The subunit structure of the eukaryotic chromosome

Influence of histone H1 on chromatin structure

Removal of histone H1 produces a transition in the structure of chromatin fibers as observed by electron microscopy. Chromatin containing all histone proteins appears as fibers with a diameter of about 250 A. The nucleosomes within these fibers are closely packed. If histone H1 is selectively removed with 50-100 mM NaCl in 50 mM sodium phosphate buffer (pH 7.0) in the presence of the ion-exchange resin AG 50 W - X2, chromatin appears as "beads-on-a-string" with the nucleosomes separated from each other by distances of about 150-200 A. If chromatin is treated in the presence of the resin with NaCl at concentrations of 650 mM or more, the structural organization of the chromatin is decreased, yielding fibers of irregular appearance.

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.

Studies on the role and mode of operation of the very-lysine-rich histone H1 in eukaryote chromatin. The three structural regions of the histone H1 molecule

Limited digestion with trypsin of both calf thymus H1 histone and the fragment 1--120 of the H1 molecule has resulted in the isolation of the fragment 35--120. This fragment assumes a globular structure under physiological conditions of pH and ionic strength. The variable N-terminal portion of the molecule, up to residue 34, is not required for the formation of the H1 globular structure. Proton nuclear magnetic resonance (NMR) and ultracentrifugation studies show that the H1 histone molecule consists of three distinct structural domains under structuring conditions: a random coil 'nose' consisting of 35 to 40 residues from the N-terminal end; a globular 'head' involving the next approximately 80 residues; and a random-coil 'tail' of the remainder of the molecule.

Binding of polylysine to chromatin subunits and cleavage by micrococcal nuclease. A comparison of accessible sites

Native chromatin and chromatin subunits (nucleosomes) were titrated with polylysine and digested with micrococcal nuclease and deoxyribonuclease I at individual lysine/nucleotide ratios. In contrast to earlier reports, which had been obtained using mechanically sheared chromatin, a comparison of the sites accessible for micrococcal nuclease and polylysine reveals that polylysine does not preferentially protect the micrococcal-nuclease-susceptible sites in chromatin. Similar results were obtained in digestion experiments with DNase I. From the experimental data presented we conclude that polylysine does not preferentially bind to the internucleosomal DNA, which is the prime target site for micrococcal nuclease, but rather to the total nucleosomal DNA moiety.

The interaction of nonhistone chromosomal proteins HMG1 and HMG2 with subfractions of H1 histone immobilized on agarose

Chromatographically isolated subfractions of calf thymus H1 histone have been covalently coupled to agarose beads and tested for their ability to form complexes with the non-histone proteins HMG1 and HMG2 (High Mobility Group proteins, Walker, J.M., Goodwin, G.H. and Johns, E.W. (1976) Eur. J. Biochem. 62, 461-469). When a mixture of HMG1 and HMG2 is passed through a column of H1 histone-agarose, the HMG2 does not bind. HMG1 does bind and can be eluted from the column with NaCl in the range of 0.05 M--0.15 M. The NaCl concentration required to elute HMG1 from each of the three H1 histone subfraction coulmns is different, suggesting that HMG1 has a different binding affinity for the three H1 histone subfractions.

Interaction of DNA with poly(L-Lys-L-Ala-Gly) and poly(L-Lys-L-Ala-L-Pro). Circular dichroism and thermal denaturation studies

Complexes of DNA with polypeptides composed of Lys, Ala, and Gly in both a sequential order, poly(L-lysine-L-alanine-glycine), and a statistical distribution, poly(L-lysine36-L-alanine28-glycine), were prepared using gradient dialysis. These polypeptide-DNA complexes were studied using ultraviolet absorption (UV) and circular dichroism (CD) to probe the conformation, binding, and melting behavior of DNA in the complex. Complexes with the sequential polypeptide showed no structural change in the DNA; however, the complexes with the random polypeptide yield CD spectra similar to phi DNA [Maniatis, T., Venable, Jr., J.S., and Lerman, L.S. (1974), J. Mol. Biol. 84, 37]. A second sequential polypeptide, poly(L-Lys-L-Ala-L-Pro)n, -DNA complex was also studied. It was found to exhibit pronounced structural changes as a function of ionic strength and poly-peptide-DNA ratio, more similar to the random sequence that the ordered sequence of the Lys, Ala, Gly polymer. Thus the importance of the composition and amino acid sequence in polypeptides which bind to DNA, even in such simple systems, is demonstrated. Evidence from thermal denaturation, employing simultaneous monitoring of CD and UV changes, supports a model in which specific polypeptides cause condensation of the DNA in the complex into an asymmetric tertiary structure. The relevance of these model systems to chromatin is discussed.

Laser Raman spectra of calf thymus histones H1, H2A, and H2B

Laser Raman spectra of the calf thymus histones H1, H2A, and H2B in aqueous solutions are presented. The amide III band in the spectrum of the very lysine-rich histone H1 in aqueous solution appears at 1245 cm-1, which is almost at the same frequency as the corresponding vibration of the ionized form of poly(L-lysine). Upon increasing the NaCl concentration to 1 M, the frequency of the amide III vibration shifts to 1250 cm-1 as a result of the formation of a more compact disordered structure of at least the N-terminal region of the protein. Changing the pH from 3 to 5 induces the same frequency shift. The amide III regions of the Raman spectra of the slightly lysine-rich histones H2A and H2B shows two bands at 1247 and 1265 cm-1 for H2A, and at 1254 and 1265 cm-1 for H2B. These doublets are attributed to vibrations involving the backbone of at least two structurally distinct parts of the histone molecules. The low frequency component is assigned to the random-coil regions of the proteins which appear to have similar conformations for H1 and H2A. The frequency of this component also suggest that the structure of the disordered regions of H2B are more compact and less extended. These conclusions confirm the conformation predictions based on the primary structures of these proteins. The high frequency component at 1265 cm-1 is assigned to the alpha-helical and rigid disordered structures of H2A and H2B, since this band increases in intensity upon addition of NaCl. The amide I' region of the histone spectra is also presented but appears to be much less sensitive to the conformation than the amide III region. The intensity of the bands due to the single bond C-C stretching modes, as well as the intensity ratio of the tyrosine Fermi doublet at 855 and 830 cm-1, are also discussed.

Specificity of the weak binding between the phage SPO1 transcription-inhibitory protein, TF1, and SPO1 DNA

The interaction of the phage SPO1 protein transcription factor 1 (TF1), with DNA has been analyzed by membrane filter binding and by sedimentation methods. Substantially specific binding of TF1 to helical SPO1 DNA can be demonstrated by nitrocellulose filter-binding assays at relatively low ionic strength (0.08). However, TF1-DNA complexes dissociate and reequilibrate relatively rapidly and this makes filter-binding assays unsuitable for quantitative measurements of binding equilibra. Accordingly, the sedimentation properties of TF1-DNA complexes have been explored and a short-column centrifugation assay has been elaborated for quantitative measurements. Preferential binding of TF1 to the hydroxymethyluracil-containing SPO1 DNA has also been demonstrated by short-column centrifugation. TF1 binds relatively weakly and somewhat cooperatively to SPO1 DNA at many sites; TF1-DNA complexes dissociate and reequilibrate rapidly. At 20 degrees C in 0.01 M phosphate, pH 7.5, 0.15 KC1, one molecule of TF1 can bind to approximately every 60 nucleotide pairs of SPO1 DNA.

Analysis of nucleosomal deoxyribonucleic acid in a higher plant

Comparisons of nuclease digestions of chromatin in nuclei from rye embryos and rat liver show that their nucleosomal DNA is similar, i.e. DNA subunits consist of 200 base-pair repeats with 140 base-pair cores of identical substructure. The identical nucleosome structure is present in nuclei from cells of rye embryos that have been non-viable (i.e. dead) for more than 7 years. These findings indicate a high degree of stability of the DNA-histone complex and are consistent with conservation of the nucleosomal structure of chromatin during evolution.

[New findings on the structure of chromosomes (author's transl)]

The structural element of eukaryotic chromosomes is the chromatin fibre consisting of histones and DNA. The chromatin fibre is about 100--200 A thick. One chromatid is built up from one chromatin fibre running through from one end to the other and laid in numerous irregular foldings. The chromatin fibre is a chain of nucleosomes. These are globular histone bodies around which the DNA winds. Nucleosomes can be observed in isolated chromatin fibrils as well as in thin sections of chromosomes after different modes of fixation. Prophasic chromosomes or early premature condensed chromosomes are thin uncoiled threads. With chromosome condensation a major coiling is seen. No constant regular arrangement of the chromatin fibril besides the major coils is observed. A rather diffuse decondensation takes place in ana- and telophase.

The effect of H1 histone on the action of DNA-relaxing enzyme

The action of DNA-relaxing enzyme on H1-DNA complexes was investigated. Complexes of superhelical and relaxed closed circular duplex DNA with H1 were treated with mammalian relaxing enzyme, deproteinized, and electrophoresed on agarose gels. At relatively low ratios of H1 to superhelical DNA, molecules of superhelical density intermediate between those of the starting material and relaxed DNA, the normal product, were generated. At relatively high H1 histone concentrations (H1:DNA greater than 0.4 w/w), the superhelical DNA was not relaxed. Further, no superhelical turns were introduced into relaxed closed duplex DNA at any concentration of H1 tested. Thus, the binding of H1 histone to DNA prevents the action of the relaxing enzyme. Moreover, H1 histone does not appear to unwind the DNA duplex upon binding. The implications of these observations and the previously demonstrated specificity of H1 histone for superhelical DNA are discussed in relation to the structure of chromatin.

Small angle neutron scattering studies of chromatin subunits in solution

Neutron scattering studies have been performed on dilute solutions of the fundamental subunit of chromatin, the nucleosome. The subunits contain approximately 195 base paris (bp) of DNA and histones H2A, H2B, H3, and H4. Measurements of the small angle scattering curves in various H2O/D2O solvents allow the contrast dependence of the radius of gyration of the subunits to be examined and give the mean scattering density of the particle. Further application of contrast variation to the higher angle scatter curves allows the contributions from the shape and internal structure of the subunits to be analyzed separately. From these results, we are able to propose a spherically averaged structure with most of the histones closely packed into a core of radius 3.2 nm surrounded by a loosely packed DNA-rich shell of 2.0 nm thickness resulting in a particle of 5.2 nm average radius. Model calculations for ellipsoids show that the outer shape of the subunit must have an axial ratio between 0.5 and 1.4 but is probably best described by more spherical particle. These results are correlated with the diffraction from chromatin films to provide an explanation for some of the diffraction rings.

Gene control in eukaryotes and the c-value paradox "excess" DNA as an impediment to transcription of coding sequences

Ways in which control of gene activity may lead to the observed high DNA content per haploid eukaryote genome are examined. It is proposed that deoxyribonucleoprotein (DNP) acts as a barrier to transcription at two distinct structural levels. At the lower level, melting of the nucleosome supercoil (quaternary structure) and of the nucleosomes (tertiary structure) might be brought about by the process of transcription itself. After unwinding the barrier section, the polymerase would eventually reach the structural gene. The transcripts of noncoding sequences, at least as far as their "unique" sequence components are concerned, may thus have filled their main function through the very process of transcription. The possibility of an inverse relationship between the length of the DNP barrier and the rates of transcription of the coding sequences is to some extent supported by available data. Different modes of coordination between the transcription of mRNA and of hnRNA from a single functional unit of gene action (funga) are considered. An analysis of gene control at high structural levels of DNP is made on the basis of other data, in relation to the concepts of eurygenic and stenogenic control. The concept of a euryon is introduced, namely of a set of linked fugas under common eurygenic control. Structure of order higher than quaternary can be inferred to exist in larger chromomeres of polytene chromosomes and in corresponding sections of ordinary chromosomes. Only moderate amounts of highest order interphase euchromatic structure are likely to be able to be accomodated in average chromomeres and none in very thin chromomeres. Puffs are interpreted as the melting of highest order interphase structure, and the absence of puffs during transcription as the absence of this highest order structure in the resting state of the chromomeres. Genes that are constantly active in all tissues may dispense with highest order interphase structure and with the corresponding control mechanism, and the fugas involved thus may not puff. Puffs, large chromomeres and highest order interphase euchromatic DNP structure seem to be correlated with genes that need to be transcribed only under certain developmental conditions. It is proposed that the function of high order structure is to sequester genetic material, namely mainly controller sequences. Since such high order structure, in most cases, would be built up to house the controller dependencies of just one structural gene, the amount of DNA per structural gene needed for gene control would be considerable, and the concept, if correct, would go a long way towards explaining the c-value paradox ("excess" DNA in eukaryotes). In eurygenic determination, the high order structure is thought to be conditioned for melting or to actually melt to an intermediate level of structure. From there, stenogenic control, leading to transcription, is considered to carry the melting process further to yet lower structural levels...

Chromatin nu bodies: isolation, subfractionation and physical characterization

Monomer chromatin subunit particles (nu1) have been isolated in gram quantities by large-scale zonal centrifugation of micrococcal nuclease digests of chicken erythrocyte nuclei. nu1 can be stored, apparently indefinitely, frozen in 0.2 mM EDTA (pH 7.0) at less than or equal to 25 degrees C. Aliquots of the stored monomers have been subfractionated by dialysis against 0.1 M KCl buffers into a soluble fraction containing equimolar amounts of H4, H3, H2A, H2B associated with a DNA fragment of approximately 130-140 nucleotide pairs, and a precipitated fraction containing all of the histones including H5 and H1 associated with DNA fragments. The total nu1 and the KCl-soluble fraction of nu1 have been examined by sedimentation, diffusion, sedimentation equilibrium ultracentrifugation, low-angle X-ray diffraction, and electron microscopy. Physical parameters from all of these techniques are presented and correlated in this study.

The subunit structure of chromatin from Physarum polycephalum

Nucleosome DNA repeat lengths in Physarum chromatin, determined by nuclease digestion experiments, are shorter than those observed in most mammalian chromatin and longer than those reported for chromatin of certain other lower eukaryotes. After digestion with staphylococcal nuclease for short periods of time an average repeat length of 190 base pairs is measured. After more extensive digestion an average repeat length of 172 base pairs is measured. Upon prolonged digestion DNA is degraded to an average monomer subunit length of 160 base pairs, with only a small amount of DNA found in lengths of 130 base pairs or smaller. Mathematical analysis of the data suggests that the Physarum nucleosome DNA repeat comprises a protected DNA segment of about 159 base pairs with a nuclease-accessible interconnecting segment which ranges from 13 to 31 base pairs. The spacing data are compatible with measurements from electron micrographs of Physarum chromatin.

Assembly of DNA with histones and nonhistone chromosomal proteins in vitro

We have examined, by protein binding assays, thermal denaturation, and circular dichroism, the possible effects of histones on nonhistone chromosomal protein (NHCP) interactions with DNA. For these studies, we have fractionated mouse Krebs II chromosomal proteins into three discrete fractions: Mo, 5 M urea-soluble NHCP; M1, 5 M urea-1 M NaCl-soluble NHCP from 5 M urea-extracted chromatin; and M3, 5 M urea-3 M NaCl-soluble chromosomal proteins from 5 M urea-1 M NaCl-extracted chromatin. These fractions contain heterogeneous populations of NHCP, and were found to differentially affect histone binding to DNA by methods of reconstitution, or by direct binding of M0, M1, or M3 to urea-salt reconstituted DNA with histones. M0 was found to exert a unique effect on the thermal denaturation and circular dichroic spectra of DNA-histone complexes. M0 from Krebs II chromatin was also found to complete for DNA sites in the presence of M0 from mouse liver chromatin. In addition, in 5 M urea, pH 8.0, histone binding to DNA reached saturation at 1.85 mg/mg of DNA, higher than the in vivo ratio of 1.00 mg/mg of DNA. Saturation of histone binding to DNA occurred only in the presence of 5 M urea, resulting in a reduction of nonspecific histone-histone interactions on DNA.

Relaxation of chromatin structure by ethidium bromide binding: determined by viscometry and histone dissociation studies

The effects of ethidium bromide intercalation on chromatin structure were monitored by viscometry and analysis of histone dissociation. Investigation of the NaCl concentration dependence of chromatin viscosity showed that the reduced viscosity (etared) was very low up to 0.4 M NaCl and increased gradually when the salt concentration was raised further. In chromatin intercalated by ethidium bromide, etared was not significantly different at low salt concentrations (up to 0.2 M NaCl). However, when the salt concentration was raised further, the viscosity response curve increased sharply to reach viscosities about 4-5 times higher than those for nonintercalated chromatin. The increase in viscosity was proportional to the increase in fluorescence intensity, when the ratio of ethidium bromide to DNA mucleotide was raised. The transition of intercalated chromatin into the relaxed form was reversible, dependent on the nature of the electrolyte and cooperative, as indicated by the small increase in salt concentration required to obtain chromatin relaxation. Investigation of the NaCl concentration dependence of histone dissociation revealed that total histones and each individual histone fraction were released from intercalated chromatin at much reduced NaCl concentrations. The midpoints of the dissociation curves of the individual histones ranged from 0.30 to 0.45 M NaCl and fell within the same range where the drastic viscosity change occurred. These results indicate that intercalation of ethidium bromide labilizes chromatin structure to relaxation by moderately elevated salt concentrations. It is suggested that the labilization is caused by changes in the DNA helix conformation due to dye intercalation decreasing the stability of histone-DNA interactions.

Model studies of chromatin structure based on X-ray diffraction data

Model calculations are presented in order to interpret the X-ray diffraction diagrams given by chromatin gels. It is shown that by taking into account the hydration of chromatin subunits, the problem of calculating the interference function in concentrated gels is greatly simplified. In this way it is spossible to fully interpret the influence of concentration on the position and intensity of the various rings present in the X-ray diffraction patterns. The possibilities and limitations of models based on spherical symmetry are also discussed. It is concluded that each chromatin subunit most likely contains three turns of DNA in each 200 base pairs segment surrounding a central protein core. With the method presented here it is possible to test if other models of chromatin based on different kinds of evidence are compatible with the X-ray diffraction data.

A model for chromatin based upon two symmetrically paired half-nucleosomes

We propose that the basic unit of chromatin is constructed of two isologously paired heterotypic protein tetramers each containing one molecule of H2A, H2B, H3, and H4 histone. These proteins form a core that holds 140 base pairs (bp) of DNA in a single left-handed, non-interwound DNA super-coil approximately 95 bp in circumference, creating a nucleosome particle (DNA and protein) organized about a dyad axis of symmetry. Such a nucleosome can open up into its separate half-nucleosomes to allow genetic readout without requiring histone displacement.

Ribosomal genes of Xenopus laevis: evidence of nucleosomes in transcriptionally active chromatin

Most of the reiterated ribosomal genes in the somatic cells of larvae of a mutant of Xenopus laevis appear to be protected from short-term nuclease digestion by being packaged in the form of chromatin subunits or nucleosomes. Since these mutant animals probably require all of their ribosomal genes to be active in order to maintain viability, at least some of the transcriptionally active gene sequences are probably associated with chromatin subunits. Thus, association of DNA with nucleosomes may not necessarily preclude template activity, although such association is probably of a dynamic rather than a static nature.

Analysis of chromatin-associated fiber arrays

Electron microscopic examination of chromatin from embryonic nuclei of Oncopeltus fasciatus and Drosophila melanogaster reveals arrays of chromatin associated fibers. The lengths and spacings of these fibers were analyzed to provide a basis for defining and interpreting regions of transcriptionally active chromatin. The results of the analysis are consistent with the interpretation of some fibers as nascent RNA with associated protein (RNP). The chromatin segments underlying these fiber arrays were classified as ribosomal or non-ribosomal transcription units according to definitions and criteria described by Foe et al. (1976). Nascent fibers on active ribosomal transcription units were analyzed and compared for Drosophila melanogaster, Triturus viridescens, and Oncopeltus fasciatus. A common feature of the fiber patterns on ribosomal TUs is that origin-distal fibers exhibit greater length variability and a lower slope relative to proximal fibers. The region of increased variability in fiber lengths is correlated with the expected location of 28S ribosomal RNA sequences in the distal half of each ribosomal transcription unit. Because 28S ribosomal RNA appears to contain more extensive regions of base sequence complementarity, we suggest that the length of ribosomal RNP fibers is influenced under our spreading conditions by the secondary structure of the nascent RNA. In order to calculate the RNA content of RNP fibers, chromatin morphology was used to estimate lengths of transcribed DNA. The packing ratio of DNA in chromatin, which we express as the length of B-structure DNA divided by length of chromatin, is 1.1-1.2 and 1.6 for the DNA in active ribosomal and non-ribosomal chromatins, respectively. These DNA packing ratios are used to determine the extent to which nascent RNP fibers are shorter than the transcribed DNA (expressed as DNA/RNP length ratio). For non-ribosomal transcription units and for proximal fibers of ribosomal transcription units. DNA/RNP length ratios are relatively constant within each array. However, considerable variability in this ratio (4-23) is observed for different arrays of fibers. Possible sources of this variability are considered by comparing ratios derived from the presumably identical ribosomal transcription units. Further analysis of the morphology of nascent fibers may elucidate the contributions of proteins and successive RNA sequences to RNP structure.

Nuclease digestion in between and within nucleosomes

In the course of digestions of rat liver nuclei with micrococcal nuclease the size of the nucleosomal DNA is shortened by 50-60 nucleotide pairs from starting lengths of about 200, 400, 600, 800, etc. nucleotide pairs in the monomeric and oligomeric nucleosomes, respectively. Acid soluble DNA material is created relatively slowly as compared to the rate of formation of subnucleosomal material. More DNA with lengths in between the 200, 400, etc. nucleotide pairs of nucleosomal DNA is formed when digestions with micrococcal nuclease are carried out at 0 to 10 degrees C compared to 40 degrees C. With DNAase II, on the other hand, formation of a 200 nucleotide pair pattern is favoured at the low temperatures. Apparently, the accessibility of potential cleavage sites in between and within nucleosomes depends strongly on the conditions of digestion. Possible reasons for this dependence are discussed.

Prediction of the conformation of the histones

The secondary structures of the histones, H1, H2A, H2B, H3, and H4 have been predicted utilizing the predictive scheme of Chou and Fasman (Biochemistry 13:211, 222[1974]) and a new set of conformational parameters based on the X-ray data of 29 protein structures. The alpha-helical, beta-sheet, reverse beta-turns, and random coil regions of these proteins are carefully delineated. Structures are specified which are most probably under various environmental conditions, i.e., for changes in ionic strength, association between histones and in association with DNA. Potential conformational changes within these histones are also predicted.

Circular dichroism as a probe of DNA structure inside reconstituted nucleohistones

Reconstituted nucleohistones were obtained by mixing in given conditions acid extracted histones and eukaryotic DNA. The histone/DNA ratio (w/w) was in the range 0.35 - 0.95. With the four histones (H2A2B) we have been able to obtain subunits (nucleosomes or upsilon-bodies). The variation of cirsular dichroism signal with temperature at 280 nm was measured to follow structural changes of the DNA inside the complex. The true change of ellipticity (see article) of histone-bound DNA regions, is similar for reconstituted nucleohistone and H1-depleted chromatin, and is therefore a physical probe of the presence of nucleosomes.

A possible explanation for the nuclease limit digestion pattern of chromatin

The general pattern of DNA fragments in the limit digest of nuclease-treated chromatin could arise from a single, unique nuclease-susceptible site per nucleosome. If DNA binds to the histone core of the nucleosome along a circularly re-entrant path, the location of the DNA entrance and exit can occur at any of a number of distinct sites. This very specific type of heterogeneity together with the natural 10-fold periodicity of DNA B can account for the observed digestion pattern. Such a general picture of the nucleosome structure could also easily explain how nucleosomes might move along the DNA. This type of structure should be easy to distinguish experimentally form more conventional explanations of the origin of the limit digest pattern of chromatin.

Chromosomal subunits in active genes have an altered conformation

Ten percent digestion of isolated nuclei by pancreatic deoxyribonuclease I preferentially removes globin DNA sequences from nuclei obtained from chick red blood cells but not from nuclei obtained from fibroblasts, from brain, or from a population of red blood cell precursors. Moreover, the nontranscribed ovalbumin sequences in nuclei isolated from red blood cells and fibroblasts are retained after mild deoxyribonuclease I digestion. This suggests that active genes are preferentially digested by deoxyribonuclease I. In contrast, treatment of red cell nuclei with staphylococcal nuclease results in no preferential digestion of active globin genes. When the 11S monomers obtained after staphylococcal nuclease digestion of nuclei are then digested with deoxyribonuclease I, the active globin genes are again preferentially digested. The results indicate that active genes are probably associated with histones in a subunit conformation in which the associated DNA is particularly sensitive to digestion by deoxyribonuclease I.

A study of the interaction between ethidium bromide and rye chromatin: comparison with calf thymus chromatin

We studied the interaction of ethidium bromide with rye and calf thymus chromatin. Both types of chromatin have the same dye accessibility, which is about 50% of that of DNA. From this result we conclude that the molecular structure of these two chromatins is similar. For rye, the extraction of H1 produces no change in the binding of ethidium bromide. The subsequent extraction of H2A and H2B produces a 14% increase in the binding, and the removal of H3 and H4, another 54% increase. At this stage, the number of binding sites is still less than that of DNA. This is presumably due to the presence of some tightly bound non-histones. Thus, the arginine-rich histones and the tightly bound non-histones are most responsible for limiting the binding of ethidium bromide to rye chromatin.

Comparative organization of active transcription units in Oncopeltus fasciatus

We have analyzed electron micrographs of chromatin-associated fiber arrays from embryos of the milkweed bug, Oncopeltus fasciatus. The analysis has revealed that the arrays have highly ordered patterns of fiber spacings and lengths. These patterns support the interpretation that the fibers are nascent RNA with associated proteins (RNP fibers) which have resulted from transcription of the DNA in the underlying chromatin segment. In particular, the patterns indicate that the chromatin underlying each array is delimited by specific sites for initiation and termination of transcription. We apply the term transcription unit to a chromatin segment thus bounded. The analysis has further revealed that transcription units can be grouped into two principal classes--ribosomal and nonribosomal. Active transcription units of these two classes differ in DNA content, in their proximity to other active transcription units, and in their chromatin morphology. For certain developmental stages, fiber frequencies (that is, the nubmers of fibers per mum of chromatin) are also useful in distinguishing ribosomal from nonribosomal arrays. The most definitive of the above classification criteria is chromatin morphology as observed under our preparative conditions. We propose that term rho chromatin for the unbeaded or smooth chromatin that underlies nascent ribosomal RNP fibers. DNA in rho chromatin has a calculated packing ratio of approximately 1.2 mum of B structure DNA per mum of chromatin. Nu chromatin is used to designate the beaded chromatin for which we calculate a DNA packing ratio of 1.6-2.3 in our preparations. This calculation for nu chromatin is based on the inference that the beads are nucleosomes (nu bodies, PS particles, unit particles). The beaded morphology is observed between fibers of nonribosomal transcription unit as well as for most fiber-free chromatin. The detection of specific sites of transcriptional initiation and termination and the classification of transcription units can provide a basis for further analysis of transcriptional control.