Restriction enzyme banding of mouse metaphase chromosomes

Heterochromatin heterogeneity in Hypostomus prope unae (Steindachner, 1878) (Siluriformes, Loricariidae)from Northeastern Brazil

Cytogenetic analyses using C-banding and chromosomal digestion by several restriction enzymes were carried out in four populations (named A, B, C and D) of Hypostomus prope unae (Loricariidae, Hypostominae) from Contas river basin, northeastern Brazil. These populations share 2n=76 and single NORs on the second metacentric pair but exclusive karyotype forms for each locality. Populations A and B presented conspicuous terminal and interstitial heterochromatic blocks on most of acrocentric chromosomes and equivalent to NORs with differences in both position and bearing pair. Population D showed evident marks at interstitial regions and interspersed with nucleolar region while population C presented interstitial and terminal heterochromatin segments, non-coincident with NORs. The banding pattern after digestion with the endonucleases Alu I, Bam HI, Hae III and Dde I revealed a remarkable heterogeneity within heterochromatin, allowing the identification of distinctive clusters of repeated DNA in the studied populations, besides specific patterns along euchromatic regions. The analysis using restriction enzymes has proved to be highly informative, characterizing population differences and peculiarities in the genome organization of Hypostomus prope unae.

Heterochromatin heterogeneity in Drosophila chromosomes detected by AluI-banding

In situ selective digestion of mitotic chromosomes from three Drosophila species (virilis, hydei, and funebris), having a chromosome number 2n = 12, was achieved with AluI restriction endonuclease. The distribution of AluI-bands, revealing a heterogeneity within heterochromatin, was compared with that of quinacrine-bands observed in standard chromosomes. The results confirmed a species-specific AluI-banding pattern, heterochromatin being selectively digested in D. virilis and D. funebris, but unaffected by the enzyme in D. hydei. The overlapping of AluI-bands and Q-bands in D. virilis and in D. funebris is discussed, since these data seem to favour the hypothesis that the induction of AluI-bands does not depend only on the presence of enzyme targets, but also on a suitable conformation of the chromatin.

Unfixed and fixed human chromosomes show different staining patterns after restriction endonuclease digestion

Restriction endonucleases (REs) have been widely used to produce banding patterns on chromosomes, but it remains uncertain to what extent the patterns are due to the sequence specificity of the enzymes, and to what extent chromatin structure influences the pattern of digestion. To throw light on this question, we have digested with restriction endonucleases unfixed chromosomes prepared in two different ways (isolated, and whole metaphase cells spread with a cytocentrifuge) and compared the results with those obtained on conventionally fixed chromosomes. Unfixed isolated chromosomes are easily destroyed by REs; after fixation with cold methanol, which produced minimal alteration to the chromatin structure, the chromosomes are resistant to the action of REs, and conventional methanol-acetic acid fixation is required to permit the induction of banding patterns by REs. Unfixed cytocentrifuge preparations, in which the chromosomes are still surrounded by cytoplasm, are much more resistant to the action of REs, and again banding patterns were only induced after methanol-acetic acid fixation. We conclude that the action of restriction endonucleases on chromosomes is strongly influenced by chromatin organisation, and that methanol-acetic acid fixation is required to permit the induction of conventional banding patterns on chromosomes.

Karyotype and genome characterization in four cartilaginous fishes

Different approaches can be used to elucidate the unsolved questions concerning taxonomic evolution in cartilaginous fish. The study of the karyological characteristics of these vertebrates by combining molecular and traditional techniques of chromosome preparation and banding has been demonstrated to be a very effective method. In this paper we studied the localization and the composition of the constitutive heterochromatin by using C- and restriction endonuclease-banding in four selachian species, belonging to two of the four superorders. We also characterized two different types of repetitive genomic sequences in these species: satellite DNA and (TTAGGG)(n) telomeric sequences. Finally, we analysed the nuclear ribosomal gene to determine the number of the nucleolar organizers and their position on chromosomes by using silver staining, chromomycin A(3), and FISH (fluorescent in situ hybridization). The results showed a prevailingly telomeric localization of constitutive heterochromatin in the Galeomorphii, the presence of additional nucleolar organizer sites in Raja asterias, an exclusively telomeric localization of the (TTAGGG)(n) sequences in Scyliorhinus stellaris and both telomeric and interstitial in Taeniura lymma. These data, together with those concerning the conservation of the satellite DNA, seem to support the hypothesis that Chondrichthyes have an evolutionary history leading them to the acquisition of large genomes rich in highly repeated sequences and subjected to some selective pressures favoring the conservation of this DNA fraction.

Asymmetric staining of Ctenomys chromosomes after treatment with AluI restriction nuclease

After treatment with the endonuclease AluI for 6 or 24 h, chromosomes of two populations of the South American rodent Ctenomys presented an asymmetric banding pattern after Giemsa staining. These asymmetric patterns were chromosome specific (each chromosome of a pair showed different banding pattern) but constant from cell to cell and between homologous chromosomes of the populations analysed. The nature of this peculiar staining is discussed in the light of the interaction between endonucleases and DNA in chromatin of fixed chromosomes.

Localization of chromosome breakpoints: implication of the chromatin structure and nuclear architecture

Restriction endonucleases and ionizing radiations have been extensively used to study the origin of chromosomal aberrations. Although a non-random distribution of chromosome breakpoints induced by these agents has been claimed by several authors, the significance of the chromatin structure and nuclear architecture in the localization of breakpoints is still not well understood. Breakpoint patterns produced by endonucleases targeted to specific genome sequences or by ionizing radiations could provide additional evidence to clarify this point. Results obtained from the localization of breakpoints induced by AluI, BamHI or DNase I as well as by neutrons or gamma-rays in G-banded Chinese hamster ovary (CHO) chromosomes are presented. AluI and BamHI were electroporated into CHO cells either during the G1 or S-phase of the cell cycle. A co-localization of breakpoints was found with a preferential occurrence in G-light bands independent of the cell cycle stage in which aberration production took place. Since AluI and BamHI recognition sequences are partitioned in the housekeeping and tissue-specific subgenomes respectively, we postulated that nuclease sensitive sites in active chromatin could be the main targets for the induction of breakpoints by these endonucleases. This assumption is supported by the finding that DNase I-induced breakpoint patterns in CHO cells are similar to those produced by AluI and BamHI. Digestion of fixed CHO chromosomes with these endonucleases induced G-banding suggesting a higher sensitivity of G-light chromatin. For comparison purposes, CHO cells were irradiated with neutrons or gamma-rays and breakpoints localized in G-banded chromosome aberrations. A higher occurrence of breakpoints in G-light bands was also observed. We detected seven breakage-prone G-light bands that were preferentially damaged by the three endonucleases and by both types of radiation. These results emphasize the possible implication of the chromatin structure and the nuclear architecture in the localization of chromosome breakpoints induced by endonucleases, neutrons and gamma-rays.

Altered patterns of DNA methylation on chromosomes from leukemia cell lines: identification of 5-methylcytosines by indirect immunodetection

An immunodetection technique has been developed to map with high resolution the methylated sites of human chromosomes. We have used this method to define the methylated areas of chromosomes from normal donors and from leukemia cell lines. The chromosomes were exposed for a short time to UV light to induce mild denaturation. The methylated sites were detected in situ by using monoclonal antibodies against 5-methylcytosine (prepared in mouse), and fluorescein-conjugated antimouse immunoglobulins. The chromosomes from normal cells exhibited a fluorescent pattern with RCT banding, although some differences from previously reported patterns could be detected. With this method we have been able to show the presence of two types of R-bands: High fluorescence R-band (HFR) and low fluorescence R-band (LFR). Chromosomes from leukemia cell lines exhibited low global staining with disrupted RCT banding of the chromosomes. The decreased level of the methylation status of the chromosomes from leukemia cells was confirmed by detection of 5-methylcytosines on total immobilized DNA. Thus, we have shown that this method can be used to determine the methylated status of chromosomes and, in turn, to map not only the structural (banding) but also the functional (methylation status) properties of the different chromosome domains in normal and pathologic human cells.

Localization of chromosome breakpoints induced by AluI and BamHI in Chinese hamster ovary cells treated in the G1 phase of the cell cycle

Intact Chinese hamster ovary cells were exposed to the restriction endonucleases (REs) AluI or BamHI. In metaphase spreads from these cells, 300 breakpoints per RE were localized in G-banded chromosome type aberrations (dicentrics, translocations, rings, terminal and interstitial deletions). The majority of breakpoints induced by both REs were localized in G-light bands and showed a similar distribution of breakpoint clusters. RE digestion of metaphase spreads with AluI induced C-banding, and with BamHI G-banding. The data indicate that nuclease sensitive sites associated with active genes are mainly responsible for the distribution of breakpoints.

The DNA fragments produced by AluI and BstNI digestion of fixed mouse chromosomes

AluI and BstNI restriction endonucleases were used to study cytological and biochemical effects on centromere DNA in fixed mouse chromosomes. These enzymes were employed, as it is known that AluI is incapable of attacking major satellite DNA, contrary to BstNI that is known to cut this DNA fraction into monomers of 234 bp. After digestion in situ, electrophoretic analysis was carried out to characterize the DNA purified (1) from the material remaining on the chromosomes and (2) from the material solubilized from chromosomes. The DNA was then transferred to a nylon filter and 32P-labelled major satellite DNA was used as a probe for hybridization experiments. Other preparations were simply stained with Giemsa after digestion in situ with AluI and BstNI. Our results show that although restriction endonuclease cleavage primarily depends on DNA base sequence, this factor is not always sufficient to explain nuclease-induced cytological effects. In fact, the structural organization of peculiar regions such as the centromeres of mouse chromosomes might affect cleavage efficiency when restriction enzyme digestion is performed in situ.

Hypomethylation of human heterochromatin detected by restriction enzyme nick translation

Using the restriction enzymes MspI and HpaII in the nick translation procedure it has been shown that decondensation of the paracentric heterochromatin of chromosome 9 during human spermatogenesis is associated with hypomethylation of the DNA sequences in this domain. Somatic cells treated with 5'-azacytidine also showed decondensation of centromeric heterochromatin. In this instance, however, hypomethylation is detected both in the extended heterochromatin at the centromeres and in the euchromatin of the chromosome arms.

Restriction endonuclease/nick translation of fixed mouse chromosomes: a study of factors affecting digestion of chromosomal DNA in situ

We used a restriction endonuclease/nick translation procedure to study the ability of certain enzymes, known to cleave mouse satellite DNA in solution, to attack satellite DNA in fixed mouse chromosomes. Although AvaII and Sau96I readily attack the mouse major satellite in fixed chromosomes, BstNI and EcoRII do not normally do so, although if the heterochromatin is uncondensed as a result of culture in the presence of 5-azacytidine, BstNI can attack it. No clear evidence was obtained for digestion in situ of the minor satellite of mouse chromosomes by MspI, the only enzyme reported to cleave this satellite. Our results show that the DNA of mouse heterochromatin is not merely not extracted by certain restriction enzymes, but is actually not cleaved by them. Chromatin conformation is therefore shown to be an important factor in determining patterns of digestion of chromosomes by restriction endonucleases.

Electron microscopy and biochemical analysis of mouse metaphase chromosomes after digestion with restriction endonucleases

Electron microscopy (EM) of whole mounted mouse chromosomes, light microscopy (LM), and agarose gel electrophoresis of DNA were used to investigate the cytological effect on chromosomes of digestion with the restriction endonucleases (REs) AluI, HinfI, HaeIII and HpaII. Treatment with AluI produces C-banding as seen by LM, cuts DNA into small fragments, and reduces the density of centromeres and disperses the chromatin of the arms as determined by EM. Treatment with HinfI produces C-banding, cuts DNA into slightly larger fragments than does AluI and increases the density of centromeres and disperses the fibres in the chromosomal arms. Exposure to HaeIII produces G- + C-banding, cuts the DNA into large fragments, and results in greater density of centromeres and reduced density of arms. Finally HpaII digestion produces G-like bands, cuts the DNA into the largest fragments found and results in greater density of centromeres and the best preservation of chromosomal arms detected by EM. These results provide evidence for: (1) REs producing identical effects in the LM (AluI and HinfI) produce different effects in the EM. (2) All enzymes appear to affect C-bands but while REs such as AluI reduce the density of these regions, other enzymes such as HpaII, HaeIII or HinfI increase their density. Conformational changes in the chromatin could explain this phenomenon. (3) The appearance of chromosomes in the EM is related to the action of REs on isolated DNA. The more the DNA is cut by the enzyme, the greater the alteration of the chromosomal ultrastructure.

Analysis of chromosome replication by a BrdU antibody technique

Chromosome replication was studied without synchronization in human lymphocyte and amniotic cell cultures visualizing very short 5-bromodeoxyuridine (BrdU) pulses by an immunologic technique (BAT). The findings agree in general with those facts known from earlier BrdU staining techniques. The very high sensitivity of BAT was shown to allow the detection of replication in a band where 1 in 200 nucleotides is replaced by BrdU. The main observations are: though the replication patterns after BAT appear strange the bands correspond to those described by the Paris Conference (1971). At the beginning of the S-phase a stepwise onset of replication in only a subset of R-bands is confirmed. There is a considerable difference in the sensitivity between early and late S (SE and SL) for the detection of BrdU pulses. This difference probably reflects a different spatial arrangement of chromatin in R-bands as compared with G-bands below the level of cytogenetic analysis. The use of short pulses did not reveal any additional subdivision of SE or SL. The correspondence between chromosomal bands and replicon clusters is discussed briefly with respect to the different time they need for replication.

The organization of the mouse satellite DNA at centromeres

The mouse genome contains a major and a minor satellite DNA family of repetitive DNA sequences. The use of 5-azacytidine has allowed us to demonstrate that these satellite DNAs are organized in two separate domains at the centromeres of mouse chromosomes. The minor satellite is closer to the short arms of the acrocentric chromosomes than the major satellite. The major satellite is farther away, flanking the minor satellite and adjacent to the euchromatic long arm of each mouse chromosome. At the level of resolution afforded by the in situ hybridization technique it would appear that the organization of the centromeric domain of the mouse is similar to that in man. That is, both contain two repetitive DNA sequence families arranged in major blocks.

Restriction enzymes MspI, HpaII, HaeIII, and HinfI applied to chicken mitotic chromosomes

The restriction enzymes MspI, HpaII, HaeIII, and HinfI were applied in situ to chicken metaphase chromosomes to determine if they denatured specific regions to produce banding patterns. Human metaphase chromosomes were treated simultaneously to serve as controls. The MspI, HpaII, and HaeIII enzymes produced no visible banding patterns in chicken chromosomes. There was slight banding on a few chromosomes in HinfI preparations, which was similar to the occasional spontaneous banding observed in chicken chromosome preparations. The results indicate that these four enzymes do not denature C-band regions in sufficient magnitude to be detected in chicken metaphase chromosomes.

Morphological and biochemical effects of endonucleases on isolated mammalian chromosomes in vitro

Endonuclease digestion of isolated and unfixed mammalian metaphase chromosomes in vitro was examined as a means to study the higher-order regional organization of chromosomes related to banding patterns and the mechanisms of endonuclease-induced banding. Isolated mouse LM cell chromosomes, digested with the restriction enzymes AluI, HaeIII, EcoRI, BstNI, AvaII, or Sau96I, demonstrated reproducible G- and/or C-banding at the cytological level depending on the enzyme and digestion conditions. At the molecular level, specific DNA alterations were induced that correlated with the banding patterns produced. The results indicate that: (1) chromatin extraction is intimately involved in the mechanism of endonuclease-induced chromosome banding. (2) The extracted DNA fragments are variable in size, ranging from 200 bp to more than 4 kb in length. (3) For HaeIII, there appears to be variation in the rate of restriction site cleavage in G- and R-bands; HaeIII sites appear to be more rapidly cleaved in R-bands than in G-bands. (4) AluI and HaeIII ultimately produce banding patterns that reflect regional differences in the distribution of restriction sites along the chromosome. (5) BstNI restriction sites in the satellite DNA of constitutive heterochromatin are not cleaved intrachromosomally, probably reflecting an inaccessibility of the BstNI sites to enzyme due to the condensed nature of this chromatin or specific DNA-protein interactions. This implies that some enzymes may induce banding related to regional differences in the accessibility of restriction sites along the chromosome. (6) Several specific nonhistone protein differences were noted in the extracted and residual chromatin following an AluI digestion.(ABSTRACT TRUNCATED AT 250 WORDS)

Use of restriction endonucleases to study relationships between DNA double-strand breaks, chromosomal aberrations and other end-points in mammalian cells

Some of the cellular effects of radiation, such as mutations, chromosomal aberrations and cell killing, can be mimicked by inducing 'pure' double-strand breaks (dsb) in DNA of cells with restriction endonucleases (RE), although the chemical structure of the ends of dsb induced by RE are likely to differ from those induced by X-rays. Chromosomal aberrations are induced by treatment of cells with a variety of RE at all stages of the cell cycle. The frequency with which RE induce dsb in the DNA may be one factor determining the number of aberrations induced. However, the structure of the dsb generated may also determine the frequencies of aberrations induced. RE which generate 'cohesive-ended' dsb in the DNA have been shown to induce lower frequencies of aberrations than those causing 'blunt-ended' dsb, when inactivated Sendai virus is used to permeabilize cells. Other methods, involving a hypertonic shock to the treated cells, have led to results in which there is little or no difference in the effectiveness between the two types of dsb. It is argued here that the use of treatments which cause a hypertonic shock may influence the frequencies of aberrations induced.

Inactive X chromosome has the highest concentration of unmethylated Hha I sites

A procedure enabling the highly sensitive detection of accessible restriction endonuclease sites on metaphase chromosomes is described. The procedure is based on the following: (i) a terminal deoxynucleotidyltransferase is used to add a biotinylated nucleotide (Bio-11-dUTP) tail to the 3' hydroxyl terminus generated by the action of a restriction enzyme and (ii) the biotinylated oligonucleotide is detected by a peroxidase-based immunocytochemical method. When used with the 5-methylcytosine-sensitive enzyme Hha I, it gives rise to a pattern close to R and T banding on autosomes. In addition, the staining of one X chromosome in females appears very unusual by its pattern and its strong intensity. This procedure, as applied on a case with a polysomy X chromosome, provides direct evidence of an overall hypomethylation of the inactive X chromosomes.

Chromosome banding in Amphibia. XII. Restriction endonuclease banding

Fixed metaphase chromosomes of several species of Amphibia were treated with various restriction endonucleases and subsequently stained with Giemsa. Metaphases of man and chicken were examined in parallel under the same experimental conditions for comparison. The restriction enzymes always induce subsets of the C-banding patterns present in the amphibian karyotypes. The heterochromatic regions can be either resistant or sensitive to the restriction enzyme. The modified C-banding patterns revealed by different restriction endonucleases in the karyotype of the same species can be either extremely dissimilar or almost completely congruent. Correspondingly, the action of the same restriction enzyme on the karyotypes of different species may vary greatly. There is only rarely a correlation between the type of C-banding patterns produced by different restriction endonucleases and their specific base pair recognition sequences. In contrast to mammalian and avian chromosomes, restriction enzymes induce no multiple G-banding patterns in amphibian chromosomes. This is attributed to the difference in organization of the DNA in the genomes of poikilothermic vertebrates. The possible mechanisms of restriction endonuclease banding and the various uses of this technique for amphibian chromosomes are discussed.

Restriction endonuclease digestion and chromosome banding in the mosquito, Culiseta longiareolata (Diptera: Culicidae)

Fixed chromosomes of the mosquito, Culiseta longiareolata (2n = 6) were treated in situ with nine restriction endonucleases and stained with ethidium bromide or Giemsa. All the heterochromatic regions were apparently protected from digestion by all enzymes except Mbo I. This enzyme selectively digested one of the three types of heterochromatin present in the species. Staining with the fluorochrome quinacrine after enzyme treatment produced a standard Q-banding pattern or a Hoechst 33258-like pattern, depending on the enzyme. These results confirmed: (a) the presence of three types of heterochromatic containing different DNA fractions in the chromosomes of this species, (b) restriction enzymes accessibility to the DNA of heterochromatin regions, and (c) the selective cleavage of particular DNA fractions without DNA removal. Moreover, quinacrine staining after enzyme digestion proved useful in detecting differential activity among enzymes which produced the same banding pattern with standard dyes.

Restriction endonuclease resistant chromatin in human chromosomes

The recent addition of restriction endonucleases in obtaining selective bands in the human genome has added a new dimension to molecular genetics. However, a considerable discrepancy exists in banding patterns produced by AluI in chromosomes 19 and 20, by MboI in chromosomes 4, 5, 8, 21 and 22 and by RsaI in chromosomes 12, 21 and 22. The principal causes of these differences are highlighted.

In situ nick translation distinguishes between C-band positive regions on mouse chromosomes

In situ nick translation of mouse metaphase chromosomes by non-radioactive detection means and DNase I digestion followed by Giemsa staining were used to analyse the DNase I resistance of two different C-band positive regions. These were the centromeric heterochromatin of acro- and metacentric chromosomes and an interstitial C-band on chromosome 1 of wild mice, IS(HSR;1C5D)1Lub. Whereas the centromeric heterochromatin was clearly resistant to DNase I, the interstitial C-band showed very high DNase I sensitivity. Among centromeric C-bands, the heterochromatin in Robertsonian fusion biarmed chromosomes was more resistant to DNase I action than was the centromeric heterochromatin of the acrocentric chromosomes.

Correlation between constitutive heterochromatin and restriction enzyme resistant chromatin in Arcyptera tornosi (Orthoptera)

Fixed mitotic chromosomes of A. tornosi have been analysed by means of C-banding, DA-DAPI and Chromomicin A3 fluorescence, as well as by digestion in situ with Alu I, Hae III, Hinf I and Hind III restriction endonucleases. From the results obtained at least nine types of chromatin can be distinguished in A. tornosi. Some C-band positive areas (constitutive heterochromatin) which show a characteristic fluorescence pattern are digested by specific endonucleases, whilst others are undigested. C-band negative areas (euchromatin) are digested by some restriction endonucleases but not by others. Regions digested are supposed to contain highly repetitive DNAs. It is noteworthy, however, that the heterochromatin associated with NORs is not attacked by any of the enzymes we used, while regions believed to contain AT-rich DNA (DA-DAPI positive) are digested by Hae III that cleaves the GG decreases CC base sequence target.

Mouse satellite DNA, centromere structure, and sister chromatid pairing

The experiments described were directed toward understanding relationships between mouse satellite DNA, sister chromatid pairing, and centromere function. Electron microscopy of a large mouse L929 marker chromosome shows that each of its multiple constrictions is coincident with a site of sister chromatid contact and the presence of mouse satellite DNA. However, only one of these sites, the central one, possesses kinetochores. This observation suggests either that satellite DNA alone is not sufficient for kinetochore formation or that when one kinetochore forms, other potential sites are suppressed. In the second set of experiments, we show that highly extended chromosomes from Hoechst 33258-treated cells (Hilwig, I., and A. Gropp, 1973, Exp. Cell Res., 81:474-477) lack kinetochores. Kinetochores are not seen in Miller spreads of these chromosomes, and at least one kinetochore antigen is not associated with these chromosomes when they were subjected to immunofluorescent analysis using anti-kinetochore scleroderma serum. These data suggest that kinetochore formation at centromeric heterochromatin may require a higher order chromatin structure which is altered by Hoechst binding. Finally, when metaphase chromosomes are subjected to digestion by restriction enzymes that degrade the bulk of mouse satellite DNA, contact between sister chromatids appears to be disrupted. Electron microscopy of digested chromosomes shows that there is a significant loss of heterochromatin between the sister chromatids at paired sites. In addition, fluorescence microscopy using anti-kinetochore serum reveals a greater inter-kinetochore distance than in controls or chromosomes digested with enzymes that spare satellite. We conclude that the presence of mouse satellite DNA in these regions is necessary for maintenance of contact between the sister chromatids of mouse mitotic chromosomes.

Endonuclease banding of isolated mammalian metaphase chromosomes

Evidence is presented that endonuclease digestion of isolated, unfixed chromosomes results in the production of banding patterns similar to those produced by digestion of fixed, air-dried chromosomes. Mouse L cell chromosomes were isolated under acidic or relatively neutral pH conditions, exposed in situ (as wet mounts on glass slides) or in vitro (in suspension) to micrococcal nuclease, Alu I or Eco RI, treated with a buffered salt solution, and stained with Giemsa. After any of these endonuclease treatments in situ, the centromeric regions of the chromosomes were intensely stained, characteristic of the C-banding observed in fixed chromosomes exposed to the same treatments. Although the fixed chromosomes were morphologically well-preserved after endonuclease digestion, the morphology of chromosomes digested in situ was variable, ranging from normal to swollen to highly distorted chromosomes. In the latter, the endonucleases induced dispersion of non-C-band chromatin; however, C-bands were still apparent as condensed, differentially-stained regions. Exposure of isolated chromosomes to Alu I in vitro also resulted in well-defined C-banding and led to the extraction of about 70% of the chromosomal DNA. From these results, the mechanism of endonuclease-induced C-banding appears to involve the dispersion and extraction of digested chromatin.

The Alu I-induced bands in metaphase chromosomes of orangutan (Pongo pygmaeus). Implications for the distribution pattern of highly repetitive DNA sequences

Restriction endonucleases have been recently proved to be active on fixed chromosomes, thus they are useful in chromatin structure studies. Within this class of enzymes, Alu I is able to detect the presence and localization of highly repetitive DNA sequences in human and in other mammalian and dipteran species. In this paper the pattern obtained on fixed metaphase chromosomes of orangutan (Pongo pygmaeus) by Alu I digestion and Giemsa staining is shown. The results are discussed in the light of the distribution, in this species, of the I-IV human satellite DNAs. It is also suggested that in Pongo some highly repetitive sequences, different from the major human satellites, are present.

Some factors affecting the action of restriction endonucleases on human metaphase chromosomes

We have investigated whether restriction endonucleases produce bands on human chromosomes by extracting DNA, using staining methods which are stoichiometric for DNA. Restriction enzymes that produce C-band patterns appear to remove DNA extensively from chromosome arms. In general, however, those restriction enzymes that produce G-bands do not extract DNA from chromosomes, and their effects are believed to be due to conformational change in the chromosomal DNA; in these cases, the chromosomal regions affected appear to be determined by the chromosome structure and not by the specificity of the enzyme. DNA loss from chromosomes due to digestion by restriction enzymes may in some cases be uniform, although a G-banding pattern is visible after Giemsa staining.

Chromosomal aberrations induced by restriction endonucleases

Restriction endonucleases (REs) are able to induce chromosomal aberrations in Chinese hamster ovary (CHO) cells. The G1 phase of the cell cycle seems to be especially sensitive for the induction of chromosomal aberrations by REs. The different capacities of REs to induce chromosomal aberrations are probably correlated with the number of recognition sites in the genome.