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Cell Rep. 2016 Sep 20;16(12):3087-96. doi: 10.1016/j.celrep.2016.08.045.

COOLAIR Antisense RNAs Form Evolutionarily Conserved Elaborate Secondary Structures.

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  • 1John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
  • 2Los Alamos National Laboratory, Los Alamos, NM 87545, USA; New Mexico Consortium, Los Alamos, NM 87544, USA.
  • 3Los Alamos National Laboratory, Los Alamos, NM 87545, USA; Pacific Northwest National Laboratory, Environmental Molecular Sciences Laboratory, Richland, WA 99354, USA.
  • 4Los Alamos National Laboratory, Los Alamos, NM 87545, USA; New Mexico Consortium, Los Alamos, NM 87544, USA. Electronic address:


There is considerable debate about the functionality of long non-coding RNAs (lncRNAs). Lack of sequence conservation has been used to argue against functional relevance. We investigated antisense lncRNAs, called COOLAIR, at the A. thaliana FLC locus and experimentally determined their secondary structure. The major COOLAIR variants are highly structured, organized by exon. The distally polyadenylated transcript has a complex multi-domain structure, altered by a single non-coding SNP defining a functionally distinct A. thaliana FLC haplotype. The A. thaliana COOLAIR secondary structure was used to predict COOLAIR exons in evolutionarily divergent Brassicaceae species. These predictions were validated through chemical probing and cloning. Despite the relatively low nucleotide sequence identity, the structures, including multi-helix junctions, show remarkable evolutionary conservation. In a number of places, the structure is conserved through covariation of a non-contiguous DNA sequence. This structural conservation supports a functional role for COOLAIR transcripts rather than, or in addition to, antisense transcription.


A. thaliana; COOLAIR; FLC; RNA structure; antisense transcripts; chemical probing; evolution; shotgun secondary structure (3S)

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