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

REYNOSO, MAURICIO; BLANCO, FLAVIO A.; ZANETTI, MARÍA EUGENIA

IUBMB LIFE

JOHN WILEY & SONS INC

Lugar: New York; Año: 2023

1521-6543

Inthis study, we aimed to identify long non-coding RNAs (lncRNAs) in root tips ofthe model legume Medicago truncatulausing previously generated nuclear, total polyA, ribosome-associated polyA(TRAP) and Riboseq RNA datasets, which might shed light on their localizationand potential regulatory roles. RNA-seq data was mapped to the version 5 of theM. truncatula A17 genome and analyzedto identify genome annotated lncRNAs and putative new root tip (NRT) lncRNAs.lncRNAs were classified according to their genomic localization relative tochromatin accessible regions, protein-coding genes and transposable elements(TE), finding differences between annotated lncRNAs and NRT lncRNAs, both intheir genomic position as well as in the type of TEs in their vicinity. Weinvestigated their response to submergence and found a set of regulated lncRNAsthat was preferentially upregulated in the nucleus, some of which were locatednearby 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-qPCRon nuclear RNA, providing additional evidence of their localization, whichcould ultimately be required for their function.