Defining the mechanisms of epigenetic information flow - Chromatin, the assemblage of protein, DNA and RNA that represents the physiologic form of the eukaryotic genome, imposes a million-fold length-scale compaction to fit DNA in the nucleus. Rather than serving as mere static packaging, chromatin structure acts as a dynamic regulator of underlying DNA function. Local chromatin structure may be stable for decades, yet is sufficiently dynamic to respond to signaling pathways, potentiating transcriptional program changes in development, disease, and environmental changes. Indeed, cellular identity and changes thereof are intimately connected to chromatin states-- keeping a neuron a neuron and not a liver cell. Apart from DNA sequence-specific transcription factors, the information carriers responsible for this structural variation are chemical modifications to the genome itself and attendant histone proteins involved in packaging (often referred to as “epigenetic” marks), as well as noncoding RNA acting at the chromatin interface. Although little known about these epigenetic information carriers, it is clear that they play crucial roles in development, cognition and disease. Elucidation of the molecular mechanisms by which epigenetic information carriers impact chromatin structure and function, particularly in the context of transcriptional activation is the unifying theme of the Ruthenburg lab. In the next four years, we will discover and characterize the detailed mechanisms of new epigenetic information carriers, focusing on nucleosome-level variation and orphaned histone modifications, defining binding partners for recently appreciated DNA modifications and their function, and performing detailed mechanistic characterization of a class of molecules we discovered--chromatin-enriched noncoding RNA that act as local transcriptional activators. In addition, we will biochemically define the function of RNA in the MLL/SET1 family of histone modification complexes and its functional consequences in cellular contexts. Our interdisciplinary work in these areas will require the development of new tools and experimental approaches—our outstanding track record of pioneering tool development with NIGMS funding makes the case that future efforts will meet with similar success. The fundamental mechanistic understanding of epigenetic information systems we will develop through these avenues will impact our understanding of nuclear function and its dysregulation in disease.
