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PLoS One DOI:10.1371/journal.pone.0002812

Conserved secondary structures in Aspergillus.

Publication TypeJournal Article
Year of Publication2008
AuthorsMcGuire, AManson, Galagan, JE
JournalPLoS One
Volume3
Issue7
Pagese2812
Date Published2008 Jul 30
ISSN1932-6203
Keywords3' Untranslated Regions, 5' Untranslated Regions, Algorithms, Aspergillus, Computer Simulation, Evolution, Molecular, Exons, False Positive Reactions, Genome, Fungal, Introns, Nucleic Acid Conformation, Nucleic Acids, Protein Structure, Secondary, RNA, Fungal, Software
Abstract

BACKGROUND: Recent evidence suggests that the number and variety of functional RNAs (ncRNAs as well as cis-acting RNA elements within mRNAs) is much higher than previously thought; thus, the ability to computationally predict and analyze RNAs has taken on new importance. We have computationally studied the secondary structures in an alignment of six Aspergillus genomes. Little is known about the RNAs present in this set of fungi, and this diverse set of genomes has an optimal level of sequence conservation for observing the correlated evolution of base-pairs seen in RNAs.

METHODOLOGY/PRINCIPAL FINDINGS: We report the results of a whole-genome search for evolutionarily conserved secondary structures, as well as the results of clustering these predicted secondary structures by structural similarity. We find a total of 7450 predicted secondary structures, including a new predicted approximately 60 bp long hairpin motif found primarily inside introns. We find no evidence for microRNAs. Different types of genomic regions are over-represented in different classes of predicted secondary structures. Exons contain the longest motifs (primarily long, branched hairpins), 5' UTRs primarily contain groupings of short hairpins located near the start codon, and 3' UTRs contain very little secondary structure compared to other regions. There is a large concentration of short hairpins just inside the boundaries of exons. The density of predicted intronic RNAs increases with the length of introns, and the density of predicted secondary structures within mRNA coding regions increases with the number of introns in a gene.

CONCLUSIONS/SIGNIFICANCE: There are many conserved, high-confidence RNAs of unknown function in these Aspergillus genomes, as well as interesting spatial distributions of predicted secondary structures. This study increases our knowledge of secondary structure in these aspergillus organisms.

URLhttp://dx.plos.org/10.1371/journal.pone.0002812
DOI10.1371/journal.pone.0002812
Pubmed

http://www.ncbi.nlm.nih.gov/pubmed/18665251?dopt=Abstract

Alternate JournalPLoS ONE
PubMed ID18665251
PubMed Central IDPMC2467506
Grant ListHHSN26620040001C / / PHS HHS / United States