Specific Structural Features of the RNA Polymerase I Core Promoter Element Targeted by Core Factor

Abstract

In yeast, Core Factor (CF) is a critical and essential RNA Polymerase I (Pol I) transcription factor that plays fundamental roles in the transcription process by recruiting Pol I and opening Pol I promoter DNA before initiation. CF binds to a ~24 bp region in the rDNA promoter called the Core Element (CE) prior to Pol I recruitment. Pol I transcribes the rDNA gene into the 35S precursor rRNA (pre-rRNA) which serves both catalytic and structural roles in the ribosome. Up-regulation of Pol I transcription has been linked to a variety of human cancers, as increased protein production can facilitate the rapid growth of cancer cells. Thus, Pol I transcription is a promising target for therapeutic development. Previous studies from our lab suggest that CF and its human orthologue, Selectivity Factor 1 (SL1), use an evolutionarily conserved mechanism to target DNA, governed by the structural features of their respective promoters. Eukaryotic rDNA promoters also exhibit conserved structural features, such as intrinsic curvature and kinks but show a distinct lack of sequence conservation. These sequence independent structurally conserved features of rDNA promoters might explain how they are being recognized by CF and its orthologues. Our findings here revealed that CF is capable of tolerating mutations at some positions of the CE while mutation in the rigid “A” patch being particularly sensitive to mutations changing structural properties. Along with conditional tolerance for sequence mutations, our results show that CF prefers a variety of structural features such as overall increased bendability and decreased curvature as well as specific profiles of bendability. Furthermore, we describe the preferences of CF for the parameters of helix twist, propeller twist, roll, and minor groove width.