AUTHOR=Kramer Marianne C. , Kim Hee Jong , Palos Kyle R. , Garcia Benjamin A. , Lyons Eric , Beilstein Mark A. , Nelson Andrew D. L. , Gregory Brian D. 

TITLE=A Conserved Long Intergenic Non-coding RNA Containing snoRNA Sequences, lncCOBRA1, Affects Arabidopsis Germination and Development

JOURNAL=Frontiers in Plant Science

VOLUME=13

YEAR=2022

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2022.906603

DOI=10.3389/fpls.2022.906603

ISSN=1664-462X

ABSTRACT=<p>Long non-coding RNAs (lncRNAs) are an increasingly studied group of non-protein coding transcripts with a wide variety of molecular functions gaining attention for their roles in numerous biological processes. Nearly 6,000 lncRNAs have been identified in <italic>Arabidopsis thaliana</italic> but many have yet to be studied. Here, we examine a class of previously uncharacterized lncRNAs termed <italic>CONSERVED IN</italic> BRASSICA RAPA (<italic>lncCOBRA</italic>) transcripts that were previously identified for their high level of sequence conservation in the related crop species <italic>Brassica rapa</italic>, their nuclear-localization and protein-bound nature. In particular, we focus on <italic>lncCOBRA1</italic> and demonstrate that its abundance is highly tissue and developmental specific, with particularly high levels early in germination. <italic>lncCOBRA1</italic> contains two snoRNAs domains within it, making it the first sno-lincRNA example in a non-mammalian system. However, we find that it is processed differently than its mammalian counterparts. We further show that plants lacking <italic>lncCOBRA1</italic> display patterns of delayed germination and are overall smaller than wild-type plants. Lastly, we identify the proteins that interact with <italic>lncCOBRA1</italic> and propose a novel mechanism of lincRNA action in which it may act as a scaffold with the RACK1A protein to regulate germination and development, possibly through a role in ribosome biogenesis.</p>