Figure 3.

Footprint of PPBF on the U4X proximal region. DNA fragments end-labeled on either the upper or lower strand were incubated with 0, 2, 6, or 18 μl of affinity-purified PPBF (as indicated above the individual lanes), subjected to partial DNase I digestions, and analyzed in denaturing gels. A + G and C + T chemical sequencing reactions were run alongside as markers. The location of the palindromic sequence in each ladder is indicated by the hexagons labeled “P,” and the extent of DNA sequences from −50 to −80 (relative to the transcription initiation site) is delineated by the lines extending from the hexagons. (In the fourth lane of the left panel [2 μl PPBF], the bands are light due to over-digestion and partial loss of sample.) At the bottom of the figure, the nucleotide sequence of the U4X proximal regulatory region is shown, and the horizontal lines indicate the protected regions on the upper and lower strands. Thick lines denote strong protection, and thinner lines weaker protection. Dots indicate sites of enhanced DNase I cleavage induced by the binding of PPBF.