Unwinding of the DNA helix in simian virus 40 chromosome templates by RNA polymerase.

We measured the distortion of the DNA helix by RNA polymerase transcribing simian virus 40 (SV40) chromosome templates and compared it with the distortion caused by the enzymes as it transcribes naked SV40 DNA, using RNA polymerase from Escherichia coli. Purified DNA topoisomerase I was added to the transcription reactions and the number of supercoil turns in DNA, after deproteinising and removal of RNA, was determined by gel electrophoresis and band-counting. The number of polymerase molecules bound per naked DNA molecule was determined by electron microscopy. Each bound RNA polymerase distorted the template in such a way as to lead to on apparent average of 0.6-0.7 negative superhelical turn in the extracted DNA. Thus only few base-pairs are melted per RNA polymerase molecule. When SV40 chromosomes were transcribed the extracted DNA had a higher number of supercoil turns than DNA extracted from the initial chromosomes. We conclude that the polymerase deforms the DNA in chromatin in the same way as it deforms pure DNA. From control experiments with inhibitors of initiation we estimated that on average 9-10 RNA polymerase molecules were bound per SV40 chromosome. This suggests that transcription can proceed while the majority or all the nucleosomal structures are intact on an SV40 DNA molecule. We discuss the implications of these findings for the mechanism of transcription of chromatin.

Transcription of Simian Virus 40 chromosomes in an extract of HeLa cells.

Simian Virus 40 (SV40) chromosomes were incubated with a concentrated extract of HeLa cells containing RNA polymerase II and other factors involved in transcription. SV40-specific RNA was synthesized. In the absence of HeLa cell extract the synthesis of labeled RNA by endogenous RNA polymerase in the chromosome preparations amounted to less than one tenth of that when the HeLa cell extract was present. Incubation with the HeLa extract increased the amount of Sarkosyl-resistant (i.e., transcribing) RNA polymerase on the SV40 chromosomes. When restriction endonucleases able to cut SV40 DNA were added to transcription reactions containing SV40 chromosomes and the HeLa cell extract, RNAs of discrete length were produced. The RNAs were identified as correctly initiated run-off transcripts of the early and late genes. Most of the RNA synthesized by the HeLa extract from SV40 chromosomes was from the region of the late genes, whereas transcription of purified SV40 DNA was from both the early and the late regions, with the early transcripts predominating.