Nuclear and cytoplasmic lncRNAs in root tips of the model legume Medicago truncatula under control and submergence

REYNOSO, MAURICIO; BLANCO, FLAVIO ANTONIO; ZANETTI, MARIA EUGENIA

IUBMB Life

IUBMB Jouirnal

Lugar: Malden ; Año: 2023

In this study, we aimed to identify long non-coding RNAs (lncRNAs) in root tips of the model legume Medicago truncatula using previously generated nuclear, total polyA, ribosome-associated polyA (TRAP) and Riboseq RNA datasets, which might shed light on their localization and potential regulatory roles. RNA-seq data was mapped to the version 5 of the M. truncatula A17 genome and analyzed to identify genome annotated lncRNAs and putative new root tip (NRT) lncRNAs. lncRNAs were classified according to their genomic localization relative to chromatin accessible regions, protein-coding genes and transposable elements (TE), finding differences between annotated lncRNAs and NRT lncRNAs, both in their genomic position as well as in the type of TEs in their vicinity. We investigated their response to submergence and found a set of regulated lncRNAs that was preferentially upregulated in the nucleus, some of which were located nearby genes of the conserved submergence upregulated gene families (SURFs), and chromatin accessible regions suggesting a potential regulatory role. Finally, the accumulation of lncRNAs under submergence was validated by RT-qPCR on nuclear RNA, providing additional evidence of their localization, which could ultimately be required for their function.