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A constant radius of curvature model for the organization of DNA in toroidal condensates.

Toroidal DNA condensates have received considerable attention for their possible relationship to the packaging of DNA in viruses and in general as a model of ordered DNA condensation. A spool-like model has primarily been supported for DNA organization within toroids. However, our observations suggest that the actual organization may be considerably different. We present an alternate model in which DNA for a given toroid is organized within a series of equally sized contiguous loops that precess about the toroid axis. A related model for the toroid formation process is also presented. This kinetic model predicts a distribution of toroid sizes for DNA condensed from solution that is in good agreement with experimental data.

Animals↗

Functional aspects of mammalian sperm chromatin.

During spermiogenesis, the histones in the round spermatid, which bind the DNA in a relatively open configuration leaving much of the DNA exposed, are replaced by the much more tightly binding protamines, which package the DNA into highly condensed toroids. This knowledge has led to models of sperm chromatin structure that characterize the DNA as highly condensed and biologically inert, a view that is substantiated by the lack of detectable mRNA transcription or DNA replication in mature sperm nuclei. However, this view of sperm chromatin structure has been challenged recently by new data from several laboratories, including our own. These data indicate that mammalian sperm nuclei can interact with exogenous DNA and undergo sperm-specific apoptosis. We propose a model for sperm chromatin structure that provides a mechanism by which the tightly compacted mammalian sperm chromatin may be capable of these activities.

Journal Article↗

Histone modification enzymes: novel targets for cancer drugs.

In eukaryotes, genomic DNA is packaged with histone proteins into the cell nucleus as chromatin, condensing the DNA > 10,000-fold. Chromatin is highly dynamic and exerts profound control on gene expression. Localised chromatin decondensation facilitates access of nuclear machinery. Chromatin displays epigenetic inheritance, in that changes in its structure can pass to the next generation independently of the DNA sequence itself. It is now clear that the post-translational modification of histones, for example, acetylation, methylation and phosphorylation, plays a crucial role in the regulation of nuclear function through the 'histone code'. There has been significant progress in identifying and understanding the enzymes that control these complex processes, in particular histone acetyltransferases and histone deacetylases. The exciting discovery that compounds inhibiting histone deacetylase activity also have antitumour properties has focused attention on their use as anticancer drugs. As a consequence, there is ongoing evaluation of several histone deacetylase inhibitor compounds in Phase I and II clinical trials with promising early results. It is likely that many of the enzymes involved in the control of histone modification will provide therapeutic opportunities for the treatment of cancer, including histone methyltransferases and Aurora kinases.

Acetylation↗

[Construction of a cDNA library of the erythrocytic stage of Plasmodium vivax].

Plasmodium vivax-infected blood samples were collected from patients in the field during malaria transmission season. Total RNA of the parasites was extracted by guanidine HCl/cesium chloride centrifugation. mRNA was purified through oligo-dT cellulose. Double stranded cDNA were synthesized with AMV reverse transcriptase by Huynh's method. lambda gt11 phage was used as the vector. A cDNA library of the erythrocytic stage P. vivax was constructed after recombination of DNA and package in vitro.

Animals↗

The herpes simplex virus 1 UL15 gene encodes two proteins and is required for cleavage of genomic viral DNA.

Previous studies have shown that a ts mutant [herpes simplex virus 1 (mP)ts66.4] in the UL15 gene fails to package viral DNA into capsids (A. P. W. Poon and B. Roizman, J. Virol. 67:4497-4503, 1993) and that although the intron separating the first and second exons of the UL15 gene contains UL16 and UL17 open reading frames, replacement of the first exon with a cDNA copy of the entire gene does not affect viral replication (J.D. Baines, and B. Roizman, J. Virol. 66:5621-5626, 1992). We report that (i) a polyclonal rabbit antiserum generated against a chimeric protein consisting of the bacterial maltose-binding protein fused in frame to the majority of sequences contained in the second exon of the UL15 gene reacted with two proteins with M(r) of 35,000 and 75,000, respectively, in cells infected with a virus containing the authentic gene yielding a spliced mRNA or with a virus in which the authentic UL15 gene was replaced with a cDNA copy. (ii) Insertion of 20 additional codons into the C terminus of UL15 exon II caused a reduction in the electrophoretic mobility of both the apparently 35,000- and 75,000-M(r) proteins, unambiguously demonstrating that both share the carboxyl terminus of the UL15 exon II. (iii) Accumulation of the 35,000-M(r) protein was reduced in cells infected and maintained in the presence of phosphonoacetate, an inhibitor of viral DNA synthesis. (iv) The UL15 proteins were localized in the perinuclear space at 6 h after infection and largely in the nucleus at 12 h after infection. (v) Viral DNA accumulating in cells infected with herpes simplex virus 1(mP)ts66.4 and maintained at the nonpermissive temperature was in an endless (concatemeric) form, and therefore UL15 is required for the cleavage of mature, unit-length molecules for packaging into capsids.

Animals↗

A convenient and adaptable package of computer programs for DNA and protein sequence management, analysis and homology determination.

We describe the further development of a widely used package of DNA/protein sequence analysis programs (1). Important revisions have been made based on user experience, and new features, multi-user capability, and a set of large scale homology programs have been added. The programs are very user friendly, economical of time and memory, and extremely transportable. They are written in a version of FORTRAN which will compile, with a few defined changes, as FORTRAN 66, FORTRAN 77, FORTRAN IV, FORTRAN IV+, and others. They are running on a variety of microcomputers, minicomputers, and mainframes, in both single user and multi-user configurations.

Amino Acid Sequence↗

Function of hexameric RNA in packaging of bacteriophage phi 29 DNA in vitro.

A cyclic hexamer of the 120-base prohead RNA (pRNA) is needed for efficient in vitro packaging of the B. subtilis bacteriophage phi 29 genome. This capacity of pRNA to form higher multimers by intermolecular base pairing of identical subunits represents a new RNA structural motif. Dimers of pRNA are likely intermediates in formation of the cyclic hexamer. A three-dimensional model of the pRNA hexamer is presented.

Bacillus Phages↗

Mechanism of DNA compaction by yeast mitochondrial protein Abf2p.

We used high-resolution atomic force microscopy to image the compaction of linear and circular DNA by the yeast mitochondrial protein Abf2p, which plays a major role in packaging mitochondrial DNA. Atomic force microscopy images show that protein binding induces drastic bends in the DNA backbone for both linear and circular DNA. At a high concentration of Abf2p DNA collapses into a tight nucleoprotein complex. We quantified the compaction of linear DNA by measuring the end-to-end distance of the DNA molecule at increasing concentrations of Abf2p. We also derived a polymer statistical mechanics model that provides a quantitative description of compaction observed in our experiments. This model shows that sharp bends in the DNA backbone are often sufficient to cause DNA compaction. Comparison of our model with the experimental data showed excellent quantitative correlation and allowed us to determine binding characteristics for Abf2p. These studies indicate that Abf2p compacts DNA through a simple mechanism that involves bending of the DNA backbone. We discuss the implications of such a mechanism for mitochondrial DNA maintenance and organization.

Binding Sites↗

Thiol WR-1065 and disulphide WR-33278, two metabolites of the drug ethyol (WR-2721), protect DNA against fast neutron-induced strand breakage.

The main metabolites of the cytoprotective drug Ethyol (Amifostine, WR-2721) are the thiol WR-1065 and the disulphide WR-33278 (formed by the oxidation of WR-1065). Both metabolites are well-known protectors against DNA damage induced by gamma-rays. Using supercoiled plasmid DNA and restriction fragments we show that they protect efficiently also in the case of fast neutrons. In anoxic conditions WR-1065 (Z = +2) protects by scavenging of OH. and by 'chemical repair' (by H donation from its SH function). WR-33278 (Z = +4) protects by scavenging of OH. and, in the case of the supercoiled plasmid DNA, by reducing the accessibility of radiolytic attack sites via the induction of packaging of DNA in liquid-crystalline condensates (observed by circular dichroism). Because of this second mechanism, the plasmid DNA is more efficiently protected by WR-33278 than by WR-1065, at concentration ratios > 1 drug/4 nucleotides. Moreover, using sequencing gel electrophoresis of irradiated fragments of known sequence, we show that the protection by the two metabolites is non-homogeneously distributed along the DNA sequence, with 'hot spots' of protection and with unprotected regions. Based on presented molecular modelling results we explain the sequence dependence of radioprotection by structural variations induced by the binding of the drugs.

Amifostine↗

Inducible covalent posttranslational modification of histone H3.

The physiological state of a eukaryotic cell is determined by endogenous and exogenous signals, and often the endpoint of the pathways that transmit these signals is DNA. DNA is organized into chromatin, a nucleoprotein complex, which not only facilitates the packaging of DNA within the nucleus but also serves as an important factor in the regulation of gene function. The nucleosome is the basic unit of chromatin and generally consists of approximately two turns of DNA wrapped around an octamer of core histone proteins. Each histone also contains an accessible N-terminal tail that extends outside the chromatin complex and is subject to posttranslational modifications that are crucial in the regulation of gene expression. Two distinct categories of histone posttranslational modification have been observed: (i) inducible or stimulation-dependent and (ii) mitosis-dependent. Stimulation by mitogens or stress leads to rapid transient posttranslational modifications of histones, in particular histone H3, which are mechanistically and temporarily distinct from modifications associated with mitosis. This Review focuses mainly on the inducible phosphorylation of histone H3 brought about by different stimuli, such as epidermal growth factor, 12-O-tetradecanoylphorbol-13-acetate, arsenite, or ultraviolet radiation. We examine the most recent, and at times controversial, research data concerning the identity of the histone H3 kinases responsible for this phosphorylation. In addition, the interdependence of phosphorylation and acetylation will be discussed in light of data showing patterns of inducible modification at specific genes.

Acetylation↗

Genetics and physiology of bacteriophage T4 3'-phosphatase: evidence for involvement of the enzyme in T4 DNA metabolism.

Mutants of bacteriophage T4D which fail to induce the deoxyribonucleotide-specific T4 3'-phosphatase have been isolated. These mutants (T4pseT) grow as well as wild-type T4 in most strains of Escherichia coli, but not in the T4-sensitive "Hospital Strain," CT196, or in a derivative strain, CTr5x. Both the formation of infectious centers and the final yield of phage are reduced by 98% when CTr5x is infected by T4pseT mutants. The growth defects are accompanied by a 50% reduction in the rate of T4 DNA synthesis, a decrease in the single-strand length of the DNA product to about one-half the mature length, and greatly reduced packaging of DNA into phage particles. Introduction of an extra-cistronic suppressor mutation (stp) into T4pseT eliminates both the requirement for the T4 3'-phosphatase in infected CTr5x and the other observed effects of the pseT mutations. The pseT gene lies between genes 63 and 31. The stp gene lies in the nonessential region between rIIB and ac. Our results suggest that 3'-phosphoryl termini can disrupt T4 DNA replication to the extent that T4 3'-phosphatase becomes required for phage production.

Alleles↗

An upper limit of the ratio of DNA volume to nuclear volume exists in plants.

The variations in nuclear DNA content from 2 x 10(2) to 2.5 x 10(5) Mbp are reported in higher plants. The major finding so far is that the genome size of plant species differs by three orders of magnitude, which are more variable than the other organisms. Investigations pertaining to the manner in which DNA is packaged in the nucleus provide us with basic information on the made of DNA existence in the plant nucleus. However, the fundamentals on nuclear DNA content and nuclear size, which underlie and enable the flexible containment of such large differences in nuclear DNA content, remain unknown. We analyzed the nuclear volumes of plants with 2C value DNA contents ranging from 3.2 x 10(2) to 1.0 x 10(5) Mbp. As a result, we obtained a constant ratio between the DNA volume and nuclear volume, which does not exceed 3%. Furthermore, we also demonstrate that the nuclear Rabl model of chromatin organisation is not a common 3-D structure, even in plants with large nuclear DNA contents. The existence of an upper limit of DNA volume ratio would present a basal parameter for the future insight into the nuclear organisation in higher plants.

Cell Nucleus↗

Differential expression of porcine major histocompatibility DNA sequences introduced into mouse L cells.

The expression of a porcine genomic DNA segment containing a major histocompatibility gene and its chromatin structure in mouse L cells have been investigated. The transformed cells, which contain about two copies of the 17.8-kilobase pig DNA insert per haploid genome, stably and uniformly express major histocompatibility antigen on their surfaces. This expression is the result of differential transcription of the 3-kilobase major histocompatibility gene; the other 14 kilobases of pig sequences flanking the coding sequence are not transcribed. Although the entire pig DNA segment is packaged into nucleosomes, only the transcriptionally active DNA sequences are packaged in a DNase I-sensitive conformation. These results suggest that the expression of this foreign DNA is actively regulated in L cells.

Animals↗

Chromatin organization and transcriptional control of gene expression in Drosophila.

It is increasingly clear that the packaging of DNA in nucleosome arrays serves not only to constrain the genome within the nucleus, but also to encode information concerning the activity state of the gene. Packaging limits the accessibility of many regulatory DNA sequence elements and is functionally significant in the control of transcription, replication, repair and recombination. Here, we review studies of the heat-shock genes, illustrating the formation of a specific nucleosome array at an activatable promoter, and describe present information on the roles of DNA-binding factors and energy-dependent chromatin remodeling machines in facilitating assembly of an appropriate structure. Epigenetic maintenance of the activity state within large domains appears to be a key mechanism in regulating homeotic genes during development; recent advances indicate that chromatin structural organization is a critical parameter. The ability to utilize genetic, biochemical and cytological approaches makes Drosophila an ideal organism for studies of the role of chromatin structure in the regulation of gene expression.

Animals↗

Herpes simplex virus type 1 portal protein UL6 interacts with the putative terminase subunits UL15 and UL28.

The herpes simplex virus type 1 (HSV-1) UL6, UL15, and UL28 proteins are essential for cleavage of replicated concatemeric viral DNA into unit length genomes and their packaging into a preformed icosahedral capsid known as the procapsid. The capsid-associated UL6 DNA-packaging protein is located at a single vertex and is thought to form the portal through which the genome enters the procapsid. The UL15 protein interacts with the UL28 protein, and both are strong candidates for subunits of the viral terminase, a key component of the molecular motor that drives the DNA into the capsid. To investigate the association of the UL6 protein with the UL15 and UL28 proteins, the three proteins were produced in large amounts in insect cells with the baculovirus expression system. Interactions between UL6 and UL28 and between UL6 and UL15 were identified by an immunoprecipitation assay. These results were confirmed by transiently expressing wild-type and mutant proteins in mammalian cells and monitoring their distribution by immunofluorescence. In cells expressing the single proteins, UL6 and UL15 were concentrated in the nuclei whereas UL28 was found in the cytoplasm. When the UL6 and UL28 proteins were coexpressed, UL28 was redistributed to the nuclei, where it colocalized with UL6. In cells producing either of two cytoplasmic UL6 mutant proteins and a functional epitope-tagged form of UL15, the UL15 protein was concentrated with the mutant UL6 protein in the cytoplasm. These observed interactions of UL6 with UL15 and UL28 are likely to be of major importance in establishing a functional DNA-packaging complex at the portal vertex of the HSV-1 capsid.

Animals↗

Accessing DNA damage in chromatin: insights from transcription.

Recently, there has been a convergence of fields studying the processing of DNA, such as transcription, replication, and repair. This convergence has been centered around the packaging of DNA in chromatin. Chromatin structure affects all aspects of DNA processing because it modulates access of proteins to DNA. Therefore, a central theme has become the mechanism(s) for accessing DNA in chromatin. It seems likely that mechanisms involved in one of these processes may also be used in others. For example, the discovery of transcriptional coactivators with histone acetyltransferase activity and chromatin remodeling complexes has provided possible mechanisms required for efficient repair of DNA in chromatin.

Animals↗

Nucleosomes, DNA-binding proteins, and DNA sequence modulate retroviral integration target site selection.

Integration of retroviral DNA can serve as a paradigm for cellular functions that are affected by the packaging of DNA into chromatin. We have used a novel polymerase chain reaction-based assay to survey DNA and chromatin for the precise distribution of many integration sites. Integration into naked DNA targets is non-uniform, implying a nucleotide sequence bias. In chromatin, integration occurs preferentially at positions where the major groove is on the exposed face of the nucleosomal DNA helix, generating a 10 bp periodic spacing of preferred sites. Chromatin assembly enhances the reactivity of many sites, so that integration occurs most frequently at sites in nucleosomal, rather than nucleosome-free, regions of minichromosomes. In contrast, integration is prevented in a region occupied by a site-specific DNA-binding protein. Comparisons of integration events mediated by viral nucleoprotein complexes or by two different retroviral integrases show that the integration machinery also affects target site selection.

Base Sequence↗