The Xenopus laevis ribosomal gene promoter contains a binding site for nuclear factor-1

Common sequence elements are important for transcription and replication of the extrachromosomal rRNA-encoding genes of Tetrahymena

Three types of conserved sequence elements have previously been identified in the generally non-conserved, 5' non-transcribed spacer region of the rRNA-encoding gene (rDNA) of Tetrahymena species. In vivo and in vitro experiments have identified the start point (tsp) for rDNA transcription. Comparative sequence analysis suggested that the type-I sequence element was likely to function as the promoter for rDNA transcription. We have used in vitro transcription assays to demonstrate that sequences in the 3' half of the type-I repeat located proximal to the tsp are essential for the accurate initiation of rRNA synthesis. These sequences define the 5' boundary of the core or minimal promoter element and include the sequences which function in rDNA replication and maintenance in the homologous regions in two upstream type-I sequence elements. These sequences may bind factors important for both the transcription and replication of rDNA.

Complex formation of nuclear proteins with the RNA polymerase I promoter and repeated elements in the external transcribed spacer of Cucumis sativus ribosomal DNA

Complex repetitive structures are located downstream of the transcription initiation site in the intergenic spacer (IGS) of the rRNA genes in Cucumis sativus (cucumber). In order to show that these repetitive elements of the 5'external transcribed spacer (ETS) are probably involved in transcriptional regulation as protein binding sites DNA-protein binding assays were carried out. The same proteins that recognize two binding sites in the promoter region analysed (upstream binding element between -164 and -105, and core promoter between -41 and +16) show binding affinity to the complex structures of the 5'external transcribed spacer. These proteins also seem to interact with the single strands of the respective DNA regions suggesting an effect on transcriptional regulation while the DNA is transcribed and, therefore, is single-stranded. Three proteins were isolated by affinity column chromatography; these proteins turned out to be much smaller (16, 22, and 24 kDa, respectively) than promoter and enhancer binding proteins in animal systems. Additionally, a 70-kDa protein could be characterized cooperating with a small segment of the repeated elements but not with the promoter.

A DNA-binding protein is required for termination of transcription by RNA polymerase I in Xenopus laevis

We describe a partially fractionated in vitro transcription system from Xenopus laevis for the assay of transcription termination by RNA polymerase I. Termination in vitro was found to require a specific terminator sequence in the DNA and a DNA-binding protein fraction that produces a footprint over the terminator sequence.

A DNA-binding protein is required for termination of transcription by RNA polymerase I in Xenopus laevis

We describe a partially fractionated in vitro transcription system from Xenopus laevis for the assay of transcription termination by RNA polymerase I. Termination in vitro was found to require a specific terminator sequence in the DNA and a DNA-binding protein fraction that produces a footprint over the terminator sequence.

Point mutation analysis of the Xenopus laevis RNA polymerase I core promoter

The core region of the Xenopus laevis pre-ribosomal RNA promoter was subjected to point mutation analysis. A total of 27 point mutants within a 78 base pair region from -64 to +14, (relative to the start of transcription at +1), were assayed by oocyte microinjection. The results locate the 3' boundary of the core promoter at +4 and the 5' boundary at between -33 and -39 and suggest that this region of the Xenopus promoter is generally similar in organisation to mammalian core promoters. In particular, the conserved guanidine nucleotides at -7 and -16 are clearly essential for promoter function. The data suggest that interactions between the transcription machinery and the promoter occur in four distinct regions around +2 to +4, -7, -17 to -20 and -28 to -33. This particular periodicity of functionally important nucleotides is consistent with a model in which all protein-DNA interactions take place from predominantly one side of the DNA helix.

The Xenopus ribosomal gene enhancers bind an essential polymerase I transcription factor, xUBF

We purified xUBF on the basis of its ability to specifically bind the enhancer elements of the Xenopus laevis rRNA genes. xUBF also binds to both upstream and downstream regions of the X. laevis ribosomal gene promoter and is essential for polymerase I transcription. Unexpectedly, xUBF binds to both upstream and downstream regions of the human ribosomal gene promoter, producing footprints that are indistinguishable from the footprints produced by hUBF, a previously described polymerase I transcription factor isolated from human cells. Despite extensive sequence divergence of vertebrate polymerase I promoters, these data suggest an evolutionary conservation of the primary DNA-protein interaction.