The inverted repeat as a recognizable structural feature in supercoiled DNA molecules

The single-strand-specific endonuclease S1 from Aspergillus oryzae introduces highly selective cleavages into supercoiled covalently closed circular DNA molecules, but not into their previously linearized counterparts. The cleavage sites are inverted repeats of unit length between 9 and 13 base pairs, separated by a nonrepetitious 2-6 base pairs. Such regions may adopt hairpin or similar structures stabilized by the negative superhelix density and may constitute recognition sites for cellular proteins.

The nature of the interaction of nucleosomes with a eukaryotic RNA polymerase II

The integrity and stability of nucleosomes under transcription assay conditions has been found to depend on concentration and ionic environment. Rifamycin AF/013, a commonly used inhibitor of initiation, is particularly effective in destabilisation of nucleosomes. Intact nucleosomes are refractory to transcription by wheat RNA polymerase II, the histone core preventing initiation. Template titration suggests that the polymerase can, however, bind to nucleosomes, and a 15--16S complex has been observed on sucrose gradients. DNase I digestion of polymerase-nucleosome incubations indicates that whilst histone is still present in the complex, the nucleosome conformation is altered resulting in enhanced nucleolysis at sites near the DNA centre but reduced overall kinetics of digestion.

The interaction of RNA polymerase II from wheat with supercoiled and linear plasmid templates

Interactions between a plant RNA polymerase II and ColE1 based plasmid DNA templates have been studied. Gel electrophoresis indicates that the enzyme binds to both supercoiled and linear species. Using the totally double stranded pMB9/SmaI fragment it is shown that transcription of completely base paired DNA is ten-fold lower than that of denatured or supercoiled plasmid, and reflects the presence of fewer initiation sites. A small proportion of the transcript remains tightly bound to supercoiled templates. 3' oligodeoxycytidine extensions on pMB9/SmaI serve to promote transcription of the linear double stranded form. Using restriction kinetics it is shown that there is a small enhancement of polymerase binding at the pMB9 tetracycline promoter, but that the selectivity of binding at this locus is lower than for the natural bacterial polymerase.

Nucleosome sub-structure during transcription and replication

We have described (Richards et al. 1977) a model for the sub-structure of the core particle (140 base pairs) of the nucleosome repeat in chromatin, based principally on results from neutron and X-ray scattering, together with data from other physico-chemical studies. Like that proposed by others (Weintraub, Worcel & Alberts 1976), a principal feature of the model is that it consists of two identical halves, each containing a heterotypic histone tetramer, which lie face-to-face about a dyad axis of symmetry. In this brief contribution we give more detail to proposals already mentioned (Richards et al. 1976, 1977) for the manner in which such a particle might linearize to accommodate the action of either the polymerase or replicase enzymes in transcription and replication, respectively

Active chromatin structure

Active gene sequences are present in the nucleosomal fraction of chromatin. Histones are attached to the DNA of transcribing non-ribosomal genes, and EM images suggest that their conformation is related to that of nucleosomes, or is readily converted to that structure on preparation for microscopy. Active nucleosomes do have, however, a changed conformation, since their DNA is more susceptible to endonucleolytic attack by DNase I. This alteration appears to reflect potential rather than actual transcriptional activity. Mechanisms for nucleosome disassembly to allow transcription without histone have been proposed. These involve alterations in histone-histone interactions without perturbation of histone-DNA contact.

The structure of the chromatin core particle in solution

The shape and size of the nucleosomal core particle from chromatin has been examined by analysis of neutron and X-ray scattering data from dilute solutions. Calculations of scattering for many different models have been made and only one model was able to account for both the X-ray and neutron profiles. This model is an oblate structure with height about 50A and diameter 110A. The DNA is mainly confined to two annuli located at the top and bottom respectively of the core particle positioned on the outside of a compact protein core which has a height of about 40A and diameter about 73A.

Structural investigations of chromatin core protein by nuclear magnetic resonance

A complex derived from chromatin containing one molecule of each of histones H2A, H2B, H3, and H4, termed core protein, was studied by 13C and 1H nuclear magnetic resonance. 13C line widths, when analyzed and compared with those of native and thermally unfolded representative globular proteins, showed that regions of the core protein possess considerable mobility. Studies of Calpha and Cbeta line widths, and Calpha spin-spin relaxation times, show that this mobility arises from sections of random-coil polypeptide. It is argued that these regions are N-terminal "tails", attached to C-terminal globular polypeptides. The 270-MHz 1H nuclear magnetic resonance spectrum shows numerous ring current shifted resonances, indicating that the C-terminal globular domain has a precise tertiary structure. The globular domain most likely forms the histone "core" of the chromatin monomer particle, whilst the basic tails probably wind around the grooves of the double helix, enabling the basic side chains to interact with the DNA phosphate groups. Some biological implications of this model are considered.

Chromatin core particle unfolding induced by tryptic cleavage of histones

Chromatin 'core particles' have been digested with trypsin to varying extents. The resulting particles are homogeneous by the criterion of ultracentrifuge boundary analysis. Sedimentation coefficients are lowered as cleavages are introduced into the histones, showing that an unfolding of the core particle occurs. This unfolding is further characterised by a lower melting temperature together with a premelting phase, higher molar ellipticity in the circular dichroism spectra at 280 nm and increased kinetics of digestion by both micrococcal nuclease and DNase I. Differences are also observed in the products of nuclease digestion. The most consistent interpretation of the data involves an unfolding process whereby free rods of DNA are released to extend from a nucleoprotein core.

An investigation of the conformational and self-aggregational processes of histones using 1H and 13C nuclear magnetic resonance

Histone self-aggregation processes have been studied by 13C and 1H nuclear magnetic resonance (NMR) as a function of ionic strength and protein concentration. Thus has led to a model involving apolar aggregation between structured regions of these molecules. This analysis supports the validity of the acquistion of conformational data on histones by the simulation of 13C NMR spectra at high concentration. Solution conformations for histones F2B and F3 are presented.

The structure and properties of histone F2a comprising the heterologous group F2a1 and F2a2 studied by 13C nuclear magnetic resonance

(13)C n.m.r. spectra have been obtained for aqueous solutions of histones F2a(1) and F2a(2), for the group F2a, for the appropriate amino acid mixturesand for the corresponding hydrolysates. These, when compared with computer simulated spectra give good agreement for secondary structure with that calculated from the known primary structure of the proteins. Evidence based on the spectra obtained at various salt concentrations leads to the conclusion that F2a is not a simple mixture but an interacting heterologous group of histones F2a(1) and F2a(2).