Acrocallosal syndrome in a child with de novo inverted tandem duplication of 12p11.2-p13.3.

Report on the child of normal unrelated parents presenting the typical features of acrocallosal syndrome (craniofacial dysmorphy, mental deficiency, convulsive disorder, agenesis of corpus callosum, preaxial polydactyly "hallux duplex" of both feet, and in addition diabetes insipidus) in which a mirror duplication of nearly the entire short arm of chromosome 12 was discovered. Since the symptomatology of trisomy and tetrasomy 12p shows some overlap with acrocallosal syndrome a common origin of the monogenic disorder and the chromosomal phenotypes is discussed.     

Partial hyperploidy of the X-chromosome inDrosophila hydei leading to duplication of male gonadal and genital structures

Summary Introduction of two doses of the X-chromosomalw ^mCo duplication next to a normal X-chromosome in males ofD. hydei leads to duplication of testis tissue and structures derived from the male genital disc. The effect of this partial hyperploidy of the X-chromosome seems restricted to the male. We tentatively conclude that this part of the X-chromosome contains some factor(s) which may specifically affect the reproductive system and analia of males.     

Circular mitochondrial genome of Candida albicans contains a large inverted duplication.

The mitochondrial DNA (mtDNA) of the dimorphic fungus Candida albicans has a molecular size of 41 kilobase pairs as judged by summation of the fragment sizes produced by digestion with restriction endonucleases EcoRI, PvuII, and a combination of both enzymes. Five of the six EcoRI fragments comprising the mitochondrial genome have been cloned into the plasmid vector, pBR322. Restriction mapping revealed a circular map as predicted by previous observations with the electron microscope. The use of nick-translated, purified mtDNA to probe digests of mtDNA from other strains of C. albicans revealed a common restriction pattern. Use of nick-translated, cloned EcoRI fragments to probe digests of mtDNA revealed a large (at least 5 kilobase pairs), inverted duplication as well as a smaller (less than 0.4 kilobase pairs) region of related sequences.     

Distinct dysmorphic syndrome in a child with inverted distal 5q duplication

In the present paper we report a moderately mentally retarded 3 1/2-year-old girl with distal inverted 5q duplication (karyotype 46,XX,inv dup(5)(pter----q35.3::q35.3----q32::q35.3----qter). A distinct dysmorphic syndrome was present corresponding to the socalled "B-type" phenotype in 5q duplications, due to a duplication of band 5q33.     

Characterization of the inverted duplication in the mitochondrial DNA of Candida albicans.

The mitochondrial DNA (mtDNA) of Candida albicans contains a large inverted duplication. As is the case with most chloroplast DNAs and one other mtDNA, the nonduplicated regions of the molecule occur in two orientations with respect to each other, indicating that internal recombination occurs. Like some other mtDNAs, the C. albicans mtDNA contains a single SalI restriction site located near one end of the large rRNA gene. In contrast to other cases, however, the inverted duplication does not appear to contain any sequences coding for rRNA.     

Different DNA replication behavior of a tandem duplication in Drosophila melanogaster

Salivary gland chromosome DNA replication of a heterozygous tandem duplication Dp(1 1)Gr/+ and a wild type strain in Drosophila melanogaster has been studied by ³H-thymidine autoradiography. Three parameters-labeling frequency, labeling intensity and labeling pattern—have been used to characterize the replication behavior of late labeling spots in the distal part (1A–9A) of the X chromosomes for both genotypes. — Differences in the labeling frequency between homologous subdivisions in both genotypes have been found. Changes of the DNA replication behavior are also indicated by the comparison of labeling patterns in both Drosophila strains. Furthermore, in comparable replication phases the labeling intensities of the Dp(1 1)Gr/+ subdivisions are different from those of the homologous subdivisions in +/+ chromosomes, even where the different DNA amount of both genotypes is taken into consideration.     

Signal for DNA methylation associated with tandem duplication in Neurospora crassa.

Most cytosine residues are subject to methylation in the zeta-eta (zeta-eta) region of Neurospora crassa. The region consists of a tandem direct duplication of a 0.8-kilobase-pair element including a 5S rRNA gene. The repeated elements have diverged about 15% by the occurrence of numerous CG to TA mutations, which probably resulted from deamination of methylated cytosines. Most but not all common laboratory strains of N. crassa have methylated duplicated DNA at the zeta-eta locus. However, many strains of N. crassa and strains of N. tetrasperma, N. sitophila, and N. intermedia have one instead of two copies of the homologous DNA and it is not methylated. A cross of strains differing at the zeta-eta locus produced progeny which all had duplicated, methylated, or unique, unmethylated DNA, like the parental strains. We conclude that a signal causing unprecedented heavy DNA methylation is present in the zeta-eta region.     

Formation of an inverted duplication can be an initial step in gene amplification.

We have developed a gene transfer approach to facilitate the identification and isolation of chromosomal regions which are prone to high-frequency gene amplification. Such regions are identified by assaying for transformants which show high-frequency resistance to PALA and/or methotrexate by amplification of a vector containing the genes which encode the enzyme targets of these antiproliferative agents. We identified 2 of 47 transformants which displayed high-frequency amplification of the transfected genes, and in this report we describe the analysis of one of them (L46). Molecular analysis of the integration site in transformant L46 revealed that the donated genes were at the center of an inverted duplication which spanned more than 70 kilobase pairs and consisted largely of host DNA. The data suggest that integration of the transfected sequences generates a submicroscopic molecule containing the inverted duplication and at least 750 kilobases of additional sequences. The donated sequences and the host sequences were readily amplified and lost in exponentially growing cultures in the absence of drug selection, which suggests that the extrachromosomal elements are acentric. In contrast to the instability of this region following gene insertion, the preinsertion site was maintained at single copy level under growth conditions which produced copy number heterogeneity in L46. The implications of our results for mechanisms of genetic instability and mammalian gene amplification are discussed.     

Physical mapping of an Xq-proximal interstitial duplication in a male

Summary A viable duplication in the proximal long arm of the X chromosome in a boy with a malformative syndrome was delineated with molecular biology techniques using 14 probes from the X cen-Xq21 region. This analysis allowed us to refine the physical map of the X cen-Xq13 region.     

Chromosomal translocation and inverted duplication associated with integrated hepatitis B virus in hepatocellular carcinomas.

Integrated hepatitis B virus (HBV) DNA is found in hepatocellular carcinomas which develop in HBV carriers. Presented here are the results of analyses of four integrants that show chromosomal rearrangements associated with the integrated HBV DNA. Two clones (p4 and C15) were found to have large inverted repeating structures, each consisting of HBV genome along with flanking cellular sequences. The structure must have arisen by duplication of the primary integrant, including the flanking cellular DNA, followed by recombination within the viral DNA. One of the two viral arms in each clone joins to the other viral arm at the "cohesive end region." Two clones (DA2-2 and DA2-6) were found to have integrated HBV sequences, each flanked by cellular DNAs from different chromosomes (chromosome X joined to 17 and chromosome 5 joined to 9). They must be the products of cellular DNA translocations using the integrated HBV DNA as the switch point. The viral DNA in each clone is a continuous stretch of a single virus genome with one end in the cohesive end region. These complex structures seem to have been produced by activation of the cohesive end of an integrant viral genome, followed by its recombination with another chromosomal DNA.     

Multiple tandem duplication of the phenylalanine ammonia-lyase genes in Cucumis sativus L.

Phenylalanine ammonia-lyase (PAL) is the first entry enzyme of the phenylpropanoid pathway, and therefore plays a key role in both plant development and stress defense. In many plants, PAL is encoded by a multi-gene family, and each member is differentially regulated in response to environmental stimuli. In the present study, we report that PAL in cucumber (Cucumis sativus L.) is encoded for by a family of seven genes (designated as CsPAL1-7). All seven CsPALs are arranged in tandem in two duplication blocks, which are located on chromosomes 4 and 6, respectively. The cDNA and protein sequences of the CsPALs share an overall high identity to each other. Homology modeling reveals similarities in their protein structures, besides several slight differences, implying the different activities in conversion of phenylalanine. Phylogenic analysis places CsPAL1-7 in a separate cluster rather than clustering with other plant PALs. Analyses of expression profiles in different cucumber tissues or in response to various stress or plant hormone treatments indicate that CsPAL1-7 play redundant, but divergent roles in cucumber development and stress response. This is consistent with our finding that CsPALs possess overlapping but different cis-elements in their promoter regions. Finally, several duplication events are discussed to explain the evolution of the cucumber PAL genes.     

Mitotic and meiotic analysis of a pericentric inversion associated with a tandem duplication in Eleutherine bulbosa

The mitotic and meiotic chromosomes of five populations of Eleutherine bulbosa were analysed after C-banding and fluorochrome (DAPI/CMA) staining. All individuals showed heterozygosity in pair number I for a pericentric inversion and a tandem duplication in the inverted region of one of the homologues. The duplication comprised the secondary constriction and ca. 40% of its associated CMA⁺ heterochromatin. All the secondary constrictions were nucleolar organizers, but the repeated one seemed to be the most active. The inverted segment constituted ca. 70% of the chromosome length and included, in addition to the duplication and the centromere, two DAPI⁺ C-bands. These markers, especially the CMA⁺ blocks which were unique in the complement, permitted a detailed analysis of meiotic pairing. In practically all examples of late zygotene the CMA blocks were paired, which seems to mean that non-homologous pairing never occurred. At this stage the duplicated CMA⁺ block was clearly unpaired. At pachytene-diplotene the inverted region formed a typical loop without chiasmata. Although male meiosis was normal, no indication of sexual reproduction was found. A causal relationship between duplication, inversion and asexual reproduction is proposed to explain the maintenance of the heterozygosity.     

Inherited Xq duplication due to a zygotic translocation t(X;X)(q23;q27)

An Xq-duplication was found in a female child with multiple malformations. The family study revealed that her mother, who has a nearly normal phenotype, carries the same duplication. The karyotype of the grandmother shows the existence of a mosaicism: 46,X,del(X) (q23)/46,X,dup(X)(q27----q23). This mosaicism can be related to a translocation t(X;X)(q23;q27) during the first cell division of the zygote.     

Structure of an inverted duplication formed as a first step in a gene amplification event: implications for a model of gene amplification.

Inverted duplications have been observed to be a common feature of gene amplification in mammalian cells and appear to be generated as a primary event in the amplification process (Ford et al., 1985; Ford and Fried, 1986). The structural features of the amplified inverted duplication, containing the polyoma virus oncogene middle T-antigen, were analysed in transformed 3B rat cells. No unusual sequences such as transposition elements were detected at the site of the inversion. The inversion was generated by a simple illegitimate recombination event in which only a single nucleotide directly at the point of the inversion cannot be accounted for from the sequence of the two parental strands. Possible structural (hairpin formation) and sequence (rich AT) features may have been involved in the illegitimate recombination event at the inversion join. In the cellular DNA near one of its joins with polyoma virus DNA an unusual sequence of 198 bp composed of 99 consecutive purine-pyrimidine pairs has been detected. A model for the generation of amplified DNA containing inverted duplications is proposed.     

Homologous recombination and chromosomal rearrangements in Escherichia coli strains carrying a heterozygous tandem duplication]

Heterozygous tandem duplications formed in conjugational matings in Escherichia coli provides a convenient model system for studying the evolution of bacterial chromosome. Heterozygous duplications segregate various classes of haploid and diploid recombinants that appear as a result of unequal crossing over between sister chromosomes. In this work, an extended tandem duplication in the deo operon of E. coli carrying deoA deoB::Tn5/deoC deoD thr::Tn9 alleles was examined. Recombination between homologous DNA repeats in the duplication was studied in strains carrying different combinations of recBC, sbcBC, recB::Tn10, recQ::Tn3 mutations. The frequency of recombination between homologous DNA repeats was very high in all strains and did not decrease when the RecBCD and RecF recombinational pathways were simultaneously damaged in strains with the recB sbcBC recQ (or recF) genotype. It is assumed that unequal crossing over between direct DNA repeats in duplications may proceed through a particular pathway of "adaptive" recombination.     

Evolutionary transition to XY sex chromosomes associated with Y-linked duplication of a male hormone gene in a terrestrial isopod

Sex chromosomes are highly variable in some taxonomic groups, but the evolutionary mechanisms underlying this diversity are not well understood. In terrestrial isopod crustaceans, evolutionary turnovers in sex chromosomes are frequent, possibly caused by Wolbachia, a vertically-transmitted endosymbiont causing male-to-female sex reversal. Here, we use surgical manipulations and genetic crosses, plus genome sequencing, to examine sex chromosomes in the terrestrial isopod Trachelipus rathkei. Although an earlier cytogenetics study suggested a ZZ/ZW sex chromosome system in this species, we surprisingly find multiple lines of evidence that in our study population, sex is determined by an XX/XY system. Consistent with a recent evolutionary origin for this XX/XY system, the putative male-specific region of the genome is small. The genome shows evidence of Y-linked duplications of the gene encoding the androgenic gland hormone, a major component of male sexual differentiation in isopods. Our analyses also uncover sequences horizontally acquired from past Wolbachia infections, consistent with the hypothesis that Wolbachia may have interfered with the evolution of sex determination in T. rathkei. Overall, these results provide evidence for the co-occurrence of multiple sex chromosome systems within T. rathkei, further highlighting the relevance of terrestrial isopods as models for the study of sex chromosome evolution.Subject terms: Evolutionary genetics, Genome evolution     

Amplification of a tandem direct repeat within inverted repeats of Marek''s disease virus DNA during serial in vitro passage.

DNA of the oncogenic strain BC-1 of Marek's disease virus contains three units of tandem direct repeats with 132 base pairs in the terminal repeat and internal repeat, respectively, of the long region of the Marek's disease virus genome, whereas the attenuated, nononcogenic viral DNA contains multiple units of the tandem direct repeats.