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A reciprocal t(17;22)(q11.2;q11.2) was found in a female patient with neurofibromatosis type 1 (NF1) and in her affected daughter. Sequence analysis of cloned junction fragments traversing the breakpoints allowed the identification of the structures involved in the rearrangement. Aberrant bands in Southern hybridizations of restriction enzyme-digested DNA of the patient pointed to the disruption of the NF1 gene in intron 31. Semispecific polymerase chain reaction analysis of the genomic DNA of the patient with the specific primer anchored at NF1 exon 31 was used to obtain the breakpoint-spanning fragment of the derivative chromosome 17. The intron 31 sequence turned out to be interrupted within a large irregular (AT) repeat. The chromosome 22-derived sequence of the der(17) junction fragment allowed us to identify cosmids of the corresponding region from a chromosome 22 specific cosmid library. With the support of the breakpoint-spanning cosmids, the chromosome 22 region upstream of the fragment carried by the der(17) was characterized. Primers deduced from the sequence of this upstream region were used in combination with a primer in NF1 intron 31 distal to the breakpoint on chromosome 17 to amplify the der(22) junction fragment. The structure of the junction sequences suggested that the translocation had arisen by unequal homologous recombination between (AT)-rich repeats on chromosome 22 and on chromosome 17 in intron 31 of the NF1 gene. However, our data support the assumption of additional rearrangements prior to, or in the course of, the recombination event, leading to a loss of the sequences between the involved (AT) repeats on chromosome 22. In the direct vicinity of these (AT) repeats, two members of a previously undescribed low-copy repetitive sequence have been found, copies of which are also present on human chromosome 13.

The autosomal dominantly inherited disease neurofibromatosis type 1 (NF1) is caused by mutations of a large gene comprising 59 exons, which code for a protein with 2818 amino acids called neurofibromin. Employing an expressed polymorphic site in exon 5 of the neurofibromin gene, the expression of its alleles was analysed quantitatively by scanning radioactive RT-PCR fragments of this exon prepared from the RNA of fibroblast cell cultures from 15 NF1 patients and of white blood cells from one NF1 patient. Thirteen of the RNA preparations yielded unequal amounts of the allelic messages. The deviations of the expression ratios (A2:A1) from 1.0 ranged from -0.9 to +25.8. The allelic messages were equally represented in the RNA preparations from five informative healthy donors. Apart from fibroblasts this phenomenon could also be detected in keratinocytes, melanocytes from normally pigmented skin and melanocytes from a café-au-lait spot of one patient. Only one of three patients affected by stop mutations exhibited unequal allelic expression. When nuclear RNA from 10 of the 13 patients was examined, equal amounts of the primary transcripts were found (average ratio A2/A1: 1.08 +/- 0.07 S.E.M.), indicating that unequal expression on the level of mRNA was not caused by mutations affecting transcriptional regulation. The ratio of the amount of neurofibromin to that of p120 GAP did not seem to be correlated with the extent of unequal allelic expression.

A new mutation, the first one close to the 5'-end of the neurofibromatosis type 1 (NF1) gene, was found when RNA preparations from various cell types of 15 NF1 patients were analysed by reverse transcription and subsequent multiplex polymerase chain reaction. This mutation removes the 84 bp of exon 3 precisely from the cDNA. Genomic Southern blots revealed a larger deletion with breakpoints within the introns flanking exon 3. This mutation suggests that the amino-terminal region of neurofibromin is functionally significant. When using this mutation to distinguish the wild type and mutant alleles, their expression could be analysed in neurofibroma fibroblasts, melanocytes from the unaffected skin, and those from a café-au-lait macule. In all these cell types, the products of both alleles were detected, confirming similar results obtained with a different NF1 gene mutation.

Approximately 50 members of the primate-specific multisequence family chAB4 are located as clusters at eight different chromosomal loci within the human genome. The whole cloned region of chAB4 represents a single-copy or low-copy sequence in all nonhuman primates tested, with the exception of the chimpanzee, for which we found chAB4 copy numbers similar to those in the human. An Alu element was inserted into chAB4 after the divergence of the Old World monkeys from the hominoids but before chAB4 was amplified. The first amplification step could be dated after the great apes and the human diverged from the Old World monkeys. We have evidence that neither the copy numbers nor the chromosomal locations remained stable after this initial step and that gross alterations in the relative copy numbers of individual family members occurred even after the divergence of the human and the chimpanzee. Taken together, our data suggest that chAB4, in an evolutionary sense, is an unusually unstable sequence family.

By screening total human DNA with probes derived from the small polydisperse circular (spc) DNA fraction of cultured human cells, we identified three clones that carry long stretches of beta-satellite DNA. Further experiments have shown that the three sequences belong to at least two different beta-satellite subfamilies, which are characterized by different higher order subunits. Members of one of these subfamilies are located in the cytological satellites of all acrocentric chromosomes, whereas members of another are located on the short arms of the acrocentrics on both sides of the stalk regions and also in the centromeric regions of chromosomes 1 and 9. This is the first time that beta-satellite sequences obtained from the spcDNA of human cells have been assigned to beta-satellite subfamilies that are organized as long arrays of tandemly arranged higher order monomers. This indicates that beta-satellite sequences can be excised from their chromosomal loci via intrastrand-recombination processes.

Small polydisperse circular DNA (spcDNA) in Fanconi anemia (FA) was analyzed from cultured fibroblast-like cells by electron microscopy. Application of the mica-press adsorption technique for the semi-quantitative determination of spcDNA amounts to three FA and three normal control skin-derived fibroblast strains revealed 85-fold increased levels of spcDNA in the FA cells. An even higher excess over controls was suggested when the FA fibroblasts were propagated for up to 11 serial in vitro passages, consistent with the short replicative life-span of primary FA cells and their rapid transition into a poorly dividing state, in which spcDNA reportedly further increases. In addition, contour length distributions of gradient-purified spcDNA preparations from five FA fibroblast strains were compared with those from five normal control strains. Mean spcDNA contour lengths were significantly greater in the FA than in the control cells. The reported findings of increased spcDNA amounts and sizes in FA coincide with a similar association of chromosome instability and abnormal spcDNA formation previously observed in cultured cells derived from angiofibromas in tuberous sclerosis. Circumstantial evidence from the present study in the paradigmatic chromosome breakage syndrome FA further supports the suggestion that a common mechanism underlies chromosome instability and the surplus generation of spcDNA. Notably, this apparent mechanism is functional in homonuclear primary cell strains with a distinct inherited basis of their chromosome instability, and is not restricted to heteroploid and neoplastoid cell lines.

A previously identified complex mutation, affecting exon 28 of the neurofibromatosis type 1 gene, was employed for the analysis of the expression pattern in primary cultures of neurofibroma cells and melanocytes from a café-au-lait macule of the patient, respectively. Reverse transcription and subsequent polymerase chain reaction amplification of the segment carrying the mutation revealed that both alleles were expressed in both cell types analysed, thus excluding loss of heterozygosity in this particular instance. Segregation of the alleles of the intragenic Alu sequence length-polymorphism disclosed the paternal origin of the mutated allele. Detection of this mutation was also used for presymptomatic direct DNA diagnosis in the younger child of the patient.

By hybridizing total human DNA with probes derived from the extrachromosomal circular DNA fraction of cultured cells, we detected a human multisequence family, called chAB4, previously unknown. Approximately 50 copies of this sequence are located in the haploid human genome. The repetition units of chAB4 are 35 kb long and the units are tandemly arranged. DNA sequence analysis of parts of the chAB4 unit revealed no direct evidence for a possible function of the family, but possibly chAB4 harbors a gene. Family members are located on human chromosomes 1, 3, and 9 and on the short arms of chromosomes 13-15, 21, and 22. Therefore, in addition to the rDNA, chAB4 is the second class of clustered repetitive sequences with a relatively long repetition unit localized on the short arms of all acrocentric chromosomes. Some evolutionary aspects arising from the structure of chAB4, the established parts of its DNA sequences, and the chromosomal localization of this new multisequence family are discussed.