A quantitative analysis of histone H1 in rabbit thymus nuclei

Role of the RB1 family in stabilizing histone methylation at constitutive heterochromatin

Here, we show a role for the RB1 family proteins in directing full heterochromatin formation. Mouse embryonic fibroblasts that are triply deficient for RB1 (retinoblastoma 1), RBL1 (retinoblastoma-like 1) and RBL2 (retinoblastoma-like 2) - known as TKO cells - show a marked genomic instability, which is coincidental with decreased DNA methylation, increased acetylation of histone H3 and decreased tri-methylation of histone H4 at lysine 20 (H4K20). Chromatin immunoprecipitation showed that H4K20 tri-methylation was specifically decreased at pericentric and telomeric chromatin. These defects are independent of E2F family function. Indeed, we show a direct interaction between the RB1 proteins and the H4K20 tri-methylating enzymes Suv4-20h1 and Suv4-20h2, indicating that the RB1 family has a role in controlling H4K20 tri-methylation by these histone methyltransferases. These observations indicate that the RB1 family is involved in maintaining overall chromatin structure and, in particular, that of constitutive heterochromatin, linking tumour suppression and the epigenetic definition of chromatin.

DNA methylation polymorphisms precede any histological sign of atherosclerosis in mice lacking apolipoprotein E

The present work investigates the occurrence and significance of aberrant DNA methylation patterns during early stages of atherosclerosis. To this end, we asked whether the genetically atherosclerosis-prone APOE-null mice show any changes in DNA methylation patterns before the appearance of histologically detectable vascular lesion. We exploited a combination of various techniques: DNA fingerprinting, in vitro methyl-accepting assay, 5-methylcytosine quantitation, histone post-translational modification analysis, Southern blotting, and PCR. Our results show that alterations in DNA methylation profiles, including both hyper- and hypomethylation, were present in aortas and PBMC of 4-week-old mutant mice with no detectable atherosclerotic lesion. Sequencing and expression analysis of 60 leukocytic polymorphisms revealed that epigenetic changes involve transcribed genic sequences, as well as repeated interspersed elements. Furthermore, we showed for the first time that atherogenic lipoproteins promote global DNA hypermethylation in a human monocyte cell line. Taken together, our results unequivocally show that alterations in DNA methylation profiles are early markers of atherosclerosis in a mouse model and may play a causative role in atherogenesis.

A single high affinity binding site for histone H1 in a nucleosome containing the Xenopus borealis 5 S ribosomal RNA gene

We have reconstituted nucleosomes containing the Xenopus borealis 5 S rRNA gene, a single histone octamer, and 1 or 2 molecules of histone H1. We determine that the 1st molecule of histone H1 to associate with the 5 S nucleosome binds with high affinity (KD approximately 2 nM), and the 2nd molecule of H1 binds with a reduced affinity (KD approximately 10 nM). This latter binding is comparable with the association of histone H1 with naked DNA. Neither molecule of histone H1 alters the helical periodicity of DNA in the nucleosome as revealed by hydroxyl radical cleavage. We conclude that although multiple molecules of histone H1 can associate with nucleosomal DNA, there is only a single high affinity binding site for histone H1 within the 5 S nucleosome.

Histone H1(0): a maintainer of the differentiated cell state?

Functional and structural effects of histones H1 and H1(0) were studied on isolated chromatin and nuclei from embryonic skeletal muscle as well as on cultured cells. The results showed that: H1 was responsible for a greater compaction of chromatin than H1(0) as evidenced by sedimentation. In contrast, H1(0) inhibited DNA synthesis in chromatin and cells to a greater extent than H1. No significant difference between the two histones on RNA synthesis inhibition was observed. histones H1 and H1(0) evidenced a quantitative increase in developing muscle cells. The results indicate that H1(0) may not be the inducer of the differentiated cell state, but rather assists in the maintenance of that state.

Activation of calcineurin by nickel ions

Calcineurin, a Ca2+- and calmodulin-dependent phosphoprotein phosphatase, was dramatically activated by Ni2+ ions. Activation by Ni2+ was independent of calmodulin and was not reversed by high concentrations of chelators. With histone H1 as substrate, the Km's obtained with Ca2+ and Ni2+ were 2.2 and 4.2 microM, and the kcat's were 0.5 and 24.3 min-1, respectively. Similar to the Ca2+- and Mn2+-supported reactions, the presence of calmodulin caused a 20-fold activation of the Ni2+-activated calcineurin over the basal rate. Incubation of calcineurin with Ni2+ resulted in 30% quenching of its Trp-fluorescence. This effect also was independent of calmodulin and not reversed by chelators. The results suggest that the Ni2+ ions are tightly bound to calcineurin and the effects may be physiologically relevant.

Histones H1 and H5: one or two molecules per nucleosome?

We have determined histone stoichiometries in nuclei from several sources by a direct chemical method, with the particular aim of quantitating histone H1 and, in chicken erythrocytes, H5, and of distinguishing between one and two molecules per nucleosome. The four histones H3, H4, H2A and H2B are found in equimolar amounts, as expected for the core histone octamer. The molar ratio of H1 in lymphocyte and glial nuclei is 1.0 per octamer, and in liver nuclei from three species 0.8 per octamer. These results suggest that each nucleosome has one H1 molecule; nucleosomes could acquire two molecules of H1 only at the expense of others containing none. The stoichiometry of H5 in chicken erythrocyte nuclei is similar to that of H1 in other nuclei, being about 0.9 molecules per nucleosome; the H1 also present in these nuclei amounts to 0.4 molecules per nucleosome.

Identification of histone H2b as a heat-shock protein in Drosophila

Total cell polypeptides synthesized, in cultured Drosophila cells under control (25 degrees C) and heat-shock (37 degrees C) conditions have been compared in two different two-dimensional polyacrylamide gel electrophoresis systems which, together, resolve polypeptides having a wide range of isoelectric points, including the most basic polypeptides of the cell. The electrophoresis of basic proteins showed that the most prominent basic polypeptide synthesized in heat shock comigrated with histone H2b. This heat-shock polypeptide was identified as histone H2b by two criteria: (a) it comigrated with authentic histone H2b in Triton-urea-acetic acid acrylamide gel electrophoresis after solubilization from nuclei with acid; and (b) partial proteolysis peptide maps of the basic heat-shock protein and histone H2b were identical. The synthesis of histone H2b was induced threefold in heat shock, whereas synthesis of the other histones was reduced from two- to tenfold. The noncoordinate synthesis of histones in Drosophila in heat shock provides an interesting system in which to investigate transcriptional and translational controls of histone synthesis as well as assembly of histones into chromatin.

Analysis of histones associated with neuronal and glial nuclei exhibiting divergent DNA repeat lengths

Total cerebral hemisphere nuclei purified from adult rabbit brain were subfractionated into neuronal and glial populations. Previous studies have shown that chromatin in neuronal nuclei is organized in an unusual nucleosome conformation compared with glial or kidney nuclei, i.e., a short DNA repeat length is present. We now analyze whether this difference in chromatin organization is associated with an alteration in the histone component of nucleosomes. Total histone isolated by acid/urea-protamine extraction of purified neuronal, glial, and kidney nuclei was analyzed by electrophoresis on SDS-polyacrylamide slab gels. Histone H1 that was selectively extracted from nuclei was also examined. Differences were not observed on SDS gels in the electrophoretic mobilities of histones associated with either the nucleosome core particle (histones (H2A, H2B, H3, H4) or the nucleosome linker region (histone H1). Total histone and selectively extracted histone H1 were also analyzed on acid/urea slab gels that resolve histones on the basis of both molecular weight and charge differences. When analyzed in this system, differences with respect to electrophoretic mobility were not detected when comparing either selectively extracted histone H1 or total histone from neuronal and glial nuclei. Quantitative analyses were also performed and neuronal nuclei were found to contain less histone H1 per milligram DNA compared with glial or kidney nuclei. Neuronal nuceli also demonstrated a lower ratio of histone H1/core histone. These results suggest that the pronounced difference in chromatin organization in neuronal compared with glial nuclei, which is reflected by a short DNA repeat length in neurons, appears to be associated with quantitative differences in neuronal histone H1.

The structure of histone H1 and its location in chromatin

On the basis of their primary structure, the lysine-rich histones are a unified family of proteins. Each has an amino acid chain which falls into three distinct domains. Only the central domain (approximately 80 residues) is in a folded conformation. It is protected from trypsin digestion in chromatin and corresponds to the segment of highest sequence conservation. Without the flanking domains it is able to close two full turns of DNA in the nucleosome and can thus locate the H1 molecule.

Ubiquitous and gene-specific regulatory 5' sequences in a sea urchin histone DNA clone coding for histone protein variants

The DNA sequences of the entire structural H4, H3, H2A and H2B genes and of their 5' flanking regions have been determined in the histone DNA clone h19 of the sea urchin Psammechinus miliaris. In clone h19 the polarity of transcription and the relative arrangement of the histone genes is identical to that in clone h22 of the same species. The histone proteins encoded by h19 DNA differ in their primary structure from those encoded by clone h22 and have been compared to histone protein sequences of other sea urchin species as well as other eukaryotes. A comparative analysis of the 5' flanking DNA sequences of the structural histone genes in both clones revealed four ubiquitous sequence motifs; a pentameric element GATCC, followed at short distance by the Hogness box GTATAAATAG, a conserved sequence PyCATTCPu, in or near which the 5' ends of the mRNAs map in h22 DNA and lastly a sequence A, containing the initiation codon. These sequences are also found, sometimes in modified version, in front of other eukaryotic genes transcribed by polymerase II. When prelude sequences of isocoding histone genes in clone h19 and h22 are compared areas of homology are seen to extend beyond the ubiquitous sequence motifs towards the divergent AT-rich spacer and terminate between approximately 140 and 240 nucleotides away from the structural gene. These prelude regions contain quite large conservative sequence blocks which are specific for each type of histone genes.

Nucleosome repeat lengths in the definitive erythroid series of the adult chicken

Morris [1] has suggested that the difference in nucleosome repeat length between chicken liver (200 base pairs) and mature chicken erythrocytes (212 base pairs) may be due to the presence of histone H5 which is found in chicken erythroid cells but not in other tissues. Levels of H5 increase during erythroid maturation in the adult chicken. To determine what influence H5 might have on repeat length, erythroid populations at various stages of maturation were isolated, and repeat lengths and levels of H5 were determined. Bone marrow cells from anemic chickens were cultured in vitro to permit non-cycling erythroblasts to mature and thus increase in density. Less dense cycling basophilic erythroblasts were then isolated by buoyant density centrifugation. This erythroblasts were then isolated by buoyant density centrifugation. This population has a repeat length of 205 base pairs and an H5 content roughly two-thirds that of mature erythrocytes, which have a repeat length of 212 base pairs. A population intermediate in maturation, consisting of cells of the anemic pheripheral blood, has a repeat length of 218 base pairs, and the predominant cell type in this population has an H5 content greater than that of mature erythrocytes. Therefore, changes in histone H5 content are reflected by the nucleosome repeat length during erythroid maturation.

Repeating oligonucleosomal units. A new element of chromatin structure

Supranucleosomal chromatin structure has been analysed by the use of histone H1 polymers crosslinked in nuclei and extended chromatin with bifunctional reagents methyl-4-mercaptobutyrimidate (MMB) and dimethyl suberimidate dihydrochloride. Almost pure H1 homopolymers were obtained in milligram amounts and examined for the distribution in molecular weights. The H1 homopolymer molecules both from nuclei and chromatin have been found to be integer multiples of an elementary structure (called "clisone") consisting of 12 histone H1 molecules. This finding strongly suggests that nucleosomal chains of chromatin are not uniform but rather organized as repeating oligonucleosomal units each consisting of 12 nucleosomes. Correlation between oligonucleosomal structures in nuclei and chromatin implies that a linearized nucleosomal chain retains the information on chromatin superstructure. The relation of the disclosed 12-nucleosome units to superbeads (nucleomeres) and other structures is discussed.

Analysis of the high mobility group proteins associated with salt-soluble nucleosomes

Two methods have recently been described for the isolation of monomer nucleosomes enriched in transcribed sequences which depend on their solubility in 0.1 M NaCl (Levy, W.B. and Dixon (1978), Nucleic Acid Res., 5, 4155-4163) or solutions containing divalent metal ions (Bloom, K.S. and Anderson, J.N. (1978), Cell, 15, 141-150). Using these procedures the proteins associated with such nucleosomes from rabbit thymus, calf liver and hen oviduct nuclei were isolated and analysed. Increased amounts of proteins HMG14 AND HMG17 and small amounts of HMG1 and HMG2 were found associated with the four core histones H2A, H2B, H3 and H4 in these nucleosomes. HMG14 and HMG17 were found to be enriched 2 - 7 fold, suggesting an involvement of these two proteins with transcribed sequences. 0.1 M NaCl-soluble monomer nucleosomes prepared by the method of Levy and Dixon were analysed by polyacrylamide gel electrophoresis and found to be composed of principally two types of particle: 1. Core particles of 145 base pairs of DNA associated with the four core histones only. 2. Nucleosomes with 160 base pairs of DNA associated with the four core histones, increased amounts of HMG14 and 17, and no H1. Small amounts of HMG1 and HMG2 are also detected. These results suggest that HMG14 and HMG17 might be interacting with the 15 base pair linker DNA. A model is presented for the structure of transcriptionally active chromatin.