Organization Of Nuclear DNA Research Articles

Abstract 2035: Alterations in nuclear DNA organization in sporadic pediatric Papillary Thyroid Carcinoma (PTC)

Abstract Pediatric papillary thyroid carcinoma (PTC) present a more aggressive disease than adults, with higher risk of malignancy, higher rates of metastasis, multifocality and larger tumor sizes. We described AGK-BRAF fusion in 19% of sporadic pediatric PTC, which is associated with lung metastasis and younger age (mean 10.67 y.o.). Super-resolved three-dimensional structured illumination microscopy (3D-SIM) allows the visualization of the DNA structure inside the interphase nucleus at microscopic length scales. 3D-SIM has shown that cancer cell nuclei exhibit chromatin remodeling, with increased amount of DNA-poor spaces, which indicates a disrupted pattern in the DNA and has been associated with aggressive behavior in other tumor subtypes. In order to understand the underlying causes of the aggressiveness of pediatric PTC, we here aimed to analyze, for the first time, the DNA organization from 13 pediatric PTC patients (≤18 y.o.), using super-resolved 3D-SIM technology. A granulometry-based measurement method quantified the size distribution of DNA structure (DNA packaging) and DNA-poor spaces. We compared the granulometry for: tumor vs normal tissues; AGK-BRAF fusion (positive vs negative tumors); distant metastasis (presence vs absence); multifocal vs unifocal tumors; age at diagnosis (≤ 10 y.o. vs > 10 y.o.); tumor size ( ≤ 2 cm vs > 2 cm) and extra-thyroidal (ET) extension (presence vs absence). Nuclei from tumor cells exhibited larger DNA structures (p=0.0001) and more DNA-poor spaces (p<0.0001) than normal cells. In relation to the clinicopathological features, patients that presented distant metastasis (p=0.001), multifocal tumors (p=0.002) and > 2 cm tumors (p=0.0029), exhibited more DNA-poor spaces in their nuclei. Regarding the analyses of the AGK-BRAF fusion, borderline results were observed for both DNA structure (p=0.058) and DNA-poor spaces (p=0.053). Similar results were observed in PTC cases with age ≤10 y.o. for DNA structure (p=0.068) and DNA-poor spaces (p=0.06). No significant difference was observed for ET extension. Our preliminary data corroborate with previous studies, where tumor cell nuclei present more DNA-poor spaces than normal cells; and suggest a progressive disruption and remodeling of the chromatin in malignant cells. Interestingly, tumor cells from patients with features of poor prognosis (distant metastasis, multifocality and tumor size) can exhibit a more disrupted DNA organization, which can be related to a more aggressive behavior of the tumor. Moreover, can also observe a trend to a more disrupted chromatin organization in AGK-BRAF tumors and tumors from <10 y.o. patients, which can be associated with the aggressiveness of the disease in these cases. Further analysis are needed to better understand wether AGK-BRAF fusion is associated with poor prognosis in pediatric PTC and if it could be related to a high genomic instability caused by this fusion. Citation Format: Luiza Sisdelli, Maria I. Cordioli, Fernanda Vaisman, Osmar Monte, Carlos Longui, Adriano N. Cury, Aline Rangel-Pozzo, Sabine Mai, Janete M. Cerutti. Alterations in nuclear DNA organization in sporadic pediatric Papillary Thyroid Carcinoma (PTC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2035.

MYCN overexpression is linked to significant differences in nuclear DNA organization in neuroblastoma

MYCN overexpression is linked to significant differences in nuclear DNA organization in neuroblastoma

Quantitative superresolution microscopy reveals differences in nuclear DNA organization of multiple myeloma and monoclonal gammopathy of undetermined significance.

ABSTRACTThe mammalian nucleus has a distinct substructure that cannot be visualized directly by conventional microscopy. In this study, the organization of the DNA within the nucleus of multiple myeloma (MM) cells, their precursor cells (monoclonal gammopathy of undetermined significance; MGUS) and control lymphocytes of the representative patients is visualized and quantified by superresolution microscopy. Three‐dimensional structured illumination microscopy (3D‐SIM) increases the spatial resolution beyond the limits of conventional widefield fluorescence microscopy. 3D‐SIM reveals new insights into the nuclear architecture of cancer as we show for the first time that it resolves organizational differences in intranuclear DNA organization of myeloma cells in MGUS and in MM patients. In addition, we report a significant increase in nuclear submicron DNA structure and structure of the DNA‐free space in myeloma nuclei compared to normal lymphocyte nuclei. Our study provides previously unknown details of the nanoscopic DNA architecture of interphase nuclei of the normal lymphocytes, MGUS and MM cells. This study opens new avenues to understanding the disease progression from MGUS to MM. J. Cell. Biochem. 116: 704–710, 2015. © 2014 The Authors. Journal of Cellular Biochemistry published by Wiley Periodicals, Inc.

Differences in Nuclear DNA Organization Between Lymphocytes, Hodgkin and Reed–Sternberg Cells Revealed by Structured Illumination Microscopy

Advances in light microscopy have enabled the visualization of DNA in the interphase nucleus with more detail than is visible with conventional light microscopy. The nuclear architecture is assumed to be different in cancer cells compared to normal cells. In this paper we have studied, for the first time, the organization of nuclear DNA and that of DNA-free space in control lymphocytes, Hodgkin cells and Reed–Sternberg cells using 3D structured illumination microscopy (SIM). We have observed detail in these SIM images that was not observed in conventional widefield images. We have measured the size distribution of the DNA structure using granulometry and noted a significant, progressive increase in the amount of sub-micron structures from control lymphocytes to Hodgkin cells to Reed–Sternberg cells. The DNA-free space changes as well; “holes” in the DNA distribution start to appear in the malignant cells. We have studied whether these “holes” are nucleoli by staining for upstream binding factor (UBF), a protein associated with the nucleolus. We have found that the relative UBF content progressively and significantly decreases—or is absent—in the DNA-free space when measured as either the Pearson correlation coefficient with the DNA-free space or as the number of “holes” that contain UBF. Similar differences exist within the population of Reed–Sternberg cells between binucleated and multinucleated cells with four or more subnuclei. To our knowledge, this is the first study that investigates the changes of the nuclear DNA structure in any disease with superresolution light microscopy. J. Cell. Biochem. 115: 1441–1448, 2014. © 2014 The Authors. Journal of Cellular Biochemistry published by Wiley Periodicals, Inc. This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.

Cell-type-specific organization of nuclear DNA into structural looped domains

In the interphase nucleus of metazoan cells the DNA is organized in supercoiled loops anchored to a proteinaceous substructure known as the nuclear matrix (NM). The DNA is anchored to the NM by means of non-coding sequences of variable length known as matrix attachment regions or MARs operationally classified in structural-constitutive, resistant to high-salt extraction and transient-functional, non-resistant to high-salt extraction. The former are also known as true loop attachment regions or LARs that determine structural DNA loops. The DNA-NM interactions define a higher order structure within the cell nucleus (NHOS). We studied in a comparative fashion the NHOS in two primary cell types from the rat: hepatocytes and naive B lymphocytes, by analyzing the topological relationships between the NM and a set of eight short gene sequences located in six separate chromosomes and as such representing a coarse-grained, large-scale sample of the actual organization of nuclear DNA into structural loop domains. Our results indicate that such an organization is cell-type specific since most of the gene sequences studied showed significant differences in their relative position to the NM according to cell type. Such cell-type specific differences in the NHOS have no obvious correlation with the tissue-specific transcriptional activity of the corresponding genes, supporting the notion that permanent, structural DNA loops are different from transient, functional DNA loops that may be associated with transcription.

Nucleic acid distribution pattern in avian erythrocytes and mammalian lymphocytes: Comparative studies by fluorescence microscopy and digital imaging analytical techniques

Nucleated erythrocytes of healthy domestic chicken and ducks, and lymphocytes of healthy Sprague Dawley rats were evaluated for nucleic acid distribution pattern, employing light and fluorescence microscopy procedures, as well as digital imaging analytical methods. The results demonstrate a unique organization of nuclear DNA of mature chicken and duck erythrocytes, as well as immature duck erythrocytes, as delineated spherical nuclear bodies that mostly corresponded with euchromatin zones of the cells in routine Wright-stain blood smears. The nuclear DNA of the rat lymphocytes, on the other hand, was observed as a more diffuse green fluorescing nuclear areas, with punctate variably-sized diffuse areas of RNA red fluorescence. RNA red color fluorescence was also evident in the narrow cytoplasm of the lymphocytes, especially in large lymphocytes, in comparison with the cytoplasm of the mature avian erythrocytes that completely lacked any nucleic acid fluorescence. Nuclear RNA fluorescence was lacking in the mature chicken erythrocytes, compared with those of the mature and immature duck erythrocytes as well as lymphocytes of both avian and rats blood. The significance of these findings lies in the establishment of normal benchmarks for the nuclear and cytoplasmic nucleic acid pattern in eukaryotic cells. These normal benchmarks become valuable in rapid diagnostic situations associated with pathologies, such as the presence of viral nuclear and cytoplasmic inclusion bodies that can alter the nucleic acid pattern of the host cells, and in conditions of cellular abnormal protein aggregations. Variability of cellular nucleic acid pattern can also aid in prognostic assessments of neoplastic conditions.

Attenuation of genotoxicity under adhesion-restrictive conditions through modulation of p53,γ H2AX and nuclear DNA organization

Interactions between tumor cells and their substratum influence cancer progression by modulating cell proliferation and survival. We now investigated whether signaling responses to UV irradiation differ on adhesion-permissive or restrictive substrates. The latter conditions diminished spreading and proliferation of neo 6.3/C8161 melanoma in which metastasis is suppressed by introduction of neo-tagged chromosome 6, but permitted proliferation of human metastatic C8161 melanoma. Apoptosis-associated PARP cleavage and DNA fragmentation induced by UV irradiation were diminished on the restrictive substrate in C8161 melanoma. Genotoxic responses to UV irradiation like persistent increases in the phosphorylation of histone H2AX, induction of the tumor suppressor p53 protein and greater binding of this protein to its DNA consensus sequence, were all decreased on the restrictive substrate. The latter also promoted a 2 fold increase of DNA condensation in chromatin and enhanced activation of the survival - and invasion-associated MMP-9 gelatinase B, preferentially in metastatic C81261 melanoma. Our data suggest that adaptation to restrictive substrates in metastatic C8161 melanoma decreases UV-induced apoptosis, partly through attenuation of DNA damage signaling responses and changes in genomic organization.

Chromatin Domains and Territories: Flexibly Rigid

The nucleus is a highly organized solid-state system, rigid and flexible at the same time, where enzymes are organized in complex processing factories. This is achieved by the organization of nuclear DNA into territories and domains, which allow compartmentalization and compaction without sacrificing accessibility. The present review discusses the implications of the organization of chromosomal domains and territories in development and carcinogenesis.

Chromatin Domains and Territories: Flexibly Rigid

The nucleus is a highly organized solid-state system, rigid and flexible at the same time, where enzymes are organized in complex processing factories. This is achieved by the organization of nuclear DNA into territories and domains, which allow compartmentalization and compaction without sacrificing accessibility. The present review discusses the implications of the organization of chromosomal domains and territories in development and carcinogenesis.

Proposals for the ISS: «Fragmentation» Experiment Influence of space flight factors on the integrity and organization of nuclear DNA

Proposals for the ISS: «Fragmentation» Experiment Influence of space flight factors on the integrity and organization of nuclear DNA

Organization of chromatin in cancer cells: role of signalling pathways

The role of mechanical and chemical signalling pathways in the organization and function of chromatin is the subject of this review. The mechanical signalling pathway consists of the tissue matrix system that links together the three-dimensional skeletal networks, the extracellular matrix, cytoskeleton, and nuclear matrix. Intermediate filament proteins are associated with nuclear DNA, suggesting that intermediate filaments may have a role in the organization of chromatin. In human hormone-dependent breast cancer cells, the interaction between cytokeratins and chromatin is regulated by estrogens. Transcription factors, histone acetyltransferases, and histone deacetylases, which are associated with the nuclear matrix, are components of the mechanical signalling pathway. Recently, we reported that nuclear matrix-bound human and chicken histone deacetylase 1 is associated with nuclear DNA in situ, suggesting that histone deacetylase has a role in the organization of nuclear DNA. Chemical signalling pathways such as the Ras/mitogen-activated protein kinase (Ras/MAPK) pathway stimulate the activity of kinases that modify transcription factors, nonhistone chromosomal proteins, and histones. The levels of phosphorylated histones are increased in mouse fibroblasts transformed with oncogenes, the products of which stimulate the Ras/MAPK pathway. Histone phosphorylation may lead to decondensation of chromatin, resulting in aberrant gene expression.Key words: histone acetylation, histone phosphorylation, nuclear matrix, cytoskeleton, histone deacetylase, cancer.

Purification and characterization of chicken erythrocyte histone deacetylase 1.

Histone acetylation is involved in nuclear processes requiring chromatin remodeling. In chicken erythrocytes, DNA replication has ceased, and active reversible histone acetylation is restricted to transcriptionally active/competent chromatin domains. In this study, we set out to identify and purify the erythroid histone deacetylase responsible for catalyzing dynamic acetylation of transcriptionally active chromatin. Histone deacetylase purified from chicken erythrocytes had a molecular mass of 66 kDa. Complementary DNA encoding the chicken histone deacetylase was cloned from erythrocytes, and analysis of the derived amino acid sequence showed the chicken histone deacetylase to be the chicken homologue of mammalian HDAC1. Purified chicken erythrocyte HDAC1 deacetylated the four core histones, with a preference for H3. We present evidence that chicken HDAC1 is a metalloenzyme, the activity of which is lost when incubated with zinc chelators. In Western blot analysis with anti-HDAC1 antibodies, we found that most erythrocyte HDAC1 is associated with the low-salt insoluble chromatin fraction and, to a lesser extent, with 150 mM NaCl-soluble oligo- and polynucleosomes. The distribution of HDAC1 in erythrocyte chromatin parallels that of dynamically acetylated class 1 histones. Further, we show that HDAC1 is associated with the erythroid nuclear matrix and that the enzyme is bound to nuclear DNA in situ. We propose that in addition to catalyzing dynamic acetylation of transcribed chromatin, the enzyme has a role in the organization of nuclear DNA.

Organization of chromatin in cancer cells: role of signalling pathways

The role of mechanical and chemical signalling pathways in the organization and function of chromatin is the subject of this review. The mechanical signalling pathway consists of the tissue matrix system that links together the three-dimensional skeletal networks, the extracellular matrix, cytoskeleton, and nuclear matrix. Intermediate filament proteins are associated with nuclear DNA, suggesting that intermediate filaments may have a role in the organization of chromatin. In human hormone-dependent breast cancer cells, the interaction between cytokeratins and chromatin is regulated by estrogens. Transcription factors, histone acetyltransferases, and histone deacetylases, which are associated with the nuclear matrix, are components of the mechanical signalling pathway. Recently, we reported that nuclear matrix-bound human and chicken histone deacetylase 1 is associated with nuclear DNA in situ, suggesting that histone deacetylase has a role in the organization of nuclear DNA. Chemical signalling pathways such as the Ras/mitogen-activated protein kinase (Ras/MAPK) pathway stimulate the activity of kinases that modify transcription factors, nonhistone chromosomal proteins, and histones. The levels of phosphorylated histones are increased in mouse fibroblasts transformed with oncogenes, the products of which stimulate the Ras/MAPK pathway. Histone phosphorylation may lead to decondensation of chromatin, resulting in aberrant gene expression.

Estrogen Regulates the Association of Intermediate Filament Proteins with Nuclear DNA in Human Breast Cancer Cells

In a previous study we showed that the levels of the intermediate filament proteins, cytokeratins 8, 18, and 19, in the nuclear matrix-intermediate filament (NM-IF) fraction from the hormone-dependent and estrogen receptor (ER)-positive human breast cancer cell line T-47D5 were regulated by estrogens. In contrast, estrogens did not regulate the cytokeratins in the NM-IF fraction of the hormone-independent and ER-positive cell line, T5-PRF. In this study, human breast cancer cells were treated with cis-diamminedichloroplatinum to cross-link protein to nuclear DNA in situ, and proteins bound to DNA were isolated. We show that cytokeratins 8, 18, and 19 of T-47D5 and T5-PRF were associated with nuclear DNA in situ. The levels of the cytokeratins 8, 18, and 19 bound to nuclear DNA or associated with the cytoskeleton of T-47D5 human breast cancer cells decreased when estrogens were depleted or the pure antiestrogen ICI 164,384 was added. In contrast, the cytokeratin levels associated with nuclear DNA or cytoskeleton were not significantly affected by estrogen withdrawal or antiestrogen administration in T5-PRF cells. These observations suggest that estrogen regulates the organization of nuclear DNA by rearrangement of the cytokeratin filament network in hormone-dependent, ER-positive human breast cancer cells and that this regulation is lost in hormone-independent, ER-positive breast cancer cells.

Regulation and regulatory parameters of histone modifications.

Histone acetylation and phosphorylation destablizes nucleosome and chromatin structure. Relaxation of the chromatin fiber facilitates transcription. Coactivator complexes with histone acetyltransferase activity are recruited by transcription factors bound to enhancers or promoters. The recruited histone acetyltransferases may acetylate histone or nonhistone chromosomal proteins, resulting in the relaxation of chromatin structure. Alternatively, repressors recruit corepressor complexes with histone deacetylase activity, leading to condensation of chromatin.This review highlights the recent advances made in our understanding of the roles of histone acetyltransferases, histone deacetylases, histone kinases, and protein phosphatases in transcriptional activation and repression. Exciting reports revealing mechanistic connections between histone modifying activities and the RNA polymerase II machinery, the coupling of histone deacetylation and DNA methylation, the possible involvement of histone deacetylases in the organization of nuclear DNA, and the role of chromatin modulators in oncogenesis are discussed. J. Cell. Biochem. Suppls. 30/31:203-213, 1998. © 1998 Wiley-Liss, Inc.

Three-dimensional organization of nuclear DNA in the higher plant nucleolonema studied by immunoelectron microscopy

Serial ultrathin sectioning of Lowicryl-embedded Vicia faba cells followed by silver impregnation added some new evidence supporting a previous suggestion that a 350 nm-thick nucleolonema filament coils up and forms a 1 μm-thick solenoid. The axial region of the solenoid was seen as low electron-opaque patches by the electron microscope. These patches usually differentiated into two regions; a moderately electron-opaque outer region (fibrillar centre) and a transparent inner region (central space). Intranucleolar localization of DNA was studied by immunoelectron microscopy using a monoclonal anti-DNA antibody. The sensitive labelling was obtained when Tween 20 (a detergent) was used as a rinse and 5 nm gold particles were used as markers. In the nucleolus gold particles were most heavily concentrated in the fibrillar centres while the central space was completely devoid of them. In the dense fibrillar component, the label gradually increased in density towards the fibrillar centres. The results presented here suggest that the fibrillar centres are laterally associated with the nucleolonema filament and reside in the axial side of the nucleolonema solenoid.

Фракционирование ДНК эукариот в пульсирующем электрическом поле. 1. Ядерная ДНК как составная часть днк-топоизомеразного комплекса

Фракционирование ДНК эукариот в пульсирующем электрическом поле. 1. Ядерная ДНК как составная часть днк-топоизомеразного комплекса

Variation in Radiation-Induced Formation of DNA Double-Strand Breaks as a Function of Chromatin Structure

The influence of chromatin structure on induction of DNA double-strand breaks (DSBs) by X radiation was studied in DNA from CHO cells. Whole cells, nuclei with condensed or relaxed chromatin, and deproteinized DNA in agarose plugs were irradiated and DSB formation was measured as a decrease in the length of DNA by nondenaturing, pulsed-field, agarose gel electrophoresis. The yield of DSBs in deproteinized DNA (2.3 x 10(-10) DSBs Da-1 Gy-1) was observed to be 70 times greater than the yield of DSBs (3.1 x 10(-12) DSBs Da-1 Gy-1) observed in DNA in the intact cell nucleus. Organization of DNA into the basic nucleosome repeat structure and condensation of the chromatin fiber into higher-order structure protected DNA from DSB induction by factors of 8.3 and 4.5, respectively. An additional twofold protection of DNA in fully condensed chromatin occurred in the intact cell nucleus. Since this protection did not appear to involve chromatin structure, we speculate that this additional protection may result from the association of soluble protein and nonprotein sulfhydryls with DNA in the intact cell nucleus. The results are consistent with the organization of nuclear DNA into both basic nucleosome repeat structure and higher-order chromatin structure providing significant protection against DSB induction.

Biophysical identification and sorting of high metastatic variants from B16 melanoma tumor.

Chromatin structure, in terms of higher order nuclear-DNA condensation (scanning cytometry) and in terms of acridine orange primary binding sites (flow cytometry), is analyzed and shown to be significantly different between high (B16-F10) and low (B16-F1) metastatic variants of B16 melanoma. Furthermore, double staining of B16-F10 and B16-F1 with ethidium bromide (chromatin) and fluorescamine (membranes) provides the identification of a homogeneous subpopulation of cells with enhanced metastatic potential based on differential fluorescamine uptake. Fluorescamine uptake and poststaining viability is shown to be dependent upon the dye/cell ratio at which staining occurs. Utilizing a sterile cell sorting technique, a subpopulation of B16-F10 with increased fluorescamine uptake representing 30% of the total "intact cell" population was isolated by means of a fluorescence activated cell sorter and replated in vitro. This subpopulation when assayed in vivo produced significantly more pulmonary metastases than its parent cell line. Scanning cytometry of the Feulgen stained sorted subpopulation reveals that the cells possess a unique nuclear morphometry characterized by a 2C-3C DNA content and a large nuclear area (disperse chromatin). Finally, when we assay simultaneously for nuclear-DNA organization and cell membrane organization a progressive uncoupling between nuclear and cell morphometry is apparent if B16-F10 (versus B16-F1).

The ovalbumin gene is associated with the nuclear matrix of chicken oviduct cells

The DNA in a eucaryotic nucleus is arranged into a series of supercoiled loops that are anchored at their bases to the nuclear matrix. Using nuclease digestion, one can progressively cleave DNA from the loops, thereby isolating residual DNA that is progressively closer to the nuclear matrix anchorage sites. We have determined that the ovalbumin gene is preferentially associated with the nuclear matrix of chicken oviduct cells, but is not preferentially associated with the nuclear matrix of chicken liver cells. As a control, the β-globin gene, which is not transcribed in oviduct cells, was found not to be preferentially associated with the oviduct nuclear matrix. The observation that the transcriptionally active ovalbumin gene is preferentially associated with the nuclear matrix may have significant implications for gene expression and the organization of nuclear DNA into supercoiled-loop domains.