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C3: The role of natural antisense long non-coding RNAs in plants

Supervisor: Dr. Selma Gago Zachert 


Specific aim(s)/topic(s)

(1)     Deciphering the role of natural antisense long non-coding RNAs in the regulation of three gene families of Arabidopsis thaliana

(2)     The role of DLCs and AGO proteins in NAT-lncRNA mediated regulation of gene expression and plant immunity (collaborative project with C2)


Background and significance

Small non-coding RNAs are involved in the defense against pathogens (small-interfering RNAs) and in the regulation of endogenous gene expression (microRNAs). Recently, it has been reported that a large fraction of the transcriptome is composed by long non-coding RNAs (lncRNAs). These include molecules longer than 200 nucleotides without protein-coding capacity. NAT-lncRNAs have been extensively studied in animals, but less is known about their function in plants. We are interested in a particular group of lncRNAs, which are transcribed from the opposite DNA strand of a coding gene (Natural Antisense long non-coding RNAs, NAT-lncRNAs). The transcription of opposite complementary RNAs produces dsRNA molecules. These can be recognized by the silencing machinery from the plant, and be processed to generate a special class of small interfering RNAs (NAT-siRNAs).  Nat-siRNAs can be loaded into RNA silencing complexes (RISC) that mediate the cleavage of the target RNA by Argonaute endonucleases (AGO). Nat-siRNAs 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. Several NAT-lncRNAs are complementary to members of different multigene families of A. thaliana. Considering the sequence conservation among members of multigene families, we hypothesize that NAT-lncRNAs could regulate not only expression of the overlapping gene (primary target) but can also modulate the expression of other closely related genes (secondary targets). This situation may allow the simultaneous (down)-regulation of several related genes and might constitute another layer in the plethora of regulatory potential of RNA molecules.