Biochemical and physiochemical characterization of chromatin fractions with different degrees of solubility isolated from chicken erythrocyte nuclei

Single-molecule and population probing of chromatin structure using DNA methyltransferases

Probing chromatin structure with DNA methyltransferases offers advantages over more commonly used nuclease-based and chromatin immunoprecipitation methods for detection of nucleosomes and non-histone protein-DNA interactions. Here, we describe two related methods in which the readout of MTase accessibility is obtained by assaying 5-methylcytosine in DNA through the PCR-based technique of bisulfite genomic sequencing. The methyltransferase accessibility protocol (MAP) determines the relative frequency at which the enzyme accesses each of its target sites over an entire population of PCR amplified product. While MAP yields much quantitative information about relative accessibility of a region of chromatin, a complementary single-molecule view of methyltransferase accessibility, termed MAP for individual templates (MAP-IT), is provided by analysis of cloned PCR products. Absolute rather than relative methylation frequencies in a region are obtained by summing the methylation status at each site over a cohort of clones. Moreover, as the integrity of individual molecules is maintained in MAP-IT, unique information about the distribution of multiple footprints along continuous regions is gleaned. In principle, the population MAP and single-molecule MAP-IT strategies can be used to analyze chromatin structure in a variety of model systems. Here, we describe the application of MAP in living Saccharomyces cerevisiae cells and MAP-IT in the analysis of a mammalian tumor suppressor gene in nuclei. This application of MAP-IT provides the first means to simultaneously determine CpG methylation of mammalian genes and their overlying chromatin structure in the same single DNA molecule.

Analytical ultracentrifugation and the characterization of chromatin structure

This mini review consists of two parts. The first part will provide a brief overview of the theoretical aspects involved in the two kinds of experiments that can be conducted with the analytical ultracentrifuge (sedimentation velocity and sedimentation equilibrium) as they pertain to the study of chromatin. In the following sections, I describe the analytical ultracentrifuge experiments which, in my opinion, have contributed the most to our understanding of chromatin. Few other biophysical techniques, with the exception of X-ray scattering and diffraction, have contributed as extensively as the analytical ultracentrifuge to the characterization of so many different aspects of chromatin structure. In the course of his scientific career, Professor Henryk Eisenberg has made many important contributions to the theoretical aspects underlying ultracentrifuge analysis, especially in the analysis of solutions of polyelectrolytes and biological macromolecules [H. Eisenberg, Biological macromolecules and polyelectrolytes in solution, Clarendon Press, Oxford, 1976]. As an example he has devoted some of his research effort to the characterization of chromatin in solution. This review includes these important contributions.

Folding of chromatin in the presence of heterogeneous histone H1 binding to nucleosomes

We have reconstituted oligonucleosome complexes containing histone H1 starting from a synthetic DNA template, consisting of 12 tandemly arranged 208-base pair fragments of the 5 S rRNA gene, purified HeLa histone octamers, and histone H1. A ratio of histone H1 per histone octamer used in the reconstitution (0.8-0.9 mol of histone H1/mol of histone octamer) similar to that observed in vivo was used. The reconstituted chromatin complexes exhibit a salt-dependent folding, which is almost indistinguishable from that exhibited by chromatin fragments obtained from nuclease digestion of native chromatin. The folding of this reconstituted chromatin complex seems to be rather independent of the symmetrical or asymmetrical position occupied by H1 in the individual nucleosomes. Binding of histone H1 to the oligonucleosome complexes, under the stoichiometric binding conditions used, had no inhibitory effect on the transcriptional potential of these complexes.

Influence of chromatin folding on transcription initiation and elongation by RNA polymerase III

Nucleosomes were assembled onto either closed circular plasmids containing a single Xenopus 5S RNA gene or a linear tandemly repeated array of Lytechinus 5S RNA genes. Both chromatin templates were found to vary in their extent of compaction, depending upon the type and concentration of cation in solution. Compaction of these chromatin templates led to a significant inhibition of both transcription initiation and elongation by RNA polymerase III. Thus, the transcriptional repression observed after incorporation of genes into chromatin depends not only on occlusion of the promoter elements through direct contact with histones but also on compaction of nucleosomal arrays which occurs under the conditions of the transcription reactions.

Chromatin dynamics and the modulation of genetic activity

Chromatin, the genetic material of eukaryotes, is a dynamic macromolecular assembly that continuously changes its composition and conformation to accommodate different stages of genetic activity, e.g. transcription and replication. Evidence is accumulating that the dynamic behavior of chromatin has important functional roles in the modulation of genetic activity, largely due to the intrinsic properties of arrays of nucleosome cores.

Preferential binding and aggregation of rabbit C-reactive protein with arginine-rich proteins

Human and rabbit C-reactive proteins (CRP) are similar in mol. wt, structure and amino acid sequence. In addition to the characteristic phosphoryline (PC)-binding specificity, both CRP molecules bind arginine- and lysine-rich proteins. The human CRP-cationic protein reactivity has been reported to be inhibited by calcium and promoted by PC in the presence of calcium. The present study compares binding and precipitation reactions of rabbit CRP (raCRP) with arginine- and lysine-rich proteins, and demonstrates the differential modulation of these interactions by calcium and acidic pH. Rabbit CRP shows preferential binding and precipitation reactivities with arginine-rich cationic molecules. Binding of raCRP to poly-L-arginine (PLA) and arginine-rich histone (ARH) occurs at pH 6.0, in the presence of calcium and is inhibitable by phosphorylcholine (PC) suggesting an interaction at or near the calcium-modulated PC binding site. The in vitro precipitation of raCRP and arginine-rich cationic molecules is significantly inhibited at pH 6.0, by the non-precipitating lysine-rich ligand PLL, and by physiological levels of calcium, and may reflect the participation of distinct "self-aggregation" sites on CRP in the precipitation response. The significance of the preferential arginine reactivity of raCRP to in vivo functions as a scavenger of chromatin during cell death and/or as a modulator of lipoprotein metabolism during the acute phase response is discussed.

Nucleoprotein hybridization: a method for isolating active and inactive genes as chromatin

The developmentally regulated sea urchin early histone gene repeat (SUEHGR) from Strongylocentrotus purpuratus was isolated as chromatin by nucleoprotein hybridization. This technique is a novel method to isolate specific sequences as chromatin. Because the purification scheme is based only on the gene sequence and is independent of other physical properties such as protein composition and transcriptional activity, we were able to isolate the same gene in different functional states. Gene size chromatin fragments were solubilized by restriction endonuclease digestion of cell nuclei. Using T7 gene 6 exonuclease, the 3'termini of the fragments were exposed and then hybridized in solution to a biotinylated oligonucleotide complementary to one end of the SUEHGR fragment. The hybrids were bound to an Avidin D matrix. DTT cleavage of the biotin linker yielded a chromatin fraction greater than 700 fold enriched in SUEHGR. Overall yields were between 2% and 15%. The purity of the isolated material was independently measured to be greater than 80%. The homogeneous native structure of the inactive genes was preserved as shown by electron microscopy and micrococcal nuclease digestion of the purified SUEHGR. Minor heterogeneity was observed for the purified active genes by micrococcal nuclease digestion but the main features of the active chromatin were preserved during isolation. This isolation offers the first opportunity to study the structure of an RNA polymerase II gene at different stages of the cell cycle and development.

Use of critical point polyacrylamide sols in thermal denaturation experiments with chromatin at physiological ionic strength

Low percentage highly crosslinked polyacrylamide gels just above the critical point in the chemically polymerized sol to gel transition are used to generate polyacrylamide sols at critical point concentrations, 7.4 g liter-1, by mild heating. We find that chromatin samples mixed with these sols induce the sol to gel transition in a process of complex coacervation. In this state, salt insoluble chicken erythrocyte chromatin is stabilized against large scale aggregation and precipitation during thermal denaturation at physiological sodium ion concentrations. The hyperchromic melting behavior of DNA in polyacrylamide sols is reproducible and consistent throughout a wide range of sodium chloride concentrations. Empirical spectroscopic techniques are discussed which isolate temperature-dependent hyperchromic signals at 260 nm due to conformational changes of DNA in chromatin and local environmental changes which promote anomalous light scattering.

The histones of the sperm of Spisula solidissima include a novel, cysteine-containing H-1 histone

The histones remaining at the end of the spermiogenic differentiation, which are found associated with a highly basic protamine-like component [Ausio, J. and K.E. Van Holde (1987) Eur. J. Biochem. 165, 363-371] in the mature sperm of Spisula solidissima, have been isolated and characterized for the first time. All four core histones H2A, H2B, H3, H4, and the lysine-rich histone H1 are present. The core histones are found in equal stoichiometric amounts. As has been observed in other bivalve molluscs, the amino acid compositions of the core histones of S. solidissima sperm are very close to those of their counterparts in the calf thymus somatic histones. The spermatic histone H1 exhibits an amino acid composition and structural features similar to other histones of the histone H1 family. Yet this latter histone seems to be sperm-specific, and it contains at least two cysteine residues per molecule, which makes it unique in its class.

The superstructure of chromatin and its condensation mechanism. IV. Enzymatic digestion, thermal denaturation, effect of netropsin and distamycin

Changes in the structure of chicken erythrocyte chromatin fibres at low ionic strength resulting from enzymatic digestion, thermal denaturation and binding of Netropsin and Distamycin were monitored by synchrotron X-ray solution scattering. Digestion with micrococcal nuclease confirms the previous assignment of the 0.05 nm-1 band to an interference between nucleosomes with an average distance of 23 nm. The results of thermal denaturation indicate that above 40 degrees C there is a progressive increase of the internucleosomal distance and that above 60 degrees C the characteristic structure of the chromatin fibre is destroyed. Binding of Netropsin and Distamycin also results in an increase of the internucleosomal distance which can be estimated to correspond to about 0.2 nm/mol.

The ubiquitinated histone species are enriched in histone H1-depleted chromatin regions

Bovine thymus and trout testis chromatin were fractionated into regions which differed in their micrococcal nuclease accessibility and solubility properties, and the distribution of the ubiquitinated histone species among these chromatin regions was elucidated. Ubiquitinated (u) species of histones H2A and H2B were enriched in the nuclease-sensitive, low-ionic-strength, soluble fraction of both chromatins. These results indicate that the presence of ubiquitinated histones may alter nucleosome-nucleosome interactions and destabilize higher-order chromatin structures. Bovine thymus chromatin was separated into aggregation-resistant, salt-soluble and aggregation-prone, salt-insoluble chromatin fractions. The aggregation-resistant chromatin fraction depleted in H1 histones was enriched in uH2A and uH2B, with uH2B showing the greater enrichment. The chromatin fragments were also stripped and reconstituted with the H1 histones prior to fractionation. The results were the same as above: uH2A and uH2B were preferentially localized in the aggregation-resistant. H1-depleted chromatin fraction, suggesting that chromatin regions enriched in ubiquitinated histone species have a reduced affinity for the H1 histones. Thus, ubiquitinated histone species may be one of the contributing factors in the differential assembly of various parts of the genome.

Affinity chromatographic purification of nucleosomes containing transcriptionally active DNA sequences

The unfolding of nucleosome cores in transcriptionally active chromatin uncovers the sulfhydryl groups of histone H3, making them accessible to SH-reagents. This has suggested that nucleosomes from active genes could be retained selectively on organomercurial/agarose columns. When nucleosomes released from rat liver nuclei by limited digestion with micrococcal nuclease were passed through an Hg affinity column, a run-off fraction of compact, beaded nucleosomes was separated from a retained nucleosome fraction. Although both contained monomer-length DNA and a full complement of core histones, histones in the retained fraction were hyperacetylated. Dot blot hybridizations showed the Hg-bound nucleosome fraction to be enriched in DNA sequences transcribed by hepatocytes (serum albumin and transferrin genes), while a brain-specific gene (preproenkephalin) was not retained, but appeared in the nucleosomes of the run-off fraction. The results are discussed in light of other evidence linking hyperacetylation of histones H3 and H4 to conformational changes at the middle of the nucleosome core.

Cell cycle-dependent changes in conformation and composition of nucleosomes containing human histone gene sequences

Unfolding of the nucleosomes in transcriptionally active chromatin uncovers the sulfhydryl groups of histone H3 and permits the selective recovery of the unfolded nucleosomes by mercury-affinity chromatography. This new technique has been used to compare the nucleosomal proteins and their postsynthetic modifications in the unfolded and the compactly beaded nucleosomes of HeLa cells in logarithmic growth, and at different stages of the growth cycle. The Hg-bound nucleosomes are shown to be deficient in replicating DNA sequences, but to remain associated with fragments of nascent RNA chains (or RNP particles) during gradient centrifugations. Both nucleosome fractions contain a full complement of "core" histones but differ with respect to postsynthetic modifications. The Hg-bound nucleosomes contain high levels of the tri- and tetra-acetylated forms of histones H3 and H4. The unbound nucleosomes are deficient in acetylated histones but enriched in phosphorylated H2A. In synchronized HeLa cells, histone H2A and H4 gene sequences occur in the Hg-bound nucleosomes during the S-phase when their transcription takes place, but not in the G2-phase when the genes are repressed.

A dual chromatin organization in the sperm of the bivalve mollusc Spisula solidissima

Most of the DNA in the sperm of the bivalve mollusc. Spisula solidissima, is found to be associated with a specific high-molecular-mass, protamine-like component, sharing features common both to protamines and to histones. We have found that this component coexists, in the mature sperm nucleus, with a complete set of histones, including an H1-like histone. Such histones account for approximately 20% of the whole protein content in the sperm chromatin, the overall protein/DNA ratio (w/w) being 0.87. These data, together with micrococcal nuclease digestions in combination with salt fractionation, have allowed us to propose a structural model for this chromatin in which short nucleosomal domains are interspersed in a highly saturated protamine-DNA complex.