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Sequence-specific and Selective Recognition of Double-stranded RNAs over Single-stranded RNAs by Chemically Modified Peptide Nucleic Acids
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COOLAIR Antisense RNAs Form Evolutionarily Conserved Elaborate Secondary Structures.

Emily J Hawkes1, Scott P Hennelly2, Irina V Novikova3

  • 1John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.

Cell Reports
|September 23, 2016
PubMed
Summary
This summary is machine-generated.

Long non-coding RNAs (lncRNAs) like COOLAIR show conserved structures, not just sequences, across species. This structural conservation suggests these molecules have important biological functions.

Keywords:
A. thalianaCOOLAIRFLCRNA structureantisense transcriptschemical probingevolutionshotgun secondary structure (3S)

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Area of Science:

  • Molecular Biology
  • Genetics
  • Bioinformatics

Background:

  • The functional relevance of long non-coding RNAs (lncRNAs) is debated, partly due to low sequence conservation.
  • Antisense lncRNAs, such as COOLAIR at the Arabidopsis thaliana FLC locus, are implicated in gene regulation.
  • Understanding lncRNA structure is crucial for deciphering their function.

Purpose of the Study:

  • To experimentally determine the secondary structure of Arabidopsis thaliana COOLAIR lncRNA variants.
  • To investigate the evolutionary conservation of COOLAIR structure in Brassicaceae species.
  • To assess the relationship between structural conservation and lncRNA functionality.

Main Methods:

  • Experimental determination of secondary structure for major COOLAIR variants.
  • Bioinformatic prediction of COOLAIR exons in related species based on structural models.
  • Validation of predicted structures using chemical probing and molecular cloning.

Main Results:

  • Major COOLAIR variants exhibit complex, exon-organized secondary structures.
  • A single non-coding SNP significantly alters the structure of a distally polyadenylated COOLAIR transcript, defining distinct FLC haplotypes.
  • COOLAIR structures, including multi-helix junctions, are remarkably conserved across divergent Brassicaceae species, often through covariation of non-contiguous sequences, despite low nucleotide identity.

Conclusions:

  • The significant evolutionary structural conservation of COOLAIR lncRNAs provides strong evidence for their functional importance.
  • Structural conservation, rather than solely sequence conservation, may be a key indicator of lncRNA function.
  • These findings challenge the notion that lack of sequence conservation negates lncRNA functionality.