Identification and experimental validation of splicing regulatory elements in Drosophila melanogaster reveals functionally conserved splicing enhancers in metazoans
RNA sequence elements involved in the regulation of pre-mRNA splicing have previously been identified in vertebrate genomes by computational methods. Here, we apply such approaches to predict splicing regulatory elements in Drosophila melanogaster and compare them with elements previously found in t...
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| Format: | Article |
| Language: | en_US |
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Cold Spring Harbor Laboratory Press
2014
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| Online Access: | http://hdl.handle.net/1721.1/88439 |
| _version_ | 1811085063885946880 |
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| author | Brooks, A. N. Aspden, J. L. Rio, D. C. Brenner, S. E. Podgornaia, Anna Igorevna |
| author2 | Massachusetts Institute of Technology. Computational and Systems Biology Program |
| author_facet | Massachusetts Institute of Technology. Computational and Systems Biology Program Brooks, A. N. Aspden, J. L. Rio, D. C. Brenner, S. E. Podgornaia, Anna Igorevna |
| author_sort | Brooks, A. N. |
| collection | MIT |
| description | RNA sequence elements involved in the regulation of pre-mRNA splicing have previously been identified in vertebrate genomes by computational methods. Here, we apply such approaches to predict splicing regulatory elements in Drosophila melanogaster and compare them with elements previously found in the human, mouse, and pufferfish genomes. We identified 99 putative exonic splicing enhancers (ESEs) and 231 putative intronic splicing enhancers (ISEs) enriched near weak 5′ and 3′ splice sites of constitutively spliced introns, distinguishing between those found near short and long introns. We found that a significant proportion (58%) of fly enhancer sequences were previously reported in at least one of the vertebrates. Furthermore, 20% of putative fly ESEs were previously identified as ESEs in human, mouse, and pufferfish; while only two fly ISEs, CTCTCT and TTATAA, were identified as ISEs in all three vertebrate species. Several putative enhancer sequences are similar to characterized binding-site motifs for Drosophila and mammalian splicing regulators. To provide additional evidence for the function of putative ISEs, we separately identified 298 intronic hexamers significantly enriched within sequences phylogenetically conserved among 15 insect species. We found that 73 putative ISEs were among those enriched in conserved regions of the D. melanogaster genome. The functions of nine enhancer sequences were verified in a heterologous splicing reporter, demonstrating that these sequences are sufficient to enhance splicing in vivo. Taken together, these data identify a set of predicted positive-acting splicing regulatory motifs in the Drosophila genome and reveal regulatory sequences that are present in distant metazoan genomes. |
| first_indexed | 2024-09-23T13:02:21Z |
| format | Article |
| id | mit-1721.1/88439 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T13:02:21Z |
| publishDate | 2014 |
| publisher | Cold Spring Harbor Laboratory Press |
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| spelling | mit-1721.1/884392022-09-28T11:37:57Z Identification and experimental validation of splicing regulatory elements in Drosophila melanogaster reveals functionally conserved splicing enhancers in metazoans Brooks, A. N. Aspden, J. L. Rio, D. C. Brenner, S. E. Podgornaia, Anna Igorevna Massachusetts Institute of Technology. Computational and Systems Biology Program Podgornaia, Anna Igorevna RNA sequence elements involved in the regulation of pre-mRNA splicing have previously been identified in vertebrate genomes by computational methods. Here, we apply such approaches to predict splicing regulatory elements in Drosophila melanogaster and compare them with elements previously found in the human, mouse, and pufferfish genomes. We identified 99 putative exonic splicing enhancers (ESEs) and 231 putative intronic splicing enhancers (ISEs) enriched near weak 5′ and 3′ splice sites of constitutively spliced introns, distinguishing between those found near short and long introns. We found that a significant proportion (58%) of fly enhancer sequences were previously reported in at least one of the vertebrates. Furthermore, 20% of putative fly ESEs were previously identified as ESEs in human, mouse, and pufferfish; while only two fly ISEs, CTCTCT and TTATAA, were identified as ISEs in all three vertebrate species. Several putative enhancer sequences are similar to characterized binding-site motifs for Drosophila and mammalian splicing regulators. To provide additional evidence for the function of putative ISEs, we separately identified 298 intronic hexamers significantly enriched within sequences phylogenetically conserved among 15 insect species. We found that 73 putative ISEs were among those enriched in conserved regions of the D. melanogaster genome. The functions of nine enhancer sequences were verified in a heterologous splicing reporter, demonstrating that these sequences are sufficient to enhance splicing in vivo. Taken together, these data identify a set of predicted positive-acting splicing regulatory motifs in the Drosophila genome and reveal regulatory sequences that are present in distant metazoan genomes. 2014-07-18T14:40:48Z 2014-07-18T14:40:48Z 2011-08 2011-04 Article http://purl.org/eprint/type/JournalArticle 1355-8382 1469-9001 http://hdl.handle.net/1721.1/88439 Brooks, A. N., J. L. Aspden, A. I. Podgornaia, D. C. Rio, and S. E. Brenner. “Identification and Experimental Validation of Splicing Regulatory Elements in Drosophila Melanogaster Reveals Functionally Conserved Splicing Enhancers in Metazoans.” RNA 17, no. 10 (October 1, 2011): 1884–1894. en_US http://dx.doi.org/10.1261/rna.2696311 RNA Article is available under a Creative Commons license; see publisher’s site for details. http://creativecommons.org/ application/pdf Cold Spring Harbor Laboratory Press Cold Spring Harbor Laboratory Press |
| spellingShingle | Brooks, A. N. Aspden, J. L. Rio, D. C. Brenner, S. E. Podgornaia, Anna Igorevna Identification and experimental validation of splicing regulatory elements in Drosophila melanogaster reveals functionally conserved splicing enhancers in metazoans |
| title | Identification and experimental validation of splicing regulatory elements in Drosophila melanogaster reveals functionally conserved splicing enhancers in metazoans |
| title_full | Identification and experimental validation of splicing regulatory elements in Drosophila melanogaster reveals functionally conserved splicing enhancers in metazoans |
| title_fullStr | Identification and experimental validation of splicing regulatory elements in Drosophila melanogaster reveals functionally conserved splicing enhancers in metazoans |
| title_full_unstemmed | Identification and experimental validation of splicing regulatory elements in Drosophila melanogaster reveals functionally conserved splicing enhancers in metazoans |
| title_short | Identification and experimental validation of splicing regulatory elements in Drosophila melanogaster reveals functionally conserved splicing enhancers in metazoans |
| title_sort | identification and experimental validation of splicing regulatory elements in drosophila melanogaster reveals functionally conserved splicing enhancers in metazoans |
| url | http://hdl.handle.net/1721.1/88439 |
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