For a long time, RNA molecules have been considered as “intermediates” transferring the information encoded into the DNA to produce proteins, but in the last years the role of several kinds of non-protein-coding RNAs (ncRNAs) in regulation of gene expression and genome organization became evident. ncRNAs include transfer and ribosomal RNAs (tRNAs and rRNAs, respectively) that participate in protein synthesis and small nuclear (snRNAs) and nucleolar (snoRNAs) RNAs, involved in splicing and in posttranscriptional chemical modifications of other RNAs, respectively. Additional small non-coding RNAs of 21 to 24 base-pairs in length involved in plant defense (small interfering RNAs, siRNAs) and in gene expression regulation [microRNAs (miRNAs), trans-acting siRNAs (tasiRNAs), natural antisense transcript siRNAs (natsiRNAs) and heterochromatic siRNAs (hcsiRNAs)] have been identified. siRNAs are produced by the silencing machinery of the cell in response to infections caused by subcellular pathogens with RNA genomes and as consequence of overexpression of exogenous sequences, whereas miRNAs, tasiRNAs, natsiRNAs and hcsiRNAs are derived from endogenous precursors. miRNAs, tasiRNAs and natsiRNAs regulate gene expression at the posttranscriptional level by binding to mRNA targets inducing their cleavage and degradation, while hcsiRNAs, originated from intergenic and repetitive regions, are associated with deposition of repressive chromatin modifications necessary to preserve genome integrity. Long non-coding RNAs (lncRNAs), transcripts longer than 200 nt and without protein-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 regulators of crucial developmental processes like germination and flowering, and are involved in the modulation of responses to hormones and abiotic stresses highlighting their biological relevance.
We are interested in natural antisense long non-coding RNAs (NAT-lncRNAs) a particular group of lncRNAs, which are transcribed from the complementary DNA strand of a protein-coding gene. The transcription of complementary RNAs produces double-stranded RNA (dsRNA) molecules. These can be recognized by the silencing machinery from the plant, and be processed to generate natsiRNAs, which can be loaded into RNA silencing complexes (RISC) to mediate the cleavage of the target RNA by Argonaute endonucleases (AGO). natsiRNAs derived from the overlapping region of transcripts corresponding to two protein-coding genes are involved in salt-stress responses, defense against bacteria, hormone regulation and plant reproduction, but less is known about overlapping RNA pairs in which one of the transcripts corresponds to a NAT-lncRNA.
Combining molecular biology tools and in vitro and in planta approaches, we aim to determine the role of NAT-lncRNAs in the regulation of the expression of multigene families in Arabidopsis thaliana, to define the processes in which they are involved, and to decipher the regulatory network subjacent to their action.