The eukaryotic CCAAT and TATA boxes, DNA spacer flexibility and looping

Regulation of RNA transcription in eukaryotic polymerase II promoters involves a complex assembly of protein factors. Some of the factors bind to their cognate DNA-sequence elements while others mediate between the DNA bound ones. In order to enable protein-protein interaction, their spatial positioning with respect to each other is critical. Here two DNA-sequence-elements are investigated, the CCAAT and the TATA boxes and their spacers. Whereas the position of the TATA is fixed at about -30, that of the CCAAT can vary substantially from -50 to -200. Despite the variable loop sizes, the CTF (CCAAT-binding) protein interacts--either directly or indirectly via a co-activator--with the general basal TATA-binding transcription factors. Sequence analysis of the spacers, as a function of their sizes, reveals that in the upstream regions of the spacers RR and YY are abundant. In the downstream, 3' region of the spacers RY and YR are very frequent. The DNA sequence elements and their intervening spacers are analyzed in terms of their geometry, anisotropic flexibility and local superhelical density. Our results indicate that the CCAAT and its vicinity is rigid, whereas the TATA and its surroundings is flexible. It is the large flexibility of this region in twist and in roll which allows DNA looping. General mechanistic implications for pol II promoters are discussed.