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

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.

Chromosomal localization of a highly repeated EcoRI DNA fragment in Megoura viciae (Homoptera, Aphididae) by nick translation and fluorescence in situ hybridization

To investigate the genome of the aphid Megoura viciae at molecular level, we have studied total DNA by agarose gel electrophoresis after cleavage with different restriction endonucleases. EcoRI digestion produced a highly repeated DNA fragment, about 600 pb long. The contribution of this EcoRI element to the total genome of M. viciae was estimated at about 6% by means of densitometric scanning of agarose gel photographs. The chromosomal localization of this fragment, investigated by fluorescent in situ hybridization (FISH), constantly showed one large and two narrower fluorescent bands located on the X chromosome, all corresponding to C-positive heterochromatic areas. These results are in full accordance with the data obtained by in situ nick translation experiments carried out after EcoRI digestion, and clearly demonstrate that a substantial amount of M. viciae heterochromatin consists of EcoRI fragments which are mainly located on the X chromosome. Using the EcoRI restriction fragment as a molecular probe may be a practical tool for the investigation of taxonomic and evolutionary relationships in this group of insects.

Molecular analysis of chromosomal polymorphism in the South American cricetid, Graomys griseoflavus

Graomys griseoflavus is a South American phyllotine rodent widespread in Argentina that shows a high frequency of Robertsonian fusions (RFs). DNA restriction with EcoRI produced a 250-bp repeated family (EG250) specific for the genus. Southern hybridization and sequencing analysis indicate that the EG250 family is heterogeneous, comprising at least two subfamilies. In situ hybridized EG250 probe showed a centromere location in almost all chromosomes. In all karyomorphs C-banding was negative, but restriction enzyme banding (Re-banding) with Alul and Mbol showed centromeric blocks in the autosomes that will generate Robertsonian fusions. Thus, we found three groups of chromosomes: (a) EG250 and Re-banding negative; (b) EG250 positive and Re-banding negative; and (c) EG250 and Re-banding positive. We consider that group (b) is more the result of chromatin condensation state than that of the frequency of recognition sites for the enzymes used. Restriction enzyme blocks would appear in regions with heterochromatic EG250 subfamilies, while lack of banding would be due to decondensed EG250 subfamilies becoming an easier target for chromosomal restriction. It is suggested that heterochromatic EG250 DNA provides a favourable molecular environment for Robertsonian fusion occurrence.

The molecular characterization of the genome of Muraena helena L. I. Isolation and hybridization of two MboI-restricted DNA fractions

To investigate the genome of the anguilliform fish Muraena helena at the molecular level we characterized total DNA by agarose gel electrophoresis after cleavage with AluI, HaeIII, MboI, and DdeI restriction endonucleases. Subsequently, we isolated the DNA from two specific electrophoretic fractions to be used as probes for Southern and in situ hybridization experiments. One such fraction showed an electrophoretic pattern typical of highly repetitive DNA localized in the centromeres of many chromosomes. The other fraction was shown to be located in the nucleolar organizer region, partially coincident with 45S rDNA, and to be composed of highly repetitive sequences.

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.