Differential compaction of transcriptionally competent and repressed chromatin reconstituted with histone H1 subtypes.

Chromatin fragments stripped of H1 histones regain the ability to form higher order structures and aggregates in 0.15 M NaCl following reconstitution with histone H1. However, transcriptionally competent chromatin fragments are resistant to chicken erythrocyte H1/H5 histone-induced 0.15 M NaCl aggregation/precipitation. In this study, we investigated the ability of stripped chromatin fragments reconstituted with one of four histone H1 subtypes (chicken erythrocyte H1, H5, trout liver H1a, H1b) at various stoichiometries to form salt precipitable higher order structures. Our results provide evidence that chicken erythrocyte histone H1 was more effective than histone H5 and trout liver histone H1b better than H1a in forming higher order structures. None of the histone H1 subtypes could render transcriptionally competent chromatin fragments insoluble in 0.15 M NaCl. These results are consistent with the ideas that the histone H1 subtypes differ in their capacities to compact chromatin fiber, and that the alterations in the structure of transcriptionally competent nucleosomes interfere with the capacity of all H1 subtypes to form higher order structures.

Effects of histone acetylation, ubiquitination and variants on nucleosome stability.

The properties of the nucleosomes of a salt-soluble, transcriptionally active gene-enriched fraction of chicken erythrocyte chromatin were evaluated by hydroxyapatite dissociation chromatography. We have demonstrated previously that the salt-soluble, transcriptionally active gene-enriched polynucleosomes are enriched in dynamically acetylated and ubiquitinated histones, and in an atypical U-shaped nucleosome that possessed about 20% less protein than a typical nucleosome. Further, newly synthesized histones H2A and H2B exchange preferentially with the nucleosomal histones H2A and H2B of this salt-soluble chromatin fraction. Analysis of the histones eluting from the hydroxyapatite-bound chromatin demonstrated that hyperacetylated and ubiquitinated (u), including multi-ubiquitinated, H2A-H2B.1 dimers dissociated at lower concentrations of NaCl than unmodified dimers or dimers with histone variants H2A.Z and/or H2B.2. Cross-linking studies revealed that at least 50% of uH2B.1 was paired with uH2A. uH2A-uH2B.1 dimers dissociated at lower NaCl concentrations than H2A-uH2B.1 dimers. Hyperacetylated histone (H3-H4)2 tetramers also eluted at lower concentrations of NaCl than unmodified tetramers. Our results support the idea that acetylation and ubiquitination of histones H2A and H2B.1 increase the lability of H2A-H2B.1 dimers in transcriptionally active nucleosomes. In contrast, our observations suggest that histone variants H2A.Z and H2B.2. stabilize the association of the H2A-H2B dimer in nucleosomes. The elevated lability of the H2A-H2B dimer may facilitate processes such as the exchange of these dimers with newly synthesized histones, the elongation process of transcription and transcription factor binding.

Expression of rainbow trout apolipoprotein A-I genes in liver and hepatocellular carcinoma.

Screening for genes overexpressed in trout aflatoxin B1-induced hepatocellular carcinomas resulted in the isolation of cDNA sequences of two apolipoprotein A-Is, apoA-I-1 and apoA-I-2. The levels of apoA-I-1 and -2 mRNAs of liver and tumor were quite different. ApoA-I-1 mRNA was the major species in liver, while apoA-I-1 and -2 mRNAs were present at similar levels in several tumors. This elevated level of apoA-I-2 mRNA was observed in seven different tumors, suggesting that the overexpression of apoA-I-2 was a general feature of aflatoxin B1-induced liver tumors. Hybridization to genomic DNA demonstrated that trout has two different apoA-I genes which is in contrast to other vertebrates which have one gene coding for apoA-I. Liver apoA-I-1 and -2 cDNA clones specified the same amino acid sequence as the tumor apoA-I-1 and -2 cDNA clones. Analysis of the cDNA-derived amino acid sequences showed that trout apoA-I-1 and -2, like human apoA-I, consist largely of multiple 22 amino acid repeats having the potential to generate an amphipathic alpha-helix. The similarity of the repeat pattern in trout and human apoA-Is suggests that all the internal repeats in these sequences arose before the fish-mammal split, some 400 million years ago.

Western blotting and immunochemical detection of histones electrophoretically resolved on acid-urea-triton- and sodium dodecyl sulfate-polyacrylamide gels.

We have developed a method for the efficient transfer of histones from acetic acid-urea-Triton X-100 (AUT)-polyacrylamide minislab gels to nitrocellulose. The AUT gel was equilibrated with 50 mM acetic acid and 0.5% sodium dodecyl sulfate and then with 62.5 mM Tris-HCl, pH 6.8, and 2.3% sodium dodecyl sulfate. An alkaline transfer buffer [25 mM 3-(cyclohexylamino)-1-propanesulfonic acid, pH 10, with 20% methanol] was used to electrophoretically transfer the strongly basic proteins from AUT or sodium dodecyl sulfate gels to nitrocellulose. The applicability of this approach in the immunochemical detection of ubiquitinated histone species is demonstrated.

Characterization and chromatin distribution of the H1 histones and high-mobility-group non-histone chromosomal proteins of trout liver and hepatocellular carcinoma.

The H1 histones serve as general repressors of gene expression by inducing the formation of a compact chromatin structure, whereas the high-mobility-group (HMG) non-histone chromosomal proteins have roles in maintaining the structure and function of transcriptionally active chromatin. The distribution of the H1 histone subtypes and HMG proteins among various trout tissues (liver, hepatocellular carcinoma, testis and erythrocyte) was determined. Histone H1b was present in the chromatin of liver, but not in the chromatin of hepatocellular carcinoma, testis or erythrocyte. Nuclease-resistant regions of liver chromatin had elevated levels of histone H1b. Histone H1b was isolated, and the N-terminal amino acid sequence of histone H1b was found to be highly similar to that of mammalian histone H1(0) and duck H5. HMG proteins T1, T2, T3, H6, C, D and F were associated with liver and hepatocellular-carcinoma chromatin, with hepatocellular carcinoma containing higher levels of HMG T1 and F. Testis and erythrocyte had HMG T2 and H6 as their predominant HMG proteins. Most of the HMG H6 of hepatocellular carcinoma, but not of liver, was located in a chromatin fraction that was soluble at physiological ionic strength and enriched in transcriptionally active DNA. These alterations in the chromatin distribution and content of hepatocyte HMG proteins and H1 histone subtypes may contribute to aberrant hepatocyte gene expression in the hepatocellular carcinoma.

Histone deacetylase is a component of the internal nuclear matrix.

In chicken immature erythrocytes, approximately 4% of the modifiable histone lysine sites participate in active acetylation. There are two categories of actively acetylated histone H4. Although both are acetylated at the same rate (t1/2 = 12 min), one is acetylated to the tetraacetylated form and is rapidly deacetylated (class 1), and the other is acetylated to mono- and diacetylated forms and is slowly deacetylated (class 2). We show that the chromatin distribution of the class 1 labeled tetraacetylated H4 species paralleled that of the transcriptionally active DNA sequences. For example, the chromatin fragments of the insoluble nuclear material contained 76% of the active DNA and 74% of the labeled tetraacetylated H4. Class 2 labeled acetylated H4 species were found in repressed chromatin and were enriched in active/competent gene-enriched chromatin fragments. The majority of the histone deacetylase activity (75-80%) was located with the insoluble residual nuclear material. Further, approximately 40-50% of the enzyme activity was associated with nuclear matrices prepared by two methods using high salt and intermediate/high salt extraction. Histone deacetylase was solubilized by extracting the nuclear matrices with high salt and 2-mercaptoethanol, a procedure that generates nuclear pore-lamina complexes. These results demonstrate that histone deacetylase is a component of the internal nuclear matrix.

Histone acetylation alters the capacity of the H1 histones to condense transcriptionally active/competent chromatin.

The relationship between histone acetylation and the capacity of H1 histones to cause the 0.15 M NaCl-induced aggregation/precipitation of transcriptionally active/competent gene chromatin fragments was investigated. Previous studies have shown that transcriptionally active/competent, but not repressed, gene chromatin polynucleosomes, which were isolated from chicken erythrocytes, remained soluble in 0.15 M NaCl after being reconstituted with H1 histones. This result suggested that some component of the active/competent gene nucleosome altered the capacity of the H1 histones to condense the chromatin fiber. Recently, Hebbes et al. (Hebbes, T.R., Thorne, A.W., and Crane-Robinson, C. (1988) EMBO J. 7, 1395-1402) demonstrated directly that active, but not repressed, gene chromatin of chicken erythroid cells contain high levels of acetylated histones. Here, we show that the solubility of active/competent gene chromatin fragments in 0.15 M NaCl is dependent on the level of acetylated histone species, with induction of hyperacetylation increasing the solubility of this gene chromatin. Also, we show that lowering the levels of the acetylated histone forms reduces the ability of the active/competent gene chromatin fragments to resist exogenously added H1-histone-induced 0.15 M NaCl aggregation/precipitation. These results suggest that histone acetylation alters the capacity of the H1 histones to form compact higher order chromatin structures such that active/competent gene chromatin is maintained in a less folded state than the bulk of chromatin.

Chromatin structure of erythroid-specific genes of immature and mature chicken erythrocytes.

The beta-globin and histone H5 genes are transcriptionally active in immature chicken erythrocytes and potentially active in mature erythrocytes. In both immature and mature erythrocytes, the majority of these erythroid-specific gene sequences are located in two chromatin fractions: the low-salt-insoluble residual nuclear material and the 0.15 M-NaCl-soluble oligo- and poly-nucleosomes. These salt-soluble chromatin fragments are enriched in hyperacetylated species of H4 and H2B, ubiquitinated and polyubiquitinated species of H2A and H2B and are depleted of linker histones H1 and H5. The competent, transcriptionally inactive embryonic epsilon-globin gene, which is part of the DNAase I-sensitive beta-globin domain, is highly enriched in the 0.15 M-NaCl-soluble polynucleosome fraction but not in the insoluble nuclear material. The repressed vitellogenin gene shows no enrichment in either of these fractions. These results suggest that only those genes that are expressed or have the potential for expression are enriched in the low-salt-insoluble nuclear material of immature or mature erythrocytes. The enrichment of active genes in the low-salt-insoluble residual nuclear material of immature erythrocytes is not dependent on on-going transcription, the presence of RNA or changes in the amount of acetylated histone species. Our results are consistent with the hypothesis that active and potentially active genes are insoluble because of the presence of preinitiation transcription complexes.

Gene-specific differences in the aflatoxin B1 adduction of chicken erythrocyte chromatin.

Mature and immature chicken erythrocyte nuclei were treated with activated aflatoxin B1 (2,3-dichloroaflatoxin B1), producing covalently bound DNA adducts. This reaction produces alkali-labile sites in the DNA which can be identified by using a variation of the Maxam-Gilbert sequencing procedure. We determined the aflatoxin B1 accessibility of defined regions of the erythroid genome by using different specific probes and monitoring the disappearance of similar-sized fragments generated by restriction enzyme digestion. The genes studied were the erythroid-specific beta-globin and histone H5 genes, which are potentially active in mature erythroid nuclei and transcriptionally active in immature erythrocytes, and the vitellogenin and ovalbumin genes, which are both transcriptionally inactive in these cells. The beta-globin and histone H5 genes were more accessible than the repressed vitellogenin and ovalbumin genes to aflatoxin B1 modification in mature and immature erythroid chromatin. Micrococcal nuclease was used to probe the nucleosomal organization of active (beta-globin and histone H5) and repressed (vitellogenin and ovalbumin) genes in chicken erythrocytes. The vitellogenin and ovalbumin genes show a canonical nucleosome repeat pattern in mature and immature chicken erythrocyte nuclei. In contrast, the beta-globin and histone H5 genes lack a distinct nucleosomal repeat pattern in these cells. These results support the hypothesis that transcriptionally active genes are preferentially accessible to carcinogen modification because of their disrupted chromatin structure.

Bovine thymus satellite I DNA sequences, which are highly methylated, are preferentially located in H1-rich chromatin.

The distribution of 5-methylcytosine among H1-rich and -poor bovine thymus chromatin regions was determined. 5-Methylcytosine was enriched in H1-rich chromatin regions, with linker and nucleosomal DNA containing similar amounts of this modified base. Satellite I DNA sequences, which constitute 5-7% of the genome and are highly methylated, were preferentially localized among H1-rich chromatin regions, in accordance with the distribution of 5-methylcytosine. In contrast to the satellite I DNA sequences, prothrombin (a single copy DNA sequence) was localized among both H1-rich and -poor chromatin regions. The results of this study are consistent with the hypothesis that DNA methylation has a role in modulating the structure of chromatin.

Reduced levels of histones H1o and H1b, and unaltered content of methylated DNA in rainbow trout hepatocellular carcinoma chromatin.

The levels of histone subtypes and DNA methylation of aflatoxin-induced rainbow trout hepatocellular carcinoma and adult liver nuclei were compared. The hepatocellular carcinoma nuclei were enriched in the ubiquitinated species of histone H2A and depleted in histones H1o and H1b. The 5-methylcytosine content and methylation patterns of the vitellogenin genes and the transcriptionally inactive TPG-3 protamine gene were not altered in the trout hepatocellular carcinoma DNA. Thus, undermethylation of DNA is not a general feature of chemically induced tumors in vivo.

DNA methylation pattern and restriction endonuclease accessibility in chromatin of a germ-line specific gene, the rainbow trout protamine gene.

The chromatin structure of a germ-line specific gene, the TPG-3 gene, one of the rainbow trout protamine genes was analyzed in various tissues. The protamine genes are expressed in early stage testis but not in late stage testis, liver or erythrocyte. Five potential CpG methylation sites in the coding and flanking regions of the TPG-3 protamine gene were monitored in early and late stage testis, nucleoprotamine, liver and erythrocyte. In all cases the patterns of methylation were identical with only one CpG site at position -740 being methylated. Thus, the methylation pattern of this protamine gene remained the same independently of the expression of the gene. Two Msp I sites at positions -293 and/or -275 and +155 were accessible to the enzyme in the TPG-3 chromatin of early stage testis. Since the Msp I site at position -293 and/or -275 was also present in the TPG-3 chromatin of liver, only the site at position +155 within the transcribed region correlated with the expression of the protamine gene.

The nonhistone chromosomal protein, H2A-specific protease, is selectively associated with nucleosomes containing histone H1.

We have determined the distribution of the nucleosomal bound nonhistone chromosomal protein, H2A-specific protease, in calf thymus and liver chromatin. The protease was unevenly distributed in chromatin with domains containing histone H1 being selectively complexed with the enzyme. Moreover, the protease had a preference for the less compact chromatin domains enriched in the H1 subtypes H1a and -c. We have demonstrated that ubiquitinated H2A is a substrate of the H2A-specific protease and that the enzyme is a serine protease which can be inactivated with protease inhibitors only after it is released from the nucleosome. Possible functions of the protease in modulating chromatin structure are discussed.