Nick Translation Method Research Articles

Universal NicE-Seq: A Simple and Quick Method for Accessible Chromatin Detection in Fixed Cells.

Genome-wide accessible chromatin sequencing and identification has enabled deciphering the epigenetic information encoded in chromatin, revealing accessible promoters, enhancers, nucleosome positioning, transcription factor occupancy, and other chromosomal protein binding. The starting biological materials are often fixed using formaldehyde crosslinking. Here, we describe accessible chromatin library preparation from low numbers of formaldehyde-crosslinked cells using a modified nick translation method, where a nicking enzyme nicks one strand of DNA and DNA polymerase incorporates biotin-conjugated dATP, dCTP, and methyl-dCTP. Once the DNA is labeled, it can be isolated for NGS library preparation. We termed this method as universalNicE-seq (nicking enzyme-assisted sequencing). We also demonstrate a single tube method that enables direct NGS library preparation from low cell numbers without DNA purification. Furthermore, we demonstrated universalNicE-seq on FFPE tissue section sample.

NicE-viewSeq: An Integrative Visualization and Genomics Method to Detect Accessible Chromatin in Fixed Cells.

A novel genome-wide accessible chromatin visualization, quantitation, and sequencing method is described, which allows in situ fluorescence visualization and sequencing of the accessible chromatin in the mammalian cell. The cells are fixed by formaldehyde crosslinking, and processed using a modified nick translation method, where a nicking enzyme nicks one strand of DNA, and DNA polymerase incorporates biotin-conjugated dCTP, 5-methyl-dCTP, Fluorescein-12-dATP or Texas Red-5-dATP, dGTP, and dTTP. This allows accessible chromatin DNA to be labeled for visualization and on bead NGS library preparation. This technology allows cellular level chromatin accessibility quantification and genomic analysis of the epigenetic information in the chromatin, particularly accessible promoter, enhancers, nucleosome positioning, transcription factor occupancy, and other chromosomal protein binding.

A refined Panax ginseng karyotype based on an ultra-high copy 167-bp tandem repeat and ribosomal DNAs

BackgroundPanax ginseng Meyer (Asian ginseng) has a large nuclear genome size of > 3.5 Gbp in haploid genome equivalent of 24 chromosomes. Tandem repeats (TRs) occupy significant portions of the genome in many plants and are often found in specific genomic loci, making them a valuable molecular cytogenetic tool in discriminating chromosomes. In an effort to understand the P. ginseng genome structure, we characterized an ultrahigh copy 167-bp TR (Pg167TR) and explored its chromosomal distribution as well as its utility for chromosome identification. MethodsPolymerase chain reaction amplicons of Pg167TR were labeled, along with 5S and 45S rDNA amplicons, using a direct nick-translation method. Direct fluorescence in situ hybridization (FISH) was used to analyze the chromosomal distribution of Pg167TR. ResultsRecently, we reported a method of karyotyping the 24 chromosome pairs of P. ginseng using rDNA and DAPI (4′,6-diamidino-2-phenylindole) bands. Here, a unique distribution of Pg167TR in all 24 P. ginseng chromosomes was observed, allowing easy identification of individual homologous chromosomes. Additionally, direct labeling of 5S and 45S rDNA probes allowed the identification of two additional 5S rDNA loci not previously reported, enabling the refinement of the P. ginseng karyotype. ConclusionIdentification of individual P. ginseng chromosomes was achieved using Pg167TR-FISH. Chromosome identification is important in understanding the P. ginseng genome structure, and our method will be useful for future integration of genetic linkage maps and genome scaffold anchoring. Additionally, it is a good tool for comparative studies with related species in efforts to understand the evolution of P. ginseng.

Selective Estrogen Receptor Modulator Inhibits Osteocyte Apoptosis during Abrupt Estrogen Withdrawal: Implications for Bone Quality Maintenance

Estrogens exert positive effects on the quantity and quality of bone, including the maintenance of osteocytes through the inhibition of their apoptosis. Ideally, selective estrogen receptor modulators (SERMs) confer all of the positive bone-associated effects of estrogens without any adverse effects. In a similar way to estrogen, the raloxifene analog LY 117018 has been shown to prevent bone loss in ovariectomized (OVX) rats. In this study, we investigated whether the osteocyte-sparing effect of 17beta-estradiol can be mimicked by the SERM LY 117018 in a rat model of OVX. Twenty-four juvenile female rats were divided into four treatment groups: sham-operated (SHAM), OVX, OVX + 17beta-estradiol (OVX+E(2)), and OVX + LY 117018 (OVX+SERM). At 7 or 14 days following the start of treatment, the radius and ulna were removed. The percentage of apoptotic osteocytes, determined using an in situ nick-translation method, was increased (2.5-fold at 7 days and sixfold at 14 days) in the OVX group compared with SHAM in both the radius and ulna. Treatment of OVX animals with either 17beta-estradiol at a dose rate of 0.125 mg/kg/day or LY 117018 at a dose rate of 3 mg/kg/day prevented these increases in osteocyte apoptosis similarly. These observations demonstrate that LY 117018 exerts a powerful inhibitory effect upon osteocyte apoptosis directly after estrogen loss, in a similar way to the known effect of 17beta-estradiol replacement. These results point to the potential benefits of SERMs on both the quantity and quality of bone in E(2)-depleted rats.

The Delayed Quinacrine Mustard Fluorescence from the C-blocks of Apodemus argenteus Is Due to the Introduction of Nicks into the DNA

"Delayed QM-fluorescence" refers to the unusual kinetics of fluorescence from most of the C-heterochromatic regions of the chromosomes of the small Japanese field mouse Apodemus argenteus. When stained with quinacrine mustard (QM-stained), these C-heterochromatic regions emit weak fluorescence immediately after exposure to blue light (BL); they emit bright fluorescence within a few minutes; and the intensity of the fluorescence gradually decreases after maximum fluorescence has been recorded. To elucidate the mechanism of this phenomenon, we used acridine orange staining (AO-staining) and a modified version of the in situ nick-translation method. Focusing on the large C-heterochromatic region (C-block) of the X chromosome, we noted that AO-stained C-blocks emitted greenish fluorescence, while QM-stained and BL-exposed (QM-BL-processed) C-blocks emitted reddish fluorescence upon AO-staining after removal of QM. These findings suggested that the C-block DNA of A. argenteus might undergo a structural change, such as strand breaks, during QM-BL processing. Application of the modified in situ nick-translation method revealed the generation of an appreciable number of nicks in the C-block DNA by QM-BL processing. No such nick formation was observed in the C-blocks of three other mammalian species: Apodemus peninsulae, Microtus montebelli, and Urotrichus talpoides. Our findings support the hypothesis that nick formation due to exposure to BL might play a primary role in inducing delayed QM-fluorescence in the C-blocks of A. argenteus. On the basis of the present and earlier findings, we propose a probable mechanism for delayed QM-fluorescence in A. argenteus chromosomes.

Compression-induced damage in a muscle cell model in vitro

Soft tissue breakdown can be initiated at the muscle layer associated with bony prominences, leading to the development of pressure ulcers. Both the magnitude and duration of pressure are important factors in this breakdown process. The present study utilizes a physical model, incorporating C2C12 mouse myoblasts in a homogeneous agarose gel, to examine the damaging effects of prolonged applied pressure. Identical cylindrical cores cut from the agarose/cell suspension were subjected to two separate compressive strains, of 10 and 20 per cent. The strain was applied for time periods ranging from 0.5 to 12 hours, using a specially designed loading apparatus. After each compression period, sections taken from the central horizontal plane of the individual constructs were stained using either haematoxylin and eosin or with the fluorescent probes, Calcein AM and ethidium homodimer-1, and assessed for cell damage. It was found that constructs subjected to the higher strain values demonstrated significantly higher values of non-viable cells for equivalent time points compared to the unstrained constructs. Further analysis on sections using the DNA nick-translation method suggested that this increase was primarily due to apoptosis. These findings imply a relationship between the duration of applied compression and damage to muscle cells seeded in the gel, which was particularly apparent at the strain level of 20 per cent, equivalent to a clinically relevant pressure of 32 mmHg (4.3 kPa). Such an approach might be useful in establishing damage threshold levels at a cellular level.

Impact of hypoglycemia and diabetes on CNS: correlation of mitochondrial oxidative stress with DNA damage.

Oxidative stress plays an important role in tissue damage caused by hypoglycemia and diabetes, which may be the result of deterioration in glucose homeostasis caused by these metabolic disorders. The present study examined the effects of insulin-induced hypoglycemia and streptozotocin induced diabetes on mitochondrial lipid peroxidation and antioxidant enzymes from different brain regions, namely, cerebral hemispheres, cerebellum, brain stem and diencephalon. In situ localization of DNA single strand breaks (SSBs) were also studied by DNA polymerase-I mediated biotin dATP labeled nick translation method after inducing hypoglycemia and diabetes. Significant decrease in mitochondrial catalase, manganese superoxide-dismutase (Mn-SOD) and reduced glutathione (GSH) content and increase in the lipid peroxidation (LPx) and glutathione peroxidase (GPx) activity was observed under these metabolic stress conditions with more pronounced effects in hypoglycemic group. We conclude that during severe energy deprivation following hypoglycemia and diabetes, mitochondrial free radicals scavenger system is down regulated, which leads to reactive oxygen species (ROS) generation. High levels of ROS in turn activate the processes leading to DNA damage. DNA SSBs, which indicates nuclear disintegration is an important feature of neuronal cell death.

A modified nick translation method used with FISH that produces reliable results with archival tissue sections.

Nick translation is used to label DNA and RNA to produce probes for in situ hybridization and Northern and Southern blotting. Fluorescence in situ hybridization (FISH) is a widely applied technique used to determine chromosomal and genetic anomalies in many biological samples. Initially the technique was applied to metaphase preparations, but the usefulness of detecting genetic anomalies in solid tumors in situ has resulted in the development of modified protocols. Formalin fixed paraffin processed tissue sections present novel challenges when applying FISH; the probes must be small (between 200 and 600 base pairs) and pretreatment is necessary before the probes can be applied to tissue sections, to promote probe access to target DNA. Here we report on a modification of a nick translation method to produce a probe that can reliably be used with FISH in paraffin processed tissue sections.

Peripheral neuroglial death induced by cisplatin administration in newborn rats

To determine the target of cytotoxicity of cisplatin (CDDP), we injected newborn rats with 2 mg/kg CDDP and examined the trigeminal ganglion for possible cell death. A nick translation method for DNA fragmentation revealed CDDP-induced glial cell death. DNA fragmentation was detected in both Schwann cells and satellite cells. Satellite cell death was observed as early as 0.5 day after injection, most frequent at 1-3 days and subsided thereafter. The incidence of neuronal death was very low and comparable to that observed in vehicle control rats. CDDP has selective toxicity to peripheral glial cells, though the damage did not culminate in cell death in adults. The glial toxicity may contribute to clinical symptoms of CDDP neuropathy.

Electron microscopic demonstration of nick end-labeled DNA fragments during capsaicin-induced apoptosis of trigeminal primary neurons in neonatal rats

DNA fragmentation was induced in the trigeminal ganglion of newborn rats by subcutaneous capsaicin injection (50 mg/kg). Twenty-four hours later, numerous roundish profiles were intensely labeled by both a DNA polymerase I-mediated nick translation method and a terminal transferase-mediated tailing method. Direct electron microscopic examination of labeled profiles indicated that the labeled profiles were neurons at earlier stages of apoptosis. DNA fragmentation signal was first detected in the nucleoplasm and later spread to the cytoplasm. The cell finally disintegrated forming many small apoptotic bodies. DNA fragmentation signal in the apoptotic bodies was readily labeled by the tailing but not the translation method.

The role of estrogen in the control of rat osteocyte apoptosis.

We have previously shown that estrogen withdrawal by gonadotrophin-releasing hormone analogs (GnRHa) induces osteocyte death via apoptosis in human bone. Although it is likely that the increase in osteocyte death via apoptosis was related to the loss of estrogen, these experiments could not rule out a direct role for the GnRHa. Therefore, in this study, we have used a rat model of ovariectomy (OVX) to determine whether the effect of estrogen withdrawal extends to other species and to clarify the role of estrogen in the maintenance of osteocyte viability. Twelve 9-week-old rats were divided into three treatment groups: sham operated (SHAM) (n = 4), OVX (n = 4), and OVX + estrogen (E2) (25 microg/day) (n = 4). At 3 weeks following the start of treatment, tibial bones were removed. The percentage of osteocytes displaying DNA breaks, using an in situ nick-translation method, was significantly higher in the OVX group compared with the SHAM control in both cortical bone (10.04% vs. 2.31%, respectively; p < 0.0001) and trabecular bone (6.44% vs. 1.58%, respectively; p = 0.003). Addition of estrogen in the OVX animals completely abrogated the increase in osteocyte apoptosis in cortical bone (0.78%) and trabecular bone (1.17%). The percentage of apoptotic osteocytes decreased with increasing distance from the primary/secondary spongiosa interface below the growth plate in the OVX model and the OVX + E2 model. Nuclear morphology and electrophoresis of DNA confirmed the presence of apoptotic cells in the samples. In conclusion, OVX in the rat results in an increase in osteocyte apoptosis as a direct or indirect result of E2 loss. Addition of estrogen in the OVX animals prevents this increase in osteocyte apoptosis. These data confirm an important role for estrogen in the control of osteocyte apoptosis and the maintenance of osteocyte viability. Estrogen deficiency might, through compromising the viability of osteocyte networks, reduce the ability of bone to respond appropriately to loading.

High sensitivity detection of HPV-16 in SiHa and CaSki cells utilizing FISH enhanced by TSA.

Detection of integrated human papillomavirus type 16 (HPV-16) DNA in SiHa and CaSki cells was used as a model system to demonstrate sensitivity and resolution of a well defined target. Using 293- to 1987-base polymerase chain reaction (PCR)-synthesized probes to the E6 and E7 open reading frames of HPV-16, several fluorescent in situ hybridization (FISH) detection methods, enhanced with tyramide signal amplification (TSA), were compared. The synthetic probes were biotin labeled by a nick translation method and the hybridized probes were detected by various fluorescent TSA methods using cyanine 3 tyramide, biotinyl tyramide and a biotin TSA Plus reagent. High sensitivity detection in SiHa cells was demonstrated using a 619-base probe to detect two single copies of integrated HPV-16 DNA. In CaSki cells, which contain up to 600 copies of HPV-16 DNA, a 293-base probe was used for detection. The results of these comparisons show that with refinement of TSA methods and reagents, increasing levels of high sensitivity detection can be achieved and that these methods allow subnuclear localization as well.

Topographic associations between DNA fragmentation and Alzheimer's disease neuropathology in the hippocampus

To identify whether the process of apoptosis bears a topographic relationship to selected aspects of Alzheimer's disease (AD) pathology, we used an in situ nick translation method (TUNEL) to map DNA fragmentation in hippocampal sections immunostained for abnormally phosphorylated tau, which exists in the neurofibrillary tangles (NFTs) and in the dystrophic neurites associated with senile plaques. To ascertain associations of DNA fragmentation with glia, TUNEL was combined with immunohistochemistry for the astrocyte marker, glial fibrillary acidic protein (GFAP), or the microglial antigen OX-42. Consistent with previous reports, the incidence of putative DNA fragmentation detected by TUNEL was much higher in the AD brain, compared to non-demented subjects. While most TUNEL-positive cells did not exhibit any systematic topographic relationship to senile plaques, which were visualized by immunostain of abnormally phosphorylated tau for dystrophic neurites, DNA fragmentation was found frequently within cells containing NFTs. In hippocampal sections prepared to visualize glia, DNA fragmentation was not observed in GFAP-positive astrocytes, but some OX-42-positive microglia exhibited TUNEL signals. Other TUNEL-positive cells were found frequently in proximity to glia. The data suggest that cells compromised by the deposition of NFTs are prone to initiate the process of apoptosis. Furthermore, some glial populations appear to be apoptotic in the AD brain.

‘Magentosis' in human lactating breast: A mode of cell death accumulating single‐stranded DNA stretches or breaks

Pale and homogeneous-looking nuclei of degenerative acinar cells selectively seen in an early regression stage of the human lactating breast were periodic acid-Schiff (PAS)-reactive. In our preceding paper, this peculiar morphologic feature was designated as 'magentosis'. The present paper was aimed at histochemically clarifying the nature of the 'magentotic' nuclei. The diffuse PAS reactivity was not influenced by pretreatments with alpha-amylase, DNase, RNase, proteinase K, nor by hydrochloric acid or heating. The nuclei were negative for acid mucosubstances and secretory glycoproteins, and were unreactive with a variety of lectins. In contrast, the presence of single-stranded DNA stretches or breaks was proven. The 'magentotic' nuclei in non-heated paraffin sections were hybridized with a heat-denatured DNA probe for human DNA consensus sequences and were focally immunoreactive with an antibody to single-stranded DNA. The terminal deoxynucleotidyl transferase-mediated dUTP nick end-labeling (TUNEL) method turned to be positive after digestion by mung bean nuclease, a single-stranded DNA-specific enzyme. The 'magentotic' nuclei were further clearly labeled by the in situ nick translation method. The nucleoli were devoid of reactivity for both the PAS and single-stranded DNA signals. We propose that 'magentosis' represents a unique mode of cell death, distinct from apoptosis and necrosis or oncosis. The PAS reactivity in the 'magentotic' nuclei may be correlated with the occurrence of single-stranded stretches or breaks in the DNA chain.

Death of neurons in the neonatal rodent and primate globus pallidus occurs by a mechanism of apoptosis

We have examined the developing rat, mouse and marmoset globus pallidus for evidence of cells dying by a process of “naturally occurring” or programmed cell death. We have demonstrated that cells in the developing mammalian globus pallidus die by a process of apoptosis and that by day 7 after birth many of the apoptotic cells possess a neuronal phenotype. Light microscopic and ultrastructural evidence of apoptotic cell death included cell shrinkage, blebbing of the extracellular membrane and condensation of the nuclear chromatin. Additionally we used an in situ nick translation method to assess the integrity of the DNA within the dying cells. This revealed that cells with the morphological characteristics of apoptosis also possessed fragmented DNA typical of cells undergoing Type 1 programmed or apoptotic cell death. The lack of lysosomal enzyme activity within the dying cells and the frequent observations of phagocytosis by neighbouring cells also suggests that the form of programmed cell death is apoptosis and not Type 2 autophagic degeneration. We found no evidence for cells dying by Type 3 non-lysosomal degeneration since all dying cells examined under the electron microscope possessed intact intracellular organelles and cell membranes. We developed a sensitive silver stain which detected balls of condensed chromatin within the apoptotic cells. This enabled identification of apoptotic cells in the developing globus pallidus at low magnification and so allowed us to map the numbers and distribution of dying cells with time. The incidence of apoptotic cells in the neonatal globus pallidus was greatest at birth and then declined such that few cells were detected at one week and none was seen in the adult rat. Although the loss of large numbers of cells in the developing nervous system is a well documented phenomenon, there are only a limited number of reports of the mechanism by which neuronal cells die, and few of these are in the developing mammalian brain. There are at least four different morphological categories of neuronal cell death which are discriminated on morphological and biochemical criteria. Our analysis suggests that apoptotic or Type 1 cell death is the major form of programmed cell death, occurring in the mammalian globus pallidus in the first week of life. This report also describes the use of two methods for the ready identification of apoptotic cells at the light microscope level. Because these methods are suitable for use on tissue sections they provide a means to assess the incidence of apoptotic cell death, in parallel with other analyses of the expression of gene products which control cell fate.

Changes in DNA strand breaks in non-parenchymal cells following hepatocyte regeneration in CCl4-induced rat liver injury.

DNA strand breaks (nicks) in non-parenchymal cells (NPCs) in CCl4-induced acute or chronic liver injury in rats were detected using an in situ nick translation method; their dynamic changes were analysed in relation to the proliferation pattern of hepatocytes and NPCs, as revealed by bromodeoxyuridine (BrdU)-uptake. In acute injury, hepatocyte proliferation started before centrilobular necrosis had occurred, whereas BrdU-labeled sinusoidal NPCs markedly increased only after centrilobular necrosis was apparent. DNA breakages in NPCs paralleled the proliferation pattern of these cells, suggesting that nicks are physiological, and reflect proliferation and activated gene expression. In chronic injury, liver cirrhosis developed after 9 weeks, but BrdU-labeling of hepatocytes was almost the same level as that in untreated liver. The number of BrdU-labeled NPCs showed only a slight increase, while those with DNA breakages were much more frequent in the cirrhotic stage, suggesting a significant role for NPCs in the fibrotic process. These results indicate that DNA strand breaks in NPCs act as a marker for activation states such as proliferation, differentiation and/or activated gene expression.

In situ nick translation at the electron microscopic level: a tool for studying the location of DNAse I-sensitive regions within the cell.

The in situ nick translation method was adapted to the ultrastructural level, to study the location of DNAse I-sensitive sequences within the cell. Ultra-thin sections of Lowicryl-embedded cells were incubated in a medium containing DNAse I, DNA polymerase I, and all four deoxyribonucleotides, some being biotinylated. The nick-translated sites were then visualized by an indirect immunogold labeling technique. The resulting labeling pattern is closely dependent on the DNAse I concentration in the nick-translation medium. The method reveals with great precision the specific DNAse I-sensitive regions within the nucleus. This technique can be used to discriminate between active and inactive regions of interphase chromatin.

Comparison of biotinylated DNA and RNA probes for rapid detection of varicella-zoster virus genome by in situ hybridization.

We describe a general method for the production of nonisotopic DNA and RNA probes for the detection of the varicella-zoster virus (VZV) genome by in situ hybridization. VZV DNA was extracted from purified viral nucleocapsids, cleaved with restriction enzyme (RE) BamHI, and cloned into plasmid pBR322 by the standard vector insert procedure. We cloned over 85% of the VZV genome and obtained 18 recombinants. Plasmids containing the B, F, G, H, and J fragments of VZV DNA were labeled by the nick translation method with biotin-11-dUTP as the dTTP analog. Additionally, the B fragment was cleaved with RE AvaI, subcloned into the plasmid pGEM-4 transcription vector, and subsequently linearized with REs PstI and EcoRI. RNA was transcribed with T7 or SP6 polymerase, with a substitution of allylamine-UTP as the UTP analog, and labeled with epsilon-caproylamidobiotin-N-hydroxysuccinimide ester. The DNA and RNA probes were used under full-stringency conditions for in situ hybridization with alkaline phosphatase as the detector and 5-bromo-4-chloro-3-indolyl phosphate-Nitro Blue Tetrazolium as the substrate. When tested under comparable conditions, the RNA probe was slightly more sensitive than was the DNA probe: both probes showed homology only with VZV-infected cells and clinical tissues and not with the other herpesviruses. Probes prepared from variable regions of the genome (fragments F and J) performed as well as did those from conserved regions (fragments B. G. and H). Biotinylated probes have distinct advantages over isotopic probes and retain their full potency for more than 2 years when stored properly.

Effects of lycobetaine on chromatin structure and activity of murine hepatoma cells.

The effects of lycobetaine (LBT) on DNA single strand break and chromatin conformation were examined by in-situ nick translation method. It was found that LBT did not cause DNA single strand break. After 2-h incubation of murine hepatoma cells with 1-50 micrograms/ml LBT in vitro, the chromatin transcription activity was inhibited gradually. This effect was time- and dose-dependent. Actinomycin D produced a similar effect; 10-hydroxycamptothecin not only caused DNA single strand break, but also altered chromatin conformation; homoharringtonine had no marked influence on either. By molecular hybridization technique, it was found that the effect of LBT on individual genes was somewhat different. After 2-h incubation of the cells with LBT, the sensitivities of c-myc, N-ras, and beta 2-microglobulin genes to DNase I were decreased from 75 +/- 6, 66 +/- 4, 70 +/- 8% to 28 +/- 8, 25 +/- 5, 28 +/- 7%, respectively, while that of c-myb and beta-globin genes (8 + 6%, 6 + 5%) did not change obviously.

T98G Glioma cells have nicks in DNA in quiescent phase

Human glioblastoma-derived cell line, T98G, is arrested in the G 1 phase of the cell cycle when serum is deprived. Using this cell line, we investigated the relation between the cell cycle and DNA single-stranded breaks, “nicks,” by an in situ nick-translation method. When T98G cells were cultured without serum for 60 h, many small cells with condensed chromatin and scanty cytoplasm appeared. These small cells that were immunohistochemically considered to be in the G 0 or early G 1 phase had many nicks in DNA. When serum was added, these small cells with nicks disappeared within 1 to 4 h. VP-16, a DNA topoisomerase II inhibitor, delayed the disappearance of these small cells with nicks. This indicated that the action of DNA topoisomerase II on the chromatin is required to repair nicks in T98G glioma cells and to promote the progression from the quiescent to the proliferating phase.