Interaction of histone H1 with superhelical DNA. Sedimentation and electron microscopical studies at low salt concentration

Linker histone H1 stimulates DNA strand exchange between short oligonucleotides retaining high sensitivity to heterology

The interaction of human linker histone H1(0) with short oligonucleotides was characterized. The capability of the histone to promote DNA strand exchange in this system has been demonstrated. The reaction is reversible at saturating amounts of H1 corresponding to complete binding of the oligonucleotide substrates with the histone. In our conditions the complete saturation of DNA with the histone occurs at a ratio of one protein molecule per about 60 nucleotides irrespectively of DNA strandedness. In contrast to the DNA strand exchange promoted by RecA-like enzymes of homologous recombination the H1 promoted reaction exhibits low tolerance to interruptions of homology between oligonucleotide substrates comparable to those for the case of spontaneous strand exchange between free DNA molecules at elevated temperatures and the exchange promoted by some synthetic polycations.

Structure of transfection-active histone H1/DNA complexes

Relationships between the structure of transfecting complexes of histone H1 and DNA and their transfection efficiency were studied. Transfection activity proved to be connected to complex aggregates. Low speed centrifugation of the complexes resulted in loss of the transfection activity. The complexes/aggregates were active with high efficiency in a broad range of weight input ratios r(i) (0.1 < r(i) < 30). Using atomic force microscopy (AFM), the complexes were imaged at negative, nearly electroneutral and positive charge conditions. Electroneutral complexes at r(i) = 1 showed a multitude of different complex forms. Fibrillar, network-like and branched structures were frequently present in one complex. Strongly positive charged complexes had a toroidal appearance. All these different forms contributed to the high transfection efficiency. Cellular uptake is supposed to be by phagocytosis.

Histone H1 preferentially binds to superhelical DNA molecules of higher compaction

In chromatin, the physiological amount of H1 is one molecule per nucleosome or, roughly, one molecule per 200 bp of DNA. We observed that at such a stoichiometry, H1 selectively binds to supercoiled DNA with magnitude of sigma > or = 0.012 (both negative and positive), leaving relaxed, linear, or nicked DNA molecules unbound. When negative and positive DNA topoisomers of varying superhelicity are simultaneously present in the binding mixture, H1 selectively binds to the molecules with highest superhelicity; less supercoiled forms are gradually involved in binding upon increasing the amount of input protein. We explain this topological preference of H1 as the consequence of an increased probability for more than one H1-DNA contact provided by the supercoiling. The existence of simultaneous contacts of H1 with both intertwined DNA strands in the supercoiled DNA molecules is also inferred by topoisomerase relaxation of H1-DNA complexes that had been prefixed with glutaraldehyde.

Gene transfer into mammalian cells using histone-condensed plasmid DNA

A recombinant histone (NLS-H1) containing both the SV40 large T antigen nuclear localization signal and the carboxy-terminal domain of human histone H1(0) was produced in bacteria. NLS-H1-plasmid DNA complexes, in the presence of chloroquine, mediated reporter gene transfer into cultured cells with similar efficiencies as plasmid DNA-cationic lipid (lipofectin) complexes. NIH-3T3 or COS-7 cells transfected with NLS-H1-plasmid DNA-lipofectin complexes expressed at least 20 times more luciferase or had at least 2.5 times more beta-galactosidase-positive cells than those transfected with plasmid DNA-lipofectin complexes. Foreign gene expression was also improved by other DNA-binding proteins and cationic lipid formulations, yet the greatest enhancement was obtained with complexes containing either NLS-H1 or calf thymus histone H1. Histone H1-plasmid DNA-lipofectin complexes were internalized by a greater number of cells than plasmid DNA-lipofectin complexes.

Theoretical analysis of gel electrophoretic data for interaction of lysine rich histone with supercoiled DNA

We demonstrate the possibility of using gel electrophoresis as a technique for the quantitative analysis of interaction of lysine rich histone with DNA. On the basis of theoretical framework for extended ligand binding to one-dimensional lattices such as DNA we have set up systems of equations which relate the ligand-to-DNA ratio to the observed gel migration distance of the complex. From the analysis of experimental data for gel electrophoresis of supercoiled DNA in the presence of lysine rich histones we have found that the observed variation of electrophoretic mobilities of the histone-DNA complexes at low histone-to-DNA ratios can be described by a non-cooperative binding behaviour. At this limit we have estimated the intrinsic binding constant to be of the order of 10(3) M-1.

Histone H1-DNA interactions and their relation to chromatin structure and function

The belief that histone H1 interacts primarily with DNA in chromatin and much less with the protein component has led to numerous studies of artificial H1-DNA complexes. This review summarizes and discusses the data on different aspects of the interaction between the linker histone and naked DNA, including cooperativity of binding, preference for supercoiled DNA, selectivity with respect to base composition and nucleotide sequence, and effect of H1 binding on the conformation of the underlying DNA. The nature of the interaction, the structure of the complexes, and the role histone H1 exerts in chromatin are also discussed.

Stabilization of chromosomes by DNA intercalators for flow karyotyping and identification by banding of isolated chromosomes

A number of structurally unrelated DNA intercalators have been studied as stabilizers of mitotic chromosomes during isolation from rodent and human metaphase cells. Seven out of the nine intercalators tested were found to be useful as chromosome stabilizing agents. Chromosome suspensions prepared in this way could be preserved for long periods of time. After isolation the chromosomal DNA was longer than 150 kb. With intercalated chromosomes high resolution flow karyotypes could be obtained as illustrated for the non-fluorescent intercalators 9-methylene-(1,3-dimethyl-2,4-dionepyrimidine-5-yl)-phenanthrid in iumchloride and 4'-aminomethyl-4,5', 8-trimethylpsoralen combined with DAPI and 33258 Hoeschst for fluorescent staining and for the fluorescent intercalator propidium iodide used as a stabilizer and as a fluorochrome. Passage of the intercalated chromosomes through the laser beam had no measurable effect on the length of the chromosomal DNA subsequently isolated. After flow analysis and collection on slides human chromosomes could easily be banded by Giemsa staining methods with the same resolution as obtained in conventional metaphase spreads. This allowed a ready identification of about 80 percent of all chromosomes in the unfractionated suspension collected after passage through the laser beam.

Formation and characterization of soluble complexes of histone H1 with supercoiled DNA

We have analyzed the interaction of rat liver histone H1 with superhelical DNA. Depending on the ratio of H1 to DNA and the concentration of salt, two different types of complexes were found. Above a critical ratio of H1 to DNA, called the aggregation point, large aggregates are formed, which have a cable-like appearance in the electron microscope. Below the aggregation point, individual soluble complexes are formed, which are the subject of this study. With increasing ionic strength, the aggregation point is shifted towards lower ratios of H1 to DNA. In the soluble complexes, H1 appears to bind along superhelically intertwined DNA strands, forming a polymer. Partial digestion of the complexes with protease suggests protection of the N-terminal tail and the globular domain of H1. Similar soluble complexes were observed with various H1 fragments but not with the core histones. In the soluble complexes, similar regions of the H1 molecule are considered to be protected from cleavage by protease, as in chromatin. Therefore, these complexes appear to be a valuable model for the interaction of H1 in chromatin fibers.

Salt-dependent co-operative interaction of histone H1 with linear DNA

The nature of the complexes formed between histone H1 and linear double-stranded DNA is dependent on ionic strength and on the H1 : DNA ratio. At an input ratio of less than about 60% (w/w) H1 : DNA, there is a sharp transition from non-co-operative to co-operative binding at a critical salt concentration that depends on the DNA size and is in the range 20 to 50 mM-NaCl. Above this critical ionic strength the H1 binds to only some of the DNA molecules leaving the rest free, as shown by sedimentation analysis. The ionic strength range over which this change in behaviour occurs is also that over which chromatin folding is induced. Above the salt concentration required for co-operative binding of H1 to DNA, but not below it, H1 molecules are in close proximity as shown by the formation of H1 polymers upon chemical cross-linking. The change in binding mode is not driven by the folding of the globular domain of H1, since this is already folded at low salt in the presence of DNA, as indicated by its resistance to tryptic digestion. The H1-DNA complexes at low salt, where H1 is bound distributively to all DNA molecules, contain thickened regions about 6 nm across interspersed with free DNA, as shown by electron microscopy. The complexes formed at higher salt through co-operative interactions are rods of relatively uniform width (11 to 15 nm) whose length is about 1.6 times shorter than that of the input DNA, or are circular if the DNA is long enough. They contain approximately 70% (w/w) H1 : DNA and several DNA molecules. These thick complexes can also be formed at low salt (15 mM-NaCl) when the H1 : DNA input ratio is sufficiently high (approximately 70%).

The role of the central globular domain of histone H5 in chromatin structure

Histone H5 contains three tyrosines in the central, apolar region of the molecule. All three tyrosines can be spin labeled at low ionic strength. When the central globular domain is folded at high ionic strength, only one tyrosine becomes accessible to the imidazole spin label. Spin labeling the buried tyrosines prevents the folding of the globular structure, which, in turn, affects the proper binding of the H5 molecule to stripped chromatin. Chromatin complexes reconstituted from such an extensively modified H5 molecule show a weaker protection of the 168 base pair chromatosome during nuclease digestion. However, when only the surface tyrosine of the H5 molecule is labeled, such a molecule can still bind correctly to stripped chromatin, yielding a complex very similar to that of native chromatin. Our data supports the idea that not just the presence of the linker histone H5, but the presence of an intact H5 molecule with a folded, globular central domain in essential in the recognition of its specific binding sites on the nucleosomes. Our data also show that during the chromatin condensation process, the tumbling environment of the spin label attached to the surface tyrosine in the H5 molecule is not greatly hindered but remains partially mobile. This suggests that either the labeled domain of the H5 molecule is not directly involved in the condensation process or the formation of the higher-order chromatin structure does not result is a more viscous or tighter environment around the spin label. The folded globular domain of H5 molecule serves in stabilizing the nucleosome structure, as well as the higher-order chromatin structure.

Interaction of histone H1 with superhelical DNA. Conformational studies and influence of ionic strength

The interaction of histone H1 with superhelical SV40 DNA at low ionic strength (approximately 0.02 M NaCl) results in the formation of DNP double-fibers and bundle- and cablelike twisted side-by-side associates of several of these double-fibers. On the basis of simple cylindrical or ellipsoidal models the sedimentation properties of these structures can be calculated in accordance with the experiment allowing a direct assignment of electron microscopical and hydrodynamic results. Sedimentation measurements in dependence on the ionic strength indicate a redistribution of H1 resulting in the formation of associates at 0.04 M NaCl and of aggregates at higher salt concentration. Double-fibers are present up to physiological salt concentrations.

Physicochemical properties of salt-soluble, unsheared chromatin. Molecular weight studies

A chromatin fraction, which can reproducibly be extracted from rat liver nuclei at moderate salt concentration (0.1 M (NH4)2SO4, 0.1 M Tris-HCl, 2 mM MnCl2, pH 7.9), was analyzed with regard to changes of its molecular weight in the range of (NH4)2SO4 concentrations between 0.1 M and 0.4 M. With the transition from 0.1 M to 0.2 M (NH4)2SO4 histone H1 is released and the molecular weight obtained from both sedimentation-viscosity and light scattering is reduced by approximately one-half. A spatial expansion of the resulting half-molecules is observed with further increasing salt concentration. On the basis of these results a double-fibrillar structure of this chromatin fraction is proposed.