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Histone H1 in G1 arrested, senescent, and Werner syndrome fibroblasts.

Histone H1 content and synthesis were examined in normal, Werner-syndrome, and transformed fibroblasts. Analysis of 3H-lysine incorporation indicated that senescent cells, but not G1-arrested young cells, had a lower ratio of molar synthesis of H1 histone to nucleosome histones than did growing young cells or gamma-ray-transformed cells. Furthermore, a biochemical study of histone H1 content plotted as a function of DNA synthesis activity and an immunocytological study using antiserum against histone H1 revealed that senescent cells had a lower histone H1 content than did young cultures at all stages of cell proliferation. Werner syndrome skin fibroblasts at early passage, however, had amounts of histone H1 comparable to those of age-matched normal control fibroblasts. We conclude that a decline, with increasing passage number, in content and synthesis of H1 histone relative to nucleosomal histones (Mitsui et al., 1980) was not simply due to passage-related accumulation of G1-arrested cells, but actually reflected age specific changes of cultured human fibroblasts. The depletion of histone H1 in the chromatin of senescent cells is a possible cause of DNA strand breakage or relaxation of gene repression.

Cell Cycle↗

Histone genes in macronuclear DNA of the ciliate Stylonychia mytilus.

DNA in the macronucleus of Stylonychia mytilus exists as discrete gene-sized fragments which are derived from micronuclear DNA through a series of well-defined developmental events. It has been proposed that each of the DNA fragments might represent a gene and its controlling elements. We have investigated this possibility using genes which code for the five histone proteins. Macronuclear DNA fragments were fractionated according to size by agarose gel electrophoresis, the fragments transferred to nitrocellulose filters using the technique of Southern, and the filter-bound DNA hybridized with labeled cloned histone genes of the sea urchin, Psammechinus miliaris. Results indicate, first, that sequences homologous to the five individual histone gene probes are present in discrete macronuclear fragments which appear as bands in the gel hybridization assay. Secondly, for each of the five individual histone gene probes the homologous DNA fragments are several in number, ranging in size in from 7.6 Kb (Kilo base pairs) to 0.73 Kb. For example, the largest of six detected fragments hybridizing to the H3 gene probe contains approximately 10 times the amount of DNA required to code for a Stylonychia H3 histone. The smallest detected fragment hybridizing to the H3 probe contains enought DNA to code for approximately two copies of the histone. Finally, in general, no two histone approximately two copies of the histone. Finally, in general, no two histone gene probes hybridized to the same macronuclear DNA fragment. This result indicates that genes coding for the five histones in Stylonychia are not located together on the same macronuclear DNA fragments and implies that the five functionally related genes would not be transcribed together as a polycistronic unit.

Animals↗

Histone mRNA in situ hybridization and Ki 67 immunohistochemistry in pediatric adrenocortical tumors.

Adrenocortical tumors in the pediatric population are rare. Classification of these tumors as adenomas or carcinomas using histological criteria is often difficult. Immunohistochemical expressions of proliferative markers are currently under investigation for utilization in the differential diagnosis and prediction of clinical outcomes. The value of histone proteins as prognostic markers in adrenocortical tumors has not yet been elucidated. We evaluated the histological features, immunohistochemical staining of Ki 67, and in situ hybridization for histone mRNA in 30 pediatric adrenocortical tumors. We investigated the relationship between these parameters and the prognosis. Using the classification proposed by Weiss, 19 tumors were classified as carcinomas and 11 as adenomas. Ki 67 and histone mRNA labeling indices (LIs, the percentage of Ki 67-positive and histone mRNA-positive tumor cells, respectively) were significantly higher in carcinomas than in adenomas (Ki 67 LI was 14.62+/-5.79 in adenomas and 20.35+/-6.23 in carcinomas, p=0.02. Histone mRNA LI was 1.73+/-1.71 in adenomas and 6.62+/-2.28 in carcinomas, p=0.00). The proliferative activity assessed by histone mRNA was lower than that assessed by Ki 67 in both diagnostic groups. The cut off point for the diagnosis of malignancy was found to be 14.55 for Ki 67 LI and 5.75 for histone mRNA LI. A correlation was found between a histone mRNA LI>or=5 and poor prognosis (recurrence, metastasis, or death). We concluded that the proliferative activity of the tumor assessed by Ki 67 and histone mRNA may assist in differentiating adrenocortical adenomas and carcinomas. In addition, our results suggest that the most reliable parameter to predict prognosis in pediatric adrenocortical tumors is the histone mRNA LI.

Adrenocortical Adenoma↗

Involvement of histone hypoacetylation in Ni2+-induced bcl- 2 down-regulation and human hepatoma cell apoptosis.

Although induction of cell apoptosis is known to be involved in the cytotoxicity of Ni(2+), little research has been aimed at the mechanism of Ni(2+)-induced apoptosis. Recent studies showed that Ni(2+) induces histone hypoacetylation in different cell lines. Since histone hypoacetylation plays important roles in the control of cell cycle progress and apoptosis, we hypothesized that histone hypoacetylation may be an unrevealed pathway in Ni(2+)-induced apoptosis. To address this, effects of Ni(2+) on cell apoptosis, bcl- 2 gene expression and histone acetylation were examined in human hepatoma Hep3B cells. We found that Ni(2+) treatment resulted in cell proliferation arrest, the appearance of detached cells, condensed chromatin, apoptotic bodies and specific DNA fragmentation, indicating the occurrence of cell apoptosis. At the same time, Ni(2+) induced a significant decrease in bcl- 2 expression and histone acetylation; the decrease of histone H4 acetylation in nucleosomes associated with the bcl- 2 promoter region was also proven by a chromatin immunoprecipitation assay, indicating the involvement of histone hypoacetylation in Ni(2+)-induced bcl- 2 down-regulation. Further studies showed that increasing histone acetylation by either 100 nM of trichostatin A or over-expressing histone acetyltranferase p300 in Hep3B cells obviously attenuated the bcl- 2 down-regulation and cell apoptosis caused by Ni(2+). Considering the importance of bcl- 2 in determining cell survival and apoptosis, the data presented here suggest that histone hypoacetylation may represent one unrevealed pathway in Ni(2+)-induced cell apoptosis, where bcl- 2 is one of its targets.

Acetylation↗

Identification and in silico analysis of a new group of double-histone fold-containing proteins.

The double-histone fold is a rare protein fold in which two consecutive regions characterized by the typical structure of histones assemble together, thus giving a histone pseudodimer. Previously, this fold was found in a few prokaryotic histones and in the regulatory region of guanine-nucleotide exchange factors of the Sos family. Standard methods of sequence comparison did not allow us to find new proteins containing a histone pseudodimer, as previously reported (Sondermann et al. 2003). However, a deeper investigation of protein sequences showed that the two histone folds included in Sos proteins share significant sequence similarity with nucleosomal histones. On the basis of this observation, we applied a specific strategy of sequence-homology search, which led to the identification of a new group of histone pseudodimers in Cca3 and proteins similar to Cca3 (Cca3S). A homology model of the histone pseudodimer included in rat Cca3 was constructed. A subsequent structure-function relationship study revealed that the histone pseudodimers included in Cca3 and Cca3S proteins, but not those present in Sos proteins, could retain the ability of mediating protein-DNA interactions, and could consequently act as DNA-binding modules.

Amino Acid Sequence↗

Inhibition of core histones acetylation by carcinogenic nickel(II).

Nickel, a well-established human carcinogen, was shown to decrease acetylation of histones H4 and H3 in cultured cells. Such a decrease is expected to suppress gene expression. However, nickel is known to not only suppress but also enhance the expression of many genes. So, perhaps, nickel can alter histone acetylation in a more complex way? In a first step of testing this presumption, we examined acetylation status of histones H2A, H2B, H3 and H4, in human (HAE) and rat (NRK) cells exposed to nickel(II) under various conditions. In both cell lines, acetylation of all four histones was down-regulated by nickel(II) in a concentration- and time-dependent manner. Acetylation of histone H2B was suppressed to greater extent than that of the others, with histone H3 being relatively least affected. The analysis of acetylation status of each of the four lysine sites at the N-terminal tail of histone H2B revealed decreases consistent with those observed in the total acetylation patterns, with the K12 and K20 residues being markedly more affected than K5 and K15 residues. Thus, the decrease in acetylation was to some degree site specific. In NRK cells, the observed uniform down-regulation of histone acetylation was consistent with a marked suppression of global gene transcription measured as [3H]-uridine incorporation into mRNA. However, in HAE cells, global RNA expression was transiently increased (in 24 h) before dropping below control after longer exposure (3 days). In conclusion, the effects of Ni(II) on histone acetylation are inhibitory, with their extent depending on the dose and exposure time. This uniform inhibition, however, is not consistently reflected in global RNA expression that in HAE cells may include both increase and decrease of the expression, clearly indicating the involvement of factors other than histone acetylation. The observed effects may contribute to neoplastic transformation of Ni(II)-exposed cells.

Acetates↗

Histone fractionation by high-performance liquid chromatography on cyanoalkysilane (CN) reverse-phase columns.

Previous work in our laboratory [Gurley et al. Anal. Biochem. 129, 132-144 (1983)] described conditions for the rapid fractionation of histones by high-performance liquid chromatography (HPLC) using a reverse-phase muBondapak C18 column. That procedure resolved the major classes of histones with one exception: the more hydrophobic H2A variant, (MHP)H2A, was not resolved from the H4 histone class. This report extends that work describing experiments using a muBondapak CN column which better resolves the classes of histones from each other including the resolution of (MHP)H2A from the H4. In addition, the less hydrophobic H2A variant, (LHP)H2A, is partially resolved from the (MHP)H2A, and the less hydrophobic H3 variant, (LHP)H3, is resolved from the more hydrophobic H3 variant, (MHP)H3. Lower trifluoroacetic acid (TFA) concentrations (0.1%) in the eluting water/acetonitrile solvent were used with the CN column than were used with the C18 column which increased the sensitivity of histone detection by ultraviolet absorption at 206 nm. Greater than 95% of the total [3H]lysine-labeled protein applied to the CN column was eluted from the column. Contaminating nonhistone proteins were found to chromatograph in the region of histone elution. These were greatly reduced by isolating nuclei prior to histone preparation. The fractionation of the histones appears to be based on the hydrophobic properties of the proteins. The histone fractions (identified by their electrophoretic mobilities) were eluted from the CN column in the following order: H1, H2B, (LHP)H2A, (MHP)H2A, H4, (LHP)H3, and (MHP)H3. Phosphorylated and acetylated histone species were not resolved from their unmodified parental species.

Animals↗

Antigenicity of histones in various chromatins.

Antisera specific to purified histone fractions are used to assess the antigenicity of the histones present in chromatin derived from various sources. The results indicate that the antigenicity of the histones present in chromatin is markedly diminished as compared to the antigenicity of the histones free in solution. The antigenicity of histones in chromatins derived from three different tissues of the rat is very similar. The antigenicity of the histones present in chromatin derived from calf thymus is higher than that of the histones present in rat thymus. It is concluded that the major reason for diminished antigenicity of histones in chromatin is that the histones are complexed in the nucleosome conformation and that the antigenic determinants residing in histones in various chromatins are exposed to similar degrees.

Animals↗

Nuclear proteins. V. Studies of histone-binding proteins from mouse liver by affinity chromatography.

We examined four extracts of mouse liver for histone-binding proteins using histone affinity chromatography and positively charged resins. The extracts used were cytoplasm and washes from isolated nuclei with buffers containing 0.05 M Tris, 0.15 M NaCl or 0.35 M NaCl. Proteins from the nuclear washes showed greater binding to the columns than proteins from the cytoplasm. The binding fractions were heterogeneous in gel electrophoresis systems. Proteins bound to affinity columns of individual histones were similar to those bound to columns of whole histone, polylysine and DEAE. A 25,000 dalton polypeptide (J2), found only in nuclear washes was a prominent histone-binding protein. It could be competitively eluted from DEAE with histones, suggesting polypeptide J2 may show a specific affinity for histones. Polypeptide J2 has an acidic to basic amino acid ratio of 1.58, and its amino acid composition is not similar to that of the high mobility group 1 protein. Polypeptide J2 binds to hydrophobic columns and may play a role in modifying histone-histone and histone-DNA interactions.

Amino Acids↗

The in situ labeling of histone H3 in chromatin by a fluorescent probe.

A sulfhydryl-specific fluorescent probe, N-3-pyrene maleimide, has been shown to label with high efficiency the sulfhydryl groups of histone H3 in nonsheared chromatin. The probe labels chromatin preparations obtained by mild homogenization or nuclease treatment of rat liver and mouse thymocyte, but not chick erythrocyte nuclei. Mononucleosomes from all nuclear preparations are labeled by the probe. The reaction is inhibited by prior reaction of the chromatin with N-ethyl maleimide. The reaction kinetics show fast and slow components representing reactions with cysteinyl sulfhydryl groups and lysyl epsilon-amino groups, respectively. Dissociation of the chromatin by urea (6 M) or sodium dodecyl sulfate (SDS) increases the fluorescence intensity (2-3 fold) and is maximal at approx. 0.01-0.02% (w/v) SDS. Histones extracted from the labelled chromatin show that approx. 80-90% of the label is associated with the histone fraction and column chromatography of this fraction shows that the label is primarily associated with histone H3. Labelling of the isolated histone fractions shows significant labelling only of histone H3. The intrinsic fluorescence of tryptophan is quenched by the labelled histone H3, but not by iodide, suggesting that non-histone (tryptophan-containing) proteins lie in close proximity to the labelled histone H3 but are not immediately accessible to external solvent. The labelled chromatin exhibits fluorescence anistropy, the anistropy parameter being 0.19 +/- 0.003 for chromatin, 0.05 +/- 0.01 for mononucleosomes and 0.0 for isolated histone H3. This demonstrates the restriction placed on the label's mobility by the chromatin fiber. The formation of a superhelix at 60-100 mM NaCl has been monitored with the probe. An increase in fluorescence intensity at 80 mM NaCl is observed with intact chromatin (but not H-1 depleted chromatin) followed by dissociation of the octamer in 1.50-2.0 M salt accompanied by a large increase in labelling.

Animals↗

Metachromatic staining with Coomassie Brilliant Blue R-250 of the proline-rich calf thymus histone, H1.

In this report, we show that calf thymus histone 1 stains metachromatically with Coomassie Brilliant Blue R-250. Histone 1 gel bands appear red instead of the more familiar blue color characteristic of the vast majority of proteins. The red color and the spectral properties of histone 1 bands are qualitatively similar to those of collagen and procollagen bands which, as previously shown by others, also stain metachromatically (Micko, S. and Schlaepfer, W.W. (1978) Anal. Biochem. 88, 566-572 and McCormick, P.J., Chandrasekhar, S. and Millis, A.J.T. (1979) Anal. Biochem. 97, 359-366). In contrast to histone 1, histones 2A, 3 and 4 stain blue; histone 2B also stains predominantly blue, but with a faint red tint. Both red and blue bands display an absorption maximum in the vicinity of 560 nm, but red bands display an additional maximum in the vicinity of 530 nm. There are quantitative differences between the red bands; the 530 nm peak is more prominent in the spectrum of the collagen band than in the spectrum of the histone 1 band. The spectra of the blue bands are all very similar except that the spectrum of the histone 2B band is shifted slightly toward lower wavelengths. To account for the spectral differences between protein bands, we propose a model in which closely-spaced proline residues are responsible for the chromotropic effect. Localized concentrations of proline residues are present in both collagens and histone 1 and a small cluster is also present in histone 2B.

Animals↗

Exposed hydrophobic regions in histone oligomers studied by fluorescence.

The interaction of the fluorescent hydrophobic probe 1-anilinonaphthalene-8-sulfonate (ANS) with histone oligomers and with histone H1 has been studied. The enhancement of ANS fluorescence produced by histones Hv (a roughly equimolar mixture of histones H2A, H2B, H3 and H4) in 2.0 M NaCl, pH 7.5, is higher than that produced by histone H1 under identical conditions. In addition, the fact that the wavelength of maximum emission of the H1-ANS complex is larger than that of the Hv-ANS complex indicates that histone H1 has a weaker hydrophobic character than histones Hv. The increase in ANS concentration produces a red shift of the emission maximum of the Hv-ANS complex, indicating some heterogeneity in the ANS binding sites. Both the H2A-H2B and the H3-H4 complexes cause a similar enhancement of the ANS fluorescence. Trypsin digestion of N-terminal sequences of histones Hv produces only small changes in the intensity of ANS fluorescence. This result indicates that the hydrophobic regions of histones Hv to which ANS binds are not located in the N-terminal portions of histone sequences. It is suggested that these exposed hydrophobic regions may be important in the maintenance of chromatin structure.

Anilino Naphthalenesulfonates↗

In vitro acylation of the xi-amino group of L-lysine in calf thymus histones by the carcinogen, beta-propiolactone.

We had previously reported that the carcinogen, beta-propiolactone (BPL) reacted in vitro with histones in whole mouse skin chromatin and that among the histone classes BPL was preferentially bound to the lysine-rich histones H1 and H1 degrees. In order to determine if in vitro reaction of BPL with calf thymus histones resulted in binding of BPL to L-lysine, we synthesized the model compounds XI-N-(3-hydroxypropionyl)lysine (HPL) and xi-N-(I-carboxyethyl)lysine (CEL) from BPL and L-lysine. The alpha-amino group of L-lysine was protected from reaction with BPL by the formation of a copper chelate. Structures were assigned on the basis of infrared spectra, pKa values and chemical analyses. BPL was reacted in vitro with calf thymus histones and the BPL-reacted calf thymus histones and control calf thymus histones were digested with trypsin followed by pronase. The respective digests were each chromatograhed on a column of AA-15 cation-exchange resin. The elution profiles of the two digests were very similar except for the appearance of a new ninhydrin-positive peak (NNPP) in the eluate of the trypsin-pronase digest of BPL-reacted calf thymus histones. When compounds HPL and CEL were added to the trypsin-pronase digest of control calf thymus histones and the mixture chromatographed on AA-15, both compounds were resolved from the other peptide (or amino acid) peaks. HPL was eluted in the same fractions as NNPP, HPL and NNPP exhibited identical RF values on silica gel TLC with acidic, alkaline and neutral solvents. CEL was not identified as a product of the reaction between BPL and calf thymus histones.

Animals↗

Regulation of histone synthesis during early Urechis caupo (echiura) development.

The histones present in mature oocytes and embryos of Urechis caupo and their pattern of synthesis during early development have been characterized. Acid-soluble proteins extracted from mature oocyte germinal vesicles and from embryonic nuclei were analyzed by two-dimensional polyacrylamide gel electrophoresis. Histones are accumulated in the mature oocytes in amounts sufficient to provide for the assembly of chromatin through the 32- to 64-cell stage of embryogenesis. Two H1 histones, which appear to be variants, were found. Germinal vesicles and cleavage-stage nuclei are enriched in H1M (maternal). During late cleavage a faster-migrating H1, H1E (embryonic), appears among the nuclear histones and, as embryogenesis continues, replaces H1M as the predominant H1. No new core histone variants are detected during early development. Examination of [3H]lysine-labeled histones from germinal vesicles and embryonic nuclei reveals stage-specific patterns of histone synthesis. H1M is the major H1 species synthesized in mature oocytes. After fertilization, a switch to the predominant synthesis of H1E occurs. Comparison of the [3H]lysine incorporated into H1E and core histones indicates that H1E synthesis is disproportionately high from midcleavage through the midblastula stage. By the gastrula stage, a balanced synthesis of H1E and each core histone is established. The results indicate that there is noncoordinate regulation of H1 and core histone synthesis during Urechis development.

Animals↗

Histone messenger RNA synthesis and accumulation during early development in the echiuroid worm, Urechis caupo.

RNA isolated from Urechis caupo mature oocytes and embryos was analyzed for the presence of histone messenger RNAs (mRNAs) by in vitro translation and by filter blot hybridization to determine the contribution of maternal and newly transcribed histone mRNAs to the pattern of histone synthesis during early development. Histone mRNAs were not detected in mature oocyte RNA which suggests that relatively few if any maternal histone mRNAs are sequestered in the mature oocytes. Histone mRNAs were detected in cleavage-stage RNA and increased in amount from midcleavage through late gastrula stages. The in vitro translation analysis also demonstrated that the amount of H1 histone mRNA in late cleavage- and early blastula-stage embryos exceeds that of the individual core histone mRNAs. The disproportionate accumulation of individual histone mRNAs correlates with the noncoordinate synthesis of H1 and core histones which occurs during early embryogenesis.

Animals↗

Histone deacetylase. A key enzyme for the binding of regulatory proteins to chromatin.

Core histones can be modified by reversible, posttranslational acetylation of specific lysine residues within the N-terminal protein domains. The dynamic equilibrium of acetylation is maintained by two enzyme activities, histone acetyltransferase and histone deacetylase. Recent data on histone deacetylases and on anionic motifs in chromatin- or DNA-binding regulatory proteins (e.g. transcription factors, nuclear proto-oncogenes) are summarized and united into a hypothesis which attributes a key function to histone deacetylation for the binding of regulatory proteins to chromatin by a transient, specific local increase of the positive charge in the N-terminal domains of nucleosomal core histones. According to our model, the rapid deacetylation of distinct lysines in especially H2A and H2B would facilitate the association of anionic protein domains of regulatory proteins to specific nucleosomes. Therefore histone deacetylation (histone deacetylases) may represent a unique regulatory mechanism in the early steps of gene activation, in contrast to the more structural role of histone acetylation (histone acetyltransferases) for nucleosomal transitions during the actual transcription process.

Animals↗

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.

Animals↗

Identification of a Caenorhabditis elegans histone H1 gene family. Characterization of a family member containing an intron and encoding a poly(A)+ mRNA.

The isolation and properties of a gene encoding a histone H1 protein of Caenorhabditis elegans, his-24, are described. The predicted protein sequence is similar to histone H1 proteins of other eukaryotes. However, the gene structure of his-24 is atypical for a histone H1 gene; it contains an intron and encodes a polyadenylated mRNA. A family of approximately five histone H1 genes is defined by cross-hybridization to his-24. All appear to encode polyadenylated mRNAs. One gene is expressed specifically in male germ cells. These histone H1 genes are dispersed individually in the genome, apart from the previously described clusters of core histone genes (H2A, H2B, H3 and H4), which probably all encode non-polyadenylated mRNAs. This histone gene organization, with clustered core histone genes, encoding non-polyadenylated transcripts, and dispersed, histone H1 genes from which it appears only polyadenylated messages arise, suggests that C. elegans is at a stage of evolution of the histone gene family intermediate between lower eukaryotes (e.g. yeast) and the most advanced forms.

Amino Acid Sequence↗