Conserved secondary structures in Aspergillus.
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 seco...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2008-07-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC2467506?pdf=render |
| _version_ | 1817982905216925696 |
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| author | Abigail Manson McGuire James E Galagan |
| author_facet | Abigail Manson McGuire James E Galagan |
| author_sort | Abigail Manson McGuire |
| collection | DOAJ |
| description | 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.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.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. |
| first_indexed | 2024-04-13T23:26:07Z |
| format | Article |
| id | doaj.art-729304bd26d24efea58fc46899a58335 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-04-13T23:26:07Z |
| publishDate | 2008-07-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-729304bd26d24efea58fc46899a583352022-12-22T02:25:03ZengPublic Library of Science (PLoS)PLoS ONE1932-62032008-07-0137e281210.1371/journal.pone.0002812Conserved secondary structures in Aspergillus.Abigail Manson McGuireJames E GalaganRecent 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.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.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.http://europepmc.org/articles/PMC2467506?pdf=render |
| spellingShingle | Abigail Manson McGuire James E Galagan Conserved secondary structures in Aspergillus. PLoS ONE |
| title | Conserved secondary structures in Aspergillus. |
| title_full | Conserved secondary structures in Aspergillus. |
| title_fullStr | Conserved secondary structures in Aspergillus. |
| title_full_unstemmed | Conserved secondary structures in Aspergillus. |
| title_short | Conserved secondary structures in Aspergillus. |
| title_sort | conserved secondary structures in aspergillus |
| url | http://europepmc.org/articles/PMC2467506?pdf=render |
| work_keys_str_mv | AT abigailmansonmcguire conservedsecondarystructuresinaspergillus AT jamesegalagan conservedsecondarystructuresinaspergillus |