Discovering structural cis‐regulatory elements by modeling the behaviors of mRNAs
Abstract Gene expression is regulated at each step from chromatin remodeling through translation and degradation. Several known RNA‐binding regulatory proteins interact with specific RNA secondary structures in addition to specific nucleotides. To provide a more comprehensive understanding of the re...
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| Format: | Article |
| Language: | English |
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Springer Nature
2009-04-01
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| Series: | Molecular Systems Biology |
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| Online Access: | https://doi.org/10.1038/msb.2009.24 |
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| _version_ | 1849225797133402112 |
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| author | Barrett C Foat Gary D Stormo |
| author_facet | Barrett C Foat Gary D Stormo |
| author_sort | Barrett C Foat |
| collection | DOAJ |
| description | Abstract Gene expression is regulated at each step from chromatin remodeling through translation and degradation. Several known RNA‐binding regulatory proteins interact with specific RNA secondary structures in addition to specific nucleotides. To provide a more comprehensive understanding of the regulation of gene expression, we developed an integrative computational approach that leverages functional genomics data and nucleotide sequences to discover RNA secondary structure‐defined cis‐regulatory elements (SCREs). We applied our structural cis‐regulatory element detector (StructRED) to microarray and mRNA sequence data from Saccharomyces cerevisiae, Drosophila melanogaster, and Homo sapiens. We recovered the known specificities of Vts1p in yeast and Smaug in flies. In addition, we discovered six putative SCREs in flies and three in humans. We characterized the SCREs based on their condition‐specific regulatory influences, the annotation of the transcripts that contain them, and their locations within transcripts. Overall, we show that modeling functional genomics data in terms of combined RNA structure and sequence motifs is an effective method for discovering the specificities and regulatory roles of RNA‐binding proteins. |
| format | Article |
| id | doaj-art-cf3d5abcf5c5435f8bf3a372a83d679a |
| institution | Kabale University |
| issn | 1744-4292 |
| language | English |
| publishDate | 2009-04-01 |
| publisher | Springer Nature |
| record_format | Article |
| series | Molecular Systems Biology |
| spelling | doaj-art-cf3d5abcf5c5435f8bf3a372a83d679a2025-08-24T11:59:45ZengSpringer NatureMolecular Systems Biology1744-42922009-04-015111410.1038/msb.2009.24Discovering structural cis‐regulatory elements by modeling the behaviors of mRNAsBarrett C Foat0Gary D Stormo1Department of Genetics, Center for Genome Sciences, Washington University School of MedicineDepartment of Genetics, Center for Genome Sciences, Washington University School of MedicineAbstract Gene expression is regulated at each step from chromatin remodeling through translation and degradation. Several known RNA‐binding regulatory proteins interact with specific RNA secondary structures in addition to specific nucleotides. To provide a more comprehensive understanding of the regulation of gene expression, we developed an integrative computational approach that leverages functional genomics data and nucleotide sequences to discover RNA secondary structure‐defined cis‐regulatory elements (SCREs). We applied our structural cis‐regulatory element detector (StructRED) to microarray and mRNA sequence data from Saccharomyces cerevisiae, Drosophila melanogaster, and Homo sapiens. We recovered the known specificities of Vts1p in yeast and Smaug in flies. In addition, we discovered six putative SCREs in flies and three in humans. We characterized the SCREs based on their condition‐specific regulatory influences, the annotation of the transcripts that contain them, and their locations within transcripts. Overall, we show that modeling functional genomics data in terms of combined RNA structure and sequence motifs is an effective method for discovering the specificities and regulatory roles of RNA‐binding proteins.https://doi.org/10.1038/msb.2009.24modelingmRNA stabilitypolysome associationpost‐transcriptional regulationsecondary structure |
| spellingShingle | Barrett C Foat Gary D Stormo Discovering structural cis‐regulatory elements by modeling the behaviors of mRNAs Molecular Systems Biology modeling mRNA stability polysome association post‐transcriptional regulation secondary structure |
| title | Discovering structural cis‐regulatory elements by modeling the behaviors of mRNAs |
| title_full | Discovering structural cis‐regulatory elements by modeling the behaviors of mRNAs |
| title_fullStr | Discovering structural cis‐regulatory elements by modeling the behaviors of mRNAs |
| title_full_unstemmed | Discovering structural cis‐regulatory elements by modeling the behaviors of mRNAs |
| title_short | Discovering structural cis‐regulatory elements by modeling the behaviors of mRNAs |
| title_sort | discovering structural cis regulatory elements by modeling the behaviors of mrnas |
| topic | modeling mRNA stability polysome association post‐transcriptional regulation secondary structure |
| url | https://doi.org/10.1038/msb.2009.24 |
| work_keys_str_mv | AT barrettcfoat discoveringstructuralcisregulatoryelementsbymodelingthebehaviorsofmrnas AT garydstormo discoveringstructuralcisregulatoryelementsbymodelingthebehaviorsofmrnas |