Sequence-specific binding of a transcription factor TFID to the promoter region of mouse ribosomal RNA gene

The binding sites of TFID, a species-dependent transcription factor, on the mouse ribosomal RNA gene (rDNA) have been analyzed by DNase I footprinting using partially purified TFID. The region -12 to -140 spanning over the upper half of the core promoter (-12 to -40) and an upstream sequence (-40 to -140) was protected. Human fraction D could not protect corresponding regions of mouse rDNA indicating that the protection was indeed caused by TFID. This was corroborated by a competition experiment using point mutants having different affinities to TFID. The analysis with deletion mutants of upstream sequence together with the competition data indicates that the binding of TFID to the core sequence is required for the binding of TFID or some co-purified proteins to the upstream sequence, while the presence of upstream sequence stabilizes the TFID binding to the core sequence. The pattern of protection of the upstream sequence suggests that at least a part of the upstream binding does not require a specific DNA sequence there but rather is caused by protein-protein interaction involving TFID bound with the core sequence. These protection patterns did not change with TFID highly purified by sequence-specific DNA affinity chromatography.