24th Annual Genetics Day
University of Rochester Medical Center
April 4, 2012|poster prize winners | schedule| flyer | poster
10th Annual Fred Sherman Lecture, Dr.
The tiny RNA pathways of C. elegans
Abstract: We explored using a full genome RNAi screen what protein co-factors are necessary for RNAi in C. elegans. To monitor RNAi in vivo, we designed an “RNAi sensor” strain that expresses both a gfp dsRNA hairpin and a gfp reporter gene in the epithelial seam cells of C. elegans. Screening of the genome-wide RNAi library identified 90 gene inactivations that reproducibly disrupt the RNAi pathway in C. elegans. We also performed an RNAi screen for miRNA function. The microRNA pathway and RNAi hits were nearly entirely distinct, endorsing the view that miRNA regulation of mRNAs is mechanistically very different from siRNA induced mRNA degradation.
Informatic analysis of the genes identified in the genome screens suggests that many fungal and protist species have deleted en masse many of the RNAi pathway genes, and validates those genes. We classified protein coding genes from eukaryotes by the presence or absence of orthologous proteins in any of 85 disparate eukaryotic genomes in plants, fungi, protists and animals. There are many orthologous genes that are present in all eukaryotes, and many other gene classes that are animal-specific for example. For the small RNA pathway, the distinction between a number of fungi and protists, and the animal, plant, and about half of the fungal genomes is key: the validated small RNA component Argonaute are not present in a number of these genomies but are present in the other animal or plant genome sequences. When we queried our database about other genes that have this pattern of loss the 85 genome sequences, a number of tantalizing gene classes were identified. Out of this set, our functional genomic screens described above identified a much larger fraction of these genes than expected by chance. The intersection of our RNAi screen and the phylogenetic profile define our highest confidence genes to follow up.