles/PMC2562518?pdf=render |
| spellingShingle | Lan Lin Shihao Shen Anne Tye James J Cai Peng Jiang Beverly L Davidson Yi Xing Diverse splicing patterns of exonized Alu elements in human tissues. PLoS Genetics |
| title | Diverse splicing patterns of exonized Alu elements in human tissues. |
| title_full | Diverse splicing patterns of exonized Alu elements in human tissues. |
| title_fullStr | Diverse splicing patterns of exonized Alu elements in human tissues. |
| title_full_unstemmed | Diverse splicing patterns of exonized Alu elements in human tissues. |
| title_short | Diverse splicing patterns of exonized Alu elements in human tissues. |
| title_sort | diverse splicing patterns of exonized alu elements in human tissues |
| url | http://europepmc.org/articles/PMC2562518?pdf=render |
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