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The Relationship Between DNA Methylation and Chromosome Imprinting in the Coccid Planococcus citri
Silvia Bongiorni1,a, Orietta Cintioa, and Giorgio Pranteraaa Dipartimento di Agrobiologia e Agrochimica, Università della Tuscia, 01100 Viterbo, Italy
Corresponding author: Giorgio Prantera, Dipartimento di Agrobiologia e Agrochimica, Università della Tuscia, Via S. Camillo De Lellis, 01100 Viterbo, Italy., prantera{at}unitus.it (E-mail)
Communicating editor: V. G. FINNERTY
| ABSTRACT |
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The phenomenon of chromosome, or genomic, imprinting indicates the relevance of parental origin in determining functional differences between alleles, homologous chromosomes, or haploid sets. In mealybug males (Homoptera, Coccoidea), the haploid set of paternal origin undergoes heterochromatization at midcleavage and remains so in most of the tissues. This different behavior of the two haploid sets, which depends on their parental origin, represents one of the most striking examples of chromosome imprinting. In mammals, DNA methylation has been postulated as a possible molecular mechanism to differentially imprint DNA sequences during spermatogenesis or oogenesis. In the present article we addressed the role of DNA methylation in the imprinting of whole haploid sets as it occurs in Coccids. We investigated the DNA methylation patterns at both the molecular and chromosomal level in the mealybug Planococcus citri. We found that in both males and females the paternally derived haploid set is hypomethylated with respect to the maternally derived one. Therefore, in males, it is the paternally derived hypomethylated haploid set that is heterochromatized. Our data suggest that the two haploid sets are imprinted by parent-of-origin-specific DNA methylation with no correlation with the known gene-silencing properties of this base modification.
THE phenomenon of chromosome, or genomic, imprinting reveals the relevance of parental origin in determining functional differences between homologous alleles or differences in the behavior of homologous chromosomes (for reviews see ![]()
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Historically, the first evidence for imprinting and its consequences for development was obtained from cytological studies of insects. In some insects, imprinting can affect the behavior of whole chromosomes or of an entire set of chromosomes. For example, in the fungal gnat Sciaridae, the zygote has three X chromosomes, two of paternal and one of maternal origin. During the syncytial embryonic divisions, maternal factors regulate whether one or two X chromosomes are eliminated. The embryos eliminating one X chromosome develop as females, while those eliminating two develop as males. In the germ line of both sexes, only one X chromosome is eliminated. Both in the germ line and in the soma, the elimination always affects the paternally derived X chromosomes; hence, the X chromosomes are parentally imprinted (![]()
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In vertebrates, considerable data exist suggesting that methylation of cytosine residues at CpG doublets in DNA plays a role in the establishment, maintenance, and erasure of the parent-of-origin imprinting at the gene level (for review see ![]()
Elucidating the molecular mechanisms underlying the imprinting of entire chromosomes or haploid chromosome sets as occurs in insects should be informative for examining the relationship between imprinting, methylation, and gene activity. In Coccids the presence of both cytosine methylation (![]()
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In these studies, we examined the relationship between DNA methylation and chromosome imprinting in mealybugs using two approaches. First, our molecular assays confirmed the presence of 5-methylcytosine in the DNA of the Coccid Planococcus citri. We did not detect differences in the overall methylation levels when male and female genomic DNAs were compared. We also used a method that permitted the detection of DNA methylation patterns in situ, at the chromosomal level. This method is called restriction enzyme-directed in situ nick translation (RE/NT) and had previously been proven to be a powerful tool to investigate DNA sequence organization at the chromosomal level (![]()
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| MATERIALS AND METHODS |
|---|
Mealybug cultures:
P. citri were raised in our laboratory on sprouting potatoes at 27°, inside glass food containers covered with gauze. The potatoes were kept in the dark to sprout for 1 mo before use.
X-ray treatment:
About 25 males at different stages of the life cycle were treated with 4000 rad of X rays delivered at a dose of 100 rad per minute. Following treatment, the males were mated en masse to virgin females. After fertilization, gravid females, containing a sufficient number of embryos for cytological analysis, were dissected as described below.
Genomic DNA extraction, digestion, and electrophoresis:
Total genomic DNA was separately isolated and purified from virgin females, gravid females, or adult males, following the method of ![]()
Chromosome preparation:
Chromosome spreads were obtained by a modification of previously described methods (![]()
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In situ nick translation:
In situ MspI, HpaII, AluI, and EcoRI/nick-translation (NT) experiments were carried out on slides containing fresh chromosome spreads (![]()
Detection and fluorescence observation:
After two washes in 10 mM Tris-HCl pH 7.4 for 5 min, the slides were treated with blocking reagent (4x SSC, 30 mg/ml BSA, 0.1% Tween 20; 1x SSC is 0.15 M NaCl, 0.015 M sodium citrate) at 37° for 30 min. Detection was carried out with avidin fluorescein isothiocyanate conjugate (avidin-FITC; Vector Laboratories, Burlingame, CA) 1:300 in detection solution (2x SSC, 1 mg/ml BSA, 0.1% Tween 20) for 30 min at 37° in a wet chamber. The slides were washed three times in 4x SSC and 0.1% Tween 20, at 42° for 5 min. The signal was amplified with biotinylated antiavidin antibody (Vector Laboratories) 1:100 in PBS for 30 min at 37° in a wet chamber. After four washes in 4x SSC and 0.1% Tween 20, at 42° for 5 min, the slides were treated again with avidin FITC for 30 min at 37° in a wet chamber. The chromosomes were counterstained with 0.2 µg/ml DAPI (Boehringer Mannheim) in 2x SSC for 5 min. After counterstaining in DAPI, the slides were mounted in antifade medium [DABCO (Sigma, St. Louis) 23.3 mg/ml, 10 mM Tris-HCl pH 7.58, 90% sterile glycerol] and observed with a Zeiss Axiophot fluorescence microscope equipped with a 100-W mercury light source. The filter combinations used were 01 for DAPI (365/11 nm excitation range) and 09 for FITC (450490 nm excitation range). Fluorescent images were captured with a CCD camera (series 200; Photometrics, Tucson, AZ) using IPLab software (Signal Analytics Corp., Vienna, VA) and processed with a Power Macintosh 8100 using Adobe Photoshop software.
| RESULTS |
|---|
Probing genomic DNA of P. citri with HpaII and MspI:
The two isoschizomers, HpaII and MspI, have the same recognition sequence (C/CGG), but are differentially sensitive to the methylation state of the internal cytosine. HpaII does not cut the sequence when the cytosine is methylated, whereas MspI is insensitive to its methylation state. Figure 1 shows ethydium bromide stain of mixed male and female P. citri genomic DNA after digestion with HpaII (lane 1) or MspI (lane 2). As expected, both enzymes produced a wide range of restriction fragments, but with HpaII the smear began just below the 23.1-kb marker band, while with MspI the smear was shifted toward the lower molecular weights, starting below the 9.4-kb band of the marker. In lanes 3 and 4 the results of the digestion with HpaII of male (lane 3) and unmated-female (lane 4) genomic DNA are shown. The two patterns are nearly identical and indistinguishable from the pattern of HpaII-digested genomic DNA from the mixed population of males and females (lane 1). Hence, this method did not detect any sex-specific differences in DNA methylation in P. citri.
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Methylation patterns of P. citri chromosomes in situ:
In P. citri males the haploid set of paternal origin becomes heterochromatized during midcleavage stages, while in females both sets appear euchromatic. To detect in situ possible differences in DNA methylation patterns between haploid sets in P. citri male and female cells (2n = 10) we digested chromosome preparations with the restriction enzymes MspI or HpaII. The endonucleolytic nicks were then expanded by nick translation in the presence of a biotinylated dUTP. The incorporation of biotinylated dUTP after nick translation is evidenced by the binding of an avidin-fluorescein complex. FITC fluorescence is thus indicative of susceptibility to the enzyme of the corresponding chromosome material. Both male and female embryonic tissues were simultaneously present in the same preparation (see MATERIALS AND METHODS), permitting comparison within an experiment. Male and female tissue patches can be easily distinguished because in male cells the heterochromatic haploid set formed a conspicuous, darkly staining structure in interphase cells. This morphological distinction between the two sets is still distinguishable in mitosis (compare male and female cells in Figure 2 and Figure 3, a1e1) until late metaphase when both euchromatic and heterochromatic sets become highly condensed.
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At digestion times of 10 min or higher, MspI and HpaII produced a similar fluorescent pattern along the chromosomes of both female and male cells, with no differential labeling of the two haploid sets in the latter. However, at the shortest digestion times (1.5 and 3 min) the two enzymes yielded different patterns along P. citri chromosomes, and the results reported below refer to these observations.
Figure 2 shows the results obtained after the MspI digestion in male (ac) and female (d and e) embryonic cells. The FITC-fluorescence pattern indicates the susceptibility of the P. citri chromosomes to digestion with MspI. In Figure 2, a1e1, the same metaphases were counterstained with the fluorescent DNA dye DAPI. Note that in both male and female cells all the chromosomes of a metaphase were FITC-labeled and that the labeling intensity of the chromosomes of a metaphase parallels their DAPI staining intensity.
The pattern obtained after HpaII-directed in situ nick translation of P. citri chromosome preparations is shown in Figure 3. In both male (Figure 3, ac) and female (Figure 3D and Figure E) embryonic cells only five chromosomes of the diploid complement are FITC labeled, while the remaining five are faint or totally unlabeled. From the comparison with DAPI images of male nuclei and metaphases (Figure 3, a1c1) it was readily apparent that the five labeled chromosomes corresponded to the heterochromatic haploid set. These results therefore indicated that the paternally derived heterochromatic haploid set was more sensitive to the digestion by the methyl-inhibited HpaII enzyme than the maternally derived euchromatic chromosomes.
The RE/NT of P. citri chromosomes after digestion with AluI (AG/CT) or EcoRI (G/AATTC) never produced a differential labeling of the heterochromatic and euchromatic sets in male cells, or the appearance in female cells of five FITC-labeled and five unlabeled chromosomes (data not shown).
In parallel control experiments, the chromosome preparations were nick translated after incubation with the digestion buffer without any restriction enzyme. At incubation times of 1.5 and 3 min the mock digestion did not produce any FITC labeling along the chromosomes, while with higher incubation times a faint, uniform labeling was produced along the chromosomes of both male and female embryonic cells.
Parental origin of the undermethylated chromosomes in female cells:
We wanted to ascertain if the five HpaII-sensitive and the five HpaII-resistant chromosomes of female embryonic cells also represented two separate haploid sets and, in this case, if they were of nonrandom parental origin. To this aim, since it is difficult to reconstruct the P. citri karyotype after DAPI staining, we carried out a different experimental approach. We applied HpaII RE/NT to the progeny of crosses between virgin females and males treated with heavy doses of X-irradiation. The X-ray-induced chromosome fragments and rearrangements were retained during spermatogenesis and transmitted to the F1 progeny because of the holocentric nature of Coccid chromosomes (![]()
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| DISCUSSION |
|---|
From the comparison of genomic DNA digestion patterns with HpaII and MspI, we expected information on the pattern of DNA methylation in the P. citri genome. In fact, these two isoschizomers cut the same DNA sequence (CCGG), but HpaII is inhibited by the methylation of the internal cytosine, while MspI is insensitive to it. Our results clearly show that MspI produces lower molecular weight DNA fragments than HpaII in DNA from a mixed population of male and female individuals, thus confirming the presence of a methylated DNA fraction in the P. citri genome, in accordance with the data obtained in mealybug species by other groups with immunochemistry (![]()
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We obtained a confirmation and extension of the results described above using the RE/NT technique. The RE/NT technique uses the differential sensitivity of HpaII and MspI to methylated cytosine residues to detect in situ DNA methylation patterns at chromosome and cellular levels (![]()
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The digestion with the methylation-sensitive HpaII does not uniformly affect all the chromosomes of the P. citri complement (2n = 10). In fact, in both male and female embryonic cells five chromosomes of the complement are intensely FITC labeled, i.e., sensitive to HpaII, while the other five are faint or unlabeled, i.e., insensitive to HpaII. These findings are in perfect accordance with the above-reported molecular evidences. In fact, these observations confirm both the presence of a methylated DNA fraction in the P. citri genome and the similarities of male and female genomic DNA with respect to the methylation pattern. In male cells, the five highly labeled chromosomes consistently correspond to the heterochromatic set. The paternally derived heterochromatic set is therefore more sensitive to HpaII and, hence, less methylated than the maternally derived euchromatic one.
The efficiency of enzyme nicking is certainly dependent upon DNA sequence and it could also be sensitive to the level of chromatin packaging (![]()
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First, it is the heterochromatic set that, because of its higher degree of chromatin compaction, would be predicted to be less accessible to enzyme digestion than the euchromatic one. But in this context it should be noted that in the mealybug P. lilacinus only the 35% of DNA in males is in a chromatin conformation resistant to nuclease digestion. The remaining 9597% of male chromatin exhibits the same level of nuclease resistance as female chromatin (![]()
Second, the two chromosome sets do not show differential sensitivity to the methyl-insensitive isoschizomer MspI. In fact, the heterochromatic set is only slightly more labeled by MspI RE/NT than the euchromatic one, but this difference, if any, parallels an analogous difference after DAPI staining (compare FITC and DAPI images of Figure 2). The two haploid sets have obviously the same DNA base compositions, and hence their differential staining with the AT-specific DNA ligand DAPI is only determined by the more condensed chromatin conformation of heterochromatic chromosomes. The higher DNA amount per chromosome unit-length of the heterochromatic material can also well account for the slightly higher FITC-labeling intensity of the heterochromatic set after MspI RE/NT. The similar sensitivity to MspI of euchromatic and heterochromatic sets is well in accordance with the above-mentioned results (![]()
Our results suggest that parent-of-origin-based differences in DNA methylation levels of the two haploid sets could account for parental chromosome imprinting in the P. citri males. The paternally derived unmethylated chromosomes undergo inactivation by heterochromatization, while their methylated maternally derived homologs remain active. From what is known about vertebrates, the findings that the functional inactivation affects the less-methylated homolog and that methylation does not hinder genetic activity appear to be surprising. In this context two considerations must be taken into account. First, for those invertebrate species in which the presence of DNA methylation has been demonstrated, this base modification is not correlated with gene inactivation. In fact, recently it has been shown that several constitutively active housekeeping genes reside in the methylated fraction of the invertebrate genome (![]()
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We observed also that in female embryonic cells 5 chromosomes of the complement are more sensitive to HpaII than the other 5, while with MspI the 10 chromosomes are equally digested. The HpaII RE/NT analysis of chromosome preparations from the daughters of irradiated fathers showed that the great majority (31 out of 39) of paternally derived chromosome fragments scored in female cells were sensitive to HpaII. Furthermore, in cells showing fragments, 5 unlabeled chromosomes can always be recognized, but 5 normally shaped FITC-labeled chromosomes cannot, indicating that the rearranged chromosome contribution of irradiated fathers is hypomethylated.
Taken as a whole, our data show that in P. citri the zygote receives from the male gamete a haploid set that is hypomethylated with respect to that received from the female gamete. In male embryos, after midcleavage stage, the heterochromatization cascade affects the hypomethylated paternally derived chromosomes. In P. citri female embryos, in the absence of the heterochromatization cascade, the paternally derived hypomethylated haploid set remains active. In conclusion, we suggest that in Coccids parental genomic imprinting is mediated by DNA methylation and that there is no correlation with the known gene silencing effects of this base modification.
| FOOTNOTES |
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1 Present address: Department of Zoology, University of Washington, Seattle, WA 98195-1800. ![]()
| ACKNOWLEDGMENTS |
|---|
We are deeply indebted to Barbara Wakimoto for helpful discussions and valuable comments on the manuscript. We also thank Julie Brill for critical reading of the manuscript. We are grateful to Angelo Schinoppi who carried out X-ray treatments and to Bruno Fazzini for his help in photographic reproduction. This work was supported by grants from the Italian Ministero dell'Università e della Ricerca Scientifica e Tecnologica and from the Consiglio Nazionale delle Ricerche of Italy (contract no. 95.02924.CT14).
Manuscript received August 5, 1998; Accepted for publication December 11, 1998.
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