Molecular organisation of the plant genome: Its relation to structure,recombination and evolution of chromosomes

Large scale changes in nuclear DNA amount accompany the evolution of species of higher plants. Much of the nuclear DNA accrued during the evolution of species does not encode genetic information and is selectively neutral. Nonetheless, the pattern of distribution of the excess DNA within and between chromosome complements suggests that there are rigid constraints underlying evolutionary changes in genome organisation. A five-fold increase in the amount of nuclear DNA has occurred in the evolution ofLathyrus species. Not withstanding this massive DNA variation, species show consistently similar patterns in base sequence proliferation, divergence and DNA distribution within and between chromosome complements. Within chromosome complements, the excess DNA is distributed evenly in all chromosomes irrespective of the large differences in chromosome size and, between complements, DNA distribution is discontinuous; species cluster into DNA groups with remarkably regular intervals. Similar constraints govern the frequency and distribution of chiasmata in the chromosome complements. Between species chiasma frequency and nuclear DNA amounts are not correlated but within complements it is positively correlated with the amount of DNA contained in each chromosome.     

STRUCTURAL ALTERATION IN ISOLATED RAT LIVER NUCLEI AFTER REMOVAL OF TEMPLATE RESTRICTION BY POLYANIONS

Specific polyanions release DNA template restrictions for DNA synthesis in isolated rat liver nuclei. The degree to which DNA synthesis is enhanced can be correlated with a spectrum of changes in nuclear structure Each polyanion which is effective in the release of template restriction produces a characteristic alteration in nuclear ultrastructure. Polyanions which have no effect on DNA synthesis do not appear to cause any change in nuclear organization or ultrastructure. Parallel measurements of nuclear DNA release and nuclear volume changes also indicate that template-activating polyanions cause remarkable changes in the structural organization of the treated nuclei. These results indicate that DNA template activation involves direct interactions between polyanions and nuclear constituents and suggest the possibility that naturally occurring polyanions might have a role in the control of gene activity     

Nuclear translocation of Acinetobacter baumannii transposase induces DNA methylation of CpG regions in the promoters of E-cadherin gene

Nuclear targeting of bacterial proteins has emerged as a pathogenic mechanism whereby bacterial proteins induce host cell pathology. In this study, we examined nuclear targeting of Acinetobacter baumannii transposase (Tnp) and subsequent epigenetic changes in host cells. Tnp of A. baumannii ATCC 17978 possesses nuclear localization signals (NLSs), (225)RKRKRK(230). Transient expression of A. baumannii Tnp fused with green fluorescent protein (GFP) resulted in the nuclear localization of these proteins in COS-7 cells, whereas the truncated Tnp without NLSs fused with GFP were exclusively localized in the cytoplasm. A. baumannii Tnp was found in outer membrane vesicles, which delivered this protein to the nucleus of host cells. Nuclear expression of A. baumannii Tnp fused with GFP in A549 cells induced DNA methylation of CpG regions in the promoters of E-cadherin (CDH1) gene, whereas the cytoplasmic localization of the truncated Tnp without NLSs fused with GFP did not induce DNA methylation. DNA methylation in the promoters of E-cadherin gene induced by nuclear targeting of A. baumannii Tnp resulted in down-regulation of gene expression. In conclusion, our data show that nuclear traffic of A. baumannii Tnp induces DNA methylation of CpG regions in the promoters of E-cadherin gene, which subsequently down-regulates gene expression. This study provides a new insight into the epigenetic control of host genes by bacterial proteins.     

Chromosomal DNA variation in Cucumis

Summary Variation in nuclear DNA amounts found in different species of Cucumis was surveyed. The DNA amounts varied from 1.373 to 2.483 pg in diploids and from 2.846 to 3.886 pg in tetraploids. DNA amount was not correlated with chromosome number and periodicity. Tetraploids were found to have double the quantity of nuclear DNA of diploids. A positive linear relationship was established between the nuclear DNA amounts and volume of chromosomes. The botanical varieties within a particular species do not differ significantly for 2C DNA amounts. A comparison of the distribution of DNA amounts among different chromosomes of haploid complement in different species revealed that the quantitative DNA changes associated with speciation affected all chromosomes. DNA changes were not however, of the same magnitude in all chromosomes of the complement. Speciation in Cucumis thus seems to have occurred through amplification or diminution of DNA proportionate to the size of chromosomes. The relationship between the basic numbers, x=7 and x=12, will have to be considered relative to the high DNA amount noticed in some species with x=12.     

Nuclear proteins and DNA in the myocardial myocytes in compensatory cardiac hypertrophy]

Using cytophotometry, the amount of DNA, total nuclear proteins and of histones were studied in the myocardial cells during days 21--36 of experimental compensatory hypertrophy of the heart (in rats). The enlargement of myocardial nuclei during the cardial hyperfunction was accompanied by accumulation of total nuclear protein, in particular, the histone fraction, without distinct changes in DNA. Analysis of correlations between nuclear proteins and DNA in the myocardial cells allows to reveal a delayed accumulation of histones in the big and gigantic nuclei, with a superfluous increase in non-histone nuclear proteins. In middle-sized nuclei, non-histone proteins have little changes against intensive accumulation of histones.     

Three-dimensional DNA image cytometry by confocal scanning laser microscopy in thick tissue blocks.

A method for the quantification of nuclear DNA in thick tissue blocks by confocal scanning laser microscopy is presented. Tissues were stained en bloc for DNA by chromomycin A3. Three-dimensional images, 60 microns deep, were obtained by stacking up confocal fluorescent images obtained with an MRC-500 (Bio-Rad, Richmond, CA). The effects due to bleaching and attenuation by depth of fluorescence emission were corrected mathematically. The DNA contents were estimated by summing up the detected emission intensities (discretized into pixel gray levels) from each segmented nucleus. Applications to an adult rat liver and to a human in situ carcinoma of theesophagus are shown to demonstrate, respectively, the precision of the method and its potential usefulness in histopathology. Comparisons are made with DNA histograms obtained on the same materials by image cytometry on smears and by flow cytometry. Ploidy peaks obtained with the confocal method, although wider than with other methods, are well separated. Confocal image cytometry offers the invaluable advantage of preserving the tissue architecture and therefore allowing, for instance, the selection of histological regions and the evaluation of the degree of heterogeneity of a tumor.     

The role of periodic changes in cyclase and protein kinase activity in the mechanism of the proliferative effect of ACTH

A prolonged effect of ACTH on the state of adenylate and guanylate cyclase systems in the adrenal glands of experimental animals was investigated. It was found that in guinea pigs injected with ACTH (4 units daily for 1-50 days) the weight of adrenal glands and the DNA content in these organs increased 2.0-2.5-fold by the end of experiment; the increase in both values was stepwise. The corticosteroid level in the blood varied throughout the experiment: the changes in the DNA content in adrenals and in the corticosteroid content in the blood were oppositely directed. This was accompanied by cyclic changes in the basal and stimulated activities of adenylate and guanylate cyclases and proteinases in the adrenal glands occurring with a periodicity of 6-15 days. The activity peaks for cyclases and protein kinases preceded the rise in the DNA content in the adrenals. A clearcut correlation between the changes in the enzyme activity and the hormone dose was observed. The changes in the basal and stimulated activities of guanylate cyclase seem to be due to the control of cAMP level in the cell (stimulation of cGMP-dependent cAMP phosphodiesterase). Apparently, the periodic changes in the activity of cAMP-dependent protein kinases in the cytoplasmic and nuclear fractions and a relatively high activation of nuclear protein kinases (by 30-60%) in comparison of cytoplasmic ones (8-10%) are related to stimulation of DNA synthesis. It is concluded that the changes in the activity of cyclases and protein kinases play a role in the mechanism of proliferative effect of ACTH.     

Beyond Repair Foci: Subnuclear Domains and the Cellular Response to DNA Damage

In the mid to late 1990's several groups identified DNA damage-dependent focal accumulations in nuclei of both DNA repair factors and the phosphorylated form of the histone variant H2A.X. The term "repair foci" has since been used to describe these protein accumulations. As a molecular marker for DNA damage, they have been immensely useful in the study of signal transduction pathways triggered by DNA damage while aiding in the identification of new factors involved in DNA repair. In spite of their importance, many other changes in the nuclear landscape correlate with DNA damage and repair processes. These include dramatic changes in chromatin ultrastructure and epigenetic modifications, which occur at the site of DNA breaks as well as globally throughout the nucleus. Besides chromatin, DNA damage also affects the dynamic behaviour, morphology and biochemical composition of various subnuclear domains, including the nucleolus, promyelocytic leukemia (PML) nuclear bodies and Cajal bodies. These changes in the nuclear landscape, the topic of this review, appear to be intimately linked to the cellular response to DNA damage and may prove as useful as repair foci in elucidating mechanisms of DNA repair.     

Molecular and cytological characteristics of nuclear DNA and chromatin for angiosperm systematics: DNA diversification in the evolution of four orchids

The species- and genus-specific DNA content, average base composition of nuclear DNA, presence or absence of satellite DNA, the percentage of heterochromatin and other characteristics of nuclear DNA and nuclear structure allow to deduce the molecular changes which accompanied, or more probably caused, cladogenesis in the orchids studied. It is suggested that saltatory replication (generative amplification) of certain DNA sequenes, diversification of reiterated DNA sequences, and loss of DNA play an important role in the evolution of orchids.—The relationship between changes of genome composition and of nuclear structure and ultrastructure is discussed on the basis of cot curves, heterochromatin staining with Giemsa (C banding), electron microscopy of nuclei, and molecular hybridization in situ.Some aspects of this paper have been presented at the Helsinki Chromosome Conference, August 1977 (Nagl & Capesius 1977).     

Review: the dynamics of the nuclear lamins during the cell cycle-- relationship between structure and function

The nuclear lamins are members of the intermediate filament (IF) family of proteins. The lamins have an essential role in maintaining nuclear integrity, as do the other IF family members in the cytoplasm. Also like cytoplasmic IFs, the organization of lamins is dynamic. The lamins are found not only at the nuclear periphery but also in the interior of the nucleus, as distinct nucleoplasmic foci and possibly as a network throughout the nucleus. Nuclear processes such as DNA replication may be organized around these structures. In this review, we discuss changes in the structure and organization of the nuclear lamins during the cell cycle and during cell differentiation. These changes are correlated with changes in nuclear structure and function. For example, the interactions of lamins with chromatin and nuclear envelope components occur very early during nuclear assembly following mitosis. During S-phase, the lamins colocalize with markers of DNA replication, and proper lamin organization must be maintained for replication to proceed. When cells differentiate, the expression pattern of lamin isotypes changes. In addition, changes in lamin organization and expression patterns accompany the nuclear alterations observed in transformed cells. These lamin structures may modulate nuclear function in each of these processes.     

A study of DNA depolyploidization and depolytenization of the heterochromatized gonosomal chromatin bodies in the secondary giant trophoblast cells of the field vole Microtus rossiaemeridionalis using cytophotometry

A study was made of the distribution of the heterochromatized gonosomal chromatin bodies (GCB) material in the course of nuclear fragmentation of secondary giant trophoblast cells resulting in polykaryocyte formation at the late stage of their differentiation. A simultaneous DNA cytophotometry in GCBs and nuclear fragments showed a progressive GCB DNA content decrease proportional to that of DNA content in nuclear fragments. DNA contents in the nuclear fragments corresponded to 2c, 4c and 8c. In most cases 1-2 GCBs were found in the nuclear fragments of different ploidy levels. Both the total DNA content in GCBs and the DNA content in separate GCBs well correlated with the ploidy levels of fragments. The data obtained demonstrate a regular, whole-genome distribution of chromosomal materials into the nuclear fragments exemplified by sex chromosome distribution in compliance with the ploidy of nuclear fragments. We discuss a possible mechanism of nuclear fragmentation that may ensure substantially a balanced genome of nuclear fragments without leading to mitotic cycle renewal in the giant trophoblast cell population.     

Chromosome diminution in Ascaris suum. Two-fold increase of nucleosomal histone to DNA ratios during development

The swine intestinal nematode, Ascaris suum, eliminates chromatin material from its primordial somatic cells during early embryogenesis. A technique for isolation of nuclei from pre- and post-diminution stage embryos has been developed and these isolated nuclei were used in investigations of nuclear events during diminution. The amount of DNA per nucleus determined by diphenylamine assays and isotope dilutions was 0.66 pg and 0.29 pg in pre- and post-diminution nuclei, respectively. Thus, A. suum loses 56% of its nuclear DNA during diminution. The loss of nuclear DNA enabled in vivo examination of histone to DNA ratios as a function of changes in DNA quantities. Ascaris histones were identified by acid extractability and tryptic fingerprint comparison with rat liver histones. Measurement of histone quantities was accomplished using linearity of Coomassie blue binding to histones separated in dodecyl sulfate gels. Ascaris nucleosomal histones levels were relatively constant in pre- and post-diminution nuclei. However, nucleosomal histone to DNA ratios approximately doubled during diminution.     

Freeze-thawing induces alterations in the protamine-1/DNA overall structure in boar sperm

The main aim of this work was to test the effects that freeze-thawing could have on the overall nuclear structure of boar sperm. This was done by analyzing both the DNA fragmentation and the protamine-1–DNA interaction of the boar-sperm nucleus. Our results indicate that freezing–thawing did not induce a significant degree of DNA fragmentation, as manifested through both the Sperm–Sus–Halomax^® stain and a random primed analysis prior to partial DNA digestion with enzymes BamHI–HinDIII. On the other hand, freeze-thawing induced significant changes in the protamine-1–DNA interaction, as revealed through both Western blot analysis and immunocytochemistry for protamine-1. These alterations caused, in turn, significant changes in the overall nuclear structure of boar sperm after thawing. Protamine-1–DNA alterations started to be apparent during the cooling phase of the freeze-thawing protocol. These results imply that one of the alterations that may be responsible for the loss of fertilizing ability of boar sperm after freeze-thawing may be an alteration in the correct formation of the overall nuclear structure, which, in turn, would induce alterations in the correct formation of the first nuclear structure after oocyte penetration.     

Changes in tissue protein pattern in relation to auxin induction of DNA synthesis

Abstract. When artichoke tuber tissue was cultured in mineral salts, the induction of DNA synthesis and subsequent cell division was dependent upon the presence of auxin in the incubation medium. Evidence is provided that an obligatory set of metabolic events precedes auxin-induced DNA synthesis, and previous work has associated these with protein synthesis. As a consequence the auxin-induced changes in nuclear and cytoplasmic proteins have been investigated. Using 2D gel electrophoresis, qualitative alterations in nuclear non-histone proteins have been detected from the earliest treatment times with auxin. These changes were progressive, starting with four novel proteins after 3 h auxin treatment and ending with about forty when DNA synthesis commences some 18–21 h later. Qualitative alterations in phosphorylated nuclear proteins due to auxin treatment were only detectable when DNA synthesis commenced. In contrast, few qualitative alterations in cytoplasmic proteins were detectable, with the major change being in phosphorylated proteins at the onset of DNA synthesis.
A possible model of auxin action is outlined which involves sequential and progressive changes in the synthesis of nuclear proteins and the control of gene expression eventually leading to DNA synthesis.     

Modulation of calcium by the carcinogenic process in the liver induced by a choline-deficient diet

A diet devoid of choline and low in methionine (CD), without any added carcinogen, has been shown to induce 100% preneoplastic nodules and more than 50% cancer in the rat liver. Attempts to understand the mechanism by which a CD diet induces liver cell cancer revealed that like chemical carcinogens, a CD diet also appears to cause alterations in DNA, perhaps mediated by free radicals. Indeed, a CD diet induces nuclear lipid peroxidation prior to the changes in DNA. The CD diet induced DNA alterations coupled with continuing liver cell proliferation may account for the induction of initiated hepatocytes by the CD diet. To gain insight into the nature of free radicals generated by the CD diet, experiments were designed to determine whether agents that modulate free radical effects influence the CD diet induced changes in the liver. We investigated the effect of Ca2+ in the modulation of CD diet induced alterations in the liver. The results show that extra Ca2+ when added to the CD diet prevented some of the early changes due to choline deficiency, such as nuclear lipid peroxidation and DNA damage, but had little or no effect on the triglyceride accumulation in the liver. Also, the same CD diet with extra Ca2+, when used as a promoter after initiation by diethylnitrosamine, decreased the number and size of early putative preneoplastic foci and nodules.     

Review: The Dynamics of the Nuclear Lamins during the Cell Cycle— Relationship between Structure and Function

The nuclear lamins are members of the intermediate filament (IF) family of proteins. The lamins have an essential role in maintaining nuclear integrity, as do the other IF family members in the cytoplasm. Also like cytoplasmic IFs, the organization of lamins is dynamic. The lamins are found not only at the nuclear periphery but also in the interior of the nucleus, as distinct nucleoplasmic foci and possibly as a network throughout the nucleus. Nuclear processes such as DNA replication may be organized around these structures. In this review, we discuss changes in the structure and organization of the nuclear lamins during the cell cycle and during cell differentiation. These changes are correlated with changes in nuclear structure and function. For example, the interactions of lamins with chromatin and nuclear envelope components occur very early during nuclear assembly following mitosis. During S-phase, the lamins colocalize with markers of DNA replication, and proper lamin organization must be maintained for replication to proceed. When cells differentiate, the expression pattern of lamin isotypes changes. In addition, changes in lamin organization and expression patterns accompany the nuclear alterations observed in transformed cells. These lamin structures may modulate nuclear function in each of these processes.     

DNA binding is required for the apoptogenic action of apoptosis inducing factor

The execution of apoptosis or programmed cell death comprises both caspase-dependent and caspase-independent processes. Apoptosis inducing factor (AIF) was identified as a major player in caspase-independent cell death. It induces chromatin condensation and initial DNA cleavage via an unknown molecular mechanism. Here we report the crystal structure of human AIF at 1.8 A resolution. The structure reveals the presence of a strong positive electrostatic potential at the AIF surface, although the calculated isoelectric point for the entire protein is neutral. We show that recombinant AIF interacts with DNA in a sequence-independent manner. In addition, in cells treated with an apoptotic stimulus, endogenous AIF becomes co-localized with DNA at an early stage of nuclear morphological changes. Structure-based mutagenesis shows that DNA-binding defective mutants of AIF fail to induce cell death while retaining nuclear translocation. The potential DNA-binding site identified from mutagenesis also coincides with computational docking of a DNA duplex. These observations suggest that AIF-induced nuclear apoptosis requires a direct interaction with DNA.     

The peculiarities of repair DNA-polymerases in the loach embryogenesis

The current concept of eukaryotic DNA polymerases is considered, which are involved in nuclear DNA repair. The data are given on a new group of DNA polymerases that maintain the integrity of DNA structures without preliminary excision of damaged regions. A special attention is paid to specific features of the functioning of repair DNA polymerases in embryogenesis of the loach. A possible existence is discussed of the previously unknown pathway of DNA repair with participation of DNA polymerase delta as independent from the nuclear antigen of proliferating cells.     

LncRNAs: the missing link to senescence nuclear architecture

During cellular senescence and organismal aging, cells display various molecular and morphological changes. Although many aging-related long noncoding RNAs (lncRNAs) are highly associated with senescence-associated secretory phenotype, the roles of lncRNAs in senescence-associated nuclear architecture and morphological changes are just starting to emerge. Here I review lncRNAs associated with nuclear structure establishment and maintenance, their aging-related changes, and then focus on the pervasive, yet underappreciated, role of RNA double-strand DNA triplexes for lncRNAs to recognize targeted genomic regions, making lncRNAs the nexus between DNA and proteins to regulate nuclear structural changes. Finally, I discuss the future of deciphering direct links of lncRNA changes to various nuclear morphology changes assisted by artificial intelligence and genetic perturbations.