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

Abstract

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 Arabidopsis thaliana but many have yet to be studied. Here, we examine a class of previously uncharacterized lncRNAs termed CONSERVED IN BRASSICA RAPA (lncCOBRA) transcripts that were previously identified for their high level of sequence conservation in the related crop species Brassica rapa, their nuclear-localization and protein-bound nature. In particular, we focus on lncCOBRA1 and demonstrate that its abundance is highly tissue and developmental specific, with particularly high levels early in germination. lncCOBRA1 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 lncCOBRA1 display patterns of delayed germination and are overall smaller than wild-type plants. Lastly, we identify the proteins that interact with lncCOBRA1 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.

LncRNA FLAIL affects alternative splicing and represses flowering in Arabidopsis

“…We found that FLAIL was efficiently purified(Appendix Fig S7D). Amplicons corresponding to spliceosomal RNAs U1, U2, and U5 were enriched in FLAIL ChIRP experiments (Fig 5F-H), yet we failed to find enrichment for ncRNAs not linked to splicing such as lncCOBRA1 (Appendix Fig S7D;Kramer et al, 2022). FLAIL knockdown controls revealed that this enrichment was specific to the expression of FLAIL (Fig 5F-H).…”

Linking discoveries, mechanisms, and technologies to develop a clearer perspective on plant long noncoding RNAs

“…Another example of a scaffolding RNA with a putative role in ribosome assembly and biogenesis is lncCOBRA1 ( CONSERVED IN BRASSICA RAPA 1 ; Kramer et al 2022 ). As the name suggests, this lncRNA was identified through an examination of Arabidopsis nuclear lncRNAs which were protein bound and conserved across Brassicaceae ( Gosai et al 2015 ).…”

“…While ∼40% of their 6,480 lincRNAs had some measure of RNA-seq-based transcriptional support, fewer than 300 of them were fully supported by their relatively deep sequencing (∼250 million reads/tissue). This updated annotation was instrumental in the discovery of many now functionally characterized lncRNAs, such as lncCOBRA1 , FLORE , DRIR , and AGAMOUS (AG)-incRNA4 ( Henriques et al 2017 ; Qin et al 2017 ; Wu et al 2018 ; Kramer et al 2022 ). In addition, these data highlighted differences between tiling arrays and RNA-seq, and also pointed to the necessity for sequencing breadth being just as, or more, important as depth when attempting to comprehensively identify lncRNAs.…”

Regulatory annotation identifies KAN1, MYB44 and PIF4 as regulators of Arabidopsis lincRNAs expressed in root

“…Arabidopsis lateral root development is regulated by the Alternative Splicing COmpetitor ( ASCO ) lincRNA, which modulates AS by interacting with the multiple splicing factors (Bardou et al, 2014; Rigo et al, 2020), and the AUXIN-REGULATED PROMOTER LOOP ( APOLO ) lincRNA, which influences the local chromatin conformation and the activity of several Auxin-Responsive genes (Ariel et al, 2020). Plants lacking CONSERVED INBRASSICA RAPA1 ( lncCOBRA1 ) were found to show a delayed germination and were overall smaller than wild-type plants (Kramer et al, 2022). Many lincRNAs are differentially expressed in various stress responses, including drought (Qi et al, 2013; Shuai et al, 2014; Li et al, 2017; Qin et al, 2017), cold (Li et al, 2017; Zhao et al, 2018; Shea et al, 2019), salinity (Deng et al, 2018; Fukuda et al, 2019), and nutrient deficiency (Fukuda et al, 2019), implying that lincRNAs may be involved in plant stress resilience (Jha et al, 2020).…”