AUTHOR=Jiao Fuchao , Pahwa Kanchan , Manning Murray , Dochy Niklas , Geuten Koen 

TITLE=Cold Induced Antisense Transcription of FLOWERING LOCUS C in Distant Grasses

JOURNAL=Frontiers in Plant Science

VOLUME=10

YEAR=2019

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2019.00072

DOI=10.3389/fpls.2019.00072

ISSN=1664-462X

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