FIG. 5.

UBF binds extensively over the human rDNA repeat. (A) The structure of the human rDNA repeat is illustrated. Solid black boxes indicate 18S, 5.8S, and 28S rRNA coding sequences. Open boxes represent 5′ and 3′ external transcribed spacers. Vertical arrows represent transcription termination elements. The cross-hatched box represents a cdc27 pseudogene. The scale bar below represents the length of the repeat, in kilobases. The position and size of subclones of the human rDNA repeat (A1 to D5) are shown below the repeat. Clones with an asterisk are devoid of alu elements. (B) Insert DNA from each of the above subclones was generated by PCR and arrayed onto nylon filters (top). Fragments derived from vector DNA (D6 to D8) provided negative controls. The identity of each insert is indicated by letters and numerals on the left and top of the array, respectively. Inserts devoid of alu elements were also arrayed independently (bottom). In panel B, the identities of each insert are shown. Arrays were hybridized with an equimolar mixture of the cosmid N68f1 and the plasmid pCD7H/B (left). In experiments shown in the middle and right panels, arrays were probed with radiolabeled DNA from α-UBF and preimmune ChIP assays, respectively. (C) The relative UBF loading values for the experiment shown above. (D) The relative UBF loading values for an independent experiment (data not shown).