PLANT RIBOSOMAL DNA EXTERNAL SPACER BINDING-FACTORS - A NOVEL PROTEINBINDS SPECIFICALLY TO A SEQUENCE CLOSE TO THE PRIMARY PRE-RIBOSOMAL-RNA PROCESSING SITE

Sequence analyses of the ribosomal DNA (rDNA) external spacer region r evealed a peculiar structure around the primary pre-rRNA processing si te in radish. Using the electrophoretic mobility shift assay, DNAse I footprinting and methylation interference analysis, we have identified in radish extracts a novel nuclear factor, NF B, that recognises this region. NF B binds to a unique CGATTTTGCCCCTGA sequence located 164 b p downstream of the transcription initiation site and immediately upst ream of the pre-rRNA processing site. Interestingly, this motif is fla nked by four homologous sequences, including the primary pre-rRNA proc essing site, which are not recognised by NF B. Based on these data and the prediction that alternative hairpin loops can be formed in this r egion of the nascent pre-rRNA, a putative role for NF B as a factor co upling transcription and pre-rRNA processing is discussed. NF B is uni que among plant and animal rDNA-binding proteins and it differs from a previously described radish factor and from other proteins that bind to plant rDNA promoters.