microRNA profiling of the nematode Caenorhabditis elegans infected by Bacillus thuringiensis

microRNAs (miRNAs) are small non-coding RNA-molecules that influence translation by binding to the target gene mRNA. Many miRNAs are found in nested arrangements within introns, or exons, of larger protein-coding host genes. miRNAs and host genes in a nested arrangement are often transcribed simultaneously, which may indicate that both have similar functions. miRNAs have been implicated in regulating defense responses against pathogen infection in C. elegans and in mammals. Here, we asked if miRNAs in nested arrangements and their host genes are involved in the C. elegans response against infection with Bacillus thuringiensis (Bt). We performed miRNA sequencing and functional genetic analysis of miRNA and/or host gene in four nested arrangements. We identified mir-58.1 and mir-2 as negative regulators of C. elegans resistance to Bt infection. However, we did not find any miRNA/host gene pair in which both contribute to defense against Bt. Overall design: microRNA profiles of wild type (WT) C. elegans exposed to either Bacillus thuringiensis B-18247, B-18679 and B-18407 or E. coli OP50 at 2h, 6h or 12h were generated by deep sequencing (4 replicates), using Illumina HiSeq2000.