Conserved Secondary Structures in Aspergillus

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.

Identification of MicroRNA-Like RNAs in Mycelial and Yeast Phases of the Thermal Dimorphic Fungus Penicillium marneffei

“…However, till 2005, no endogenous miRNAs have been reported in fungi but only reports of antisense transcripts encoded in the genome of C. neoformans [66]. No plant or animallike miRNAs was found in Aspergillus species by computational analysis of six Aspergillus genomes (Aspergillus nidulans, Aspergillus oryzae, Aspergillus fumigatus, Aspergillus terreus, Aspergillus clavatus, and Neosartorya fischeri) [67]. It was therefore uncertain whether fungi have microRNAs until the recent discovery of milRNAs in the filamentous fungi, N. crassa, S. sclerotiorum and M. anisopliae, as well as the human pathogenic yeast, C. neoformans [30][31][32][33].…”

Known and novel post-transcriptional regulatory sequences are conserved across plant families

“…The conservation of such primary sequence elements is typically easier to interpret because similarity in secondary structure is often a result of nucleotide composition (Rivas and Eddy 2000) and, even when constrained structure can be identified via covariance, these structures are difficult to generalize across the genes that harbor them (McGuire and Galagan 2008;Rabani et al 2008). Since most intergenic or untranslated DNA evolves at a neutral rate, primary sequences separated by a large evolutionary distance cannot be aligned with confidence.…”

Rnaz 2.0:

“…RNAz 1.0 has been used successfully to map structural ncRNAs in a wide variety of genomes. [15][16][17][18][19][20] A large number of these predictions have also been verified experimentally. [21][22][23] Moreover, the generic approach and many algorithmic details developed for RNAz 1.0 have been re-used, extended, and adapted to other problems in the field of RNA gene-finding.…”