Research Program
Physiology and pathogenesis yield a dynamic genome
The genetic landscape faced by a living cell is constantly changing. Developmental transitions, environmental shifts, and pathogenic invasions lend a dynamic character to both the genome and its activity pattern. We study a variety of natural mechanisms that are utilized by cells adapting to genetic change. These include mechanisms activated during normal development and systems for detecting and responding to foreign or unwanted genetic activity. At the root of these studies are questions of how a cell can distinguish "self" versus "nonself" and "wanted" versus "unwanted" gene expression.
Silencing Responses to Foreign DNA and RNA:
We can mimic certain aspects of genetic response to viral pathogens by injecting foreign DNA or RNA into cells. Using the nematode C. elegans as a model system, we find that injected DNA or RNA is often poorly expressed, even when carried to the proper cellular compartment. More surprisingly, experiments in which the introduced DNA or RNA is homologous to a cellular gene often result in the silencing of the endogenous gene, even in cases where that gene provides an essential physiological function for the organism.
Double stranded RNA as a major mediator in gene silencing:
In investigating the mechanisms by which injected genetic information is silenced in C. elegans, we have found a number of structural features that provide an indication of unwanted nucleic acid. The most prominent of these features has been double stranded RNA (dsRNA). Absent during "normal" gene expression, dsRNA is an essential component in the life cycle of most viruses. By flagging dsRNA as an indicator of unwanted RNA replication, and by scrupulously avoiding the production of dsRNA during most normal gene expression, the cell acquires a modicum of protection from viral infection. The mechanism by which dsRNA segments are utilized to trigger silencing of homologous genes, termed RNAi, has been a major focus in the lab for the last six years, with our efforts primarily directed toward understanding the efficacy of a system that can use just a few molecules of dsRNA to silence a large population of target molecules.
Other mediators of gene silencing:
Double stranded RNA is not the only trigger of genetic silencing for C. elegans. In addition, several aspects of DNA context (copy number, position, and tertiary structure) and RNA structure (as yet unknown) allow the system to recognize foreign invaders in the genetic makeup of the cell. The precise character of these determinants and the mechanisms underlying their ability to evoke a response are currently under investigation.
Gene silencing processes in development and pathogenesis:
We continue to investigate the roles for gene silencing components in normal development. C. elegans is an opportune system for these analyses, as development is readily followed and analyzed on a number of levels. Many of the components that have key roles in gene silencing also have critical developmental functions in C. elegans. Particularly interesting are a number of connections between silencing processes and germline development. Of all tissues, the germline goes to greatest lengths to prevent expression of unwanted genes. In particular we observe strikingly efficient silencing for factors whose normal role is to restrict cell fates in somatic tissue. Mechanisms for recognizing and silencing of such genes are essential to maintain a totipotent germline and are being analyzed by a combination of genetic and biochemical approaches.
Silencing responses to unusual DNA and RNA structures are by no means specific to C. elegans. Although mechanistic details may be different in different organisms, the underlying responses to several "aberrant" DNA and RNA triggers appear to be present in plants and fungi in addition to a broad spectrum of animal species. Silencing responses in plants have clearly been shown to reflect and respond to pathogenic challenges. In animal systems, the connections have yet to be fully worked out. In particular, we are interested in the roles of gene silencing processes in viral pathogenesis and tumor progression in mammalian systems.
