Conserved Secondary Structures in Aspergillus

Abigail Manson Mcguire,James E Galagan,Alan Christoffels

doi:10.1371/journal.pone.0002812

Abstract

BackgroundRecent 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 FindingsWe 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 ∼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/SigificanceThere 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.

Highlights

Recent experimental evidence in mammals has indicated that the portion of the genome that is transcribed, as well as the number of functional RNAs in the genome, is much higher than previously thought [1,2,3,4,5,6,7,8,9,10]
Exons contain primarily long, branched hairpins, 59 UTRs primarily contain groupings of short hairpins located near the start codon, and 39 UTRs contain very little secondary structure compared to other regions
Complete genomes were available for A. nidulans [32], A. oryzae [33], and A. fumigatus [34]

Summary

Introduction

Recent experimental evidence in mammals has indicated that the portion of the genome that is transcribed, as well as the number of functional RNAs in the genome, is much higher than previously thought [1,2,3,4,5,6,7,8,9,10]. RNAz compares the minimum free energy of the predicted structure to that of random sequences of the same base composition to calculate a z-score, which is an index of the thermodynamic stability of the structure. It calculates a ‘‘structure conservation index’’ (SCI), which is the ratio of the free energy of the consensus structure to the average of the free energies of the individual sequences. We used RNAz to search for sequences likely to form conserved secondary structures in an alignment of six Aspergillus genomes, and cluster the predicted secondary structures by structural similarity to find structural classes. 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

Methods

Results and Discussion

Conclusions