Probing with DNase I of nucleosomal core particles assembled in vitro in the presence of polyglutamic acid

When a dream comes true: birth of the African Crystallographic Association (AfCA)

This paper summarizes brief perspectives on the historic process of establishing an African Crystallographic Association (AfCA) and includes representative references. It covers activities within four arbitrarily selected, approximate time slots, i.e., 1890s-1999, 2000-2013, 2014-2019 and 2020-2023. A genuine attempt is made to include appropriate role players, organizations and accompanying events within these periods. It concludes with the official admission of AfCA as the fifth Regional Associate of the IUCr at the 26th Congress and General Assembly of the IUCr in Melbourne, Australia in 2023.

A novel nucleosome assembly procedure (with a little help from pectin)

The acidic polysaccharide pectin (alpha-1,4-polygalacturonic acid) has been introduced as a nucleosome assembly facilitator as a substitute for polyglutamic acid. The pectin-assembled nucleosomes were indistinguishable from polyglutamic acid-assembled nucleosomes by thermal denaturation and DNAse I digestion. Pectin had two major advantages over polyglutamic acid-the yield of assembled cores was approximately 50% higher and the pectin could be easily removed after completion of the reassembly procedure by dialysis following pectinase cleavage.

Solution studies of the interactions between the histone core proteins and DNA using fluorescence spectroscopy

The equilibrium interactions between histone H2A-H2B and H3/H4 subunits with 200 base pair chicken erythrocyte DNA have been studied by monitoring the fluorescence polarization of a long-lived fluorescence probe covalently bound to the histone subunits. These studies have brought to light the formation of highly asymmetric complexes exhibiting very high histone/DNA stoichiometries as well as very high apparent affinities. The stoichiometries observed for these non-nucleosome complexes depended both upon the concentration of the histones and the concentration of the DNA 200mer. The observed stoichiometries varied approximately between 4 and 16 histone octamers/DNA 200mer and the affinities were in the nanomolar range. These results are discussed in terms of their in vitro as well as their possible in vivo significance.

Extended C-terminal tail of wheat histone H2A interacts with DNA of the "linker" region

The preparation of hybrid histone octamers with wheat histone H2A variants replacing chicken H2A in the chicken octamer is described. The fidelity of the reconstituted hybrid octamers was confirmed by dimethyl suberimidate cross-linking. Polyglutamic-acid-mediated assembly of these octamers on long DNA and subsequent micrococcal nuclease (MNase) digestion demonstrated that, whereas chicken octamers protected 167 base-pairs (representing 2 full turns of DNA), hybrid histone octamers containing wheat histone H2A(1) with its 19 amino acid residue C-terminal extension protected an additional 16 base pairs of DNA against nuclease digestion. The protection observed by hybrid histone octamers containing wheat histone H2A(3) with both a 15 residue N-terminal and a 19 residue C-terminal extension was identical with that observed with H2A(1)-containing hybrid histone octamers with only the 19 residue C-terminal extension. These results suggest that the role of the C-terminal extension is to bind to DNA of the "linker" region. The thermal denaturation of chicken and hybrid core particles was identical in 10 mM-Tris.HCl.20 mM-NaCl, 0.1 mM-EDTA, confirming that there was no interaction between the basic C-terminal extension and DNA of the core particle. Denaturation in EDTA, however, showed that hybrid core particles had enhanced stability, suggesting that the known conformational change of core particles at very low ionic strength allows the C-terminal extension to bind to core particle DNA under these conditions. A model accounting for the observed MNase protection is presented.

Preparation of fluorescently labelled hybrid histone octamers

Labelling hybrid histone octamers (the Cys variant of histone H4 replaced histone H4 in the chicken erythrocyte octamer) with the fluorescent probe 5-(2(iodoacetyl)aminoethyl)aminonapthalene- 1-sulfonic acid, IAEDANS, resulted in significant non-specific incorporation of label. Fluorescently labelled hybrid histone octamers were prepared by reconstitution methodology after labelling the isolated histone Cys-H4 and separation of specifically and non-specifically labelled histone. Core particles prepared from these octamers have identical thermal denaturation to unlabelled core particles demonstrating that the incorporation of a fluorescent probe at this site has no overall effect on either histone-histone or histone-DNA interactions. DNase 1 digestion of 32P end-labelled fluorescent core particles yielded the anticipated asymmetric cutting pattern with a 10 bp interval between fragments. Comparison of the cutting pattern with those previously obtained in these laboratories for both polyglutamic acid reconstituted and 'native' core particles demonstrated that fluorescent core particles had an enhanced susceptibility to digestion at site 7.

Isolation and characterisation of a 167 bp core particle isolated from stripped chicken erythrocyte chromatin

We have digested chicken erythrocyte soluble chromatin, both unstripped and stripped of histones H1 and H5 with either 0.6 M NaCl or DNA-cellulose, with micrococcal nuclease (MNase). Digestion of unstripped chromatin to monomeric particles initially paused at 188 bp DNA; continued digestion resulted in another pause at 177 before the 167 bp chromatosome and 146 bp core particle were obtained. Digestion of stripped chromatin to monomeric particles paused transiently at 177 bp; continued digestion resulted in marked pauses at 167 and 156 before the 146 bp core particle was obtained. These results suggested that 167 bp DNA representing two complete turns are bound to the histone octamer. Histone H1/H5 binds an additional two helical turns of DNA, thereby protecting up to 188 bp DNA against nuclease digestion. Monomeric particles containing 167 bp DNA were isolated from stripped chromatin and found by DNase I digestion to be a homogeneous population with a 10 bp DNA extension to either end relative to the 146 bp core particle. Thermal denaturation and circular dichroism spectroscopy showed stronger histone-DNA interactions and increased DNA winding as the length of DNA attached to the core histone octamer was decreased. Thermal denaturation also showed three classes of histone-DNA interaction: the core particle containing 167 bp DNA had tight binding of ten helical turns of DNA, intermediate binding of two helical turns and looser binding of four helical turns.

Limitations of the poly(glutamic acid) reconstitution method in the reassembly of mono- and dinucleosomes

Reconstitution of mononucleosomes and dinucleosomes at physiological ionic strength by means of poly(glutamic acid) is not efficient at physiological histone octamer:DNA ratios, unlike that with the salt dialysis method. The shorter the DNA is, the less transfer of octamers from poly(glutamic acid) to DNA occurs. By increasing the octamer:DNA ratio it is possible to involve all the DNA in the assembly, but for DNA longer than core particle length, nucleoprotein particles containing extra histones are concomitantly generated. Except for core particle and chromatosome lengths of DNA reassembled at 0.6:1 or 1:1 octamer:DNA ratio (and thus with low yield), reconstituted nucleoprotein particles proved to be different from native nucleosomes by their insolubility upon isolation. In the aggregates, DNA ends seemed to be sufficiently loose to allow exonuclease III digestion up to a certain limit. This resulted in patterns that for some cloned DNA fragments could give the impression, without knowledge of the above, of resulting from a unique octamer position. In view of the small range of length of DNA and the low yield of faithful reconstitution, the assembly method using poly(glutamic acid) is only of limited use in mono- or dinucleosome reconstitution experiments, at least in our hands.

Fluorescent labelling of histone H3: effect on histone-histone interaction and core particle assembly

Substitution of Cys 110 of chicken histone H3 with N-iodoacetyl-N1-(5-sulpho-1-naphthyl)ethylenediamine or iodoacetamide prevents octamer formation in 2 M NaCl but does not prevent polyglutamic acid-mediated core particle assembly.