Cold Induced Antisense Transcription of FLOWERING LOCUS C in Distant Grasses

Abstract

Functional conservation of RNAs between different species is a key argument for their importance. While few long non-coding RNAs are conserved at the sequence level, many long non-coding RNAs have been identified that only share a position relative to other genes. It remains largely unknown whether and how these lncRNAs are conserved beyond their position. In Arabidopsis thaliana, the lncRNA COOLAIR is transcribed antisense from FLOWERING LOCUS C (FLC) in response to cold. Despite relatively low sequence similarity, the COOLAIR expression pattern and in vitro RNA secondary structure are highly conserved across the family Brassicaceae, which originated some 50 mya. It is unclear, however, whether COOLAIR functions in distantly related species such as monocots, which diverged some 150 mya. Here, we identified antisense lncRNAs from FLC homologs in various monocot species that share no sequence similarity with A. thaliana COOLAIR. Yet similar to COOLAIR, we found that BdODDSOC1 antisense (BdCOOLAIR1) and BdODDSOC2 antisense (BdCOOLAIR2) are induced by cold in a Brachypodium distachyon winter accession. Across B. distachyon accessions, the sequences of BdCOOLAIR1 and BdCOOLAIR2 are less conserved than exons but more conserved than flanking regions, suggesting a function for the transcript itself. Knock down of the BdODDSOC2 non-overlapping BdCOOLAIR2 transcript did not show a morphological phenotype, but did result in significantly higher BdODDSOC2 expression during cold, indicating that BdCOOLAIR2 performs a role in cis in the rate of BdODDSOC2 silencing. This functional similarity between eudicot and monocot species reveals ancient conservation or convergent evolution of FLC antisense transcription. Either scenario supports its functional importance.

Long Non-coding RNA in Plants in the Era of Reference Sequences

“…COOLAIR is involved in FLC repression by both autonomous and vernalization pathways, which leads to flowering in spring. Homology-based search was performed to find FLC locus and antisense FLC transcripts in other monocots, and the results showed that although there is no sequence conservation between antisense FLC transcripts and Arabidopsis COOLAIR lncRNA, the locations of these transcripts were conserved in six grass species including T. aestivum (Jiao et al, 2019). COLDAIR was identified as another lncRNA potentially regulating FLC expression.…”

The Role of FLOWERING LOCUS C Relatives in Cereals

“…Brachypodium has also been shown to encode lncRNAs, similar to COOLAIR , which target FLC -like genes for downregulation during vernalization ( Jiao et al, 2019 ). Two high confidence lncRNAs were detected for BdOS2 , while one lncRNA could be detected for BdOS1 .…”

“…Expression of these lncRNAs is induced by vernalization, and their induction is significantly higher in a winter accession compared to a facultative accession, while their expression is absent in a spring accession. Knockdown of BdCOOLAIR2 via RNAi also affects the rate of silencing of BdOS2 in BdTR3C, though it is not essential for the complete silencing of BdOS2 ( Jiao et al, 2019 ). This information suggests that lncRNAs complement the mechanisms which silence FLC -like genes in grasses, in a similar fashion to FLC regulation in Arabidopsis , although this mode of regulation is accession dependent.…”

Linking Brassinosteroid and ABA Signaling in the Context of Stress Acclimation

“…Histone acetylation is important in the FCA-mediated thermal adaptation of developing seedlings, chlorophyll biosynthesis, and seedling photosynthetic fitness [ 56 ]. The FLC/FCA module functions not only in hot conditions, but also in cold, providing adaptation to winter conditions through an FLC antisense transcript COOLAIR [ 53 , 57 ]. This may explain why BRL3ox plants demonstrated high gene expression not only in the category “Response to Water Deprivation”, but also in the categories “Response to Temperature Stimulus” and “Cold Acclimation” [ 2 ].…”