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Conserved secondary structures in Aspergillus.

Abigail Manson McGuire1, James E Galagan

  • 1The Broad Institute of M.I.T. and Harvard, Cambridge, Massachusetts, United States of America. amcguire@broad.mit.edu

Plos One
|July 31, 2008
PubMed
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This study identified thousands of conserved RNA structures in Aspergillus fungi, including novel hairpin motifs within introns. These findings reveal a rich landscape of functional RNAs and their genomic distribution.

Area of Science:

  • Genomics
  • Bioinformatics
  • RNA Biology

Background:

  • Functional RNA discovery is expanding, necessitating advanced computational prediction methods.
  • The Aspergillus genus presents a unique opportunity for studying RNA evolution due to conserved sequences across its genomes.

Purpose of the Study:

  • To computationally identify and analyze conserved RNA secondary structures across six Aspergillus genomes.
  • To cluster predicted RNA structures by similarity and investigate their genomic distribution.

Main Methods:

  • Whole-genome computational search for conserved RNA secondary structures.
  • Clustering of predicted structures based on structural similarity.

Main Results:

  • Identified 7450 conserved secondary structures, including a novel ~60 bp hairpin motif in introns.

Related Experiment Videos

  • Found distinct genomic distributions: exons host long hairpins, 5' UTRs have short hairpins near start codons, and 3' UTRs show minimal structure.
  • Observed increased density of intronic RNAs with intron length and mRNA structures with gene intron count. No microRNAs were detected.

    • Conclusions:

    • Aspergillus genomes harbor numerous conserved RNAs with unknown functions.
    • The study highlights specific spatial arrangements of RNA secondary structures within different genomic regions.
    • This research significantly enhances understanding of RNA secondary structures in Aspergillus organisms.