Originally discovered in a search for RNA polymerase II-associated factors, the Paf1 complex (Paf1C) is best characterized for its roles in regulating transcription elongation. The complex co-localizes with RNA polymerase II from the promoter to the 3’ end of genes and has been linked to a growing list of transcription-related processes including: elongation through chromatin, histone modifications, and recruitment of factors important in transcript maturation. The complex is conserved throughout eukaryotes and is comprised of the proteins Paf1, Ctr9, Cdc73, Rtf1, and Leo1. The domain structures of Paf1C subunits are largely undefined and have few clear homologs, making it difficult to postulate for or localize functions to the individual subunits. To understand mechanistically how Paf1C coordinates its functions and interactions, I took an approach utilizing biochemical, biophysical, and structural techniques to characterize proteins within Paf1C, specifically focusing on the Rtf1 subunit.
The goal of my thesis work was to determine the molecular mechanism by which Rtf1 influences transcription and chromatin structure. To this end I focused on studying different functional domains within Rtf1. I provided a molecular description of how Rtf1 mediates Paf1C recruitment to elongating RNA polymerase II. Recruitment of Rtf1 is controlled by its centrally located Plus3 domain and a direct interaction with the conserved elongation factor Spt5. I solved the co-crystal structure of the human Plus3 domain bound to a phosphorylated C-terminal repeat of Spt5. The structure revealed the basis for recognition of the repeat motif of Spt5, an important component in the recruitment of regulatory factors to RNA polymerase II. I have performed further structural characterization of Rtf1, studying the N-terminal histone modification domain. To gain insight into the molecular mechanism underlying the domain’s function, I successfully crystallized and solved the structure of a minimal region of Rtf1 that is necessary and sufficient for Rtf1-mediated histone modifications. The structure, paired with conservation analysis and genetic phenotype data, have allowed us to identify important surfaces on Rtf1 that function in regulating chromatin structure. Taken together these studies shed new light onto the mechanism by which Paf1C influences the complex network of regulatory interactions required for eukaryotic transcription
