DNA-Encoded Chromatin Structural Intron Boundary Signals Identify Conserved Genes with Common Function
The regulation of metazoan gene expression occurs in part by pre-mRNA splicing into mature RNAs. Signals affecting the efficiency and specificity with which introns are removed have not been completely elucidated. Splicing likely occurs cotranscriptionally, with chromatin structure playing a key reg...
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| Format: | Article |
| Language: | English |
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Wiley
2015-01-01
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| Series: | International Journal of Genomics |
| Online Access: | http://dx.doi.org/10.1155/2015/167578 |
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| _version_ | 1841524666677592064 |
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| author | Justin A. Fincher Gary S. Tyson Jonathan H. Dennis |
| author_facet | Justin A. Fincher Gary S. Tyson Jonathan H. Dennis |
| author_sort | Justin A. Fincher |
| collection | DOAJ |
| description | The regulation of metazoan gene expression occurs in part by pre-mRNA splicing into mature RNAs. Signals affecting the efficiency and specificity with which introns are removed have not been completely elucidated. Splicing likely occurs cotranscriptionally, with chromatin structure playing a key regulatory role. We calculated DNA encoded nucleosome occupancy likelihood (NOL) scores at the boundaries between introns and exons across five metazoan species. We found that (i) NOL scores reveal a sequence-based feature at the introns on both sides of the intron-exon boundary; (ii) this feature is not part of any recognizable consensus sequence; (iii) this feature is conserved throughout metazoa; (iv) this feature is enriched in genes sharing similar functions: ATPase activity, ATP binding, helicase activity, and motor activity; (v) genes with these functions exhibit different genomic characteristics;
(vi) in vivo nucleosome positioning data confirm ontological enrichment at this feature; and (vii) genes with this feature exhibit unique dinucleotide distributions at the intron-exon boundary. The NOL scores point toward a physical property of DNA that may play a role in the mechanism of pre-mRNA splicing. These results provide a foundation for identification of a new set of regulatory DNA elements involved in splicing regulation. |
| format | Article |
| id | doaj-art-d8808cafe3d244f0ad5ab8c60b8b46c8 |
| institution | Kabale University |
| issn | 2314-436X 2314-4378 |
| language | English |
| publishDate | 2015-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | International Journal of Genomics |
| spelling | doaj-art-d8808cafe3d244f0ad5ab8c60b8b46c82025-02-03T05:47:48ZengWileyInternational Journal of Genomics2314-436X2314-43782015-01-01201510.1155/2015/167578167578DNA-Encoded Chromatin Structural Intron Boundary Signals Identify Conserved Genes with Common FunctionJustin A. Fincher0Gary S. Tyson1Jonathan H. Dennis2Department of Computer Science, Florida State University, Tallahassee, FL 32306, USADepartment of Computer Science, Florida State University, Tallahassee, FL 32306, USADepartment of Biological Science, Florida State University, Tallahassee, FL 32306, USAThe regulation of metazoan gene expression occurs in part by pre-mRNA splicing into mature RNAs. Signals affecting the efficiency and specificity with which introns are removed have not been completely elucidated. Splicing likely occurs cotranscriptionally, with chromatin structure playing a key regulatory role. We calculated DNA encoded nucleosome occupancy likelihood (NOL) scores at the boundaries between introns and exons across five metazoan species. We found that (i) NOL scores reveal a sequence-based feature at the introns on both sides of the intron-exon boundary; (ii) this feature is not part of any recognizable consensus sequence; (iii) this feature is conserved throughout metazoa; (iv) this feature is enriched in genes sharing similar functions: ATPase activity, ATP binding, helicase activity, and motor activity; (v) genes with these functions exhibit different genomic characteristics; (vi) in vivo nucleosome positioning data confirm ontological enrichment at this feature; and (vii) genes with this feature exhibit unique dinucleotide distributions at the intron-exon boundary. The NOL scores point toward a physical property of DNA that may play a role in the mechanism of pre-mRNA splicing. These results provide a foundation for identification of a new set of regulatory DNA elements involved in splicing regulation.http://dx.doi.org/10.1155/2015/167578 |
| spellingShingle | Justin A. Fincher Gary S. Tyson Jonathan H. Dennis DNA-Encoded Chromatin Structural Intron Boundary Signals Identify Conserved Genes with Common Function International Journal of Genomics |
| title | DNA-Encoded Chromatin Structural Intron Boundary Signals Identify Conserved Genes with Common Function |
| title_full | DNA-Encoded Chromatin Structural Intron Boundary Signals Identify Conserved Genes with Common Function |
| title_fullStr | DNA-Encoded Chromatin Structural Intron Boundary Signals Identify Conserved Genes with Common Function |
| title_full_unstemmed | DNA-Encoded Chromatin Structural Intron Boundary Signals Identify Conserved Genes with Common Function |
| title_short | DNA-Encoded Chromatin Structural Intron Boundary Signals Identify Conserved Genes with Common Function |
| title_sort | dna encoded chromatin structural intron boundary signals identify conserved genes with common function |
| url | http://dx.doi.org/10.1155/2015/167578 |
| work_keys_str_mv | AT justinafincher dnaencodedchromatinstructuralintronboundarysignalsidentifyconservedgeneswithcommonfunction AT garystyson dnaencodedchromatinstructuralintronboundarysignalsidentifyconservedgeneswithcommonfunction AT jonathanhdennis dnaencodedchromatinstructuralintronboundarysignalsidentifyconservedgeneswithcommonfunction |