Poising chromatin for transcription

Association of actin with DNA and nuclear matrix from Guerin ascites tumour cells

The protein composition of nuclear matrices containing different amount of DNA was examined. It was found that, in matrices containing 2% to 80% of total DNA, the quantity of DNA-bound proteins remains relatively constant varying from 10% to 15% of total nuclear proteins. Electrophoretic patterns do not differ substantially, but autoradiograms with in vitro 125I labelled proteins show quantitative variations in the actin content. Application of radioimmunoassay (RIA) enabled to determine the exact content of actin in GAT nuclei and nuclear matrices - 5 micrograms/ml in nuclei, of which 50% are bound to DNA and 30% being a component of the protein part of the nuclear matrix. These results are supported by electron microscopic data, where immunogold technique was performed on thin sections and spread material. The applied methods suggest that part of the nuclear actin is tightly bound (resistant to 2 M NaCl) to DNA and represents a component of the internal nuclear matrix.

The ultrastructure of upstream and downstream regions of an active Balbiani ring gene

When active, the 37 kb Balbiani ring genes are known to form transcription loops with an almost fully extended chromatin axis. Here we examine the upstream and downstream regions of such transcription loops by electron microscopy. We demonstrate that a loop starts and ends in tightly packed chromatin; the two anchoring sites are clearly separated from each other in space. The upstream, nontranscribed region consists of a thin, extended, apparently flexible and nucleosome-free fiber corresponding to about 0.5 kb DNA. The downstream, nontranscribed region appears as a 200 nm long nucleofilament loosely coiled into a short, thick chromatin fiber and estimated to contain about 3 kb DNA.

Genes expressed in cortical neurons--chromatin conformation and DNase I hypersensitive sites

DNase I sensitivity experiments were performed utilizing DNA probes to genes which are either transcribed in rat cortical neurons (the 68 kDa neurofilament gene and the neuron-specific enolase gene) or are transcriptionally silent (albumin). Results suggest that unlike liver, in which a hierarchy in chromatin conformation exists between transcribed and nontranscribed genes, the majority of protein coding sequences in cortical neurons may be relatively sensitive to nuclease digestion. This supports our previous observation of an increased DNase I sensitivity of total chromatin in cortical neurons. Nuclease sensitivity experiments also revealed the presence of brain-specific DNase I hypersensitive sites associated with the two neuron-specific genes.

An evolutionarily conserved protein fraction stably linked to DNA

Chromatins from four evolutionarily remote species (insect, fish, amphibian and bird) were isolated, high-salt-extracted and extensively deproteinized to remove noncovalently associated proteins. A protein fraction resisting the extraction procedures was found firmly linked to DNA in all four chromatins. Two-dimensional tryptic peptide mapping revealed a remarkable evolutionary conservativeness of this protein component, suggesting an indispensable function for it in the nucleus.

The protamine gene chromatin in developing trout testis exists in an altered state

Micrococcal nuclease was used to probe the nucleosomal organization of the rainbow trout germ-line-specific protamine multi-gene family in testis and erythrocytes. In erythrocyte chromatin, the repressed protamine genes show a distinct nucleosomal repeat pattern. However, in early-stage testis chromatin, where the protamine genes are expressed, they lack a distinct nucleosomal repeat pattern, indicating that the disrupted chromatin structure is related to their transcriptional activity. Micrococcal nuclease-digested testis and erythrocyte chromatin was separated into soluble and insoluble fractions. Transcriptionally active/competent genes of testis that had been labeled by nuclear nick-translation were enriched in the low-salt eluted, micrococcal nuclease-sensitive chromatin fraction. This fraction was not enriched in protamine DNA sequences. In testis, but not erythrocytes, protamine DNA sequences were slightly enriched in chromatin that fractionated with insoluble nuclear material, suggesting that transcriptionally active protamine gene chromatin has an insoluble character. Since the different protamine genes may not be simultaneously expressed, our results show the distribution of both transcriptionally active and inactive protamine genes. However, our observations indicate that the active germ-line-specific protamine gene chromatin shares several, but not all, of the features associated with other active tissue-specific genes.

Endogenous degradation of rat liver chromatin studied by agar gel electrophoresis of nuclei

Direct agar gel electrophoresis of incubated rat liver nuclei revealed that most of the chromatin is rapidly converted to stable, large fragments, showing identical electrophoretic mobility. Short and long term incubation gave the same results. The analysis of deproteinized DNA under nondenaturing as well as denaturing conditions showed, however, a correlation between the DNA size pattern and the time of incubation. Our data on the persistance of large and uniform in size chromatin fragments despite the presence of cleaved DNA in them may indicate naturally footprinted regions of chromatin, implying most probably some strong ordered interactions of chromatin constituents. It seems that some substantial unknown features of higher order structure of chromatin are preserved in rat liver nuclei isolated and digested under the experimental conditions used.

Chromatin folding modulates nucleosome positioning in yeast minichromosomes

Based on the chromatin structures of the yeast URA3 gene and the TRP1ARS1 circle, we have designed circular minichromosomes of different sizes that should each form a tight tetranucleosome. This structure was assumed to be stiff and bulky and therefore likely to be sensitive to packaging into a three-dimensional structure. The structures of the minichromosomes were determined using micrococcal nuclease. Only one of the minichromosomes showed a protected region of about 570 bp, compatible with the predicted tight tetranucleosome, while all other constructs showed alternative structures. A comparison of the structures revealed that neither histone-DNA interactions nor influences from flanking boundaries are sufficient determinants of nucleosome positions. The data strongly suggest that chromatin folding modulates the nucleosome arrangement along the DNA.

Localization, in human placenta, of the tightly bound form of DNA methylase in the higher order of chromatin organization

In human placenta, the DNA of all subfractions of the third level of chromatin organization exhibits similar values of the methylcytosine-to-cytosine ratio. The tightly bound form of DNA methyltransferase is mostly recovered in the 'stripped loop' fraction, although, on the basis of the DNA content, the 'stripped loops' and the 'stripped matrix' appear to possess a similar amount of the enzyme. DNA methyltransferase activity is instead totally absent from the 'digested matrix', i.e., from the fraction remaining after digestion of the 'stripped matrix' with DNAase I. Upon addition of exogenous DNA methyltransferase, however, the DNA of this fraction, which is only 1% (in weight) of the total chromatin DNA and which has a length of approx. 9 kbp, can readily undergo methylation.

Doxorubicin induces the acetylation of histone H1 in a human colon cancer cell line (LoVo/DX) selected for resistance to the drug, but not in the sensitive parental line (LoVo)

The effect of doxorubicin (DX) treatment on H1 synthesis and acetylation was studied in two human colon adenocarcinoma cell lines, sensitive (LoVo) and resistant (LoVo/DX) to this drug. Histone variants were resolved by a high resolution two-dimensional gel electrophoresis system coupled to fluorography for the detection of radioactive incorporation. The relative synthesis of H1.4 and H1.5 variants was slightly reduced by DX. This is probably related to the inhibition of DNA synthesis consequent to drug treatment. The main effect is that DX induces the acetylation of H1 isoproteins in the LoVo/DX resistant line but not in the parental line, which is 30 times more sensitive to anthracyclines. The different behavior of the two cell lines cannot be attributed to different cellular drug retention since the DX doses chosen (1.25 for LoVo and 40 micrograms/ml for LoVo/DX cells) correspond to similar intracellular drug concentrations. H1 acetylation persisted after exposure to cycloheximide in DX treated LoVo/DX cells, indicating that it is a postranslational event. The induction of H1 acetylation appears rather specific since no increase was found in 3H-acetate incorporation on the total cellular TCA-precipitable fraction. In addition DX treatment did not modify the acetylation of core histones in either LoVo or LoVo/DX cell lines.

A domain model for eukaryotic DNA organization: a molecular basis for cell differentiation and chromosome evolution

A model for eukaryotic chromatin organization is presented in which the basic structural and functional unit is the DNA domain. This simple model predicts that both chromosome replication and cell type-specific control of gene expression depend on a combination of stable and dynamic DNA-nuclear matrix interactions. The model suggests that in eukaryotes, DNA regulatory processes are controlled mainly by the intranuclear compartmentalization of the specific DNA sequences, and that control of gene expression involves multiple steps of specific DNA-nuclear matrix interactions. Predictions of the model are tested using available biochemical, molecular and cell biological data. In addition, the domain model is discussed as a simple molecular mechanism to explain cell differentiation in multi-cellular organisms and to explain the evolution of eukaryotic genomes consisting mainly of repetitive sequences and "junk" DNA.

Methylation of single CpG dinucleotides within a promoter element of the Herpes simplex virus tk gene reduces its transcription in vivo

The binding of the transcription factors Sp1 and CTF immediately upstream from the TATA box of the Herpes simplex virus (type 1) thymidine kinase-coding gene (tk) facilitates efficient transcription of this gene in microinjected Xenopus laevis oocytes. To establish whether the presence of methylated CpG dinucleotides within the binding sites of these two factors affects transcription of the tk gene in vivo, we replaced a 33-bp promoter segment, consisting solely of the Sp1 and CTF binding sites, with synthetic oligodeoxynucleotide duplexes containing 5-methylcytosine residues at selected positions. We show that symmetrical methylation (modification of both strands) of any of the four CpGs within this promoter segment resulted in an approximately 20-fold reduction in the specific transcription of the tk gene in Xenopus oocytes, as shown by primer extension analysis of the isolated mRNA. As no other methylated CpG dinucleotides were present within the entire 9.2-kb vector, our results demonstrate that the presence of a single mCpG dinucleotide within the promoter region is sufficient for transcriptional inactivation of the tk gene. The possible mechanisms of this downregulation are discussed.