Conservation and function of COOLAIR long non-coding RNAs in Brassica flowering time control

Hawkes, Emily (2017) Conservation and function of COOLAIR long non-coding RNAs in Brassica flowering time control. Doctoral thesis, University of East Anglia.

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Since their discovery long non-coding RNAs (lncRNAs) have in turn been described as essential genomic regulators or as transcriptional noise. Examples of lncRNAs with experimentally-validated function are limited, with poor nucleotide sequence conservation calling apparent functionality into question. COOLAIR lncRNAs are transcribed in the antisense direction at the Arabidopsis thaliana floral repressor gene, Flowering Locus C (FLC). Previous work has revealed a role for COOLAIR antisense RNAs in regulation of the FLC protein-coding sense transcript and, consequently, flowering time.

FLC homologues are wide-spread in flowering plants, but nucleotide sequence conservation of COOLAIR-specific regions is low. COOLAIR has a complex secondary structure, and covariant base-pair mutations predict strong conservation of this secondary structure across flowering plants. Syntenic transcription of COOLAIR was confirmed in vivo for several species within the family Brassicaceae, including three commercially important Brassica crops: B. rapa, B. oleracea and B. napus. COOLAIR transcription was detected from at least three of four ancient FLC clades within the latter three polyploid and paleopolyploid species. Each FLC homologue has distinct nucleotide sequence, expression patterns, and COOLAIR isoforms. Further variation in COOLAIR was identified between winter and spring cultivars. It was hypothesised that this could affect cis-regulation of FLC. Correlation between COOLAIR modifications and flowering time was tested by introducing antisense splice site mutations into Brassica FLC transgenes in A. thaliana. These experiments suggested that a shorter COOLAIR isoform with a disrupted structural motif was a weaker negative regulator of FLC.

This work supports conservation of COOLAIR expression, structure and function in Brassica crop plants, and a role for RNA structure in COOLAIR function. We propose an evolutionarily conserved lncRNA that is neither essential regulator nor transcriptional noise, but rather adapts with the environment to fine-tune the transition to flowering.

Item Type: Thesis (Doctoral)
Faculty \ School: Faculty of Science > School of Biological Sciences
Depositing User: Bruce Beckett
Date Deposited: 23 Jul 2018 11:59
Last Modified: 04 Jun 2021 00:43


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