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Title: COOLAIR Antisense RNAs Form Evolutionarily Conserved Elaborate Secondary Structures

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. Here, 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.
Authors:
 [1] ;  [2] ;  [3] ;  [1] ;  [1] ;  [2]
  1. Norwich Research Park, Norwich (United Kingdom). John Innes Centre
  2. Los Alamos National Lab. (LANL), Los Alamos, NM (United States); New Mexico Consortium, Los Alamos, NM (United States)
  3. Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Publication Date:
Grant/Contract Number:
AC05-76RL01830
Type:
Published Article
Journal Name:
Cell Reports
Additional Journal Information:
Journal Volume: 16; Journal Issue: 12; Journal ID: ISSN 2211-1247
Publisher:
Elsevier
Research Org:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org:
USDOE Laboratory Directed Research and Development (LDRD) Program; European Research Council (ERC)
Country of Publication:
United States
Language:
English
Subject:
60 APPLIED LIFE SCIENCES; RNA structure; antisense transcripts; COOLAIR; FLC; chemical probing; A. thaliana; evolution; shotgun secondary structure (3S)
OSTI Identifier:
1377996
Alternate Identifier(s):
OSTI ID: 1335861