Naked DNA Templates Research Articles

Role of Nucleosomal Cores and Histone H1 in Regulation of Transcription by RNA Polymerase II

The relation between chromatin structure and transcriptional activity was examined by in vitro transcription analysis of chromatin reconstituted in the absence or presence of histone H1. To maintain well-defined template DNA, purified components were used in the reconstitution of chromatin. Reconstitution of nucleosomal cores to an average density of 1 nucleosome per 200 base pairs of DNA resulted in a mild reduction of basal RNA polymerase II transcription to 25 to 50 percent of that obtained with naked DNA templates. This nucleosome-mediated repression was due to nucleosomal cores located at the RNA start site and could not be counteracted by the sequence-specific transcription activators Sp1 and GAL4-VP16. When H1 was incorporated into the chromatin at 0.5 to 1.0 molecule per nucleosome (200 base pairs of DNA), RNA synthesis was reduced to 1 to 4 percent of that observed with chromatin containing only nucleosomal cores, and this H1-mediated repression could be counteracted by the addition of Sp1 or GAL4-VP16 (antirepression). With naked DNA templates, transcription was increased by a factor of 3 and 8 by Sp1 and GAL4-VP-16, respectively (true activation). With H1-repressed chromatin templates, however, the magnitude of transcriptional activation mediated by Sp1 and GAL4-VP16 was 90 and more than 200 times higher, respectively, because of the combined effects of true activation and antirepression. The data provide direct biochemical evidence that support and clarify previously proposed models in which there is depletion or reconfiguration of nucleosomal cores and histone H1 at the promoter regions of active genes.

Transcription on nucleosomal templates by RNA polymerase II in vitro: inhibition of elongation with enhancement of sequence-specific pausing.

The process by which RNA polymerase II elongates RNA chains in vivo, where the template is at least partially in a nucleosomal configuration, remains poorly understood. To approach this question we have partially purified RNA polymerase II transcription complexes paused early in elongation. These complexes were then used as substrates for chromatin reconstitution. Elongation of the nascent RNA chains on these nucleosomal templates is severely inhibited relative to elongation on naked DNA templates. Elongation on the nucleosomal templates results in a reproducible template-specific pattern of transcripts generated by RNA polymerase pausing. The RNA polymerases are not terminated because the large majority will resume elongation upon the addition of Sarkosyl or 400 mM KCl. The effectiveness of RNA polymerase II pause/termination sites is enhanced by the presence of nucleosomes. For example, a pause site similar in sequence to the c-myc gene exon 1 terminator is used four to seven times more effectively in reconstituted templates. A comparison of elongation on templates bearing phased nucleosomes and on reconstituted templates that show no predominant phasing pattern indicates that the locations of pause sites are not related to the positions of the nucleosomes. Rather, the major determinant of RNA polymerase pausing on the nucleosomal templates appears to be the underlying DNA sequence.

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

An assay that employs guanosine 5'-O-(2-thiotriphosphate) was used to measure correct initiation of RNA chains in isolated cell nuclei, where chromatin structure is relatively undisturbed. RNA chains initiated with guanosine 5'-O-(2-thiotriphosphate) were separated from the remaining RNA by mercury-Sepharose column chromatography and analyzed for correctly initiated mouse mammary tumor virus RNA with a T1 nuclease protection assay. The monovalent cation concentration dependence for initiation in isolated nuclei was similar to that previously observed for initiation from naked DNA templates (optimum near 90 mM) but different from that for elongation of nascent RNA chains. However, in contrast to the systems that employ naked DNA templates, initiation efficiency in the nuclear system was relatively unaffected by moderate changes in pH (6.7-8.3), temperature (25-37 degrees C), and magnesium ion concentration (1-9 mM). The optimized assay was used to assess the inhibitory activity of several compounds that have been reported to be specific inhibitors of transcription initiation on naked DNA templates. Both Sarkosyl and heparin were effective inhibitors of specific initiation by RNA polymerases I and II in isolated nuclei without inhibiting elongation of nascent chains, but 5,6-dichlorobenzimidazole riboside was relatively ineffective as a specific inhibitor of initiation by RNA polymerase II.

A bacteriophage RNA polymerase transcribes in vitro through a nucleosome core without displacing it

Small linear DNA molecules containing histone octamers (nucleosome cores) are transcribed by SP6 RNA polymerase with only slightly lower efficiency than naked DNA templates. The position of the histone octamer on the DNA remains unchanged even after multiple passages by the polymerase. The histone octamer is not released even transiently from the DNA by polymerase transit. We conclude that histone octamers do not impede transcription elongation.

Fractionation of aurintricarboxylic acid and effects of its components on nuclear swelling and nucleic acid synthesis

Crude aurintricarboxylic acid synthesized by the conventional method was fractionated into 8 components (A1-A8) by silica gel thin layer chromatography. Some of the components were isolated and their effects were tested on nuclear swelling and on in vitro RNA synthesis and DNA synthesis using isolated polymerases. Only two components with low R F (A7 and A8) induced strong nuclear swelling. The other components were almost inactive. Formaurindicarboxylic acid, a contaminating polyanion of crude aurintricarboxylic acid, was synthesized separately. It was as effective as the two active components in nuclear swelling and inhibited RNA and DNA polymerases on naked DNA template. However, it stimulated RNA synthesis on chromatin template probably by dissociating histones from DNA. Unfractionated aurintricarboxylic acid showed the same effects at higher concentrations. A preliminary analysis indicated one of the inactive components (A4) is genuine aurintricarboxylic acid. The results suggest that the observed activity of crude aurintricarboxylic acid is due to some contaminating substances, one of which is formaurindicarboxylic acid.