Contact points between a positive transcription factor and the Xenopus 5S RNA gene

We have investigated the contact points of a positive transcription factor with the internal control region of the 5S ribosomal RNA genes of Xenopus. The methylation of any one of eight G residues clustered at the 3′ end of the internal control region on the noncoding strand of the DNA or the ethylation of their surrounding phosphates interferes with the binding of this protein. The importance of the 5′ half of the control region is shown by a binding affinity of the protein to oocyte 5S RNA genes that is one fourth that to somatic 5S RNA genes. This can be attributed to two base changes at residues 53 and 55 in the 5′ part of the control region. The different affinities of the transcription factor for the oocyte and somatic 5S RNA genes may contribute to their differential expression in somatic cells. The almost exclusive location of strong contact points on the noncoding strand of the gene suggests how transcription events could proceed repeatedly along a gene that is assembled into a stable transcription complex. It is proposed that the complex is transiently shifted to the noncoding strand as each round of RNA synthesis occurs from the coding strand.