Restriction endonucleases in the study of eukaryotic chromosomes

Heterochromatin heterogeneity revealed by restriction endonuclease digestion and subsequent C-banding on bovine metaphase chromosomes

Conventional alkaline C-banding was found to be an effective additional step in restriction endonuclease banding to improve staining contrast and to reveal hidden changes in the heterochromatic blocks. Examples of these cases are demonstrated on the bovine chromosome set using Hinf I and Taq I endonucleases in the digestion experiments.

Characterization of the heterochromatin of the darkling beetle Misolampus goudoti: cloning of two satellite DNA families and digestion of chromosomes with restriction enzymes

The darkling beetle Misolampus goudoti Er. has 58% of C-banded chromosome material. In this paper we deal with the study of the heterochromatin of this insect both by molecular and cytogenetical methods. Two different satellite DNA families have been characterized in Misolampus goudoti by agarose gel electrophoresis of EcoRI and PstI restriction fragments, respectively. The EcoRI family is composed of a monomeric unit of 196 bp (64.3% A-T rich) DNA sequence, representing about 120,000 copies per haploid genome. The presence of frequent intermediate-size satellite variants and an internal direct repetition of 61 bp in the EcoRI repetitive main monomer suggest that the evolution of this satellite proceeded by unequal crossing-over, occurring both within and between the 196 bp unit. Another highly repetitive sequence, defined by digestion of genomic DNA with PstI, has a more complex unit of 1.2 kb with about 70,000 copies per haploid genome. In situ digestion of M. goudoti chromosomes with restriction enzymes shows a non-specific chromosome DNA extraction from pericentromeric positions with EcoRI and chromosome specific extraction of DNA with PstI and HinfI. This is discussed in relation to the chromosomal location of both satellites.

Sau3A in situ digestion of human chromosome 3 pericentromeric heterochromatin. I. Differential digestion of α-satellite and satellite 1 DNA sequences

In situ digestion with the restriction endonuclease (RE) Sau3A (Sau3A REISD) uncovers a polymorphism for the pericentromeric heterochromatin of human chromosome 3, which can be positively stained (3+) or not (3–), and has proven useful to differentiate donor and recipient cells after sex-matched bone marrow transplantation and to analyze the so-called hemopoietic chimerism. The aim of the present investigation was to obtain insight into the molecular basis of such polymorphism to optimize its use for chimerism quantification using methodological approaches other than REISD. To this end, fluorescence in situ hybridization (FISH) assays using probes for the satellite DNA sequences that mainly constitute chromosome 3 pericentromeric heterochromatin (α-satellite and satellite 1 DNA) were performed on control and Sau3A-digested chromosomes. The results obtained suggest that chromosome 3 α-satellite DNA is digested in all individuals studied, irrespective of the karyotype obtained by Sau3A REISD (3++, 3+–, 3--), and thus it does not seem to be involved in the polymorphism uncovered by Sau3A on this chromosome. Satellite 1 DNA is not digested in any case, and shows a polymorphism for its domain size, which correlates with the polymorphism uncovered by Sau3A in such a way that 3+ chromosomes show a large domain (3L) and 3– chromosomes show a small domain (3S). It seems, therefore, that the cause of the polymorphism uncovered by Sau3A on the pericentromeric region of chromosome 3 is a difference in the size of the satellite 1 DNA domain. Small satellite 1 DNA domains fall under the resolution level of REISD technique and are identified as 3–.Key words: heterochromatin, α-satellite DNA, classical satellite DNA, satellite 1 DNA, restriction endonucleases, FISH.

R- and G-band patterns in Astyanax scabripinnis paranae (Pisces, Characiformes, Characidae)

The absence of longitudinal bands in fish chromosomes has been associated with technical problems in chromosome preparations or the absence of a structural compartmentalization in the fish genome. In the present study, a R-banding pattern was obtained using a replication banding technique by in vivo treatment with 5-bromodeoxyuridine (5-BrdU). G-banding patterns were obtained after trypsin treatment and also after chromosome cleavage by in situ treatment with the restriction endonuclease BamHI. A similar G-banding pattern was also obtained after cleavage with the endonuclease HinfI. Presence of a resolute R- and G-banding patterns shows that Astyanax scabripinnis paranae chromosomes could present an isochore-like structure similar to that found in other vertebrates.

The effects of enzyme inactivation and incubation buffer on digestion in situ with restriction endonucleases

Previous studies have shown that components of the incubation reaction other than the restriction endonucleases in an in situ restriction enzyme digest of chromosomes may induce G-like banding patterns. To determine whether factors other than DNA base composition play a role in determining restriction enzyme induced bands, we investigated the effect of reaction buffers alone or in the presence of heat inactivated enzymes. Our results show that enzymes such as AluI, RsaI and MspI become inactivated during 3-24 hr incubations at 37 C and that reaction buffers alone failed to produce G-like bands when inactive endonucleases were included.

Cytogenetic studies in some species of Scorpaeniformes (Teleostei: Percomorpha)

Cytogenetic studies were performed in four species of two scorpaeniform teleost families: Scorpaenidae and Triglidae. The karyotypes of Trigla lucerna, Trigloporus lastoviza (Triglidae), Scorpaena porcus and S. notata (Scorpaenidae) were analysed using various banding methods and in situ hybridization with a telomeric probe. In the two Scorpaena species, modest morphological divergence corresponded to considerable karyotype reorganization, while in the two Triglidae substantial phenotypical divergence corresponded to limited chromosomal changes. These data stress the need for a taxonomical re-evaluation of these teleosts based on characters independent of morphology.

Molecular cytogenetic analysis of heterochromatin in the chromosomes of tilapia, Oreochromis niloticus (Teleostei: Cichlidae)

The structure of the heterochromatic bands in mitotic chromosomes of the important tropical aquaculture species of tilapia, Oreochromis niloticus, was investigated by the combination of the C-banding technique, chromosomal digestion with two restriction endonucleases and fluorescence in situ hybridization (FISH) of two satellite DNAs (SATA and SATB). The tilapia chromosomes presented heterochromatic bands in the centromeres and in the short arms of almost all chromosomes that were differentially digested by the restriction endonucleases HaeIII and EcoRI. FISH of SATA showed that this satellite sequence is distributed in the centromeric region of all chromosomes of tilapia. FISH also revealed an intense hybridization signal for SATB in only one chromosome pair, but less intense signals were also present in several other pairs. The digestion of tilapia chromosomes by HaeIII and EcoRI was positively correlated with the position of SATA and SATB in chromosomes as revealed by FISH. The results obtained may be useful in future molecular and genetic studies of tilapias.

Dynamics of Sau3A in situ digestion of human chromosomes analyzed with computerized imaging

The differential DNA removal obtained after in situ digestion of human metaphase chromosomes with the restriction endonuclease Sau3A was analyzed on complete and partially digested nuclei using computerized imaging. The results obtained permit the discrimination of Sau3A-resistant chromosome regions (pericentromeric constitutive heterochromatin on chromosomes 3 and 9) from those partially digested (Yq12 and pericentromeric heterochromatin on other chromosomes), according to the digestion dynamics deduced from the grey intensity profile along each chromosome. This approach permits an accurate labelling of chromosome markers for the identification of genomes from different individuals. This is of special interest for the analysis of the chimeric status found in patients after allogenic bone marrow transplantation.

Restriction endonuclease in situ digestion (REISD) and fluorescence in situ hybridization (FISH) as complementary methods to analyze chimerism and residual disease after bone marrow transplantation

The efficiency of restriction endonuclease in situ digestion (REISD) with Sau3A to analyze chimerism and residual disease (RD) has been tested before and after an allogenic bone marrow transplant (BMT) in an acute lymphoblastic leukemia (ALL) patient. The combined results obtained with REISD and FISH using the appropriate probes for detecting chromosome rearrangements have proven to be useful for the identification and quantification of both the hemopoietic chimerism achieved after BMT and the RD persistent in the patient. The sensitivity of REISD has been determined to be around 95%, i.e., similar to that obtained by FISH. REISD with Sau3A was particularly useful in the analysis of chimerism since this enzyme revealed the polymorphic status of constitutive heterochromatin in human chromosome 3 and thus allowed discrimination of cells derived from donor and recipient. The method itself seems promising since neither a donor/recipient sex mismatch nor a cytogenetic disease marker are needed for its application.

Difference in constitutive heterochromatin behaviour between human amniocytes and lymphocytes detected by a sequential in situ exonuclease III digestion-random primer extension procedure

Fixed chromosomes from human amniotic fluid cells and peripheral blood lymphocytes were digested in situ with exonuclease III and the single stranded DNA obtained was used as template for an in situ random primer extension. Under these conditions an R banding pattern, more evident in lymphocytes than in amniocytes, was obtained. Nevertheless, constitutive heterochromatin of chromosomes 1, 16, Yq, and mainly the pericentromeric region of chromosome 9 was far more intensely labelled in amniocytes than in lymphocytes. Fluorescence in situ hybridisation with a specific classical satellite DNA probe, showed that this differential labelling was dependent on a greater sensitivity of chromosome 9 constitutive heterochromatin to exonuclease III digestion in amniocytes than in lymphocytes, thus indicating qualitative differences in this region between both human cellular materials.

Tenebrio obscurus satellite DNA is resistant to cleavage by restriction endonucleases in situ

Satellite DNA from the mealworm beetle, Tenebrio obscurus, is composed of 344 bp long monomers of high AT content (68%), and represents 15% of the total DNA. In situ hybridization reveals the positions of the satellite on the pericentromeric heterochromatin of all T. obscurus chromosomes. To compare restriction enzyme (RE) effects with those on naked DNA, fixed chromosomes were digested with REs having recognition sites in most of the satellite monomers, and also with enzymes having target sites present only partially, or very rarely in the satellite units. All enzymes produce similar C-like banding patterns showing heterochromatin resistance to digestion regardless of the enzyme used. In situ nick translation suggests the inability of REs to cleave satellite DNA rather than the inefficient extraction of DNA fragments. DNA in heterochromatin was only extensively digested when the chromosomes were preincubated with proteinase K, indicating that accessibility of REs to DNA is increased by the removal of chromosomal proteins. This is in contrast to recently obtained results in Tenebrio molitor, where cleavage of satellite DNA is equally efficient in both fixed chromosomes and in naked DNA. The satellite DNAs of the two congeneric species differ in their AT content, and their primary and higher order structure, which could influence both heterochromatin structure and the accessibility of REs to satellite DNA.

5-azacytidine produces differential undercondensation of alpha, beta and classical human satellite DNAs

Fluorescence in situ hybridization employing human alphoid, beta and classical satellite DNA probes was performed on 5-azacytidine treated and untreated chromosomes obtained from human lymphocytes. The individual used in this study presented a polymorphism of constitutive heterochromatin of chromosomes 1 and 9 as revealed by in situ digestion with the restriction endonuclease Alul. Neither the alphoid nor the beta satellite DNA domains were susceptible to condensation-inhibition by 5-azacytidine. Only the classical satellite localized on chromosome 9 was affected. The constitutive heterochromatin size polymorphism was shown to depend mainly on variations of the classical satellite DNA domain. Therefore, condensation-inhibition, as a phenomenon which may modify the natural folding of the chromatin fibre, regionally affects human constitutive heterochromatin and seems to be dependent on the heterochromatic family.

Satellite III DNA: regions of extreme endonuclease resistance and inter-individual polymorphism in the Mb size range

Southern analysis of within-gel digested and restricted human cells has revealed very large Satellite III restriction fragments which show clear inter-individual length polymorphism. The Mb and sub-Mb length of these fragments indicate that they arise from regions of heterochromatin which contain homogeneous Satellite III sequences of peculiar resistance to common endonucleases. Based on sequence alone, such regions would be little digested by endonuclease digestion of chromatin in metaphase, regardless of its method of preparation. Polymorphic regions such as these might be expected to stain as part of the C-banding seen in endonuclease treated metaphase chromosomes, and may in part account for inter-individual C-band heteromorphisms.