Effect of transcription of yeast chromatin on DNA topology in vivo

Coding regions of transcribed and non-transcribed genes typically differ in chromatin structure. However, it is not known what kind of alterations in nucleosome or chromatin structure these differences reflect. To determine whether changes in nucleosome topology accompany transcription, we introduced into yeast a multicopy plasmid bearing the gene coding for the heat shock protein HSP26. The plasmid-borne gene is assembled into chromatin, and is induced by heat shock in the same manner as the endogenous HSP26 gene. A small change in linking number in the HSP26 plasmid accompanies heat shock. This change is consistent with that previously reported for thermal untwisting of DNA in yeast chromatin, and is equivalent in magnitude to that observed in control plasmids which lack heat-shock response elements. These data indicate that no stable alteration in nucleosome topology accompanies transcription of the heat shock gene. Moreover, the kinetics of the observed changes in linking number indicate that topoisomerase relaxes the thermally induced torsional stress in 1-5 min. We conclude that if alterations in nucleosome topology accompany polymerase passage, recovery must take place within this time period.

The transcription complex of the Xenopus somatic 5 S RNA gene. A functional analysis of protein-DNA interactions outside of the internal control region

We have defined protein-DNA interactions associated with the transcription complex of a Xenopus somatic 5 S RNA gene under efficient in vitro transcription conditions. Transcription factor IIIA, the internal control region of the 5 S RNA gene and specific DNA sequences 5' and 3' of the internal control region are all involved in the formation of a multiprotein complex. Specific protein-DNA interactions outside of the 5 S RNA gene itself, revealed by DNase I footprinting, have no apparent role in the transcription process. Sequences within the 5 S RNA gene, 5' of the internal control region, are not essential for transcription by RNA polymerase III in vitro, but do contribute to its efficiency.

Nucleosomes inhibit both transcriptional initiation and elongation by RNA polymerase III in vitro

To examine the effect of nucleosomes on in vitro transcription, purified chicken erythrocyte core histones and plasmid DNA bearing the Xenopus 5S RNA gene were assembled into nucleosomes and used as templates for transcription in a Xenopus oocyte nuclear extract. Plasmids having a nucleosome incorporating a specific region of the gene were selected by treating the reconstituted molecules with restriction endonucleases. In this way, it was shown that a nucleosome on or close to the internal control region of the 5S RNA gene inhibits transcription. Furthermore, experiments with 5S maxigenes showed that RNA polymerase III, in contrast to SP6 RNA polymerase, will not transcribe through a nucleosome in vitro.

Yeast nucleosomes allow thermal untwisting of DNA

Thermal untwisting of DNA is suppressed in vitro in nucleosomes formed with chicken or monkey histones. In contrast, results obtained for the 2 micron plasmid in Saccharomyces cerevisiae are consistent with only 30% of the DNA being constrained from thermal untwisting in vivo. In this paper, we examine thermal untwisting of several plasmids in yeast cells, nuclei, and nuclear extracts. All show the same quantitative degree of thermal untwisting, indicating that this phenomenon is independent of DNA sequence. Highly purified yeast plasmid chromatin also shows a large degree of thermal untwisting, whereas circular chromatin reconstituted using chicken histones is restrained from thermal untwisting in yeast nuclear extracts. Thus, the difference in thermal untwisting between yeast chromatin and that assembled with chicken histones is most likely due to differences in the constituent histone proteins.

Effect of trypsinization and histone H5 addition on DNA twist and topology in reconstituted minichromosomes

Free DNA in solution exhibits an untwisting of the double helix with increasing temperature. We have shown previously that when DNA is reconstituted with histones to form nucleosome core particles, both the core DNA and the adjacent linker DNA are constrained from thermal untwisting. The origin of this constraint is unknown. Here we examine the effect of two modifications of nucleosome structure on the constraint against thermal untwisting, and also on DNA topology. In one experiment, we removed the highly positively charged histone amino and carboxy termini by trypsinization. Alternatively, we added histone H5, a histone H1 variant from chick erythrocytes. Neither of these modifications had any major effect on DNA topology or twist in the nucleosome.

Nucleosome core particles suppress the thermal untwisting of core DNA and adjacent linker DNA

Covalently closed circular DNA is known to undergo a temperature-dependent change in helical twist. We have reconstituted nucleosome core particles onto closed circular DNA and measured the thermal untwisting of the DNA as a function of nucleosome density. The results demonstrate that the DNA associated with the nucleosome core particle does not alter its twist when the temperature is varied between 4 degrees C and 37 degrees C, and that the length of DNA prevented from thermal untwisting includes the linker as well as the core DNA.