Determination of occupancies of the SPH and GT-IIC transcription factor binding motifs in SV40: Evidence for two forms of transcription elongation complex

Occupancies of the SPH and GT-IIC sequence motifs in the native SV40 late transcription elongation complex were determined by assessing blockage to restriction enzyme cleavage. Cleavages specific to the transcription elongation complex were quantified by radioactive extension labeling and polymerase run-off analysis. The SPH motif was assayed by SphI digestion and found to be unoccupied. In contrast, digestion with PvuII at the GT-IIC site was blocked in 36% of the complexes, indicating that approximately a third of the complexes are occupied by factor. This fractional occupancy indicates that there are at least two forms of SV40 late transcription elongation complexes, one form with the GT-IIC site occupied by a factor and another with the site vacant. (C) 1996 Academic Press, Inc.