|Faculty and Research
Jack Keene, PhD
James B. Duke Professor
The Keene Laboratory has a long-term interest in the structures and functions of viral and mammalian genomes. In the early 1980's, they determined the first genomic sequences for rabies, Ebola and VS viruses, and discerned the origins of defective interfering viruses. Their research focused on small noncoding RNAs called the leader RNAs that are generated by these viruses. They found that leader RNAs of VSV and rabies bind to a cellular host RNA-binding protein (RBP) called La that is now known to assist virus infectivity by blocking access of the RIG-I protein to the leader RNA. RIG-I activates the type I interferon response when it binds to small noncoding RNAs like the leader RNAs. In 1984, the Keene lab derived cDNA clones of the La RBP using sera from patients with autoimmune diseases such as Lupus and Sjogren's syndrome. Novel procedures developed in the Keene lab to clone the La gene led to the cloning of several other human genes involved in autoimmunity and to the development of the first recombinant diagnostic test for autoantibodies. These autoimmune RBPs were found to contain a common RNA-binding motif that Keene named the RNA Recognition Motif (RRM) and demonstrated that the RRM forms the core of a functional unit RNA-binding domain. Since 1991, the lab has focused on the functions of human RRM-ELAV/Hu RBPs demonstrating that they bind to AU-rich sequences, and increase the stability and translation of their mRNA targets.
More recently, the Keene lab devised methods to identify structurally and functionally related cellular mRNAs and microRNAs that cluster together based upon their association with ELAV/Hu RBPs and other RNA-binding proteins. This general approach has been termed ribonomics because it uses microarrays or Solexa sequencing to determine mRNAs and microRNAs associated with ribonucleoprotein complexes. This novel approach to functional genomics is has been used and adapted in many laboratories to analyze biological responses such as virus infectivity, tumorigenesis, genotoxic agents, radiation and developmental inducers. These studies have revealed that functionally related mRNA subsets are post-transcriptionally coordinated, thereby, representing the organizational state of genetic information between the genome and the proteome. Based on these findings, Keene proposed the concept of Post-Transcriptional RNA Operons and Regulons (PTRO) based upon the combinatorial regulation of mRNAs at all steps between transcription and translation, potentially revealing a RNP-regulatory code or "USER-code". The PTRO is a simplifying model that explains the organization and dynamic properties of multiple mRNA and noncoding RNAs located in the nucleus and cytoplasm. Many dozens of PTROs have since been reported in archaea, yeasts, worms, flies, trypanosomes, plants, humans and other mammals, and unexpectedly, in bacteria. The PTRO model has a variety of therapeutic implications as it can be used to identify dynamic changes in time and space of all cellular mRNAs and noncoding RNAs involved in growth regulation, neuronal plasticity, immune regulation and cancer.