The composition and structure of isolated chromosomes

Histone Deacetylase Inhibitors as Therapeutic Interventions on Cervical Cancer Induced by Human Papillomavirus

The role of epigenetic modifications on the carcinogenesis process has received a lot of attention in the last years. Among those, histone acetylation is a process regulated by histone deacetylases (HDAC) and histone acetyltransferases (HAT), and it plays an important role in epigenetic regulation, allowing the control of the gene expression. HDAC inhibitors (HDACi) induce cancer cell cycle arrest, differentiation, and cell death and reduce angiogenesis and other cellular events. Human papillomaviruses (HPVs) are small, non-enveloped double-stranded DNA viruses. They are major human carcinogens, being intricately linked to the development of cancer in 4.5% of the patients diagnosed with cancer worldwide. Long-term infection of high-risk (HR) HPV types, mainly HPV16 and HPV18, is one of the major risk factors responsible for promoting cervical cancer development. In vitro and in vivo assays have demonstrated that HDACi could be a promising therapy to HPV-related cervical cancer. Regardless of some controversial studies, the therapy with HDACi could target several cellular targets which HR-HPV oncoproteins could be able to deregulate. This review article describes the role of HDACi as a possible intervention in cervical cancer treatment induced by HPV, highlighting the main advances reached in the last years and providing insights for further investigations regarding those agents against cervical cancer.

Substantial intraspecific genome size variation in golden-brown algae and its phenotypic consequences

BACKGROUND AND AIMS

While nuclear DNA content variation and its phenotypic consequences have been well described for animals, vascular plants and macroalgae, much less about this topic is known regarding unicellular algae and protists in general. The dearth of data is especially pronounced when it comes to intraspecific genome size variation. This study attempts to investigate the extent of intraspecific variability in genome size and its adaptive consequences in a microalgal species.

METHODS

Propidium iodide flow cytometry was used to estimate the absolute genome size of 131 strains (isolates) of the golden-brown alga Synura petersenii (Chrysophyceae, Stramenopiles), identified by identical internal transcribed spacer (ITS) rDNA barcodes. Cell size, growth rate and genomic GC content were further assessed on a sub-set of strains. Geographic location of 67 sampling sites across the Northern hemisphere was used to extract climatic database data and to evaluate the ecogeographical distribution of genome size diversity.

KEY RESULTS

Genome size ranged continuously from 0.97 to 2.02 pg of DNA across the investigated strains. The genome size was positively associated with cell size and negatively associated with growth rate. Bioclim variables were not correlated with genome size variation. No clear trends in the geographical distribution of strains of a particular genome size were detected, and strains of different genome size occasionally coexisted at the same locality. Genomic GC content was significantly associated only with genome size via a quadratic relationship.

CONCLUSIONS

Genome size variability in S. petersenii was probably triggered by an evolutionary mechanism operating via gradual changes in genome size accompanied by changes in genomic GC content, such as, for example, proliferation of transposable elements. The variation was reflected in cell size and relative growth rate, possibly with adaptive consequences.

Genome size and lifestyle in gnesiotrochan rotifers

Gnesiotrochan rotifers display a variety of life styles ranging from taxa with free-swimming larval and sessile adult stages to those with motile adult stages and colonial habits. Several explanations for the C- value enigma posits that genome size is correlated with lifestyle. To investigate this, 13 gnesiotrochan species representing nine genera were measured by flow cytometry. Genome sizes (1C) within Gnesiotrocha ranged from 0.05 pg (Hexarthra mira and Hexarthra fennica) to 0.25 pg (Sinantherina ariprepes). Genome sizes varied within genera and species; e.g., H. fennica (El Huérfano, Mexico) was estimated to be 15% larger than that of H. mira and H. fennica (Keystone Wetland, TX, USA). Gnesiotrochan genome sizes are similar to those reported within Ploima, which range from 0.06 pg (Brachionus rotundiformis, B. dimidiatus) to 0.46 pg (B. asplanchnoidis). Within Gnesiotrocha, genome size was found to be significantly smaller in sessile versus motile species as well as in solitary versus colonial species. To account for phylogenetic background, Linear Mixed Models with hierarchical taxonomic ranks showed that there is a taxonomic component underlying genome size. This study provides the first estimates of genome size within the superorder, providing a baseline for genomic and evolutionary studies within the group.

Origin of the concept of the quiescent centre of plant roots

Concepts in biology feed into general theories of growth, development and evolution of organisms and how they interact with the living and non-living components of their environment. A well-founded concept clarifies unsolved problems and serves as a focus for further research. One such example of a constructive concept in the plant sciences is that of the quiescent centre (QC). In anatomical terms, the QC is an inert group of cells maintained within the apex of plant roots. However, the evidence that established the presence of a QC accumulated only gradually, making use of strands of different types of observations, notably from geometrical-analytical anatomy, radioisotope labelling and autoradiography. In their turn, these strands contributed to other concepts: those of the mitotic cell cycle and of tissue-related cell kinetics. Another important concept to which the QC contributed was that of tissue homeostasis. The general principle of this last-mentioned concept is expressed by the QC in relation to the recovery of root growth following a disturbance to cell proliferation; the resulting activation of the QC provides new cells which not only repair the root meristem but also re-establish a new QC.

CHANGES IN NUCLEAR HISTONES DURING FERTILIZATION, AND EARLY EMBRYONIC DEVELOPMENT IN THE PULMONATE SNAIL, Helix aspersa

Calf thymus histories comprising two fractions, one rich in lysine, the other having roughly equal amounts of lysine and arginine, Loligo testes histones rich in arginine, and salmine, are compared with respect to their amino acid compositions, and their staining properties when the proteins are fixed on filter paper. The three types of basic proteins; somatic, arginine-rich spermatid histones, and protamine can be distinguished on the following basis. Somatic and testicular histones stain with fast green or bromphenol blue under the same conditions used for specific staining of histones in tissue preparations. The former histones lose most or all of their stainability after deamination or acetylation. Staining of the arginine-rich testicular histones remains relatively unaffected by this treatment. Protamines do not stain with fast green after treatment with hot trichloracetic acid, but are stained by bromphenol blue or eosin after treatment with picric acid. These methods provide a means for the characterization of nuclear basic proteins in situ. Their application to the early developmental stages of Helix aspersa show the following: After fertilization the protamine of the sperm is lost, and is replaced by faintly basic histones which differ from adult histones in their inability to bind fast green, and from protamines, by both their inability to bind eosin, and their weakly positive reaction with bromphenol blue. These "cleavage" histones are found in the male and female pronuclei, the early polar body chromosomes, and the nuclei of the cleaving egg and morula stages. During gastrulation, the histone complement reverts to a type as yet indistinguishable from that of adult somatic cells.

Organization of chromatin in the interphase mammalian cell

The use of imaging techniques has become an essential tool in cell biology. In particular, advances in fluorescence microscopy and conventional transmission electron microscopy have had a major impact on our understanding of chromatin structure and function. In this review we attempt to chart the conceptual evolution of models describing the organization and function of chromatin in higher eukaryotic cells, in parallel with the advances in light and electron microscopy over the past 50 years. In the last decade alone, the application of energy filtered transmission electron microscopy (EFTEM), also referred to as electron spectroscopic imaging (ESI), has provided many new insights into the organization of chromatin in the interphase nucleus. Based on ESI imaging of chromatin in situ, we propose a 'lattice' model for the organization of chromatin in interphase cells. In this model, the chromatin fibers of 10 and 30nm diameter observed by ESI, produce a meshwork that accommodates an extensive and distributed interchromosomal (IC) space devoid of chromatin. The functional implications of this model for nuclear activity are discussed.

An analysis of the inactivation of the frog sperm nucleus by toluidine blue

Toluidine blue, applied to frog sperm under appropriate conditions, inactivates specifically the sperm nucleus, leaving the extranuclear parts of the cell undamaged. Thus, the dye-treated spermatozoa stimulate eggs to cleave normally, but contribute no chromosomes to the resulting embryos, which develop as typical gynogenetic haploids. The concentration of dye required to produce this inactivation varies with pH. Measurements made over the entire pH range which can be tolerated by sperm cells showed that in the lower part of the range (5 to 7) the effective dye concentration was about 5 x 10^–6M; in the intermediate range (7 to 8.5) it was 1 x ^–6 to 1 x ^–7M; and for the higher pH values (8.5 to 10.0) it was about 5 x ^–8M. Using sperm suspensions containing 1500 cells per c. mm. these concentrations of dye produced specific inactivation of the sperm nuclei within 7 to 60 minutes at 18°C. Tests of the reversibility of the inactivation were made by transferring the sperm from the dye to a dilute Ringer's solution after a known degree of inactivation had been produced. Following removal of the dye the sperm cells were tested on eggs over a period of 2 hours. During this time there was no indication of a reversal of the inactivation. Microscopic observations of sperm treated with ^–5M or 5 X ^–5M dye show that the dye is taken up by the sperm nucleus, which is faintly but definitely stained. The dye appears to be uniformly distributed in the nucleus, while extranuclear structures remain unstained. Measurements of the amount of dye bound per sperm nucleus indicate that the minimal quantity required for complete inactivation is about 6.7 x ^–18 mole, while the maximal amount which can be bound without injury to extranuclear structures is about 1.5 x ^–16 mole. The value obtained for the minimal requirement (6.7 X ¹⁶ mole = 4 X ⁶ molecules) suggests that there are roughly 4 million binding sites in the nucleus which, when blocked by dye molecules, somehow prevent the sperm chromosomes from participating in the development of the egg.

The absence of histone in the bacterium Escherichia coli. I. Preparation and analysis of nucleoprotein extract

The deoxyribonucleic acid (DNA) from Escherichia coli has been isolated as an extract containing about 50 per cent by weight protein. The protein component differs both in composition and chemical behaviour from histone which occurs in combination with the DNA in most cells of higher organisms. Although this result suggests the absence of histone-like protein, it is not clear whether the bacterial protein found is naturally bound to the bacterial DNA in the cell or becomes attached to the DNA during the course of isolation.

Cytological evidence that both RNA and DNA may form a complex with the same protein

Deoxyribonucleic acid can be added back to protein sites from which the original nucleic acid, ribo- or deoxyribo-, is removed. If sections of frozen-substituted ovarian follicle cells of a leafhopper are first extracted by hot trichloracetic acid to remove nucleic acids and then immersed in a solution of a commerical preparation of deoxyribonucleic acid, the nucleic acid becomes attached to nuclear and cytoplasmic sites and can be rendered visible by the Feulgen reaction. The addition occurs in certain other tissues as well. The results are discussed in relation to biochemical and other cytochemical investigations of the nucleoprotein complex.

STUDIES ON ISOLATED NUCLEI. II. ISOLATION AND CHEMICAL CHARACTERIZATION OF NUCLEOLAR AND NUCLEOPLASMIC SUBFRACTIONS

This paper describes the subfractionation of nuclei isolated from guinea pig liver by the procedure presented in the first article of the series (8). Centrifugation in a density gradient system of nuclear fractions disrupted by sonication permits the isolation of the following subfractions: (a) a nucleolar subfraction which consists mainly of nucleoli surrounded by a variable amount of nucleolus-associated chromatin and contaminated by chromatin blocks derived primarily from von Kupffer cell nuclei; (b) and (c), two nucleoplasmic subfractions (I and II) which consist mainly of chromatin threads in a coarser (I) or finer (II) degree of fragmentation. The protein, RNA, and DNA content of these subfractions was determined, and their RNA's characterized in terms of NaCl-solubility, nucleotide composition, and in vivo nucleotide turnover, using inorganic ₃₂P as a marker. The results indicate that there are at least three types of RNA in the nucleus (one in the nucleolus and two in the nucleoplasm or chromatin), which differ from one another in NaCl-solubility, nucleotide composition, turnover, and possibly sequence. Possible relations among these RNA's and those of the cytoplasm are discussed.

INACTIVATION OF A BACTERIOPHAGE BY CHEMICAL ANTIBACTERIAL AGENTS

An extinction method has been used to examine the inactivation of coliphage T6r by a number of chemical antibacterial agents. A marked difference in the effect of concentration on inactivation efficiency has been shown for different agents, chloramine-T and formaldehyde having concentration exponents of approximately 2 and 3 respectively; crystal violet, cetrimide and phenol having concentration exponents of approximately 11, 13 and 15 respectively. It is suggested that a low concentration exponent is associated with inactivation of the phage by an effect on the protein coat of the particle and a high concentration exponent with an effect on its internal structure.

A histochemical approach to the knowledge about the neuron nucleus: the "pre-alarm chromatin"

Chromatin as a functional whole. Since the nineteen-fifties (1,2), studies on the histochemistry of the nucleus have been based on its concept as a whole: measurement of the DNA content, and the ratio between nucleus size and cell size appeared to be (and were in effect) an indication of the functional status of the single cell and of the cell population. Two decades later, the already well-known morphological distinction between the chromatins as euchromatin and heterochromatin was reinterpreted on the basis of the degree of spiralization of the nucleosomal fiber and its complexity (3). Subsequently, considerable information about the non-random interphasic position of the chromosomal domains in the nucleus was obtained by in situ hybridization, and the successive reconstruction of their location in the nucleus by image processing with Normarski optics and rotating stage or by confocal microscopy (4-8). Moreover, immunological studies using monoclonal antibodies raised against the splicing factors acting on nuclear pre-mRNAs in discrete nuclear regions (spliceosomes) (9,10), lent support to the notion that the chromatin machinery operates as a whole.

Isolation of matrices from maize leaf nuclei: identification of a matrix-binding site adjacent to the Adh1 gene

Nuclear matrices were isolated from maize leaves by the two conventional methods usually employed for the preparation of the corresponding structures of animal origin. It is demonstrated that functionally competent matrices, recognizing and specifically binding the MAR-containing DNA of the mouse kappa-immunoglobulin gene may be prepared by both 2 M NaCl and LIS extractions of maize nuclei. A DNA region with a high affinity for the nuclear matrix was identified at the 5' end of the maize Adh1-S gene, distal to the promoter region. The presence of sites of reported altered chromatin structure in this particular region is discussed. While the proximity and the cohabitation of MARs with different regulatory elements is a common feature of matrix association regions in animal systems, this is the first plant MAR identified in a region of known significance for gene regulation.

Binding of sequences from the 5'- and 3'-nontranscribed spacers of the rat rDNA locus to the nucleolar matrix

Nucleolar matrix structures were obtained under different extraction conditions from highly purified isolated nucleoli. Their ultrastructural appearance, protein composition and capacity to bind rDNA preferentially were studied in a model binding system. A region spanning approximately 25 kb in the rat ribosomal gene locus was screened for DNA sites capable of specifically interacting with the proteins of the nucleolar matrix (MARs). Two such sites were identified: one is located on an EcoRV-KpnI fragment in the 5'-nontranscribed spacer region, between two repetitive elements and close to the transcription initiation site; the other MAR is on a PvuII-BamHI fragment located in the 3'-nontranscribed region, encompassing an element 85% homologous to a B2-sequence. The two MARs are located in regions rich in polypyrimidine/polypurine tracks and contain a few elements homologous to the consensus sequence for topoisomerase II. This indicates that the "attachment sites" for the ribosomal genes belong to the same class of sequences as the MARs attaching the chromosomal DNA to the nuclear matrix.

Interaction of MAR-sequences with nuclear matrix proteins

The recent discovery of DNA sequences responsible for the specific attachment of chromosomal DNA to the nuclear skeleton (MARs/SARs) was an important step towards our understanding of the functional and structural organization of eukaryotic chromatin [Mirkovitch et al.: Cell 44:273-282, 1984; Cockerill and Garrard: Cell 44:273-282, 1986]. A most important question, however, remains the nature of the matrix proteins involved in the specific binding of the MARs. It has been shown that topoisomerase II and histone H1 were capable of a specific interaction with SARs by the formation of precipitable complexes [Adachi et al.: EMBO J8:3997-4006, 1989; Izaurralde et al.: J Mol Biol 210:573-585, 1989]. Here, applying a different approach, we were able to "visualize" some of the skeletal proteins recognizing and specifically binding MAR-sequences. It is shown that the major matrix proteins are practically the same in both salt- and LIS-extracted matrices. However, the relative MAR-binding activity of the individual protein components may be different, depending on the method of matrix preparation. The immunological approach applied here allowed us to identify some of the individual MAR-binding matrix proteins. Histone H1 and nuclear actin are shown to be not only important components of the matrix, but to be involved in a highly efficient interaction with MAR-sequences as well. Evidence is presented that proteins recognized by the anti-HMG antibodies also participate in MAR-interactions.

Structure-function relationships in eukaryotic nuclei

It may be that eukaryotic nuclei contain a collection of operationally independent units (genes), each controlled through its interactions with soluble protein factors which diffuse at random throughout the nucleoplasmic space. Alternatively, nuclei might be organized in such a sophisticated fashion that specific genes occupy distinct sites and that spatially ordered RNA synthesis, processing and transport delivers mature RNAs to predestined sites in the cytoplasm. Different fields of research support each of these extreme views. Molecular biologists inspecting the precise details of specific interactions, usually in vitro, inevitably favour the former, while cell biologists working with far more complicated systems generally assume that more elaborate arrangements exist. In considering the importance of nuclear architecture, I have attempted to relate a collection of experiments each of which intimates some close relationship between structural aspects of chromatin organization and the precise mechanisms underlying nuclear function. I will argue that higher-order structures are crucial for achieving the observed efficiency and coordination of many nuclear processes.

Coordinate replication of dispersed repetitive sequences in Physarum polycephalum

The synchronous macroplasmodial growth phase of the slime mould Physarum polycephalum was used to study the in vivo replication of large chromosomal DNA segments. Newly replicated DNA was isolated at various points in S-phase by its preferential association with the nuclear matrix. This DNA was then used to probe cosmid clones of the Physarum genome. The results indicate that certain dispersed repetitive sequences in the genome are coordinately replicated. The observed pattern of replication may be due either to the presence of a replication origin within each repetitive sequence or to the systematic arrangement of these sequences around a replication origin. The latter appears more likely since the repetitive sequences are probably not randomly scattered within the genome.

Alterations in nuclear anatomy by chemical modification of proteins in isolated rat liver nuclei

Whole rat liver nuclei were treated with citraconic anhydride, a reagent specific for primary amines. Dramatic changes were observed in nuclear morphology and light scattering properties. An analysis for DNA and RNA content suggested that DNA was released from the nuclei with a short half-time, approximately 2-4s demonstrating a biphasic release profile. RNA was similarly released but with a monophasic profile. Analysis of SDS-PAGE gels of modified nuclei demonstrated a progressive enrichment of nuclear matrix (lamins) polypeptides with extent of modification. H1 histone was quantitatively lost as a function of modification reagent concentration, while approx. 50% of the nucleosomal histones cosedimented with DNA- and RNA-free nuclei. Modification in the presence of 2 mM EGTA released all the DNA and RNA [less than or equal to 1% remaining) while retaining structures characteristic of nuclear matrix, nucleoli, and ribonucleoprotein (predominantly hnRNA group A and B). These nucleic acid-deficient structures have been termed nuclear fossils to differentiate them from high salt detergent-prepared empty nuclear sacks, nuclear remnants, or nuclear scaffolds. Modification in the presence of 2% Triton X-100 results in structures similar to the nuclear fossils (EGTA treatment), but missing the double bilayer and a 51K polypeptide that is a major component of the other structures. The use of chemical modification on the nucleus provides an experimental approach for examining the role of ionic interactions in controlling nuclear structure. Citraconylation may thus serve two functions: (a) as a protein-specific perturbant of nuclei capable of simply and rapidly preparing a range of structural variants for the analysis of nuclear interactions; (b) offer a paradigm for control of nucleic acid-polypeptide interactions based on post-translational alterations in protein charge.

Monoclonal antibodies specific for tight-binding human chromatin antigens reveal structural rearrangements within the nucleus during the cell cycle

The class of nonhistone chromosomal proteins that remains bound to DNA in chromatin in the presence of 2.5 M NaCl-5 M urea has proven refractile to biochemical analysis. In order to study its role in chromatin organization, we have produced monoclonal antibodies that are specific for the HeLa DNA-protein complex that remains after extraction of chromatin with high salt and urea. The antibody-producing clones were identified with an ELISA assay. Of the six clones selected, five were stabilized by limiting dilution. All clones are IgG producers. None cross-react significantly with native DNA, core histones, or the high-mobility group nonhistone proteins. All antibodies are specific for nuclear or juxtanuclear antigens. Indirect immunofluorescence shows that three antibodies, which are nonidentical, stain three different nuclear networks. Available evidence indicates that two of these networks are the nuclear matrix. A fourth antibody reveals structures reminiscent of chromocenters. A fifth antibody, AhNA-1, binds to interphase HeLa chromatin and specifically decorates metaphase chromosomes. AhNA-1 similarly recognizes rat chromosomes. Each of these monoclonal antibodies also reveals a changing pattern of nuclear staining as cells progress through the cell cycle. Presumably, this reflects the rearrangement of the cognate antigens.

Chromatin-associated RNA: differential extraction and characterization

Mammalian cells in different states of cytodifferentiation exhibited different RNA-synthesizing and processing patterns that could be used as markers for phenotypic variability. Inherent in these patterns was an RNA class which was differentially extracted from the cellular homogenate by elevating the temperature and pH of the buffer used in the phenol procedure. This class of RNA was initially designated fraction B (chromatin-associated RNA). In the characterization of fraction B, human myeloma cells labeled for 3 and 24 h were fractionated into subcytoplasmic and subnuclear components and the [3H]-RNA was differentially extracted. After 3 and 24 h labeling 84% and 73%, respectively, of the labeled RNA in the chromatin was extracted in fraction B. Only 10-20% of the polysomal RNA was extracted in fraction B with little enrichment in poly(A) RNA. These and other observations suggested that fraction B was a subpopulation of heterogeneous nuclear RNA which was tightly bound to the chromatin complex.

Isolation and characterization of the nuclear matrix in Friend erythroleukemia cells: chromatin and hnRNA interactions with the nuclear matrix

Nuclear matrices from undifferentiated and differentiated Friend erythroleukemia cells have been obtained by a method which removes DNA in a physiological buffer. These matrices preserved the characteristic topographical distribution of condensed and diffuse "chromatin" regions, as do nuclei in situ or isolated nuclei. Histone H1 was released from the nuclear matrix of undifferentiated cells by 0.3 M KCl; inner core histones were released by 1 M KCl. Nuclear matrix from differentiated cells did not maintain H1, and histone cores were fully released in 0.7 M KCl. KCl removed the core histones as an octameric structure with no evidence of preferential release of any single histone. Electron microscopy of KCl-treated matrix revealed no condensed regions but rather a network of fibrils in the whole DNA-depleted nuclei. When nuclear matrices from both types of cell were exposed to conditions of very low ionic strength, inner core histones and condensed regions remained. These observations support the contention that inner core histones are bound to matrix through natural ionic bonds or saline-labile elements, and that these interactions are implicated in chromatin condensation. hnRNA remained undegraded and tenaciously associated to the matrix fibrils, and was released only by chemical means which, by breaking hydrophobic and hydrogen bonds, produced matrix lysis. Very few nonhistone proteins were released upon complete digestion of DNA from either type of nuclei. The remaining nonhistone proteins represent a large number of species of which the majority may be matrix components. The molecular architecture in both condensed and diffuse regions of interphase nuclei appears to be constructed of two distinct kinds of fibers; the thicker chromatin fibers are interwoven with the thinner matrix fibers. The latter are formed by a heteropolymer of many different proteins.

A model of the breakdown and removal of the chromatin components during Feulgen acid hydrolysis

A stochastic model of Feulgen hydrolysis is proposed. The model, constructed so as to embody the main features of chromatin structure, is simple enough to allow the calculation of extraction rates. Extraction rate curves generated by the model are compared with experimental curves obtained under various conditions (different fixatives and hydrolysis solutions). A good correspondence is found between the experiments and the predictions of the model.

Accessibility of DNA in chromatin to DNA polymerase and RNA polymerase

The accessibility of DNA in chromatin to both exogenous DNA polymerase and RNA polymerase is slight when compared to isolated DNA. DNA in extracted chromatin is somewhat more accessible to these enzymes than is DNA in the chromatin of isolated nuclei; and the DNA template of chromatin is more accessible to DNA polymerase than to RNA polymerase. In these experiments we have given much attention to the technique of scintillation counting, since artifacts arising in this procedure can lead to erroneous conclusions.

Blocking by histones of accessibility to DNA in chromatin

The effect of histones on accessibility of DNA to DNase in chromatin of thymus nuclei has been studied by selective extraction of either lysine-rich or arginine-rich histones. It was found that all histones block accessibility but that, weight for weight, lysine-rich histones block much more effectively than do arginine-rich histones. We point to the contrast between accessibility of DNA to DNase and of DNA to RNA polymerase, and to what may be the similarity between accessibility to DNase and DNA polymerase.