Host-infection interaction through short dsRNAs

Double-stranded small RNA (dsRNA) molecules are known to be able to silence genes [1]. The plant-infecting fungus Botrytis cinerea produces such RNAs to silence genes in infected hosts (Arabidopsis, tomato), in particular immune-response genes [2]. Similarly, plants can produce dsRNA targeting genes in the fungus (host-induced gene silencing) to avoid infection. This latter mechanism may be underlie situations described in literature where the fungus grows without killing the host: pant-produced dsRNAs may silence genes regulating production of toxins or cell-wall degrading enzymes.

In this project, the goal is to find potential dsRNA-silencing mechanisms between host and infection. A starting point could be to develop a tool similar to [3], to scan both genomes for potential targets. The dsRNA sequences could be measured in the host-infection system or could be derived from literature. The target list can be refined by incorporating prior knowledge on plant infection, e.g. by prioritizing genes involved in immume-response pathways. A related question is how these dsRNAs are transported: perhaps RNA-binding proteins with a signal peptide play a role.

[1] S. Hammond et al. (2010). Post-transcriptional gene silencing by double-stranded RNA. Nature Reviews Genetics 2:110-119. [2] A. Weiberg et al. (2013) Fungal small RNAs suppress plant immunity by hijacking host RNA interference pathways. Science 342:118. [3] Y. Naito et al. (2005) dsCheck: highly sensitive off-target search software for double-stranded RNA-mediated RNA interference. Nucleic Acids Research 33(suppl 2):W589-91.

Used skills: Programming, statistics

Requirements: INF-22306 Programming in Python, BIF-30806 Advanced bioinformatics