Long non-coding RNAs (lncRNAs), transcripts longer than 200 nt and without protein-coding capacity, have been identified due to the massive use of deep-sequencing methods, which revealed that most of the genome is transcribed. Based on their position relative to protein-coding genes, lncRNAs are classified into intergenic (located between two protein genes), intronic (transcribed from intronic regions) and antisense (transcribed from the opposite DNA strand of a protein-coding gene). Despite the fact that only a few lncRNAs have been characterized in plants, it has been shown that they are key regulators of crucial developmental processes including germination and flowering, and that are involved in the modulation of responses to hormones and abiotic stresses highlighting their biological relevance.
The focus of our research is the functional characterization of natural antisense long non-coding RNAs (lncNATs) overlapping protein-coding genes of multigene families. It was reported that synthesis of complementary RNAs during transcription of sense and antisense genes can lead to dsRNAs generation and, consequently, to the production of a particular class of small RNAs derived from the overlapping regions called natural antisense transcript siRNAs (nat-siRNAs). Generation of nat-siRNAs can be particularly relevant in the context of multigene families due to sequence conservation among closely related members, and, in this context, to its potential to regulate not only the overlapping gene (primary target) but also the expression of other family members (secondary targets). Additionally, lncNATs can modulate gene expression by other mechanisms, acting in cis or trans in the nucleus, interacting with proteins in the cytosol or by the activity of small peptides encoded in their sequences.
Using sequence information from the model plant Arabidopsis thaliana we identified several lncNATs encoding genes that overlap with members of multigene families and hypothesized that they could regulate the expression of their potential targets by the previously described mechanisms.
Combining several approaches, we ambition to understand the role of lncNATs in the context of multigene families of A. thaliana, to define the processes in which they are involved and to decipher the regulatory network subjacent to their action.