Differential DNase I sensitivity of the two complementary nucleosomal DNA strands in cycloheximide-treated Ehrlich ascites tumor cells

The accessibility of the two complementary DNA strands in newly replicated chromatin of Ehrlich ascites tumor (EAT) cells grown under conditions of cycloheximide-inhibited protein synthesis was studied by analysis of the DNase I digestion of isolated nuclei. Bulk DNA was labeled with 14C-thymidine and the newly synthesized strands - with bromodeoxyuridine and 3H-thymidine. The DNase I digests were fractionated in two successive CsCl density gradient centrifugations to obtain a dense fraction containing 15-20% newly replicated DNA. Analysis of the distribution of 14C-labeled parental DNA fragments complementary to the 3H-nascent strand has shown that the 14C-labeled fragments prevail in the region of 30-50 nucleotides. Simulation experiments using the rate constants for DNase I attack show that this result may be explained by an enhanced accessibility at the nucleosomal 5'-end region of the parental strands, where the H2a-H2b dimer interacts with DNA. This asymmetry seems to be induced by interactions in the chromatin.     

Patterns of nuclease protection during strand exchange. recA protein forms heteroduplex DNA by binding to strands of the same polarity

recA protein, in the presence of ATP, polymerizes on single-stranded DNA (plus strand) to form a presynaptic nucleoprotein filament that pairs with linear duplex DNA and actively displaces the plus strand from the recipient molecule in a polarized fashion to form a new heteroduplex molecule. The interaction between recA protein and DNA during strand exchange was studied by labeling different strands and probing the intermediate with pancreatic deoxyribonuclease I (DNase I) or restriction endonuclease. The incoming single strand was resistant to DNase I in the original nucleoprotein filament and remained resistant even after extensive strand exchange had occurred. Both strands of the parental duplex molecule were sensitive to DNase I in the absence of joint molecule formation; but as strand exchange progressed following homologous pairing, increasing stretches of the parental plus strand became resistant, whereas the complementary parental minus strand remained sensitive to DNase I throughout the reaction. Except for a region of 50-100 base pairs at the end of the newly formed heteroduplex DNA where strand exchange was initiated, the rest of the heteroduplex region was resistant to cleavage by restriction endonucleases. The data suggest that recA protein promotes strand exchange by binding both the incoming and outgoing strands of the same polarity, whereas the complementary strand, which must switch pairing partners, is unhindered by direct contact with the protein.     

Sex-specific alterations in chromatin conformation of the brain of aging mouse

Chromatin conformation has been analysed in the brain cortex of adult (24±2 weeks) and old (65±4 weeks) male and female mice. Nuclei purified from different groups of mice were digested with MNase and DNase I for varying time periods (0–90 min), and with endogenous endonucleases for 1 h. MNase and DNase I digestion kinetics showed that the percentage of acid solubility of chromatin was relatively lower in old than adult and in female than male. This was further supported by electrophoretic analysis of nuclease digested DNA fragments. When the nuclei were incubated with only Ca²⁺or mg²⁺, no endonuclease digestion was observed. However, under similar conditions, the liver DNA was cleaved substantially. When divalent cations were added together, they activated endogenous endonucleases and digested the brain chromatin. The activity of Ca²⁺/Mg²⁺-dependent endogenous endonucleases was higher in male than female. Thus the accessibility of chromatin to MNase, DNase I and endogenous endonucleases was higher in male than female, and MNase as well as DNase I were more active in adult than old. Such sex- and age-dependent conformation of chromatin may attribute to differential expression of genes in the mouse brain.     

TSH-treatment of thyroid slices increases the amount of DNA released from nuclei by mild DNase-I digestion

Nuclei from TSH-treated and control thyroid slices were subjected to very limited digestion by DNase I, and then centrifuged at 1200×g. The amount of DNA released into supernatants was increased significantly by TSH when <0.1% to 3% of total DNA was rendered acid-soluble. This effect could be detected in buffers containing 2mM Mg⁺⁺ (with chromatin condensed) or <0.05mM Mg⁺⁺ (chromatin decondensed). Gel electrophoresis showed that the length of the majority of the DNA fragments in the supernatants (<0.1% of DNA acid-soluble) was greater than 4 kilobases; no TSH-dependent shift in size distribution was observed. We speculate that TSH may affect specific DNase I-hypersensitive sites in chromatin.     

Mechanism of degradation of duplex DNA by the DNase induced by herpes simplex virus

Reaction intermediates formed during the degradation of linear PM2, T5, and λ DNA by herpes simplex virus (HSV) DNase have been examined by agarose gel electrophoresis. Digestion of T5 DNA by HSV type 2 (HSV-2) DNase in the presence of Mn²⁺ (endonuclease only) gave rise to 6 major and 12 minor fragments. Some of the fragments produced correspond to those observed after cleavage of T5 DNA by the single-strand-specific S1 nuclease, indicating that the HSV DNase rapidly cleaves opposite a nick or gap in a duplex DNA molecule. In contrast, HSV DNase did not produce distinct fragments upon digestion of linear PM2 or λ DNA, which do not contain nicks. In the presence of Mg²⁺, when both endonuclease and exonuclease activities of the HSV DNase occur, most of the same distinct fragments from digestion of T5 DNA were observed. However, these fragments were then further degraded preferentially from the ends, presumably by the action of the exonuclease activity. Unit-length λ DNA, EcoRI restriction fragments of λ DNA, and linear PM2 DNA were also degraded from the ends by HSV DNase in the same manner. Previous studies have suggested that the HSV exonuclease degrades in the 3′ → 5′ direction. If this is correct, and since only 5′-monophosphate nucleosides are produced, then HSV DNase should “activate” DNA for DNA polymerase. However, unlike pancreatic DNase I, neither HSV-1 nor HSV-2 DNase, in the presence of Mg²⁺ or Mn²⁺, activated calf thymus DNA for HSV DNA polymerase. This suggests that HSV DNase degrades both strands of a linear double-stranded DNA molecule from the same end at about the same rate. That is, HSV DNase is apparently capable of degrading DNA strands in the 3′ → 5′ direction as well as in the 5′ → 3′ direction, yielding progressively smaller double-stranded molecules with flush ends. Except with minor differences, HSV-1 and HSV-2 DNases act in a similar manner.     

Precise location of DNase I cutting sites in the nucleosome core determined by high resolution gel electrophoresis.

The precise locations of the DNase I cutting sites in the nucleosome core have been determined by analysis of the DNA products of a DNase I digestion of 32P end-labelled mucleosome cores on a high resolution gel electrophoresis system. This system is capable of resolving fragments of mixed sequence DNA differing by one base into the region of 160 bases in length. The DNase I cutting sites in the core are found to be spaced at multiples of about 10.4 (i.e. clearly different from 10.0) bases along the DNA, but show significant variations about this value. In addition to the location of the sites, the stagger between individual sites on opposite strands has been determined and is found to be inconsistent with at least one proposed mechanism for nuclease cleavage of chromatin DNA. Finally, a calculated distribution of fragment lengths in a DNase I digest of nuclei has been determined from the data obtained from the nucleosome core and found to be in reasonable agreement with the observed distribution. The periodicity of 10.4 is discussed with respect to the number of base pairs per turn of chromatin DNA and the number of superhelical turns of DNA per nucleosome.     

Template active chromatin structures: Degradation by deoxyribonuclease I

Chicken embryos were pulse-labelled in vivo with [³H]uridine (10 min), the chromatin isolated and treated with DNAse I. The residual chromatin was separated from the degradation products by centrifugation. The nascent pulse-labelled RNA is completely recovered in the residual chromatin even after prolonged incubation with DNAase I, whereas the DNA is completely degraded to 80 base polynucleotide fragments and smaller fragments.Abbreviations cDNA DNA complementary to mRNA - DOC deoxycholate - EDTA ethylendiamintetraacetic acid - SDS sodium-dodecylsulfate     

Measuring Arabidopsis Chromatin Accessibility Using DNase I-Polymerase Chain Reaction and DNase I-Chip Assays

DNA accessibility is an important layer of regulation of DNA-dependent processes. Methods that measure DNA accessibility at local and genome-wide scales have facilitated a rapid increase in the knowledge of chromatin architecture in animal and yeast systems. In contrast, much less is known about chromatin organization in plants. We developed a robust DNase I-polymerase chain reaction (PCR) protocol for the model plant Arabidopsis (Arabidopsis thaliana). DNA accessibility is probed by digesting nuclei with a gradient of DNase I followed by locus-specific PCR. The reduction in PCR product formation along the gradient of increasing DNase I concentrations is used to determine the accessibility of the chromatin DNA. We explain a strategy to calculate the decay constant of such signal reduction as a function of increasing DNase I concentration. This allows describing DNA accessibility using a single variable: the decay constant. We also used the protocol together with AGRONOMICS1 DNA tiling microarrays to establish genome-wide DNase I sensitivity landscapes.Chromatin has a major impact on genome organization and gene activity. Differential accessibility of DNA is thought to be a major consequence of locally different chromatin composition and structure (Li et al., 2007). Chromatin sensitivity to nucleases has proven to be a powerful tool to probe DNA accessibility in chromatin. Frequently used nucleases include DNase, micrococcal nuclease, and restriction enzymes. The resolution of restriction enzymes is limited by their sequence specificity, and micrococcal nuclease is more often used to determine nucleosome occupancy (Schones and Zhao, 2008). Chromatin sensitivity to DNase I has often been used to define the “openness” of chromatin relative to its higher order structures. Its applicability has been manifested by detecting regulatory elements, such as promoters, enhancers, and insulators, as DNase I-hypersensitive sites (Wang and Simpson, 2001; Crawford et al., 2004, 2006; Dorschner et al., 2004; Sabo et al., 2006; Boyle et al., 2008; Naughton et al., 2010; Pique-Regi et al., 2011). DNase I sensitivity can also be used as a measure for the general accessibility of chromatin (Weil et al., 2004).Initially, the chromatin accessibility of local genomic regions to DNase I was probed by Southern blotting (Mather and Perry, 1983; Bender et al., 2000; Wang and Simpson, 2001; Bulger et al., 2003). However, Southern blotting is tedious and lacks sensitivity, and the interpretation of results can be challenging. Therefore, analysis methods based on PCR have been developed (Pfeifer and Riggs, 1991; Feng and Villeponteau, 1992; McArthur et al., 2001; Dorschner et al., 2004; Martins et al., 2007). In recent years, DNase I assays were coupled to high-throughput genome-wide profiling strategies such as genome tiling arrays and next-generation sequencing (Crawford et al., 2004, 2006; Sabo et al., 2004, 2006; Weil et al., 2004). While much has been learned about the accessibility of chromatin in animal and yeast systems, our knowledge of chromatin accessibility in plants is limited. Most studies have focused on selected genomic regions such as the general regulatory factor1 (GRF1) gene and the alcohol dehydrogenase1 (Adh1) and Adh2 genes in maize (Zea mays; Paul and Ferl, 1998a, 1998b) or the GRF gene, the Adh gene, and an 80-kb genomic region harboring 30 protein-coding genes in Arabidopsis (Arabidopsis thaliana; Vega-Palas and Ferl, 1995; Paul and Ferl, 1998a, 1998b; Kodama et al., 2007). The technique used in these reports was exclusively DNase I treatment and analysis of accessibility using Southern blotting. More recently, we have combined the DNase I sensitivity assay with whole-genome tiling arrays in Arabidopsis to generate a genome-wide chromatin accessibility profile (Shu et al., 2012).Here, we present a robust, optimized DNase I sensitivity assay protocol for Arabidopsis tissues based on PCR. This protocol can be adapted to different samples or experimental objectives; the strategies for optimizing each step are also discussed. Analysis of relatively large fragments by PCR has proven to be highly robust as a first step in probing DNase I sensitivity in any region of the genome. We also introduce a new strategy for presenting the DNase I sensitivity of the tested regions using a decay constant calculated by fitting PCR product intensity values from a gradient digestion. In this way, the sensitivity of each region is characterized by a single value, facilitating comparisons between different regions or samples. Finally, we describe how our protocol can be combined with genomic techniques for genome-wide profiles of chromatin accessibility.     

The mechanism and pattern of banding induced by restriction endonucleases in human chromosomes

The mechanism of chromosome banding induced by restriction endonucleases was analyzed by measuring the amount of radioactivity extracted from [¹⁴C]thymidine-labeled chromosomes digested first with restriction enzymes and subsequently with proteinase K and DNase I. Restriction enzymes with a high frequency of recognition sites in the DNA produced a large number of short DNA fragments, which were extracted from chromosomes during incubation with the enzyme. This loss of DNA resulted in decreased chromosomal staining, which did not occur in regions resistant to restriction enzyme digestion and thus led to banding. Subsequent digestion of chromosomes with proteinase K produced a further loss of DNA, which probably corresponded to long fragments retained in the chromosome by the proteins of fixed chromatin. Restriction enzymes induce chromatin digestion and banding in G1 and metaphase chromosomes, and they induce digestion and the appearance of chromocenters in interphase nuclei. This suggests that the spatial organization and folding of the chromatin fibril plays little or no role in the mechanism of chromosome banding.It was confirmed that the pattern of chromosome banding induced by AluI, MboI, HaeIII, DdeI, RsaI, and HinfI is characteristic for each endonuclease. Moreover, several restriction banding polymorphisms that were not found by conventional C-banding were detected, indicating that there may be a range of variability in the frequency and distribution of restriction sites in homologous chromosome regions.     

Assembly of newly replicated chromatin.

Mild staphylococcal nuclease digestions under isotonic conditions release fragments of a 200 Å diameter fiber from nuclei of Drosophila melanogaster tissue culture cells. These soluble fragments have high sedimentation coefficients (30–100S) and show tightly packed nucleosomes in the electron microscope. Under the same conditions, newly replicated chromatin is released as more slowly sedimenting fragments (14S). Within 20 min after DNA replication, the nascent chromatin gradually matures into compact supranucleosomal structures which are indistinguishable from bulk chromatin on the isokinetic sucrose gradients.We have used this fractionation technique to examine the question of the fate and assembly of the new histones. After short pulses with either ³⁵S-methionine or ³H-lysine, the radioactive histones do not co-sediment with the bulk chromatin but appear instead in the fractions where the newly replicated DNA is found. Furthermore, the various nascent histones appear in different fractions on the gradient: histones H3 and H4 in 10–15S structures, histones H2A and H2B in 15–50S structures and histone H1 in 30–100S structures. These results, together with the analysis of pulse and pulse-chase experiments of both nascent DNA and histones, strongly suggest that histones H3 and H4 are deposited first on the nascent DNA (during or slightly after the DNA is replicated), histones H2A and H2B are deposited next (2–10 min later) and histone H1 is deposited last (10–20 min after DNA replication). A high turnover 20,000 dalton protein is also associated with the newly replicated chromatin.     

Studies on the mode of segregation of histone nu bodies during replication in HeLa cells

Two models were tested for the mode of distribution of histone nu bodies at the replication fork. The replication fork was labeled by brief incubation of cells with ³H-thymidine. Nuclei were isolated and digested with low levels of micrococcal nuclease, and the kinetics of cleavage of the pulse-labeled chromatin DNA were compared to the kinetics of cleavage of parental chromatin DNA. In chromatin labeled for 30 sec to 10 min, the rate of cleavage of the pulse-labeled region into monomeric nu body-sized units exceeded the rate of cleavage of parental chromatin by a factor of 2, but did not approach the predicted value of 5–6 for random segregation. This value dropped to 1.6 in 15 min and was euivalent to parental chromatin in 20 min labeling experiments. DNA synthesized in the presence of cycloheximide was also digested at twice the rate of parental chromatin DNA.A Poisson analysis of the kinetics of cleavage by micrococcal nuclease further confirmed these observations. The predicted difference in the rate of production of monomeric, dimeric, and trimeric deoxyribonucleoprotein units was very similar to the experimental values of both total chromatin and nascent chromatin. Thus the nu body spacings in newly replicated chromatin closely approximate those in parental chromatin.These results agree well with a conservative or nondispersive model of nucleosome distribution in which the proteins are associated with one of the two daughter chromosomes during replication.     

Enzymatic conversion of long DNA to small DNA fragments for the construction of short hairpin RNA expression libraries

Several techniques to enzymatically construct a short hairpin RNA (shRNA) expression library have been reported as tools for comprehensive genetic analyses by RNA interference. Our technique constructs an shRNA expression library from 25- to 35-bp DNA fragments by fragmenting given double-stranded DNA (dsDNA). We compared the following two procedures to efficiently prepare such small DNA fragments: one is the cleavage of dsDNA with deoxyribonuclease I (DNase I) in the presence of Mn²⁺ followed by blunting with T4 DNA polymerase, and the other is the introduction of nicks with DNase I in the presence of Mg²⁺ followed by blunting with the Klenow fragment. Consequently, the latter yielded the DNA fragments more efficiently. However, these DNA fragments were contaminated with fused DNA fragments that had originated from two regions of original dsDNA. Therefore, we used single-strand-specific exonucleases and succeeded in suppressing the production of such fused DNA fragments. Our technique allows the efficient conversion of given dsDNA to small DNA fragments.     

Breakage of Parental DNA Strands in Haemophilus influenzae by 313 nm Radiation after Replication in the Presence of 5-Bromodeoxyuridine

Haemophilus influenzae was labeled with thymidine-³H (dThd), then grown in the presence of 5-bromodeoxyuridine (BrdUrd), and then irradiated with 313 nm light (a wavelength that selectively photolyzes DNA containing 5-bromouracil [BrUra]). Irradiation with 313 nm light induced breaks in the ³H-labeled strands in cells grown with BrdUrd at a much higher frequency than in ¹⁴C-labeled DNA of cells not exposed to BrdUrd. Breakage of the ³H-labeled strands was about 0.6% as efficient as that of fully BrUra-substituted DNA. During growth in the presence of BrdUrd, susceptibility to 313 nm-induced breakage of the ³H-labeled DNA strands increased, reaching a maximum in about one generation, and it decreased to zero during subsequent growth for one generation in medium containing dThd instead of BrdUrd. Heat denaturation of DNA extracted from dThd-³H-labeled cells grown in the presence of BrdUrd eliminated 313 nm-induced breakage of the ³H-labeled strands. It is concluded that breakage of the ³H-labeled DNA strands resulted from reaction with photoproducts in the base-paired, BrUra-containing strands, rather than from photolysis of BrdUrd incorporated into parental strands. It may be possible to utilize the phenomenon of interstrand breakage in physical studies of DNA replication.     

Deoxyribonuclease I produces staggered cuts in the DNA of chromatin

The relationship of cuts made by deoxyribonuclease I (DNase I, EC. 3.1.4.5) on the two strands of DNA of chromatin has been investigated. DNA was extracted from a DNase I digest of rat liver nuclei and incubated with the large fragment of DNA polyrnerase I. Analysis of the products of this incubation indicates the cuts made by DNase I on opposite strands are staggered with respect to one another. A cut on one strand is about two bases in the 3′ direction or eight bases in the 5′ direction from the position on its own strand which is directly across from the cut on the other strand. A different result is obtained when a DNase I digest of native DNA is analyzed. Current models for the organization of DNA in the nucleosome are discussed with respect to these results.     

Analysis of chromatin of skeletal muscle of developing rats using micrococcal nuclease and DNase I

Conformational changes in the chromatin of skeletal muscle of 3-, 14-and 30 day-old developing rats have been studied using DNase I and micrococcal nuclease (MCN). Purified nuclei were digested separately by MCN and DNase I. The rate and extent of digestion by MCN decreases gradually as development proceeds. The electrophoretic pattern of MCN digested DNA, however, shows no change. The kinetics of digestion of nuclei by DNase I show no change with development. However, the electrophoretic pattern of DNase I digested DNA shows a gradual decrease in the amount of 10–30 bp fragments with progressive development. These studies show that the chromatin of the skeletal muscle undergoes certain conformational changes during postnatal development, and such changes in chromatin may be necessary for terminal differentiation of this tissue.     

Deoxyribonucleic acid synthesis in isolated DNA-membrane complexes

The DNA synthesized by isolated Escherichia coli DNA-membrane complexes has been analysed by centrifugation techniques. The in vitro synthesized DNA sediments after deproteinization, in part with the parental bulk DNA and in part as a spectrum of fragments with sedimentation coefficients between 10 and 25 s. The fragments are, at least partially, precursors to the fast sedimenting DNA. The DNA fragments are mostly double stranded and contain (i) parental DNA pieces non-covalently bound to newly synthesized DNA strands of similar length, as well as (ii) one well-defined fraction in which parental DNA and newly synthesized DNA are covalently joined. The results are discussed in terms of the “prefork synthesis” model of Haskell & Davern (1969).     

Conformational changes in the chromatin of the brain of developing rats and its modulation by zinc chloride

Conformational changes in the chromatin of the brain were studied during the development of the rat (3-, 14-and 30-day old) using microccoccal nuclease (MCN) and DNase I. The rate and extent of digestion of chromatin by MCN is not altered during development. However, pre-incubation of slices of the cerebral cortex with ZnCl₂ increases the initial rate of digestion by MCN by 2–3-fold, and also enhances the production of monomer DNA. The rate and extent of digestion of chromatin by DNase I is greater in an early stage of development. The initial rate of digestion by DNase I is stimulated by 3–4-fold after ZnCl₂ treatment. These data show that changes occur in the conformation of chromatin, particularly in the internucleosomal region of brain cells as they pass from dividing to the non-dividing state.