Oral Presentation Australasian RNA Biology and Biotechnology Association 2026 Conference

Structural Conservation of Long Non-Coding RNAs Across the Brassicaceae (144836)

Gabriela Santos-Rodriguez 1 2 , Christopher Klapproth 3 , Jose Antonio Corona-Gomez 4 , Caylyn Railey 5 , Andrew Nelson 5 , Sven Findeiss 3 , Peter Stadler 3 , Selene L Fernandez-Valverde 1 2
  1. UNSW RNA Institute, UNSW, Sydney, NSW, Australia
  2. School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, Australia
  3. Bioinformatics Group, Department of Computer Science and Interdisciplinary Center of Bioinformatics, University of Leipzig, Leipzig, Germany
  4. Centro de Investigación sobre el Envejecimiento, Centro de Investigación y de Estudios Avanzados del IPN, Mexico City, Mexico
  5. Boyce Thompson Institute, Ithaca, New York, United States

Long-noncoding RNAs (lncRNAs) are transcripts of over 200 nt involved in the regulation of gene expression. In plants, lncRNAs have been implicated in diverse regulatory processes, including modulation of chromatin topology, interactions with microRNAs, regulation of alternative splicing, and scaffolding of protein complexes. Despite their biological importance, identifying evolutionarily conserved lncRNAs remains methodologically challenging, largely because of their limited sequence conservation. Nonetheless, lncRNAs have alternative forms of conservation, such as the preservation of secondary RNA structure, which is crucial for their molecular functionality.

Here, we assessed the secondary structure conservation of lncRNAs within the Brassicaceae clade in the recently released telomere-to-telomere genome of Arabidopsis thaliana. Using a comparative genomics approach, we screened Arabidopsis thaliana lncRNAs, leveraging sequence similarity and whole-genome alignments across 13 Brassicaceae species spanning ~19 MYA. We find that about ~18% of screened RNAs had statistically significant signals of RNA secondary conservation as measured by RNAz. Importantly, a substantial number of these structurally conserved lncRNAs could only be identified by combining sequence-based orthologue assessment with genomic conservation analysis. Overall, we identify a highly reliable group of structurally conserved lncRNAs whose biological functions may depend on their structure.