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International Journal of Genomics
Volume 2015, Article ID 167578, 10 pages
http://dx.doi.org/10.1155/2015/167578
Research Article

DNA-Encoded Chromatin Structural Intron Boundary Signals Identify Conserved Genes with Common Function

1Department of Computer Science, Florida State University, Tallahassee, FL 32306, USA
2Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA

Received 1 October 2014; Accepted 15 February 2015

Academic Editor: Soraya E. Gutierrez

Copyright © 2015 Justin A. Fincher et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

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.