Journal
CELL REPORTS
Volume 16, Issue 12, Pages 3087-3096Publisher
CELL PRESS
DOI: 10.1016/j.celrep.2016.08.045
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Funding
- US DOE LANL LDRD
- European Research Council (ERC) under the European Union's Seventh Framework Programme
- UK Biotechnology and Biological Sciences Research Council (BBSRC) Institute Strategic Program [BB/C517633/1]
- BBSRC iCASE Studentship [BB/K012371/1]
- Bayer CropScience
- BBSRC [BBS/E/J/000C0625] Funding Source: UKRI
- Biotechnology and Biological Sciences Research Council [BBS/E/J/000C0625, 1366599, BB/C517633/1] Funding Source: researchfish
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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.
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