Effect of intercalating agents on RNA polymerase I promoter selection in Xenopus laevis

Inhibition of topoisomerase II does not inhibit transcription of RNA polymerase I and II genes

Injection of VM-26 (teniposide) into Xenopus oocytes inhibits the activity of topoisomerase II but does not inhibit transcription by RNA polymerases I and II. A specific assay for topoisomerase II, resolution of catenated DNA molecules into product rings, was used to quantitate VM-26 inhibition in vivo. When catenanes were injected without VM-26, about 60% of them were separated into product rings in the first 5 min after injection, and decatenation of the remainder was complete within 15 min. When VM-26 was coinjected, 60% of the catenanes were separated into product rings in the first 5 min after injection, but the remaining 40% were stable over the next 40 min. At 1 h after injection catenanes were no longer detected in the gel analysis, but the increasing numbers of linear product rings indicated that topoisomerase II continued to be inhibited by VM-26. These results suggest that a short lag of approximately 5 min is required for VM-26 to inhibit topoisomerase II and that after this initial period topoisomerase II is inhibited by more than 90%. There was no detectable decrease in transcription of injected rRNA and thymidine kinase (TK) genes or in the activity of the rRNA enhancer when these transcription templates were coinjected with VM-26. The time required for assembly of injected DNA into chromatin doubled in the presence of VM-26.

Inhibition of topoisomerase II does not inhibit transcription of RNA polymerase I and II genes

Injection of VM-26 (teniposide) into Xenopus oocytes inhibits the activity of topoisomerase II but does not inhibit transcription by RNA polymerases I and II. A specific assay for topoisomerase II, resolution of catenated DNA molecules into product rings, was used to quantitate VM-26 inhibition in vivo. When catenanes were injected without VM-26, about 60% of them were separated into product rings in the first 5 min after injection, and decatenation of the remainder was complete within 15 min. When VM-26 was coinjected, 60% of the catenanes were separated into product rings in the first 5 min after injection, but the remaining 40% were stable over the next 40 min. At 1 h after injection catenanes were no longer detected in the gel analysis, but the increasing numbers of linear product rings indicated that topoisomerase II continued to be inhibited by VM-26. These results suggest that a short lag of approximately 5 min is required for VM-26 to inhibit topoisomerase II and that after this initial period topoisomerase II is inhibited by more than 90%. There was no detectable decrease in transcription of injected rRNA and thymidine kinase (TK) genes or in the activity of the rRNA enhancer when these transcription templates were coinjected with VM-26. The time required for assembly of injected DNA into chromatin doubled in the presence of VM-26.

High initiation rates at the ribosomal gene promoter do not depend upon spacer transcription

We report experiments that test the model that in Xenopus laevis, RNA polymerase I is "handed over" in a conservative fashion from the T3 terminator to the adjacent gene promoter. We have introduced transcription-terminating lesions into the ribosomal DNA repeat by irradiating cultured cells with ultraviolet light. We used isolated nuclei to measure the effect of such lesions on transcription. UV damage sufficient to prevent all elongating RNA polymerase from reaching T3 from upstream had no adverse effect on the density of RNA polymerase at the very 5' end of the gene. We conclude that high rates of transcription initiation at the gene promoter do not depend upon polymerase passing from one repeat to the next or on polymerase initiating at the spacer promoters.

A test of 'polymerase handover' as a mechanism for stimulating initiation by RNA polymerase I

On the tandemly linked ribosomal genes of Xenopus laevis, the RNA polymerase transcribes past the 3' end of the 40S coding region and terminates at T3 just upstream of the gene promoter. The close proximity of T3 to the gene promoter, and the functional interdependence of these two elements, has led to the suggestion that polymerase terminating at T3 might be passed directly to the gene promoter. Such a mechanism might be necessary to maintain the characteristic high rate of transcription initiation seen on the ribosomal genes. We have performed a direct test of this model by introducing chain-terminating psoralen adducts into a circular plasmid containing a single gene promoter with its attendant T3 region upstream. We find that the psoralen adducts can completely prevent polymerase from traveling around the template circle (and thus prevent polymerase from approaching the promoter from upstream) without affecting the rate of transcription initiation at the gene promoter. This result suggests that recycling of polymerase from T3 to the promoter is not a significant mechanism in maintaining high initiation rates.

Inhibition of transcription in eukaryotic cells by X-irradiation: relation to the loss of topological constraint in closed DNA loops

X irradiation was found to inhibit in vivo transcription in mammalian, yeast, insect and avian cells in a dose-dependent manner. Measurements of DNA nicking indicated that about one DNA single-strand break per estimated DNA loop (domain) length is sufficient to explain the effect. The inhibitory effect was partially reversed by post-irradiation incubation of cells. During such incubation DNA nicking was considerably repaired. The size of transcripts was not changed by irradiation. The in vitro (run on) activity of RNA polymerase in nuclei isolated from irradiated cells also was not altered. The dose-response curves were different in various cells, correlating with the reported unequal average domain size of supercoiled DNA (and also replicon size) in diverse organisms.

In vivo transcription from multiple spacer rRNA gene promoters during early development and evolution of the intergenic spacer in the brine shrimp Artemia

The control of ribosomal RNA (rRNA) gene expression during development can be productively studied by examination of the relationship between promoter structure and function as well as the processing of primary transcripts. Toward this end total cell RNA was extracted from embryos at various stages and probed with cloned rRNA genes using the "dot blot" method. This exercise showed that rRNA gene expression is a stage-specific process and is thus under developmental control. S1 nuclease protection experiments localized fourteen different upstream DNA sites encoding 5'-termini of pre-rRNAs during this synthetic phase of development. There is no indication of any spacer fail-safe terminator function. The S1 approach contributed to the sequencing of several of the sites. Comparative sequence alignments reveal short conserved regions in DNAs corresponding to these sites, which are shown to fall into two structural classes. Sites 3, 4, 6 and 9 are proposed to function in transcription initiation and are found to have the consensus sequence 5'...T-A-T-A-T-Pu-Pu-Pu-G-Pu-Pu-G-T-C-A 3'. Sites 1, 2, 5 and 8 which are proposed to function in 5'-processing have the consensus sequence; 5'...Pu-G-T-Pu-T-T-G 3'. These short sequence conserved regions are hypothesized to serve as recognition signals for proteins within the rDNA transcription initiation complex and for 5'-processing enzymes, respectively. Sequencing of the intergenic spacer region from which a model for spacer evolution is derived shows that tandem ca 600 bp subrepeats explain much of the multiplicity observed within control sites.

Expression of ribosomal insertion in Drosophila: sensitivity to intercalating drugs

Ribosomal insertions in Drosophila are transcribed at very low levels. The abundance of the most prominent 0.8 kb type 1 insertion transcript increased up to 60-fold when cultured cells were exposed to the DNA intercalating drug chloroquine. After injection of insertion-containing rDNA in circular form into Xenopus laevis oocytes an apparently identical 0.8 kb insertion transcript was synthesized, and its accumulation was stimulated several fold by coinjection of chloroquine or ethidium bromide. We suggest that ribosomal insertions are assembled in a chromatin conformation that lacks unconstrained torsional stress, accounting for the inactivity of these DNA regions; introduction of stress by intercalation results in activation of transcription from the insertion sequences.