Chromatin structure and gene activity: the role of nonhistone chromosomal proteins

Identification of a nonhistone chromosomal protein associated with heterochromatin in Drosophila melanogaster and its gene

Monoclonal antibodies were prepared against a fraction of nuclear proteins of Drosophila melanogaster identified as tightly binding to DNA. Four of these antibodies were directed against a 19-kilodalton nuclear protein; immunofluorescence staining of the polytene chromosomes localized the antigen to the alpha, beta, and intercalary heterochromatic regions. Screening of a lambda gt11 cDNA expression library with one of the monoclonal antibodies identified a recombinant DNA phage clone that produced a fusion protein immunologically similar to the heterochromatin-associated protein. Polyclonal sera directed against the bacterial lacZ fusion protein recognized the same nuclear protein on Western blots. A full-length cDNA clone was isolated from a lambda gt10 library, and its DNA sequence was obtained. Analysis of the open reading frame revealed an 18,101-dalton protein encoded by this cDNA. Two overlapping genomic DNA clones were isolated from a Charon 4 library of D. melanogaster with the cDNA clone, and a restriction map was obtained. In situ hybridization with these probes indicated that the gene maps to a single chromosome location at 29A on the 2L chromosome. This general strategy should be effective for cloning the genes and identifying the genetic loci of chromosomal proteins which cannot be readily assayed by other means.

Simian virus 40 protein VP1 is involved in spacing nucleosomes in minichromosomes

We have investigated the average nucleosome spacing in the chromatin from several simian virus 40 virion assembly mutants temperature-sensitive in the major capsid protein VP1. Viral assembly intermediates that accumulate in cells infected with mutants that block virion assembly at the propagation step (tsB) have an average nucleosome repeat length similar to that of wild-type SV40 chromatin, approximately 198(+/- 4) base-pairs. This repeat length is longer than that of the host (BSC-40) cellular chromatin, which has a value of 187(+/- 4) base-pairs. In contrast, SV40 chromatin from cells infected with virus containing a mutation that blocks virion assembly at the initiation step (tsC) has a significantly shorter average repeat length of 177(+/- 4) base-pairs. At the permissive temperature (33 degrees C), tsC chromatin has a nucleosome spacing periodicity essentially the same as that of wild-type SV40 chromatin. In addition to possessing a chromatin structure with nucleosomes that are, on the average, closer together, tsC chromatin contains a nuclease-hypersensitive or open region in nearly all molecules, but apparently the same number of nucleosomes. These findings suggest that nucleosomes are deposited initially on newly replicated SV40 chromatin in such a way as to leave the DNA region containing the origin of replication and transcription enhancers uncovered. Subsequent interaction with capsid proteins appears to increase the average nucleosome spacing and consequently to cover the open region for encapsidation.

DNase I-hypersensitive sites in the 5'-flanking region of the rat serum albumin gene: correlation between chromatin structure and transcriptional activity

As tested by DNase I digestion, the chromatin structure in several regions 5' to the rat serum albumin gene varies in tissues and cell lines that differ in transcription rate of this gene. Three DNase I-hypersensitive regions were found in hepatocyte nuclei but not in kidney cell nuclei. The sites were approximately 2.8 kbp (site 1), 0.2 kbp (site 2), and 0.05 kbp (site 3) upstream from the cap site of the gene. In rat fetal liver tissue and rat hepatoma cell lines (FaO, C2, and C2-rev7), as well as in cultured primary hepatocytes where the rate of albumin gene transcription is lower than in adult liver, hypersensitive site (HSS) 1 was absent while sites 2 and 3 were present. In addition, the C2 cell line, which does not express albumin mRNA, contains a different HSS at position -1.5 kbp. Factors (proteins) bound to sites 2 and 3 may allow cell-specific transcription, but the additional factor interaction at site 1 could be required for a maximal rate of albumin gene transcription.

Tubulin-chromatin interactions: evidence for tubulin-binding sites on chromatin and isolated oligonucleosomes

The interaction of tubulin with chromatin has been studied using a radiolabeled tubulin binding assay and velocity sedimentation analysis on isokinetic sucrose gradients. Soluble chromatin was prepared by mild micrococcal nuclease digestion of rat liver nuclei and tubulin was purified from rat brain by temperature-dependent assembly-disassembly and phosphocellulose chromatography. The tubulin-binding assay is based on the ability of chromatin to precipitate quantitatively at physiological ionic strength allowing separation of free tubulin from chromatin-bound tubulin. The binding of tubulin to unfractionated soluble chromatin was rapid, reversible and saturable. Saturation of binding sites was obtained using tubulin concentrations ranging from 0.5 to 400 micrograms/ml, in the presence of a high concentration (2.5 mg/ml) of another acidic protein, bovine serum albumin. The Scatchard and Hill plots showed that tubulin bound to a single class of non-interacting sites and yielded values of (0.5-0.6) X 10(7) M-1 for an apparent Ka and a maximal binding capacity of 0.8 nmol tubulin/mg DNA, i.e. about 1 molecule of tubulin/10 nucleosomes. Similar binding parameters were obtained when binding experiments were performed with insoluble chromatin in 0.15 M NaCl. Velocity sedimentation analysis of tubulin-chromatin complexes revealed that tubulin bound to all classes of chromatin oligomers, irrespective of the length of the nucleosomal chain. Tubulin-trinucleosome complexes formed from isolated trinucleosome in the presence of an excess of tubulin were separated from free reactants. It was found that 10-15% of the starting oligonucleosomal species reacted with tubulin, in a stoichiometry of about 0.8 molecule of tubulin/nucleosome. Given the characteristics of the binding and the expected cellular free tubulin concentration, the tubulin-chromatin interaction could possibly take place in vivo, when the nuclear membrane breaks down during the first steps of mitosis.

DNA engineering shows that nucleosome phasing on the African green monkey alpha-satellite is the result of multiple additive histone-DNA interactions

The mechanism underlying sequence-specific positioning of nucleosomes on DNA was investigated. African green monkey alpha-satellite DNA was reconstituted in vitro with histones. Histone octamers were found to adopt one major and several minor positions on the satellite repeat unit, very similar to those positions found previously in vitro, demonstrating that sequence-specific histone-DNA interactions are responsible for nucleosome positioning on this DNA. In order to understand the nature of these interactions in more detail, we have constructed a variant satellite fragment containing an insertion of half a helical DNA turn. The parent fragment directs histones to one major and two overlapping minor positions that are all affected by the insertion. All three frames respond in a unique fashion to the additional five base-pairs. From a quantitative analysis of the nucleosome positions on the engineered fragment, consensus "phasing boxes" as the basis for nucleosome positioning can be ruled out. Instead, our results argue very strongly that nucleosome positioning is due to the independent contribution of many different DNA-histone contacts along the entire core particle, in an apparently additive fashion.

Protein-DNA interactions and nuclease-sensitive regions determine nucleosome positions on yeast plasmid chromatin

To study mechanisms of nucleosome positioning, small circular plasmids were constructed, assembled into chromatin in vivo in Saccharomyces cerevisiae, and their chromatin structures were analysed with respect to positions of nucleosomes and nuclease-sensitive regions. Plasmids used include insertions of the URA3 gene into the TRP1 gene of the TRP1ARS1 circular plasmid in the same (TRURAP) or opposite (TRARUP) orientation. The URA3 gene has six precisely positioned, stable nucleosomes flanked by nuclease-sensitive regions at the 5' and 3' ends of the gene. Three of these nucleosome positions do not depend on the flanking nuclease-sensitive regions, since they are formed at similar positions in a derivative plasmid (TUmidL) that contains the middle of the URA3 sequence but not the 5' and 3' ends. These positions are probably due to protein-DNA interactions. In both TRURAP and TRARUP, the positions of the nucleosomes on the TRP1 gene were, however, shifted compared with the positions on the parental TRP1ARS1 circle and TUmidL. These changes are interpreted to be due to changes in the positions of flanking nuclease-sensitive regions that might act as boundaries to position nucleosomes. Thus, two independent mechanisms for nucleosome positioning have been demonstrated in vivo. The ARS1 region contains the 3' end of the TRP1 gene and the putative origin of replication. Since in TRURAP and TRARUP the TRP1 gene is interrupted, but the ARS1 region remains nuclease sensitive, this non-nucleosomal conformation of the ARS1 region probably reflects a chromatin structure important for replication.

Drosophila histone H2A.2 is associated with the interbands of polytene chromosomes

Drosophila chromatin contains two antigenically distinct H2A histones, H2A.1 and H2A.2. Indirect immunofluorescence analyses revealed that anti-H2A.1 binding was distributed throughout polytene chromosomes, whereas anti-H2A.2 binding was interband-specific. Thus, H2A.2 probably contributes to the less compacted structure of interbands. Since each band-interband region is thought to contain a single gene, our results suggest that the distribution of H2A.2 echoes the functional organization of the Drosophila genome. Similar H2A histones occur in eukaryotes ranging from protozoa to mammals. Their placement might be an important determinant of chromatin structure.

Effect of exogenous histone H5 on integration of histone H1 in rat liver chromatin. Correlations with aberrant epsilon-N-methylation of histone H1

Binding modes of histones H1 and H5, and their competition for chromatin-binding sites in rat liver nuclei, were correlated with aberrant N-methylation of H1 histone lysine residues, induced by chicken erythrocyte histone H5, in order to gain more insight into the integration of lysine-rich histones in chromatin. Addition of approx. 2.5 molecules of histone H5 per nucleosome to rat liver nuclei increases the ratio of total basic residues in histones to DNA nucleotides (BR/NT) in the nuclear chromatin from 1.0 to 1.5. At this concentration, approx. 0.7 molecule of histone H5 is bound per nucleosome, and there is no displacement of histone H1 from the nuclear chromatin. If S-adenosyl[Me-3H]methionine is present in the incubation mixture, the aberrant incorporation of labeled methyl groups into histone H1 reaches a maximum at this concentration of histone H5. The radioactivity present in histone H1 from nuclei incubated with labeled AdoMet at a total BR/NT ratio of 1.5: resides mainly in a histone H1 subfraction tentatively identified by Bio-Rex 70 chromatography and acrylamide gel electrophoresis as histone H1c; presents as a single spot upon peptide mapping of tryptic hydrolysates by means of two-dimensional thin-layer chromatography; and elutes in the position of mono-N-methyllysine upon ion-exchange chromatography of histone H1 hydrolysates. Upon further increase of the BR/NT ratio, the following changes are produced: a gradual decrease in radioactive methyl uptake into histone H1; a gradual displacement of histone H1 from the chromatin; increased binding of histone H5 in chromatin, up to a maximum of 3.4 residues per nucleosome; and a slowly increasing uptake of label into histone H5. The combined data from histone H1/H5 binding and histone H1 methylation studies suggest that upon addition of exogenous histone H5 to rat liver nuclei the binding of two lysine-rich histones per nucleosome plays a significant role in the induction of specific changes in chromatin structure, which in vivo may have important functional implications in terms of chromatin condensation and suppression of transcription.

Chromatin superstructure. A study with an immobilized trypsin

Hen erythrocyte chromatin was treated with trypsin immobilized on collagen membranes and the unfolding of chromatin fiber was followed by light scattering at 90 degrees and flow linear dichroism. Chromatin was found almost completely decondensed when the bulk of H1 and H5 was digested while H3 was still intact. Further digestion leading to degradation of both H3 and the rest of H1 and H5 accounted for no more than 10-15% of the total effect. When chromatin with trypsin-cleaved H1 and H5 was titrated with increasing amounts of spermidine it folded similarly to the control sample. This finding suggests that charge neutralization appears a likely mechanism for maintaining the structure of the 30 nm chromatin fiber by the C-terminal domain of H1 and H5.

Isolation of oligonucleosomes from active chromatin using HMG17-specific monoclonal antibodies

We report the preparation of HMG17-containing oligonucleosomes from chicken embryos and from liver and oviduct of laying hens. Monoclonal antibodies against HMG17 were used for their isolation. An unusual size distribution with respect to their repeat number was observed. The oligonucleosomes of repeat number up to N6 were highly enriched for DNA of the vitellogenin II gene (liver) and for DNA of the ovalbumin and lysozyme genes (oviduct).

Methidiumpropyl-EDTA-iron(II) cleavage of ribosomal DNA chromatin from Dictyostelium discoideum

We have used methidiumpropyl-EDTA-iron(II) [MPE.Fe(II)] in parallel with micrococcal nuclease to investigate the chromatin structure of the extrachromosomal palindrome ribosomal RNA genes of Dictyostelium. Confirming our earlier results with micrococcal nuclease (1,2), MPE.Fe(II) digested the coding region of rapidly transcribing rRNA genes as a smear, indicating the absence or severe disruption of nucleosomes, whereas in slowly transcribing rRNA genes, a nucleosomal ladder was produced. In the central non-transcribed spacer region of the palindrome, MPE.Fe(II) digestion resulted in a normal nucleosomal repeat, whereas micrococcal nuclease gave a complex banding pattern. The difference is attributed to the lower sequence specificity of MPE.Fe(II) compared to micrococcal nuclease. In the terminal region of the palindrome, however, both substances gave a complex chromatin digestion pattern. In this region the DNA appears to be packaged in structures strongly positioned with respect to the underlying DNA sequence.

Structure of hyperacetylated chromatin: light scattering and flow linear dichroism study

Cation-induced folding of 10 nm chromatin filament to 30 nm fiber was studied with hyperacetylated chromatin using light scattering at 90 degrees and flow linear dichroism. Acetylated chromatin folded in a way indistinguishable from that of the control chromatin: both the compactness of chromatin and the orientation of nucleosomes relative to the fiber axis were identical at a given salt concentration.

A mammalian high mobility group protein recognizes any stretch of six A.T base pairs in duplex DNA

alpha-Protein is a high mobility group protein originally purified from African green monkey cells based on its affinity for the 172-base-pair repeat of monkey alpha-satellite DNA. We have used DNase I footprinting to identify 50 alpha-protein binding sites on simian virus 40 DNA and thereby to determine the DNA binding specificity of this mammalian nuclear protein. alpha-Protein binds with approximately equal affinity to any run of six or more A X T base pairs in duplex DNA, to many, if not all, runs of five A X T base pairs, and to a small number of other sequences within otherwise (A + T)-rich regions. Unlike well characterized sequence-specific DNA binding proteins such as bacterial repressors, alpha-protein makes extensive contacts within the minor groove of B-DNA. These and related findings indicate that, rather than binding to a few specific DNA sequences, alpha-protein recognizes a configuration of the minor groove characteristic of short runs of A X T base pairs. We discuss possible functions of alpha-protein and the similarities in DNA recognition by alpha-protein and the antibiotic netropsin.

Nonhistone protein BA is a glutathione S-transferase localized to interchromatinic regions of the cell nucleus

A DNA-binding nonhistone protein, protein BA, was previously demonstrated to co-localize with U-snRNPs within discrete nuclear domains (Bennett, F. C., and L. C. Yeoman, 1985, Exp. Cell Res., 157:379-386). To further define the association of protein BA and U-snRNPs within these discrete nuclear domains, cells were fractionated in situ and the localization of the antigens determined by double-labeled immunofluorescence. Protein BA was extracted from the nucleus with the 2.0 M NaCl soluble chromatin fraction, while U-snRNPs were only partially extracted from the 2.0 M NaCl-resistant nuclear structures. U-snRNPs were extracted from the residual nuclear material by combined DNase I/RNase A digestions. Using an indirect immunoperoxidase technique and electron microscopy, protein BA was localized to interchromatinic regions of the cell nucleus. Protein BA was noted to share a number of chemical and physical properties with a family of cytoplasmic enzymes, the glutathione S-transferases. Comparison of the published amino acid composition of protein BA and glutathione S-transferases showed marked similarities. Nonhistone protein BA isolated from saline-EDTA nuclear extracts exhibited glutathione S-transferase activity with a variety of substrates. Substrate specificity and subunit analysis by SDS polyacrylamide gel electrophoresis revealed that it was a mixture of several glutathione S-transferase isoenzymes. Protein BA isolated from rat liver chromatin was shown by immunoblotting and peptide mapping techniques to be two glutathione S-transferase isoenzymes composed of the Yb and Yb' subunits. Glutathione S-transferase Yb subunits were demonstrated to be both nuclear and cytoplasmic proteins by indirect immunolocalization on rat liver cryosections. The identification of protein BA as glutathione S-transferase suggests that this family of multifunctional enzymes may play an important role in those nuclear domains containing U-snRNPs.

Developmental changes in the chromatin of the brain of the rat: analysis by nick-translation

Nick translation of nuclei of the brain of 3- 14- and 30-day old rats was carried out following their digestion by DNase I. The incorporation of 3H-dTMP at 14- and 30-day is significantly lower than at 3-day. This may be due to a lower proportion of active chromatin (DNase I hypersensitive sites) and condensation of chromatin with progressive development. When nuclei were digested by EcoRI and then nick-translated, the incorporation of 3H-dTMP showed the same pattern. Since the EcoRI sites are believed to be randomly distributed, the overall conformation of chromatin including the DNase I sensitive sites seems to undergo increasing compaction with development.

Histones and their modifications

Histones constitute the protein core around which DNA is coiled to form the basic structural unit of the chromosome known as the nucleosome. Because of the large amount of new histone needed during chromosome replication, the synthesis of histone and DNA is regulated in a complex manner. During RNA transcription and DNA replication, the basic nucleosomal structure as well as interactions between nucleosomes must be greatly altered to allow access to the appropriate enzymes and factors. The presence of extensive and varied post-translational modifications to the otherwise highly conserved histone primary sequences provides obvious opportunities for such structural alterations, but despite concentrated and sustained effort, causal connections between histone modifications and nucleosomal functions are not yet elucidated.

Structure of transcriptionally active chromatin

Transcriptionally active or potentially active genes can be distinguished by several criteria from inactive sequences. Active genes show both an increased general sensitivity to endonucleases like DNase I or micrococcal nuclease and the presence of nuclease hypersensitive sites. Frequently, the nuclease hypersensitive sites are present just upstream of the transcription initiation site covering sequences that are crucial for the promoter function. Viral or cellular transcription enhancer elements are also associated with DNase I hypersensitive sites. At least for the SV40 enhancer, it was shown by electronmicroscopic studies that the DNase I hypersensitive DNA segment is excluded from nucleosomes. It is highly plausible that the binding of regulatory proteins to enhancer or promoter sequences is responsible for the exclusion of these DNA segments from nucleosomes and for the formation of nuclease hypersensitive sites. We speculate that the binding of such proteins may switch on a change in the conformation and/or the protein composition of a chromatin segment or domain containing one to several genes. Biochemical analysis of fractionated nucleosome particles or of active and inactive chromatin fractions have revealed differences in the composition as well as in the degree of modification of histones in these two subfractions of the chromosome. However, until present it is impossible to define unambiguously what are the crucial structural elements that distinguish between particles present on active and inactive chromatin.

The modifications in the methylation patterns of H2B and H3 after heat shock can be correlated with the inactivation of normal gene expression

The potential significance of the important post-synthetic methylation changes of core histones observed upon heat shock or after an arsenite treatment has been studied in Drosophila Kc cells. The changes in the histone methylation patterns appeared to be linked with the repression of normal gene expression rather than with the activation of the heat shock genes. Thus following a brief heat shock, the kinetics of recovery of the normal pattern of gene expression could be correlated with those of the return to a normal pattern of methylation of histones H2B and H3. Experiments with different inducers and a transcriptional inhibitor also suggest that the decreased methylation of H3 and the increase in that of H2B are an effect of the repression of transcription processes.

Histone phosphorylation in native chromatin induces local structural changes as probed by electric birefringence

In order to understand how the phosphorylation of histones affects the chromatin structure, we used electron microscopy, sedimentation velocity, circular dichroism and electric birefringence to monitor the salt-induced filament reversible solenoid transition of phosphorylated and native chromatin. Phosphorylation in vitro of chicken erythrocyte chromatin by cyclic-AMP-dependent protein kinase from porcine heart led to the modification of the histones H3 and H5 only, which were modified at a level of one phosphate and about three phosphate groups per molecule, respectively. In contrast to circular dichroism and sedimentation studies, which tend to suggest that phosphorylation of H3 and H5 does not affect chromatin structure, electron microscopy reveals that phosphorylation causes a relaxation of structure at low ionic strength. Electric birefringence and relaxation time measurements clearly prove that local structural changes are induced in chromatin: we observe a decrease of the steady-state birefringence with the appearance of a negative contribution in the signal and a marked increase of the flexibility of fibres. The component with the negative birefringence presents very short relaxation times, like those exhibited by small DNA fragments or individual nucleosomes. Two possibilities are then suggested. First, the conformational change is consistent with what would be expected from the presence of DNA segments loosely associated with the core histone H3. That the length of such segments could correspond to about one to two base-pairs per nucleosome strongly suggests that phosphorylation induces changes affecting some specific H3-DNA interactions only. This result could corroborate previous observations indicating that the N-terminal region of H3, where the site of phosphorylation is located, plays a decisive role in maintaining the superstructure of chromatin. Second, phosphorylation could introduce hinge points between each nucleosome. In this case, the negative birefringence results from partial orientation of the swinging nucleosomes. A possible mode of action of phosphorylation might be to weaken structural restraints imposed by histone H3, thus facilitating further condensation of chromatin.

Effect of X-ray induced DNA damage on DNAase I hypersensitivity of SV40 chromatin: relation to elastic torsional strain in DNA

The effect of X-irradiation on DNAase I hypersensitivity of SV40 minichromosomes within nuclei or free in solution was investigated. The susceptibility of the specific DNA sites in the control region of minichromosomes to DNAase I decreased in a dose dependent manner after irradiation of isolated nuclei. On the other hand, the irradiation of minichromosomes extracted from nuclei in 0.1 M NaCl-containing buffer almost did not affect the level of their hypersensitivity to DNAase I. This suggests that DNAase I hypersensitivity may be determined by two different mechanisms. One of them may be connected with elastic torsional strain within a fraction of minichromosomes and another seems to be determined by nucleosome free region. The first mechanism may be primarily responsible for the hypersensitivity of minichromosomes within nuclei. After irradiation of the intact cells, DNAase I hypersensitivity tested in nuclei substantially increased. This was connected with activation of endogeneous nucleases by X-irradiation which led to accumulation of single- and double-strand breaks superimposed to DNAase I induced breaks in the control region of SV40 DNA.

Single-strand-specific degradation of DNA during isolation of rat liver nuclei

We have investigated structural change in rat liver DNA produced by different isolation procedures and specifically compared the integrity of DNA derived by phenol extraction from isolated and purified nuclei with preparations extracted immediately from a crude liver homogenate containing intact nuclei. As indicated by stepwise elution from benzoylated DEAE-cellulose, most structural change in DNA was evident following nuclei isolation. Damage principally involved generation of single-stranded regions in otherwise double-stranded DNA fragments; totally single-stranded DNA was not detected by hydroxylapatite chromatography. Caffeine gradient elution suggested formation of single-stranded regions extending for up to several kilobases. In neutral sucrose gradients, differences in sedimentation rates of respective DNA samples consequent upon S1 nuclease digestion could be detected after isolation of nuclei, though not in other circumstances. The observed single-strand-specific nuclease digestion of DNA could apparently be reduced if steps were taken to reduce autodigestion during nuclei isolation by reduction of temperature and covalent cation concentration. The results are discussed in terms of the use of exogenous and endogenous nucleases in chromatin fractionation studies involving isolated nuclei and possible artifactual findings that may be generated by single-strand-specific autodigestion.

Analysis of conformation and function of the chromatin of the brain of young and old rats

Digestion of nuclei of the cerebral hemisphere of young (18-20 week) and old (90-97 week) rats by DNase I shows that the rate and extent of digestion is lower in the old. Time course analysis of the DNA fragments produced by DNase I by polyacrylamide gel electrophoresis shows that more of the lower base pair fragments are produced in the young. Also, the rate of production of these fragments is higher in the young than in the old. Assay of template-engaged RNA polymerase II (alpha-amanitin sensitive) shows that in the old it is only about 50% of that of the young. Addition of exogenous eukaryotic (wheat germ) RNA polymerase II is not able to restore transcription of the chromatin in the old to the level of the young. These data show that chromatin undergoes increasing condensation as a function of age, resulting in decreased transcriptional activity in old age.

Transient alterations of the chromatin structure of sea urchin early histone genes during embryogenesis

We describe features of the chromatin structure of the early histone gene family of Strongylocentrotus purpuratus during development. Before and after the histone genes are transcriptionally active, chromatin structure is quite similar with well-defined spaced nucleosomes and no major 5'-flanking sites hypersensitive to nucleases. During the period when the genes are active, marked changes in chromatin structure occur. Micrococcal nuclease digestion generates monomer nucleosomes and only trace amounts of higher multimers. Regions hypersensitive to an endogenous nuclease and DNAase I appear in the 5'-flanking regions of genes for H2A, H2B and H3. Each region consists of four sites spanning a DNA length of 200-250 base pairs. In each case, one major cutting site is near the TATA box; the bulk of the sensitive region is in the nontranscribed spacer. Other sites, in 3'-flanking regions of the genes, are sensitive to nucleases only when the histone genes are no longer transcribed.

Spermine induced phosphorylation of a 42 kD/pI 5.9 nuclear protein in different human tumor cell lines

In vitro phosphorylation of 5 M urea extracts from nuclei obtained from different human tumor cell lines leads to incorporation of phosphate from 32P-gamma-ATP in more than 20 polypeptides with an acidic pI. Whereas heparin at a concentration of 1 microgram had no effect on the phosphorylation pattern, spermine stimulated the total phosphorylation up to twofold. Furthermore, in the presence of this polyamine, the two-dimensional polyacrylamide gel revealed an additional phosphoprotein with an apparent pI of 5.9 and a relative molecular mass of 42 000. Phosphoamino acid analysis of the most prominent phosphoproteins showed serine and threonine as phosphoacceptors.

Distribution of tightly bound non-histone proteins in chromatin fractions obtained by DNAase II digestion

Digestion of pig liver chromatin with DNAse II afforded three different fractions which were characterized in terms of their DNA, RNA and tightly bound non-histone protein content, their DNA fragment size and their template activity. Two of these fractions are soluble after digestion with DNAase II and have been separated on the basis of their different solubility in MgCl2. A third fraction is not solubilized even after extensive digestion, although the size of its DNA is comparable to that of the enzyme solubilized fractions. The three fractions show qualitatively and quantitatively different distribution of tightly bound non-histone proteins, with specific protein components in each fraction; furthermore the non-solubilized fraction is greatly enriched in proteins tightly bound to DNA. From all the data obtained it can be suggested that the tightly bound proteins of the insoluble fraction may play, directly or indirectly, a role in maintaining an organized chromatin structure.

Nuclear antigens in the HeLa cell cycle

Antisera to 0.35 M NaCl extracts and residues of S phase HeLa nuclei were reacted with electrophoretically separated proteins from the nuclei or nuclear material of HeLa cells synchronized in G1, S, G2 or M phases of the cell cycle. Quantitative evaluation of the peroxidase-antiperoxidase stained nitrocellulose transfers (Western blots) revealed significant changes in the quantities of nuclear non-histone proteins during the cell cycle. Immunochemical staining of electrophoretically separated nuclear antigens permits their selective detection in minute quantities and in the presence of many additional proteins.

The effect of histone H1 on the compaction of oligonucleosomes. A quasielastic light scattering study

The structural properties of H1-depleted oligonucleosomes are investigated by the use of quasielastic laser light scattering, thermal denaturation and circular dichroism and compared to those of H1-containing oligomers. To obtain information on the role of histone H1 in compaction of nucleosomes, translational diffusion coefficients (D) are determined for mono-to octanucleosomes over a range of ionic strength. The linear dependences of D on the number of nucleosomes show that the conformation of stripped oligomers is very extended and does not change drastically with increasing the ionic strength while the rigidness of the chain decreases due to the folding of linker DNA. The results prove that the salt-induced condensation is much smaller for H1-depleted than for H1-containing oligomers and that histone H1 is necessary for the formation of a supercoiled structure of oligonucleosomes, already present at low ionic strength.

Primary organization of nucleosomal core particles is invariable in repressed and active nuclei from animal, plant and yeast cells

A refined map for the linear arrangement of histones along DNA in nucleosomal core particles has been determined by DNA-protein crosslinking. On one strand of 145-bp core DNA, histones are aligned in the following order: (5') H2B25,35-H455,65-H375,85,95/H488-H2B105,11 5-H2A118-H3135,145/H2A145 (3') (the subscripts give approximate distance in nucleotides of the main histone contacts from the 5'-end). Hence, the histone tetramer (H3,H4)2 and two dimers (H2A-H2B) are arranged on double-stranded core DNA in a symmetrical and rather autonomous way: H2A/H3-(H2A-H2B)-(H3,H4)2-(H2B-H2A)-H3/H2A. The primary organization was found to be very similar in core particles isolated from repressed nuclei of sea urchin sperm and chicken erythrocytes, from active in replication and transcription nuclei of Drosophila embryos and yeast and from somatic cells of lily. These data show that (i) the core structure is highly conserved in evolution and (ii) the overall inactivation of chromatin does not affect the arrangement of histones along DNA and thus does not seem to be regulated on this level of the core structure.

Local protein-DNA interactions may determine nucleosome positions on yeast plasmids

The structure of the nucleosome core particle, the basic structural subunit of chromatin, is well known. Although nucleosomes often appear to be positioned randomly with respect to DNA sequences, in some cases they seem to occupy precisely defined positions on the DNA. The yeast plasmid TRP1ARS1 contains three precisely positioned, stable nucleosomes, I, II and III, which are flanked by nuclease-sensitive regions. Our aim in the present study was to determine whether the positions of these three nucleosomes relate to (1) protein-DNA interactions; (2) the limited space between nuclease-sensitive regions, which is just long enough to accommodate three yeast nucleosomes (that is, boundary conditions); or (3) proximity to the putative origin of replication in one of the nuclease-sensitive regions. We have tested these alternatives by analysing the positions of nucleosomes after insertion of various lengths of DNA into this region and assembly of chromatin in vivo. Our results suggest that specific protein-DNA interactions are the most likely determinants of these nucleosome positions.

Analysis of chromatin of the brain of young and old rats by nick-translation

Chromatin of the brain of young (22-23 week) and old (118-119 week) rats has been analysed by nick-translation reaction following its digestion by DNaseI, EcoRI, MspI and HpaII. The incorporation of (3H)-dTMP in the old is only about 50 percent of that of the young. The difference in the incorporation following digestion of nuclei by MspI and HpaII that quantitate the degree of methylation of internal cytosines in the 5' CCGG 3' sequences, is nearly two-fold higher in the old. These data indicate that the chromatin undergoes increasing condensation as a function of age. One of the contributory factors may be increasing methylation of DNA. This may decrease the active fraction of chromatin.

Higher order structure of chromatin: influence of ionic strength and proteolytic digestion on the birefringence properties of polynucleosomal fibers

Effects of ionic strength and proteolytic digestion on the conformation of chromatin fibers were studied by electric birefringence and relaxation measurements. The results confirm that at low ionic strength chromatin presents structural features reflecting those observed in the presence of cations. Soluble chromatin prepared from rat liver nuclei by brief nuclease digestion exhibits a positive birefringence. As the salt concentration is increased, the transition to a compact solenoidal structure is deduced from changes in electro-optical properties: the positive birefringence gradually decreases and the observed reduction in 40 mM NaCl is nearly 95%; the relaxation time decreases dramatically and the character of the kinetic changes since the decay of birefringence described initially by a spectrum of relaxation times becomes monoexponential. On digestion with proteases at low ionic strength we observe at first a rapid increase of the positive birefringence concomitant with an increase of the relaxation time. Then the birefringence decreases and becomes negative. Chromatin undergoes two successive transitions: the first transition is explained by a lengthening of nucleosomal chains without modification of the orientation of nucleosomes within the superstructure and the second one by the unwinding of the DNA tails and internucleosomal segments. When chromatin is digested at 30 mM NaCl we find a single unfolding transition characterized by the decrease of birefringence and a slight increase in the relaxation time. The results imply that the positive birefringence of chromatin does not depend on the presence of whole histone H1 and that a salt concentration of 30 mM NaCl is sufficient to modify the initial site or/and the effects of proteolytic attack.

Monoclonal antibodies to a phosphoprotein from chromatin of rat liver

Three monoclonal antibody subclasses (IgG1, IgG2a, and IgM) were raised to the phosphoprotein B2 (Mr 68000, pI6.5-8.2) which has been shown previously to be associated with the nucleosomes of rat liver nuclei. These antibodies do not show any significant cross reactivity with CM-cellulose 'unbound' non-histone chromosomal proteins, bovine serum albumin or histones. Further verification of the specificity of these antibodies to this phosphoprotein was carried out using both 'dot' blot and immunological transfer analysis ('Western blot'). The monoclonal antibodies (IgG1 and IgG2a) could also be used to semi-quantify the phosphoprotein B2 in rat liver nuclei. The high specificity and unlimited availability of this type of probe provides a means to study the role(s) of this phosphoprotein in the overall scheme of actively transcribed chromatin.

A lysine-rich protein functions as an H1 histone in Dictyostelium discoideum chromatin

Mononucleosomes released from Dictyostelium discoideum chromatin by micrococcal nuclease contained two distinctive DNA sizes (166-180 and 146 bp). Two dimensional gel electrophoresis suggested a lysine-rich protein protected the larger mononucleosomes from nuclease digestion. This was confirmed by stripping the protein from chromatin with Dowex resin. Subsequently, only the 146 bp mononucleosome was produced by nuclease digestion. Reconstitution of the stripped chromatin with the purified lysine-rich protein resulted in the reappearance of the larger mononucleosomes. Two-dimensional gel electrophoresis showed the protein was associated with mononucleosomes. Hence, the protein functions as an H1 histone in bringing the two DNA strands together at their exit point from the nucleosome. Trypsin digestion of the lysine-rich protein in nuclei resulted in a limiting peptide of approx. 10 kilodaltons. Trypsin concentrations which degraded the protein to peptides of 12-14 kilodaltons and partially degraded the core histones did not change the DNA digestion patterns obtained with micrococcal nuclease. Thus, the trypsin-resistant domain of the lysine-rich protein is able to maintain chromatosome structure.

Transcriptional block caused by a negative supercoiling induced structural change in an alternating CG sequence

Using supercoiled plasmids containing a (CG)16 sequence downstream of a promoter, it is shown that purified E. coli RNA polymerase can transcribe through the sequence when it is in the B helical form. However, the polymerase together with its nascent transcript is blocked at the boundary of the CG sequence proximal to the promoter when the template is negatively supercoiled to flip the CG sequence to the left-handed Z-form. S1 nuclease mapping of in vivo transcripts from an E. coli gyrase temperature-sensitive mutant harboring the plasmids indicates that the bulk of the transcripts at either permissive or nonpermissive temperatures can proceed through the CG sequence, suggesting that the sequence is normally in the B helical form in vivo. The almost total blockage of transcription in vitro by the (CG)16 sequence in a highly negatively supercoiled DNA is not observed for a d(CA)21 X d(TG)21 insert.

A transcription enhancer acts in vitro over distances of hundreds of base-pairs on both circular and linear templates but not on chromatin-reconstituted DNA

We have analyzed the effect of nucleosome formation and of the simian virus (SV40) enhancer on the efficiency of in vitro transcription. In a whole cell extract made from HeLa cells, nucleosome assembly on DNA results in the formation of chromatin-like complexes. However, transcription was detectable only when the DNA templates were partially or totally depleted of nucleosomes. On nucleosome-free templates, when the SV40 enhancer was present upstream from the complete SV40 early or rabbit beta-globin promoters, there was a five- to tenfold stimulation of specific transcription. When present upstream from its homologous promoter, the SV40 enhancer activated SV40 early transcription independently of its orientation with respect to the coding sequence. Point mutations known to impair the SV40 enhancer function in vivo had a similar effect in vitro. The extent of the enhancing effect was the same with linear or circular templates. When the SV40 enhancer was inserted upstream from the rabbit beta-globin gene, the activation of transcription was reduced with increasing distance between the enhancer and beta-globin upstream promoter elements, but was still significant over a distance of more than 400 base-pairs.

Age changes of chromatin. A review

The age-related studies of chromatin and DNA has attracted significant interest in recent years. However, individual works describe only some and a few of the many changes of chromatin. It is often difficult to decide whether these changes have secondary or primary nature. The overview of these studies makes it possible to realize how many very complex and interdependent changes occur in chromatin during ageing. Chromatin is the most complex among self-reproducible parts of the cell. A very sophisticated structure of chromatin makes possible the differential transcription of a genetic programme which supports the accurate specialized functions of each cell in interphase and also provides a mechanism for perfect reproduction of this complex machinery of genetic information during cell division. It is known that chromatin proteins, more than chromatin DNA show tissue specificity and developmental changes. There are many theories of cellular ageing which select some special types of DNA, RNA or protein changes and to promote them as the main or primary causes of cellular senescence. However, if these changes are considered within the more comprehensive picture of functional structure of chromatin the results show the interdependence of individual alterations and their proper place in the complex, multichannel, species and tissue-specific character of actual ageing. An attempt to summarize the basic facts and theories about age changes of the two main parts of chromatin structure, proteins and DNA is being made in this review. At the same time the author tried to develop a concept of non-random distribution of the age changes in chromatin and a possible higher rate of accumulation of different alteration and lesions in the transcribed and functionally active parts of chromatin.

DNA replication and chromatin structure of simian virus 40 insertion mutants

Insertion of DNA segments into the nuclease-sensitive region of simian virus 40 alters both replication efficiency and chromatin structure. Mutants containing large insertions between the simian virus 40 origin of replication (ori site) and the 21-base-pair repeated sequences replicated poorly when assayed by transfection into COS-1 cells. Replication of mutants with shorter insertions was moderately reduced. This effect was cis-acting and independent of the nucleotide sequence of the insert. The nuclease-sensitive chromatin structure was retained in these mutants, but the pattern of cleavage sites was displaced in the late direction from the ori site. New cleavage sites appeared within the inserted sequences, suggesting that information specifying the nuclease-sensitive chromatin structure is located on the late side of the inserts. Accessibility to BglI (which cleaves within the ori site) was reduced in the larger insertion mutants. These results support the conclusion that efficient function of the viral origin of replication is correlated with its proximity to an altered chromatin structure.

Control of RNA polymerase binding to chromatin by variations in linker histone composition

We have measured the frequency of initiation sites in chromatin for RNA polymerase in vitro as a function of the composition of linker histones (H1 and its analogues). In linker histone-depleted chromatin, RNA chain initiation appears to be restricted to the exposed linker DNA. On titration with purified linker histones, initiation is further restricted to an extent determined by the amount and type of linker histone, and the source of depleted chromatin. The extent of repression is correlated with the capacity of linker histones to induce the formation of higher-order structure in the complex. The results suggest that the effects of linker histones are mediated through the higher-order structure of chromatin, which prevents access of polymerase to the linker DNA. Accordingly, we find that structures imposed by the linker histones after polymerase binding are not inhibitory. Microscopy reveals that the higher-order structure in partially condensed chromatin is discontinuous, with solenoidal units spaced by sections of unravelled nucleosomes. Since salt stimulation of linker histone exchange does not result in derepression of linkers in our assay, we conclude that the distribution of higher-order units in chromatin is static and that the linker histones exchange between high-affinity sites in established units. We have previously shown that the globin gene is selectively unfolded in tissues that express the gene. The present results suggest that the transcriptional activity of specific genes is maintained by differential linker histone binding within chromatin.

Structure and regulated expression of the SpoC1 gene cluster from Aspergillus nidulans

We have previously described the organization of a 13.3 kb region of the Aspergillus nidulans genome, designated SpoC1, coding for multiple poly(A)+ RNAs that accumulate in asexual spores but not in somatic cells. We have determined the limits of the SpoC1 gene cluster by investigating the transcriptional features of 53 kb of chromosomal DNA. This segment of the genome codes for at least 19 poly(A)+ RNAs, some of which are transcribed from overlapping regions. The area of developmental regulation is approximately 38 kb in length and is delimited by 1.1-kb direct repeats. With one exception, RNAs transcribed from the central part of the cluster appear late during conidiophore development and accumulate specifically in spores. The exceptional transcript appears earlier during development and accumulates specifically in cells of the conidiophore. In contrast, RNAs encoded at the borders of the cluster occur in both somatic cells and spores. The results indicate that if a chromatin-level control mechanism operates to regulate expression of the SpoC1 gene cluster, as previously suggested by us, additional levels of regulation must also exist.

Age-related changes of the pattern of non-histone proteins in active and condensed fractions of mouse liver chromatin and hepatocarcinoma

Electrophoretic analysis of histones and non-histone acid-soluble proteins in active (nuclease sensitive) and inactive chromatin from liver of young and old CBA mice and in age-related hepatocarcinomas showed a higher ratio of NHP:histones in active chromatin in old cells. Some liver- and hepatoma-specific fractions of non-histone proteins have been identified as chromatin matrix proteins.

Phosphorylation of chromosomal proteins during the transition of a normal plant cell to a crown gall tumor cell

The transition of a wounded plant cell to a crown gall tumor cell, which is induced by infection with virulent Agrobacterium tumefaciens cells, is accompanied by enhancement of chromatin-bound protein phosphokinase activity. Various protein kinases with different substrate specificity (viz. histone, phosvitin, casein phosphokinases) are distinctly more active in tumor cells. The phosphate is introduced into seryl and threonyl residues of proteins and is stable under standard assay conditions, thus indicating the absence of protein phosphatases. Acyl or histidyl phosphates are not involved. The properties of protein phosphokinases change during tumor induction, giving rise to kinases which are sensitive to spermine or spermidine. The pattern of chromatin proteins is tissue-specific and consequently different in wounded and tumorous plant cells, as is the phosphorylation pattern of these proteins.

The structural organization of oligonucleosomes

We have used electric birefringence to study the structure of oligonucleosomes and to show the influence of histone H1 depletion on their conformation in solution. Measurements are made at low ionic strength on monodisperse samples containing up to 8 nucleosomes. For each oligomer, having H1 or not, the analysis of both relaxation and orientation times gives information about the particle's orientation mechanism through the ratio r of permanent over induced dipole terms. For native oligomers, the data confirm the previous finding of a discontinuity in hydrodynamic behavior between pentamer and heptamer: the rotational times are multiplied by 10 and r increases from 0.2 to 0.7 showing the appearance of a non-negligible contribution of a permanent dipole to the orientation mechanism. We suggest a model for the hexanucleosome at low ionic strength and discuss its implications for the higher-order structure of chromatin. The treatment for H1 depletion abolishes the transitions in electro-optical properties: the value of r remains constant, r = 0.15, and both rotational times increase progressively with the number of nucleosomes in the chain. That reflects an important unfolding of oligonucleosomal structure which we attributed to the unwinding of DNA tails and internucleosomal segments. The disc planes of nucleosomes become closely parallel to the nucleosomal chain axis.