Investigation of RNA interference and related gene regulatory mechanisms

PROJECT SUMMARY Over evolutionary time, species access innovations that evolve in parallel lineages. The mitochondrion and chloroplast genome-transfers provide stunning examples. The experimental transfer of DNA has begun to provide a glimpse at—and a handle to explore—this fundamental process. C. elegans, whose rapid life cycle

calls upon the germline to function every few days, is an ideal animal in which to investigate transgenerational systems that regulate information. This project will explore the following questions: 1) How do cells distinguish ‘licensed’ from potentially dangerous ‘unlicensed’ information? 2) How do Argonautes and chromatin regulators

coordinate to propagate gene-expression states? 3) How do distinct Argonaute systems integrate to achieve surveillance and how is transcriptome surveillance organized spatially? A remarkable feature of RNA surveillance in the worm germline is that both silenced and expressed states are communicated to offspring via small RNAs.

These small-RNA signals comprise approximately one million different guide-RNA species that engage a dozen different germline Argonautes. Initiators of silencing—e.g., dsRNA, piRNAs, and recently intronless mRNAs— have been relatively easy to identify. Yet, insights into mechanisms that ensure pathway specificity have been

elusive. Moreover, the coordination between small RNA pathways and heterochromatin remains murky. Preliminary studies suggest that peri-nuclear nuage domains marked by RNA-binding proteins differentiate from each other to direct distinct RNA-silencing tasks, and nuage domains appear to communicate or associate with

the small-RNA source loci in the nucleus. This compartmentalization could dramatically simplify the math for whole transcriptome silencing. Instead of millions of guide complexes in each nuage domain, only about 20,000 distinct guide-RNA species would be needed to silence adjacent heterochromatin. Understanding the cascading

effects that shift the balance of RNA binding and surveillance in nuage and heterochromatin could shed light on related perturbations that cause a myriad of human disorders.