PUBLICATION
Variation in sequence and organization of splicing regulatory elements in vertebrate genes
- Authors
- Yeo, G., Hoon, S., Venkatesh, B., and Burge, C.B.
- ID
- ZDB-PUB-041028-4
- Date
- 2004
- Source
- Proceedings of the National Academy of Sciences of the United States of America 101(44): 15700-15705 (Journal)
- Registered Authors
- Venkatesh, Byrappa
- Keywords
- Fugu, zebrafish, G triplets, exonic splicing enhancers, intronic splicing enhancers
- MeSH Terms
-
- Animals
- Base Sequence
- Conserved Sequence
- DNA/genetics
- Enhancer Elements, Genetic
- Exons
- Genes, Regulator
- Genetic Variation
- Humans
- Introns
- Mice
- Models, Genetic
- RNA Splicing/genetics*
- Species Specificity
- Tetraodontiformes/genetics
- Vertebrates/genetics*
- Zebrafish/genetics
- PubMed
- 15505203 Full text @ Proc. Natl. Acad. Sci. USA
Citation
Yeo, G., Hoon, S., Venkatesh, B., and Burge, C.B. (2004) Variation in sequence and organization of splicing regulatory elements in vertebrate genes. Proceedings of the National Academy of Sciences of the United States of America. 101(44):15700-15705.
Abstract
Although core mechanisms and machinery of premRNA splicing are conserved from yeast to human, the details of intron recognition often differ, even between closely related organisms. For example, genes from the pufferfish Fugu rubripes generally contain one or more introns that are not properly spliced in mouse cells. Exploiting available genome sequence data, a battery of sequence analysis techniques was used to reach several conclusions about the organization and evolution of splicing regulatory elements in vertebrate genes. The classical splice site and putative branch site signals are completely conserved across the vertebrates studied (human, mouse, pufferfish, and zebrafish), and exonic splicing enhancers also appear broadly conserved in vertebrates. However, another class of splicing regulatory elements, the intronic splicing enhancers, appears to differ substantially between mammals and fish, with G triples (GGG) very abundant in mammalian introns but comparatively rare in fish. Conversely, short repeats of AC and GT are predicted to function as intronic splicing enhancers in fish but are not enriched in mammalian introns. Consistent with this pattern, exonic splicing enhancer-binding SR proteins are highly conserved across all vertebrates, whereas heterogeneous nuclear ribonucleoproteins, which bind many intronic sequences, vary in domain structure and even presence/absence between mammals and fish. Exploiting differences in intronic sequence composition, a statistical model was developed to predict the splicing phenotype of Fugu introns in mammalian systems and was used to engineer the spliceability of a Fugu intron in human cells by insertion of specific sequences, thereby rescuing splicing in human cells.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping