Functional Genomics
We believe it is possible to extract more complete informational content from sequenced genomes and advance the operational definition of "genetic meaning." We combine unbiased determinations of transcriptional activity at high resolution with innovative functional tests in sophisticated model systems.
In a pilot study, we applied "saturation tiling" for unbiased mapping of noncanonical transcripts from a defined interval of the Drosophila genome. Three findings provide an exciting glimpse at under-appreciated transcriptional activity:
- The scope of unannotated transcription is widespread.
- Much of this noncanonical activity responded to stimulus challenge.
- Stimulus-dependent RNAs were clearly linked to a master regulator that intimately regulates conventional outputs.
To determine whether non-canonical RNAs encode authentic biologic function, we are interrogating unannotated transcripts for relevant phenotypes. Noncanonical RNAs could exert subtle activities and produce subtle phenotypes if eliminated.
Consequently, as a means to both enhance sensitivity and narrow the scope of functional experiments, we focus on stimulus-induced transcripts, since it is reasonable that they might promote adaptive responses when challenged and, if removed, cause stimulus-conditional phenotypes. The stimulus chosen for these studies exploits a standard protocol of radiation stress that we developed over the last decade.
We are analyzing custom mutations that eliminate a selected collection of noncanonical RNAs for relevant phenotypes and other indicators of molecular activity.
Mobile Elements
In humans, p53 is implicated in age-related diseases and altered in most human cancers. As transcription factors, p53 genes mediate selective activation and repression of targets to specify adaptive responses. However, despite extensive characterization, precisely how p53 acts to suppress tumors and mitigate age-related disease remains poorly understood. Since p53 genes are broadly conserved, ancestral properties of these genes offer promising routes towards understanding functions of p53 that become deranged in human diseases. Toward this goal, we are exploring the p53 regulatory network in the Drosophila system.
This genetic model offers uniquely powerful opportunities for interrogating conserved networks that support human pathologies and, like its mammalian counterparts, the Drosophila p53 gene specifies adaptive responses to damage that preserve genome stability. Leveraging experimental tools that visualize real-time p53 action in vivo, we discovered that p53 normally contains the activity of transposons, which are mobile elements broadly implicated in sporadic and heritable human disease. We also showed that p53 genetically interacts with the piRNA pathway, an ancient and highly conserved pathway dedicated to the suppression of transposons in all animals. In addition, by exchanging the fly p53 gene with human p53 counterparts, we found that normal human p53 genes can restrain transposons but mutated p53 alleles from cancer patients can not.
These combined discoveries suggest that p53 acts through highly conserved mechanisms to contain transposons. Furthermore, since human p53 mutants are disabled for this activity, our findings raise the possibility that p53 mitigates disease by suppressing the movement of transposons. Consistent with this, we uncovered preliminary evidence for unrestrained retrotransposons in p53 mutant mice and in p53-driven human cancers.