The Bartel laboratory has identified a novel class of C. elegans small RNAs predicted to play a role in RNA silencing. RNA silencing refers to several related mechanisms, in which different classes of small RNA molecules target mRNAs for degradation or translational down regulation, or target DNA for transcriptional down regulation. In animals, transcriptional down regulation is the least understood mode of RNA silencing. I hypothesize that this novel class of C. elegans small RNA, termed hsiRNA (heterochromatic short interfering RNA), transcriptionally silences target genomic regions through alterations to chromatin. I propose three broad goals to further our understanding of hsiRNA silencing. (i) Development of an hsiRNA detection assay, and use of this assay to investigate genes involved in hsiRNA expression and processing. (ii) Creation of a reporter system to monitor hsiRNA silencing, and use of this reporter to identify genes required for hsiRNA silencing. (iii) Investigation of chromatin at hsiRNA silenced sites. It is anticipated that these studies will contribute to our understanding of RNA silencing, hsiRNA function, chromatin, and the intersection of RNA silencing and chromatin biology.
