Sensitivity of regions of chromatin containing hyperacetylated histones to DNAse I.

We have used DNase I as a probe for structural changes in regions of chromatin containing highly acetylated histones. The enzyme preferentially digests regions of chromatin that are associated with rapidly or highly acetylated histones, suggesting that nucleosomes in these regions are in a more accessible conformation. This sensitivity to DNase I may be related to the same factors which cause the differential digestion of active genes.     

Linker DNA bending induced by the core histones of chromatin

We have previously reported that ionic conditions that stabilize the folding of long chromatin into 30-nm filaments cause linker DNA to bend, bringing the two nucleosomes of a dinucleosome into contact [Yao, J., Lowary, P. T., & Widom, J. (1990) Proc. Natl. Acad. Sci. U.S.A. 87, 7603-7607]. Dinucleosomes are studied because they allow the unambiguous detection of linker DNA bending through measurement of their nucleosome-nucleosome distance. Because of the large resistance of DNA to bending, the observed compaction must be facilitated by the histones. We have now tested the role of histone H1 (and its variant, H5) in this process. We find that dinucleosomes from which the H1 and H5 have been removed are able to compact to the same extent as native dinucleosomes; the transition is shifted to higher salt concentrations. We conclude that histone H1 is not essential for compacting the chromatin filament. However, H1 contributes to the free energy of compaction, and so it may select a single, ordered, compact state (the 30-nm filament, in long chromatin) from a family of compact states which are possible in its absence.     

A chromatin core particle obtained by selective cleavage of histones by clostripain.

Rat liver chromatin core particles digested with clostripain yield a structurally well-defined nucleoprotein particle with an octameric core made up of fragmented histone species (designated H'2A, H'2B, H'3 and H'4, respectively) after selective loss of a sequence segment located in the N-terminal region of each core histone. Sequential Edman degradation and carboxypeptidase digestion unambiguously establish that histones H2A, H2B, H3 and H4 are selectively cleaved at the carboxyl side of Arg 11, Lys 20, Arg 26 and Arg 19 respectively and that the C-terminal sequences remain unaffected. Despite the loss of the highly basic N-terminal regions, including approximately 17% of the total amino acids, the characteristic structural organization of the nucleosome core particle appears to be fully retained in the proteolyzed core particle, as judged by physicochemical and biochemical evidence. Binding of spermidine to native and proteolyzed core particles shows that DNA accessibility differs markedly in both structures. As expected the proteolyzed particle, which has lost all the in vivo acetylation sites, is not enzymatically acetylated, in contrast to the native particle. However, proteolyzed histones act as substrates of the acetyltransferase in the absence of DNA, as a consequence of the occurrence of potential acetylation sites in the core histones thus rendered accessible. The possible role of the histone N-terminal regions on chromatin structure and function is discussed in the light of the present observations with the new core particle obtained by clostripain proteolysis.     

Interactions between core histones and chromatin at physiological ionic strength

Addition of core histones to chromatin or chromatin core particles at physiological ionic strength results in soluble nucleohistone complexes when polyglutamic acid is included in the sample. The interaction between nucleosomes and added core histones is strong enough to inhibit nucleosome formation on a closed circular DNA in the same solution. Complexes consisting of core particles and core histones run as discrete nucleoprotein particles on polyacrylamide gels. Consistent with the electrophoretic properties of these particles, protein cross-linking with dimethyl suberimidate indicates that added core histones are bound as excess octamers. Histones in the excess octamers do not exchange with nucleosomal core histones at an ionic strength of 0.1 M and can be selectively removed from core particles by incubating the complexes in a solution containing sufficient DNA. Under conditions where added histones are confined to the surface of chromatin, the excess histones are mobile and can migrate onto a contiguous extension of naked DNA and form nucleosomes.     

Equimolar proportions of somatic-type,core histones in chromatin of spermatogonia

[³H]Leucine incorporation into histones of seminiferous epithelial cells of hypophysectomized rats was used to calculate the molar proportions of the core histones of spermatogonia. The molar proportions H3:H2B:(H2A + protein A24):H4 are 1:1:1:1, viz. identical with those reported by others for somatic cells. Similar results were obtained when molar proportions of histones of seminiferous epithelial cells from immature rat testis (predominantly populated with spermatogonia) were determined by the dye-binding method. These data are relevant to mechanisms for the replacement of some of the core histones by variants during the primary spermatocyte stages.     

Isolation of four core histones from human sperm chromatin representing a minor subset of somatic histones

Using high performance liquid chromatography we have successfully purified four core histones from mature human sperm chromatin. The H2A variants present in sperm (H2A.X and limited H2A.Z) have been shown previously to be minor variants in somatic chromatin. The histones are highly modified as evidenced by extensive acetylation and an as yet uncharacterized multicharge modification of H2B. Based on our data, we conclude that histone proteins are a minor component of each mature spermatozoa. Given the unique nature of the histone variants present in sperm, we propose that this chromatin component has a specific function and may possibly facilitate the programming of genes which will be active in early development.     

DNA folding by histones: the kinetics of chromatin core particle reassembly and the interaction of nucleosomes with histones.

The kinetics of the chromatin core particle reassembly reaction in solution were quantitatively studied under conditions such that nucleohistone aggregation did not occur. Core particles, salt-jumped rapidly by dilution from 2.5 m-NaCl (in which DNA and histones do not interact) to 0.6 m-NaCl (in which core particles are nearly intact), reassemble in two distinct time ranges. Approximately 75% of the DNA refolds into core particle-like structures “instantaneously” as measured by several physical and chemical techniques with dead times in the seconds to minutes time range. The remaining DNA refolds with relaxation times ranging from 250 minutes at 0 °C to 80 minutes at 37 °C; this slow effect cannot be attributed to sample heterogeneity. The fraction of slowly refolding DNA and the slow relaxation time are independent of the core particle concentration. Transient intermediates present during the slow phase of refolding were identified as free DNA and core particle-like structures containing excess histone. Mixing experiments with DNA, histones, and core particles showed that core particle-histone interactions are responsible for the slow kinetics of DNA refolding. Upon treatment of reassembling core particles with the protein crosslinking reagent, dimethylsuberimidate, the slow phase of the reassembly reaction was arrested and a 13 S particle containing DNA and two octamers of histone was isolated. Consistent with the nature of this kinetic intermediate, it is shown that in 0.6 m-NaCl, core particles co-operatively bind at least one additional equivalent of histones with high affinity in the form of excess octamers. Also, core particles continue to adsorb considerably more histones with a weaker association constant of the order 10⁵m^?1 (in units of octamers) to a maximum value of 12 ± 2 equivalents (octamers) per core particle. The sedimentation coefficient increases with the two-thirds power of the molecular weight of the complex, as it would in the case of clustered spheres.A reassembly mechanism consistent with the data is presented, and other simple mechanisms are excluded. In the proposed mechanism, core particles reassemble very rapidly and compete effectively with DNA for histones such that approximately one-third of the particles initially formed are complexed with an excess octamer of histones, and 25% of the total DNA remains uncomplexed. The amount of this unusual reaction intermediate decays slowly to an equilibrium value of about 10%, thereby leaving 9% of the total DNA uncomplexed. Approximate values are calculated for the free energies, rate constants, and two of the activation energies which characterize this migrating octamer mechanism. This mechanism provides a means whereby histone octamers can be temporarily stripped off DNA at a modest free energy cost, approximately 2.6 kcal per nucleosome. Also, the properties of excess histone adsorption by chromatin and octamer migration suggest an efficient mechanism, consistent with observations by others, for nucleosome assembly in vivo during replication.     

Acetylation and phosphorylation of Drosophila histones. Distribution of acetate and phosphate groups in fractionated chromatin.

The phosphorylation and acetylation patterns of Drosophila histones were studied after whole cell incubation with ortho [32P] phosphate or [3H] acetate. Radioactive phosphate associated mainly with H1, H3, and H4 and radioactive acetate was associated mainly with H3, H4, and H2B. H3 showed the highest specific activity of both labels. Two chromatin fractionation methods were employed to investigate the distribution of acetate and phosphate groups in histones form template-active and template-inactive regions. The levels of both acetate and phosphate groups were higher in histones from template-active regions.     

The core histone N termini function independently of linker histones during chromatin condensation

The relationships between the core histone N termini and linker histones during chromatin assembly and salt-dependent chromatin condensation were investigated using defined chromatin model systems reconstituted from tandemly repeated 5 S rDNA, histone H5, and either native "intact" core histone octamers or "tailless" histone octamers lacking their N-terminal domains. Nuclease digestion and sedimentation studies indicate that H5 binding and the resulting constraint of entering and exiting nucleosomal DNA occur to the same extent in both tailless and intact chromatin arrays. However, despite possessing a normal chromatosomal structure, tailless chromatin arrays can neither condense into extensively folded structures nor cooperatively oligomerize in MgCl(2). Tailless nucleosomal arrays lacking linker histones also are unable to either fold extensively or oligomerize, demonstrating that the core histone N termini perform the same functions during salt-dependent condensation regardless of whether linker histones are components of the array. Our results further indicate that disruption of core histone N termini function in vitro allows a linker histone-containing chromatin fiber to exist in a decondensed state under conditions that normally would promote extensive fiber condensation. These findings have key implications for both the mechanism of chromatin condensation, and the regulation of genomic function by chromatin.     

Characterization and nucleosomal core localization of Achlya histones involved in stress-induced chromatin condensation

To better understand the basis for heat shock-induced chromatin condensation in Achlya, a further characterization of the histones of this organism was carried out. The nucleosomal location (i.e., core vs linker), partial peptide map, and electrophoretic behavior of each Achlya histone was determined and compared to the well-characterized histones of rabbit kidney. The results of this and previous studies suggest that in Achlya, no nucleosome linker-associated histone analogous to histone H1 of higher eucaryotes is observed and that the Achlya histone designated alpha is a novel nucleosomal core histone. These observations may reflect the existence of a mechanism of stress-induced chromatin condensation which does not involve histone H1.     

On the arrangement of histones in chromatin.

It was found that nucleoprotein particles formed after DNase I action on calf thymus chromatin contain single-stranded DNA fragments, associated with histones only by ionic linkages. These results suggest that histones in chromatin are bound ionically only to one polynucleotide strand of double-helical DNA, protecting it against nucleolytic attack.     

Cryo-EM structure of the nucleosome core particle containing Giardia lamblia histones

Giardia lamblia is a pathogenic unicellular eukaryotic parasite that causes giardiasis. Its genome encodes the canonical histones H2A, H2B, H3, and H4, which share low amino acid sequence identity with their human orthologues. We determined the structure of the G. lamblia nucleosome core particle (NCP) at 3.6 Å resolution by cryo-electron microscopy. G. lamblia histones form a characteristic NCP, in which the visible 125 base-pair region of the DNA is wrapped in a left-handed supercoil. The acidic patch on the G. lamblia octamer is deeper, due to an insertion extending the H2B α1 helix and L1 loop, and thus cannot bind the LANA acidic patch binding peptide. The DNA and histone regions near the DNA entry-exit sites could not be assigned, suggesting that these regions are asymmetrically flexible in the G. lamblia NCP. Characterization by thermal unfolding in solution revealed that both the H2A–H2B and DNA association with the G. lamblia H3–H4 were weaker than those for human H3–H4. These results demonstrate the uniformity of the histone octamer as the organizing platform for eukaryotic chromatin, but also illustrate the unrecognized capability for large scale sequence variations that enable the adaptability of histone octamer surfaces and confer internal stability.     

Laser Raman identification of an interaction site on DNA for arginine containing histones in chromatin.

Comparisons of the Raman spectra of DNA, chromatin, and complexes of DNA with poly-L-arginine and N-α-acetylarginine have been made. Both in native chromatin and in complexes of DNA with the arginine derivatives there is a marked decreased in the Raman intensity of the 1490±2 cm^?1 band due to guanine. Considerable evidence is presented to show that a decrease in the intensity of the 1490 cm^?1 Raman band of quanine in DNA is strong indication of a hydrogen bond being attached to the N-7 position of quanine. A specific model is presented for the interaction of the arginine residues with the guanine residues in the major groove of DNA. The Raman frequency of the histone Amide 1 band indicates that these protein molecules have a high α-helical content while the phosphate diester stretch frequency of the DNA shows the DNA to be in the B-family.     

Hyperacetylated histones facilitate chromatin assembly in vitro.

We have examined the effect of histone acetylation on the in vitro assembly of nucleosomes with DNA and purified histones at physiological ionic strength in the presence of polyglutamic acid. We have found that hyperacetylated histones assemble nucleosomes with greater efficiency, and to a greater extent, than either control or hypoacetylated histones. Assembly reactions were performed over a range of histone to DNA ratios (0.25 to 3.0, w/w) and polyglutamic acid to histone ratios (0 to 1.6, w/w). Although polyglutamic acid may act as a sink to prevent nonspecific histone-DNA interactions, our data suggest that the polyanion primarily facilitates the assembly of nucleosomes by organizing histones into a form that is amenable to deposition.     

Purification and the histones of Dictyostelium discoideum chromatin.

Dictyostelium chromatin has been purified from nuclei in high yield by differential centrifugation and nuclease cleaving. Its chemical composition has been assayed, and its histones have been analyzed by gel electrophoresis, peptide fingerprints, amino acid composition, and ion-exchange chromatography. The mass ratios of DNA/RNA/histone/nonhistone are 1.0:0.18:0.98:1.02. There are four histones including one unusual histone, H7, which is the most abundant histone in the slime mold. The H4-like protein is the most conserved protein, while the other histones show both similarities and differences with mammalian histones.     

Nucleosomes containing histones H1 or H5 are closely interspersed in chromatin

The distribution of histones H1 and H5 along chromatin fibers has been examined in the nucleated hen erythrocyte. Nucleosome oligomers, produced by micrococcal nuclease digestion of nuclei, were sequentially reacted with affinity-chromatography purified rabbit anti-H5 and sheep anti-rabbit antibodies. Quantitation of the relative amounts of H1 and H5 in the precipitated and supernatant fractions as a function of the oligomer number was consistent with a close interspersion of both types of histones, probably a random one. This conclusion was supported by the immunoprecipitation of longer chromatin fibers. This pattern of distribution appears to apply both to bulk chromatin and to chromatin inactivated during the maturation of the erythrocyte.