RNA silencing is a conserved eukaryotic gene regulatory mechanism, integral for taming endogenous (repetitive elements and transposons) or exogenous (viruses and bacteria) invasive nucleic acids to minimize their impact on genome integrity and function. RNA silencing also is essential for controlling the expression of protein coding genes throughout development or in response to environmental stimuli. RNA silencing is guided by small RNAs, which mostly are produced by a class of RNaseIII enzymes called Dicer. Recently, a growing number of Dicer-independent small RNAs have been found, resulting from the action of RNA-dependent RNA polymerases, RNaseH-like Argonaute proteins or exoribonucleases. Small RNAs also are subjected to regulatory mechanisms. However, the list of enzymes that regulate the fate of small RNAs or small RNA precursors is far from being complete.

In this project, we will examine the role of uncharacterized RNaseIII enzymes in the regulation of small RNA in plants. These enzymes exhibit RNaseIII and double-stranded RNA binding (DRB) domains but lack RNA helicase and PAZ domains that Dicer enzymes have. Therefore, they resemble bacterial or fungal RNaseIII enzymes and thus are referred to as RTL (for Rnase Three Like). Genetic, molecular and bioinformatic results previously obtained indicate that Arabidopsis RTL1 and RTL2 modulate small RNA accumulation. Therefore, modulating the expression of RTL enzymes may alter the epigenome.

This project aims at understanding the function and biological role of RTL enzymes by a combination of genetics, bioinformatics and biochemistry approaches. We will explore the physiological consequences of RTL deregulation by analyzing the transcriptome and methylome of plants that have inherited phenotypic modifications after elimination of the RTL trigger.