Optimized reaction conditions and specific inhibitors for initiation of transcription by RNA polymerase II in nuclei from cultured mammalian cells

Differential RNA elongation controls the variant surface glycoprotein gene expression sites of Trypanosoma brucei

The protozoan parasite Trypanosoma brucei develops antigenic variation to escape the immune response of its host. To this end, the trypanosome genome contains multiple telomeric expression sites competent for transcription of variant surface glycoprotein genes, but as a rule only a single antigen is expressed at any time. We used reverse transcription-PCR (RT-PCR) to analyse transcription of different segments of the expression sites in different variant clones of two independent strains of T. brucei. The results indicated that RNA polymerase is installed and active at the beginning of many, if not all, expression sites simultaneously, but that a progressive arrest of RNA elongation occurs in all but one site. This defect is linked to inefficient RNA processing and RNA release from the nucleus. Therefore, functional transcription in the active site appears to depend on the selective recruitment of a RNA elongation/processing machinery.

Post-transcriptional transfer of gamma-thio affinity label to RNA in isolated parsley nuclei

As an alternative to soluble plant transcription systems, we examined the reinitiation capacity of isolated parsley nuclei. Nuclear chalcone synthase in vitro transcripts were affinity-labelled with gamma-thio-ATP, gamma-thio-GTP or beta-thio-ATP, and purified by chromatography on a mercury Sepharose affinity column. Primer extension and subsequent PCR amplification of these in vitro transcripts revealed gamma-thio-ATP-dependent, but no beta-thio-ATP-dependent, signals, although affinity labelling of overall in vitro transcripts still occurred with beta-thio-ATP. We conclude that the described plant nuclei reinitiated transcription non-specifically and that post-transcriptional transfer of the gamma-thio affinity label severely interfered with the detection of reinitiated transcripts.

Specific transcription and reinitiation of 2,4-D-induced genes in tobacco nuclei

In order to study the effects of trans-acting factors on cis-acting elements in plant genes an in vitro reinitiating nuclear transcription system is needed. Here we report that run-on experiments with nuclei isolated from 2,4-D-treated auxin-starved early-stationary-phase cells of tobacco clearly show reitintiation of transcription of specific 2,4-D-induced genes. Using gamma-thio nucleotides and [alpha-32P]-UTP we were able to demonstrate the presence of reinitiated labelled specific RNAs after isolation on a mercury-agarose affinity column. Addition of heparin as an inhibitor blocked this reinitiation. In a primer extension assay we found that the new transcripts initiate at approximately the same site as used in vivo.

Specific transcription and reinitiation of class III genes in wheat embryo nuclei and chromatin

Chromatin isolated from wheat germ embryos has a transcription efficiency for RNA polymerase III (pol III) closely approaching that for isolated wheat germ nuclei. Transcription in nuclei and chromatin is inhibited 5-10-fold by the addition of heparin, suggesting that free pol III molecules bind to chromatin and initiate transcription during thein vitro incubation. Nuclei were shown to have similar transcriptional activity in potassium chloride and potassium acetate. Nuclei and chromatin exhibited different salt optima for transcription. Neither nuclei nor chromatin were strongly stimulated by exogenous protein fractions. The data presented here suggest that in wheat germ nuclei the complete transcriptional apparatus is stably bound to the chromatin. Wheat germ nuclei may serve therefore as an enriched source for a solublein vitro transcription system.