Dark Matter: Functional Analyses of Noncanonical Transcript

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.