HMG proteins and DNA flexibility in transcription activation

The relative stiffness of naked DNA is evident from measured values of long itudinal persistence length (similar to 150 bp) and torsional persistence l ength (similar to 180 bp). These parameters predict that certain arrangemen ts of eukaryotic transcription activator proteins in gene promoters should be much more effective than others in fostering protein-protein interaction s with the basal RNA polymerase II transcription apparatus. Thus, if such i nteractions require some kind of DNA looping, DNA loop energies should depe nd sensitively on helical phasing of protein binding sites, loop size, and intrinsic DNA curvature within the loop. Using families of artificial trans cription templates where these parameters were varied, we were surprised to find that the degree of transcription activation by arrays of Gal4-VP1 tra nscription activators in HeLa cell nuclear extract was sensitive only to th e linear distance separating a basal promoter from an array of bound activa tors on DNA templates. We now examine the hypothesis that this unexpected r esult is due to factors in the extract that act to enhance apparent DNA fle xibility. We demonstrate that HeLa cell nuclear extract is rich in a heat-r esistant activity that dramatically enhances apparent DNA longitudinal and torsional flexibility. Recombinant mammalian high-mobility group 2 (HMG-2) protein can substitute for this activity. We propose that the abundance of HMG proteins in eukaryotic nuclei provides an environment in which DNA is m ade sufficiently flexible to remove many constraints on protein binding sit e arrangements that would otherwise limit efficient transcription activatio n to certain promoter geometries.