A simple and efficient procedure for isolating plant chromatin which is suitable for studies of DNase I-sensitive domains and hypersensitive sites

Summary A simple and rapid procedure has been developed for the isolation of chromatin from plant leaves. The molecular weight of the DNA extracted from these chromatin preparations is comparable to that of DNA isolated by a conventional purification procedure (CTAB-CsCl-method). These results suggest that almost no degradation occurs during the isolation procedure. The effect of DNase I on three different groups of genes was studied; one of them, encoding the NADPH-protochlorophyllide oxidoreductase (PCR), represents a gene which is actively transcribed in etiolated leaf tissue. The other genes examined encode the hordein seed storage protein and 26S ribosomal RNA. The hordein genes are known to be inactive in leaves.The hordein and rDNA genes were found to be resistant to low levels of DNase I, while the gene for the PCR was highly sensitive to DNase I. During the course of digestion of the PCR gene, discrete cleavage products are generated. These indicate the presence of DNase I hypersensitive sites in the vicinity of the PCR gene in etiolated leaves. As a control naked DNA has been digested with DNase I. No differences in sensitivity between the PCR gene and the hordein genes can be detected.     

Quantitation of DNase I sensitivity in Xenopus chromatin containing active and inactive globin, albumin and vitellogenin genes.

The disappearance of defined restriction fragments of the beta 1-globin, an albumin and the A1 vitellogenin gene was quantitated after DNase I digestion and expressed by a sensitivity factor defined by a mathematical model. Analysis of naked DNA showed that the gene fragments have similar but not identical sensitivity factors. DNase I digestion of chromatin revealed for the same gene fragments sensitivity factors differing over a much wilder range. This is correlated to the activity of the genes analyzed: the beta 1-globin gene fragment is more sensitive to DNase I in chromatin of erythrocytes compared to hepatocytes whereas the albumin gene fragment is more sensitive to DNase I in chromatin of hepatocytes. The A1 vitellogenin gene has the same DNase I sensitivity in both cell types. Comparing the DNase I sensitivity of the three genes in their inactive state we suggest that different chromatin conformations may exist for inactive genes.     

The distribution of NADPH-protochlorophyllide oxidoreductase in relation to chlorophyll accumulation along the barley leaf gradient

The possible regulatory role of NADPH-protochlorophyllide oxidoreductase for chlorophyll accumulation has been investigated in barley plants. Within the primary leaf of etiolated plants the different maturation stages of etioplasts are found in a linear series with the youngest in cells near the base and the oldest in cells near the tip. This distribution of different plastid forms is paralleled by drastic differences in the NADPH-protochlorophyllide-oxidoreductase content of the plastids and their capacity to accumulate chlorophyll during illumination. The amount of enzyme and the rate of chlorophyll accumulation are highest in the mature etioplast in the tip of the leaf and both decline rapidly with decreasing age of the leaf tissue, being almost undetectable in the leaf base. The translatable mRNA coding for the enzyme shows a different distribution pattern within the leaf. The highest concentration is found in the middle part of the leaf while in the top part only traces of this mRNA are detectable. It is concluded that during leaf development the enzyme is synthesized rapidly only during a limited time period and that it is stored subsequently in the mature etioplast as a stable protein. The close correlation between the distribution of the enzyme within the barley leaf and that of the potential to accumulate chlorophyll during illumination would favour a control of chlorophyll accumulation by the amount of NADPH-protochlorophyllide oxidoreductase. Dark-grown plants which were exposed to far-red light were used to test this possibility. The far-red-absorbing form of phytochrome (P_fr) has an inverse effect on the kinetics of chlorophyll accumulation and the enzyme concentration. Our results indicate that the rate of chlorophyll accumulation in barley is not determined by the level of NADPH-protochlorophyllide oxidoreductase present in the leaves.     

Regreening of senescent Nicotiana leaves. I. Reappearance of NADPH-protochlorophyllide oxidoreductase and light-harvesting chlorophyll a/b-binding protein

Decapitation of Nicotiana rustica L. plants above a single senescent leaf induced regreening, which was promoted by cytokinin treatment. Regreening required low light. The decline in leaf protein content and increase in protease activity seen during senescence were reversed on regreening. Western blotting showed that light-harvesting chlorophyll a/b-binding protein declined considerably during senescence, but on regreening it increased back to the levels seen in green leaves. NADPH-protochlorophyllide oxidoreductase (POR) was found by Western blotting at high levels in etiolated cotyledons, but at low levels in green leaves and not at all in senescent leaves. However, POR reappeared in regreening leaves, and cytokinin accelerated its increase.     

Rearranged and germline immunoglobulin kappa genes: different states of DNase I sensitivity of constant kappa genes in immunocompetent and nonimmune cells

The rearrangement of a variable (V) and a constant (C) gene appears to be a necessary prerequisite for immunoglobulin gene expression. Multiple different rearranged kappa genes were found in several mouse myelomas, although these cells produce only one type of kappa chain [Wilson, R., Miller, J., & Storb, U. (1979) Biochemistry 18, 5013--5021]. It is therefore of interest to understand how only one allele within a lymphoid cell becomes expressed, while the other allele remains nonfunctional ("allelic exclusion"). We have studied the chromatin conformation of kappa genes by making use of the preferential digestion of potentially active genes by DNase I described, for example, for globin genes [Weintraub, H., & Groudine, M. (1976) Science (Washington, D.C.) 193, 848--856]. The DNase I sensitivity of kappa genes in myeloma tumors, in a B cell lymphoma, and in liver was determined by hybridization with DNA on Southern blots. It was found that rearranged C kappa genes are DNase I sensitive in myelomas in which several kappa genes are rearranged, regardless of whether the rearranged genes code for the kappa chains synthesized by the cell. Furthermore, the C kappa gene in germline configuration is also DNase I sensitive in a B cell lymphoma; i.e., it is in the same chromatin state as the rearranged C kappa gene which probably codes for the kappa chains produced by the cell. The altered chromatin state appears to be localized: V kappa genes in germline context are not DNase I sensitive in myeloma or B lymphoma cells while C kappa genes present in a kappa gene cluster on the same chromosomes are sensitive. When rearranged, however, the V kappa genes are as sensitive to DNase I as are rearranged C kappa genes. V lambda and C lambda genes are not DNase I sensitive in kappa myelomas. Thus, commitment to kappa gene expression is apparently correlated with a chromatin conformation which confers increased DNase I sensitivity to the DNA in the vicinity of all C kappa genes in the cell. "Allelic exclusion" does not operate on the level of chromatin conformation which can be detected by altered DNase I sensitivity.     

Deoxyribonuclease I sensitivity of the ovomucoid-ovoinhibitor gene complex in oviduct nuclei and relative location of CR1 repetitive sequences

The location of CR1 middle repetitive sequences within or near the boundaries of the ovalbumin DNase I sensitive domain has suggested that CR1 sequences may play a role in defining transition regions of DNase I sensitivity in hen oviduct nuclei. We have examined this apparent relationship of CR1 sequences and transitions of chromatin structure by determining the DNase I sensitivity in oviduct nuclei of a 47-kilobase region that contains five CR1 sequences and the transcribed ovomucoid and ovoinhibitor genes. We find that three of the CR1 sequences occur within a broad transition region of decreasing DNase I sensitivity downstream of the ovomucoid gene. Another CR1 is in a region of decreased DNase I sensitivity within the ovoinhibitor gene. The fifth CR1 sequence is in a DNase I sensitive region between the two genes but which is less sensitive to DNase I digestion than the region immediately upstream from the ovomucoid gene. Thus, the CR1 sequences occur within regions of reduced relative DNase I sensitivity, suggesting that CR1s could facilitate the formation of a chromatin conformation that is less sensitive to DNase I digestion. Unexpectedly, the noncoding strand of sequences within and immediately adjacent to the 5' end of the actively transcribed ovomucoid and ovalbumin genes was less sensitive to DNase I digestion than their respective coding strands.     

Nonradioactive in situ nick translation combined with counterstaining: Characterization of C-band and silver positive regions in mouse testicular cells

The DNase I sensitivity of three different chromatin regions in mouse testicular cells was analysed by in situ nick translation with biotin-dUTP combined with various counterstaining techniques. The regions were: (i) the constitutive centromeric heterochromatin, (ii) an interstitial C-band positive insertion on chromosome 1, Is(HSR1;C5)1Lub, and (iii) the chromatin containing rDNA (designated nucleolar chromatin herein). Incorporated biotin was detected either by the horseradish peroxidase reaction with diaminobenzidine (DAB) or the alkaline phosphatase reaction with fast red. The latter resulted in a water insoluble red precipitate, which was easily removable by any organic solution thus allowing the application of various counterstaining protocols. DNase I sensitivity of the three chromatin regions was screened in different cell types of the mouse testis. The interstitial Is(HSR) region was highly DNase I sensitive when it was recognizable by strong mithramycin fluorescence. The centromeric heterochromatin was DNase I resistant when it was compacted into microscopically visible chromosomal structures (mitosis, pachytene, metaphase I and II). In interphase nuclei from Sertoli cells and spermatogonia it became highly DNase I sensitive. In round spermatids it displayed medium DNase I sensitivity. Nucleolar chromatin was not labelled by in situ nick translation when silver staining demonstrated strong protein production. Sperm cells were highly DNase I sensitive from stages 11 to 15, but resistant as mature spermatozoa.     

Estrogen induces tissue specific changes in the chromatin conformation of the vitellogenin genes in Xenopus.

Nuclei from male Xenopus liver were digested extensively with DNase I and the residual amount of the four vitellogenin genes measured by hybridization with a moderate excess of vitellogenin cDNA. The saturation value was about twofold lower in chromatin isolated from liver cells of estrogen treated than from untreated males or from erythrocytes. Analyzing the disappearance of several defined restriction fragments specific for the A1 and A2 vitellogenin genes, after limited digestion with DNase I, suggested that the entire A1 and A2 vitellogenin genes are about twofold more sensitive to DNase I in chromatin of hepatocytes isolated from estrogen treated than from untreated males. Using the same assay no change in the DNase I sensitivity of the two vitellogenin genes in erythrocyte chromatin was observed. Analysis of the beta 1-globin and an albumin gene demonstrated that the DNase I sensitivity of these genes in both cell types is not altered by estrogen. All these data indicate that estrogen stimulation results in an increased DNase I sensitivity specific for the vitellogenin genes in hepatocytes.     

DNase I hypersensitivity and expression of the Shrunken-1 gene of maize

The local chromatin structure of the Shrunken-1 (Sh) gene of maize was probed by analyzing DNase I hypersensitivity. Sh encodes the gene for sucrose synthetase, a major starch biosynthetic enzyme, which is maximally expressed in the endosperm during seed maturation. In addition to general DNase I sensitivity, specific DNase I hypersensitive sites were identified in endosperm chromatin that mapped near the 5 end of the Sh gene. The pattern of hypersensitive sites and their relative sensitivity were altered in other non-dormant tissues that produce little or no enzyme. However, some changes in chromatin structure appear to be independent of Sh gene expression and may reflect general alterations associated with plant development. The chromatin structure of several sh mutations, induced by Ds controlling element insertions, was also analyzed. Although the insertions perturbed expression of the gene, there were no notable effects on local chromatin structure.     

Nuclease sensitivity of active chromatin.

The active regions of chicken erythrocyte nuclei were labeled using the standard DNase I directed nick translation reaction. These nuclei were then used to study the characteristics and, in particular, the nuclease sensitivity of active genes. Although DNase I specifically attacks active genes, micrococcal nuclease solubilizes these regions to about the same degree as the total DNA. On the other hand micrococcal nuclease does selectively cut the internucleosomal regions of active genes resulting in the appearance of mononucleosomal fraction which is enriched in active gene DNA. A small percentage of the active chromatin is also released from the nucleus by low speed centrifugation following micrococcal nuclease treatment. The factors which make active genes sensitive to DNase I were shown to reside on individual nucleosomes from these regions. This was established by showing that isolated active mononucleosomes were preferentially sensitive to DNase I digestion. Although the high mobility group proteins are essential for the maintenance of DNase I sensitivity in active regions, these proteins are not necessary for the formation of the conformation which makes these genes preferentially accessible to micrococcal nuclease. The techniques employed in this paper enable one to study the chromatin structure of the entire population of actively expressed genes. Previous studies have elucidated the structure of a few special highly prevalent genes such as ovalbumin and hemoglobin. The results of this paper show that this special conformation is a general feature of all active genes irregardless of the extent of expression.     

Light modulation of the activity of protochlorophyllide reductase.

Illumination of etiolated plants effects the activity of protochlorophyllide reductase (NADPH-protochlorophyllide oxidoreductase) in the plastids. Constant illumination or a 2-min light-triggering of etiolated plants leads to an approx. 80% decrease in activity of the enzyme, a change that can be reversed by returning the plants to darkness. The change in activity results from an alteration of the Vmax. rather than Km. Despite the fact that exogenous pigments effect the activity of the enzyme in vitro, no correlation could be drawn between the concentrations of pigments in vivo and activity of the enzyme.     

Chromatin structure of transferred genes in transgenic plants

The chromatin structure of foreign genes in transgenic tobacco plants was investigated by digestion of nuclei with DNase I and micrococcal nuclease, respectively, followed by restriction and Southern analysis of the digestion products. The results were compared to the differential expression of the different transgenes. Two model systems were used: plants harbouring vector DNA derived from the disarmed vector pGV 3850 and plants harbouring the light-regulated and organ-specifically expressed potato ST-LS1 gene and the cotransferred ncpaline synthase (nos) reporter gene. Our results show that transferred genes are located in DNase l-sensitive domains in all transformants. Slight variations of DNase l-sensitivity of the transferred ST-LS1 constructs in different transformants neither reflected the between-transformant variability of expression nor the organ-specific activity of the transgenes. A deletion event was found responsible for silencing the ST-LS1 gene but not the nos gene in one of the transformants. Whereas no DNase l-hypersensitive sites were found within the 3850-T-DNA and the ST-LS1 gene, one prominent site was mapped to the nos promoter within the ST-LS1 construct in all transformants. Digestion of chromatin harbouring 3850-T-DNA with micrococcal nuclease resulted in a blurred nucleosomal pattern as compared to nucleolar and bulk chromatin, the extent of blurring being independent of the expression of transferred genes. The present results favour the “permissive domain” hypothesis which capitalizes on the chromatin surrounding the integration site as the determining factor for the chromatin structure of incoming alien genes. However, between-transformant variability of expression is not reflected by differential sensitivity to DNase I. Hence, other factors than chromatin structure must be involved in creating “position effects”.     

Gamma rays and bleomycin nick DNA and reverse the DNase I sensitivity of beta-globin gene chromatin in vivo.

The active beta-globin genes in chicken erythrocytes, like all active genes, reside in large chromatin domains which are preferentially sensitive to digestion by DNase I. We have recently proposed that the special structure of chromatin in active domains is maintained by torsional stress in the DNA (Villeponteau et al., Cell 39:469-478, 1984). This hypothesis predicts that nicking of the DNA within any such chromosomal domain in vivo will relax the DNA and lead to loss of the special DNase I-sensitive state. Here we have tested this prediction by using gamma irradiation and bleomycin treatment to cleave DNA within intact chicken embryo erythrocytes. Both treatments cause reversal of DNase I sensitivity. Moreover, reversal occurs at approximately one nick per 150 kilobase pairs for both agents despite their entirely unrelated modes of cell penetration and DNA attack. These results suggest that the domain of DNase I sensitivity surrounding the beta-globin genes comprises 150 kilobase pairs of chromatin under torsional stress and that a single DNA nick in this region is sufficient to reverse the DNase I sensitivity throughout the entire domain.     

Streptomycin mimics the cool temperature response in rice plants

Exogenous application of streptomycin to etiolated seedlings of rice (Oryza sativa L.) during growth in darkness at moderate temperatures induced the same type of chlorosis as that elicited by cool temperatures. A comparison of sensitive (Indica) and tolerant (Japonica) cultivars indicated a close relationship between sensitivity to streptomycin and cool temperatures. Immunoblot (Rubisco LSU, SSU; CF1 complex of H⁺-ATPase; NADPH-protochlorophyllide oxidoreductase) and Northern blot analyses of plastid-encoded genes (16S rRNA; rbcL; rpoB; petB) in the streptomycin-treated sensitive cultivars revealed that the normal etioplast development was specifically inhibited by the antibiotic. Furthermore, the antibiotic did not affect the expression of mitochondrion-encoded genes (18S rRNA; atpA), which are also unaffected by cool temperatures. These result suggest that the effect of the antibiotic is quite similar to that of cool temperatures.     

Differential expression of two types of sucrose synthase-encoding genes in wheat in response to anaerobiosis, cold shock and light

The expression of two types of sucrose synthase-encoding genes, Ss1 and Ss2, in hexaploid wheat (Triticum aestivum, L.), has been investigated using type-specific probes, corresponding to the 250-270 bp C-terminal portions of the respective cDNA clones. Both types of genes are highly expressed in developing endosperm, where the expression of the Ss2 type slightly precedes in time that of the Ss1 type. Expression of Ss genes is lower in etiolated leaves and in roots than in endosperm. In the first two tissues, the Ss1 mRNA is much more abundant than the Ss2 mRNA, and the Ss1 mRNA level sharply increases in response to anaerobiosis and to cold shock (6 degrees C), while the level of Ss2 mRNA is not significantly affected. Upon illumination of etiolated leaves, the Ss1 level mRNA decreases significantly and the Ss2 mRNA level increases.