Different sensitivity of DNA in situ in interphase and metaphase chromatin to heat denaturation

Heat denaturation of DNA in situ, in unbroken cells, was studied in relation to the cell cycle. DNA in metaphase cells denatured at lower temperatures (8 degrees-10 degrees C lower) than DNA in interphase cells. Among interphase cells, small differences between G1, S, and G2 cells were observed at temperatures above 90 degrees C. The difference between metaphase and interphase cells increased after short pretreatment with formaldehyde, decreased when cells were heated in the presence of 1 mM MgCl2, and was abolished by cell pretreatment with 0.5 N HCl. The results suggest that acid-soluble constituents of chromatin confer local stability to DNA and that the degree of stabilization is lower in metaphase chromosomes than in interphase nuclei. These in situ results remain in contrast to the published data showing no difference in DNA denaturation in chromatin isolated from interphase and metaphase cells. It is likely that factors exist which influence the stability of DNA in situ are associated with the super-structural organization of chromatin in intact nuclei and which are lost during chromatin isolation and solubilization. Since DNA denaturation is assayed after cell cooling, there is also a possibility that the extent of denatured DNA may be influenced by some factors that control strand separation and DNA reassociation. The different stainability of interphase vs. metaphase cells, based on the difference in stability of DNA, offers a method for determining mitotic indices by flow cytofluorometry, and a possible new parameter for sorting cells in metaphase.     

Caffeine increases sensitivity of DNA to denaturation in chromatin of L1210 cells

Abstract.
Exposure of exponentially growing L1210 cells to 5 mM and higher concentrations of caffeine perturbs their progression through the cell cycle and results in increased sensitivity of DNA in situ to denaturation. The latter is detected by the increased metachromatic stainability of DNA with acridine orange (AO) and sensitivity to S₁ nuclease, measured by flow cytometry. Decreased DNA stability is generally characteristic of chromatin condensation and in untreated cells is observed in mitosis or quiescence (G₀). The caffeine-induced decrease in DNA stability affects the interphase cells regardless of their position in the cycle and the changes are stochastic, concentration- and time-dependent. Populations of cells responding to caffeine are very heterogenous with respect to the degree of destabilization of DNA; sensitivity of DNA to denaturation of the maximally affected cells is similar to that of untreated cells in mitosis. The present method allows one to quantitatively express effects of caffeine on nuclear chromatin in individual cells of large cell populations and may be employed in studies correlating chromatin changes induced by this agent with its effects in modulation of cell sensitivity to radiation or antitumour drugs.     

Caffeine increases sensitivity of DNA to denaturation in chromatin of L1210 cells.

Exposure of exponentially growing L1210 cells to 5 mM and higher concentrations of caffeine perturbs their progression through the cell cycle and results in increased sensitivity of DNA in situ to denaturation. The latter is detected by the increased metachromatic stainability of DNA with acridine orange (AO) and sensitivity to S1 nuclease, measured by flow cytometry. Decreased DNA stability is generally characteristic of chromatin condensation and in untreated cells is observed in mitosis or quiescence (G0). The caffeine-induced decrease in DNA stability affects the interphase cells regardless of their position in the cycle and the changes are stochastic, concentration- and time-dependent. Populations of cells responding to caffeine are very heterogenous with respect to the degree of destabilization of DNA; sensitivity of DNA to denaturation of the maximally affected cells is similar to that of untreated cells in mitosis. The present method allows one to quantitatively express effects of caffeine on nuclear chromatin in individual cells of large cell populations and may be employed in studies correlating chromatin changes induced by this agent with its effects in modulation of cell sensitivity to radiation or antitumour drugs.     

Thermal denaturation of DNA in situ as studied by acridine orange staining and automated cytofluorometry

Thermal denaturation of nuclear DNA is studied in situ in individual cells or isolated cell nuclei by employing the property of the fluorochrome acridine orange (AO) to differentially stain native and denatured DNA and by using an automated flow-through cytofluorimeter for measurement of cell fluorescence. RNAse-treated cells, or cell nuclei, are heated, stained and measured while in suspension and AO-DNA interaction is studied under equilibrium conditions. Measurements are made rapidly (200 cells/sec); subpopulations of cells from a measured sample can be chosen on the basis of differences in their staining or light-scattering properties and analysed separately. DNA denaturation in situ is rapid; it approaches maximum during the first 5 min of cell heating. Divalent cations stabilize DNA against denaturation. At low pH the transition occurs at lower temperature and the width of the transition curves (‘melting profiles’) is increased. Decrease in ionic strength lowers the DNA melting temperature. This effect is much more pronounced in cells pretreated with acids under conditions known to remove histones. Histones thus appear to stabilize DNA in situ by providing counterions. At least four separate phases can be distinguished in melting profiles of DNA in situ; they are believed to indicate different melting points of DNA in complexes with particular histones. A decrease in cell (nuclear) ability to scatter light coincides with DNA melting in situ, possibly representing altered refractive and/or reflective properties of cell nuclei. Formaldehyde, commonly used to prevent DNA renaturation, is not used in the present method. The heat-induced alterations in nuclear chromatin are adequately stabilized after cell cooling in the absence of this agent. Cells heated at 60–85 °C exhibit increased total fluorescence after AO-staining, which is believed to be due to unmasking of new sites on DNA. This increase is neither correlated with DNA melting, nor with the presence of histones. Possibly, it reflects destruction of DNA superstructure maintained at lower temperatures by DNA associations with other than histone macromolecules (nuclear membrane).     

Cytofluorometric studies on conformation of nucleic acids in situ. II. Denaturation of deoxyribonucleic acid.

Thermal denaturation of deoxyribonucleic acid (DNA) in situ in individual unbroken cells is studied by a cytofluorometric method. This method allows us to investigate DNA denaturation in the presence of divalent cations at concentrations reported to be necessary to maintain native structure of nuclear chromatin. Under these conditions the pattern of DNA denaturation is very different than when studied in the presence of ethylenediaminetetraacetate or citrate. The results suggest that with divalent cations present, the histone basic charges are more uniformly distributed along whole nuclear DNA. Various cell types exhibit great differences in sensitivity to DNA denaturation when assayed in the presence of 1 mM MgCl2. Human lymphocytes, monocytes and certain kinds of human leukemic cells show differences large enough to be used as a parameter for their recognition in mixed samples. Possible applications of the method in basic research on chromatin conformation and as a tool for cell recognition in diagnostic cytology or in the classification of human leukemia are proposed.     

Rapid analysis of drug effects on the cell cycle

Using a flow cytometric technique to analyse DNA content and chromatin structure simultaneously, the following parameters of cell cycle progression were estimated in control and drug-treated L1210 cell cultures: (a) the kinetics of cell exit from the G1 phase; (b) the probability of cell exit from the indeterminate portion of the G1 phase, measured as the half-time of cell residence in that state; (c) the duration of the deterministic portion of G1 phase; (d) the rates of cell transit through selected "windows" in S phase; (e) the rate of cell entrance into mitosis; (f) the mean duration of the cell cycle (Tc). These parameters are obtained in a single stathmokinetic experiment from measurements of individual samples withdrawn at 30 min-1 hr intervals from Vinblasatine-treated cultures. In the same experiment mitotic indices are obtained with high statistical accuracy, and may be used to determine the terminal point of drug action. In addition to cell cycle analysis the method makes it possible to detect drug-induced changes in nuclear chromatin that are manifested by varying sensitivity of DNA in situ to denaturation by acid. Such changes were found to be associated with defective chromatin condensation, altered histone modifications or intercalation of the drugs into DNA. Using this technique the effects of sodium n-butyrate and two new antitumor drugs on L1210 cells were investigated.     

Quantitative cytochemical changes induced by dexamethasone and adrenalectomy in rat liver chromatin

Physiochemical changes in the state of chromatin shortly following glucocorticoid stimulation of target cells are predicted by the proposed mechanism of steroid action. These changes had not been previously demonstrated in situ. The present experiments demonstrate that in the intact rat, or in one which has been adrenalectomized but given a moderate dose of dexamethasone, the thermal stability of liver cell chromatin is significantly reduced over the level observed in the adrenalectomized untreated animal. This alteration was rated by measuring nuclear acridine orange metachromasia following chromatin denaturation. These data also show an enhanced binding of the dye by the liver cell nuclei under the same conditions. Feulgen dye binding was also found to be enhanced by dexamethasone stimulation but to a level indicative of configurational changes in the chromatin rather than an increase in the amount of DNA in the cells.     

Methods of denaturation and renaturation of DNA in interphasic chromatin: cytochemical quantitative analysis by Methyl Green staining

Almost diploid nuclei (as judged from the microdensitometric evaluation of the Feulgen positive material) of granular and Purkinje cells of the rat cerebellar cortex, were submitted to in situ DNA denaturation and renaturation experiments. We assessed the double-strandedness of DNA, by Methyl Green staining according to Scott (1967). Under these conditions a stoichiometric ratio between bound dye and DNA exists, suitable for quantitative microdensitometric measurements. Our data show that DNA in the interphasic chromatin is never completely denatured after the treatments we used. Furthermore, the renaturation takes place in a different way in the two cell types. Owing to the unlike chromatin packing of granular and Purkinje nuclei, we suggest that nuclear proteins must interfere differently on the in situ denaturation and renaturation processes.     

Single-strand nuclease action on heat-denatured spermiogenic chromatin.

The aim of this study was to compare the sensitivity of chromatin from representative cellular stages of spermiogenesis to a single-strandeded nuclease after heat denaturation. Thermal denaturation of chromatin was assayed in situ in fixed round, elongating and elongated spermatids and in testicular sperm from mice. Production of single-stranded deoxyribonucleic acid (DNA) at elevated temperatures was monitored by digesting chromatin with endonuclease specific for single-stranded DNA (S1 nuclease), staining the residual DNA with gallocyanin-chrome alum (GAC) and measuring the stain content by absorption cytophotometry. Changes in GCA staining were minimal over the temperature range of 22-90 degrees C in each cell type not exposed to nuclease. Staining of undigested cells decreased progressively with advancing cell maturity. Nuclease had no effect on the GCA content of round spermatids below 60 degrees C, but above this temperature there was a progressive decrease in GCA-stainable chromatin. Both round and elongating spermatid stages showed a significantly greater sensitivity to nuclease digestion than did more mature stages; sperm showed no effects of nuclease action below 80 degrees C. Progressive chromatin condensation and a concomitant decrease in the number of available DNA phosphate groups during spermiogenic cell maturation may be responsible for the observed decline in sensitivity to nuclease and decreased GCA staining. Thermal denaturation of round spermatids labeled with 3H-thymidine produced no change in autoradiographic mean nuclear grain counts, indicating no loss of thymidine-labeled DNA from the slides during denaturation. When round spermatids and sperm were hydrolyzed with hot tricholoroacetic acid before staining, both nuclear GCA content and autoradiograph grain count were partially reduced, indicating incomplete DNA removal. Almost complete loss of Feulgen-stainable material occurred in these cells and may be due to depurination and elimination of Feulgren-reactant aldehyde groups.     

In situ factors affecting stability of the DNA helix in interphase nuclei and metaphase chromosomes

The data from earlier cytochemical studies, in which the metachromatic fluorochrome acridine orange (AO) was used to differentially stain single vs double-stranded DNA, suggested that DNA in situ in intact metaphase chromosomes or in condensed chromatin of G0 cells is more sensitive to denaturation, induced by heat or acid, than DNA in decondensed chromatin of interphase nuclei. Present studies show that, indeed, DNA in permeabilized metaphase cells, in contrast to cells in interphase, when exposed to buffers of low pH (1.5-2.8) becomes digestible with the single-strand-specific S1 or mung bean nucleases. A variety of extraction procedures and enzymatic treatments provided evidence that the presence of histones, HMG proteins, and S-S bonds in chromatin, as well as phosphorylation or poly(ADP)ribosylation of chromatin proteins, can be excluded as a factor responsible for the differential sensitivity of metaphase vs interphase DNA to denaturation. Cell treatment with NaCl at a concentration of 1.2 N and above abolished the difference between interphase and mitotic cells, rendering DNA in mitotic cells less sensitive to denaturation; such treatment also resulted in decondensation of chromatin visible by microscopy. The present data indicate that structural proteins extractable with greater than or equal to 1.2 N NaCl may be involved in anchoring DNA to the nuclear matrix or chromosome scaffold and may be responsible for maintaining a high degree of chromatin compaction in situ, such as that observed in metaphase chromosomes or in G0 cells. Following dissociation of histones, the high spatial density of the charged DNA polymer may induce topological strain on the double helix, thus decreasing its local stability; this can be detected by metachromatic staining of DNA with AO or digestion with single-strand-specific nucleases.     

RNA content and chromatin structure of CHO cells arrested in metaphase by colcemid

To evaluate the stability of cells arrested in metaphase, cell viability, RNA content, and chromatin structure (the latter probed by the DNA in situ sensitivity to acid-induced denaturation) were studied in uniform-age mitotic CHO cell populations maintained either at 37 degrees C (in the presence of Colcemid) or at 0-4 degrees C for up to 6 h. No significant changes in cell viability and RNA content were seen throughout the experiment for both groups of cells. The sensitivity of DNA in situ to denaturation was significantly increased during the initial 40 min of cell arrest in mitosis. However, no further chromatin changes for up to 6 h were evident regardless of whether cells were kept at 37 degrees C with Colcemid or at 0-4 degrees C in its absence. The data indicate that neither significant deterioration of metaphase cells nor progressive chromatin changes are expected during stathmokinesis experiments in vitro or during the metaphase cell arrest in cytogenetic studies lasting up to 6 h. Also, no RNA turnover can be detected in mitotic cells during this time interval.     

Detection of 5-bromodeoxyuridine (BrdUrd) incorporation by monoclonal antibodies: role of the DNA denaturation step

Immunochemical detection of cells that incorporate 5-bromodeoxyuridine (BrdUrd) requires prior denaturation of DNA in situ to make BrdUrd binding sites accessible to the antibodies. A technique is described in which the DNA denaturation step is facilitated by a) prior dissociation of histones from DNA and b) the use of low ionic strength buffer in which the cells are suspended during heating. Dissociation of histones is achieved by cell treatment with 0.08N HCl at 0 degree C, which a) increases accessibility of DNA to propidium iodide (and following the denaturation to the antibodies); b) lowers stability of DNA to thermal denaturation; c) decreases differences between various cell types due to variability in chromatin structure; and d) ensures more complete DNA denaturation. Cell heating (80-95 degrees C) at low ionic strength (1 mM Na+) eliminates the need for formamide and results in extensive and rapid DNA denaturation. The method was applied in Friend leukemia, L1210 and HL-60 cell lines, and to bone marrow, experimental animal tumor and primary human tumor cells.     

Changes in nuclear chromatin related to apoptosis or necrosis induced by the DNA topoisomerase II inhibitor fostriecin in MOLT-4 and HL-60 cells are revealed by altered DNA sensitivity to denaturation.

The antitumor drug fostriecin (phosphotrienin, FST) has been reported to exert its cytostatic and cytotoxic effects via inhibition of DNA topoisomerase II. The sensitivity of human lymphocytic leukemic MOLT-4 and promyelocytic HL-60 leukemic cells to a wide range of FST concentrations was studied by analyzing the cell cycle-specific effects and changes in nuclear chromatin induced by this inhibitor. The latter was evaluated by assaying the sensitivity of DNA in situ to acid-induced denaturation cytofluorimetrically, with the use of the metachromatic fluorochrome acridine orange (AO), which differentially stains double-stranded and denatured DNA. The cytostatic effects were observed soon after addition of FST (at concentrations of 1-30 microM for MOLT-4 cultures and 1-5 microM for HL-60 cultures) as a perturbation of cell progression through S and G2 phases of the cell cycle. Cell progression through the cycle was halted at greater than 30 microM FST in MOLT-4 cultures and at greater than 5 microM in HL-60 cultures; the effect was instantaneous and affected all phases of the cycle, so that no changes in the cell cycle distribution were apparent with increasing length of exposure to the drug. Instead, at these high FST concentrations, immediate cytotoxic effects became evident, manifesting either as cell apoptosis or necrosis. Apoptosis was observed only in the case of HL-60 cells, at FST concentrations of 5-100 microM, and was characterized by markedly increased sensitivity of DNA to denaturation combined with a decrease in overall DNA stainability, either with the DNA-specific dye DAPI or with AO, indicative of the activation of endogenous nucleases. Necrotic cell death was observed at FST concentrations of 1 mM and at greater than 30 microM for HL-60 and MOLT-4 cells, respectively: in both cases the overall DNA stainability, with either DAPI or AO, was unchanged compared to the control, but their DNA was very sensitive to denaturation. Interestingly, DNA in G2 and late S phase MOLT-4 cells, which were undergoing necrotic death, was much more sensitive to denaturation than was DNA in G1 cells of this lineage. The data indicate that chromatin changes induced by DNA topoisomerase II inhibitors in cells that undergo apoptotic or necrotic death can be conveniently monitored by the assay of DNA in situ sensitivity to denaturation.     

Changes in cell nuclei during S phase: progressive chromatin condensation and altered expression of the proliferation-associated nuclear proteins Ki-67, cyclin (PCNA), p105, and p34.

Using multiparameter flow cytometry we have measured the nuclear DNA content of exponentially growing HL-60 cells in conjunction with protein content, nuclear forward light scatter, DNA in situ sensitivity to denaturation, DNA accessibility to 7-aminoactinomycin D (7-AMD), and content of the proliferation-associated proteins: cyclin (PCNA), p105, p34, and Ki-67. Multivariate analysis of the data made it possible to correlate changes in each parameter with the degree of cell advancement through S phase (amount of replicated DNA). A decrease of the protein/DNA ratio, lowered DNA accessibility to 7-AMD, increased sensitivity of DNA to denaturation, and increased ability of isolated nuclei to scatter light all paralleled cell progression through S phase. These changes indicate that during S phase chromatin progressively condenses and suggest that the condensation is associated with the efflux of nonhistone proteins from the nucleus. The increase in the content of the antigen detected by the Ki-67 antibody was observed to exceed the increase in DNA content during S phase and the rate of the Ki-67/DNA increase was higher during the second half of S phase. Thus, this protein appears to be primarily synthesized during S, especially late in S phase, and is degraded in G1. The ratio of cyclin (PCNA)/DNA remained rather constant whereas the contents of p105 and p34 proteins, when expressed per unit of DNA, both decreased during S phase. The data indicate that significant changes in structure and composition of chromatin take place during S phase and suggest that the composition of chromatin associated with the nonreplicated DNA is different compared to chromatin associated with the newly replicated DNA.     

Cross-linking of estrogen receptor to chromatin in intact MCF-7 human breast cancer cells: optimization and effect of ligand

To investigate the effect of ligand (be it hormone, antihormone, or no hormone) on the interaction between estrogen receptor (ER) and chromatin, we have used formaldehyde as a cross-linking agent in intact MCF-7 human breast cancer cells. After a 1- to 2-h hormone treatment, the cells are exposed for 8 min to formaldehyde, which is added directly to their culture medium to minimize environmental perturbation. Nuclei are prepared from formaldehyde-treated cells and their contents are fractionated on CsCl density gradients to separate DNA-protein complexes from free protein. Peak gradient fractions are assayed for the presence of specific proteins by immunoblot of sodium dodecyl sulfate-polyacrylamide gel patterns. Using this approach, we find that 0.15% formaldehyde is optimal for cross-linking ER to chromatin. We detect ER and the large subunit of RNA polymerase II with DNA from formaldehyde-treated, but not from untreated cells. On the other hand, actin (a cytoplasmic protein) and small nuclear ribonucleoprotein particle proteins (nuclear RNA binding proteins) are not cross-linked to DNA. Therefore, cross-linking appears to be selective and fractionation is efficient. Interestingly, we detect similar levels of ER (as well as RNA polymerase II) with DNA from formaldehyde-treated cells, regardless of whether the cells are preexposed to estrogen (17 beta-estradiol at 10(-8) M), antiestrogen (ICI 164,384 at 10(-7) or 10(-6) M), or no hormone. These results, using covalent cross-linking in intact cells, indicate that both ligand-occupied and unoccupied ER are associated with chromatin.     

Acridine orange binding to chromatin of individual cells and nuclei under different staining conditions. Thermadenaturation of Chromatin.

The thermodenaturation of chromatin in situ was studied by staining heat-treated nuclei with acridine orange. It was found that formaldehyde, which under the present conditions had to be used to prevent extensive renaturation of DNA, seriously affects the results of standard acridine orange staining in an unspecific manner. In particular the acetylation step involved in this staining method is strongly inhibited. Thus the standard method of staining can only give qualitative information about the effects of thermodenaturation. On the other hand, acridine orange staining at defined equilibrium, without prior acetylation is insensitive to formaldehyde and multiphasic thermodenaturation profiles are obtained with this method. At low temperatures these profiles mainly reflect changes in the protein-DNA interaction whereas at higher temperatures DNA denaturation also contributes to the curves. Although these two processes cannot be separately quantitated by simple measurements of dye binding, the thermodenaturation profiles still contain biologically significant information about the properties of chromatin in situ.     

维甲酸诱导的人大肠癌细胞凋亡

本研究应用光镜、电镜技术、DNA凝胶电泳、流式细胞术及末端脱氧核苷酰转移酶原位标记(TUNEL法),观察全反式维甲酸ATRA诱导的人大肠癌CCL229细胞凋亡特征。RA诱导CCL229细胞凋亡,光、电镜下观察到凋亡小体形成等典型的形态学改变,琼脂糖凝胶电泳上呈现特征性的DNA ladder,DNA直方图上显示亚二倍体峰。10-8mol/L-105mol/L范围内,RA诱导CCL229细胞凋亡表现出时间和剂量依赖性。     

Evidence for a role of RNA in eukaryotic chromosome structure. Metabolically stable, small nuclear RNA species are covalently linked to chromosomal DNA in HeLa cells

An investigation of metabolically stable, chromatin-associated RNA in HeLa cells has revealed that three small RNA species, 193, 171 and 127 nucleotides in length, are covalently linked to double-stranded chromosomal DNA through phosphodiester bonds. These DNA-linked RNAs appear to be members of the small nuclear RNA species that have been identified in a wide variety of eukaryotic cells, and they are tentatively identified as species C, D and G′, in the nomenclature system currently employed for HeLa cell small nuclear RNAs. These DNA-linked RNAs do not appear to be involved in priming DNA replication, since they are of relatively high metabolic stability ($\text{t}{}_{\mathrm{<mtext>1</mtext><mtext>2</mtext>}}\text{= 19}$ hours in HeLa cells with a 21·5-hour cell generation time) and since their covalently contiguous DNA stretches are not enriched in newly replicated material. They lack saturated pyrimidine bases (level of detection = 0·15 mol %) and are therefore not “chromosomal RNA”, as defined by its proponents. The covalent linkage of these small RNA species with chromosomal DNA was discovered by virtue of the fact that when highly purified HeLa cell chromatin is dissociated by chaotropic solutes, these RNAs are released in association with small pieces of double-stranded DNA (approx. 475 nucleotide pairs). These DNA-RNA complexes can then be purified by removing the bulk, high molecular weight DNA by ultra-centrifugation. The resulting DNA-RNA complexes are shown to be covalently joined by several criteria, including equilibrium density-gradient centrifugation in either Cs₂SO₄/dimethylsulfoxide or aqueous Cs₂SO₄/formaldehyde after thermal denaturation (90 °C in 50% formamide, which is 55 deg. C above the melting temperature of this DNA), by the chromat ographicbehavior of the complexes on hydroxylapatite before and after thermal denaturation, and by the demonstration of alkali-resistant ribonucleotides flanking the 3′ hydroxyl termini of the DNA, the latter criterion providing evidence for 3′ to 5′ DNA-RNA phosphodiester bonds. Reconstruction experiments involving addition of the purified RNAs to nuclei or chromatin demonstrate that the covalent DNA-RNA linkages do not arise by ligation events during cell fractionation. Further experiments indicate the existence of a dynamic equilibrium of these small nuclear RNA species between chromosomal and nucleoplasmic loci in vivo, and other considerations suggest that this equilibrium may be cell cycle-dependent. The DNA adjacent to these covalently linked RNAs has the same melting temperature as total HeLa chromosomal DNA and its reassociation kinetics reveal the presence of both repeated and non-repeated sequences, implying that the DNA-linked RNAs are widely distributed throughout the HeLa cell genome. It is proposed that these DNA-linked RNAs are involved in the tertiary structure of chromatin, particularly in relation to the cell cycle.     

Intranuclear relocalization of matrix binding sites during T cell activation detected by amplified fluorescence in situ hybridization

We describe a method for analyzing the nuclear localization of specific DNA sequences, with special emphasis on their binding status to the nuclear matrix, depending on the developmental stage of the cells. This method employs high-resolution fluorescence in situ hybridization procedures. For our studies, it was important to examine the nuclear localization of a particular gene locus. Previously, however, it was not possible to detect a single-copy genomic sequence using a DNA probe less than several kilobases in size. We describe here a signal amplification technique based on tyramide which makes such a task possible. Using this method, we monitored single-copy loci using a short, 509-bp DNA sequence that binds in vivo to the T cell factor SATB1 within T cell nuclei, high-salt-extracted nuclei (histone-depleted nuclei generating "halos" with distended chromatin loops), and the nuclear matrix, before and after T cell activation. We found that these loci were anchored onto the nuclear matrix, creating new bases of chromatin loops, only after T cell activation. This experimental strategy, therefore, enabled us to detect the changes in higher order chromatin structure upon activation and study gene regulation at a new dimension: the loop domain structure. The methods shown here can be widely applied to explore other functions involving chromatin, including recombination and replication.