Expression of the tryptophan operon in merodiploids of Escherichia coli. I. Gene dosage, gene position and marker effects.
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Diploidy↗
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Gene dosage and gene expression in the HLA region: evidence from deletion variants.
Among variants selected in a human cell line for nonexpression of a single gene product in the HLA complex, most are single-gene variants, but several have been isolated that are cis-acting and abolish expression of a series of closely linked genes. The two most plausible mechanisms by which such variants could arise are mitotic crossing-over and chromosome deletion. In two HLA variants the presence of a visible chromosome deletion, a 50% reduction in activity of glyoxalase I (a closely linked marker), or both provided evidence for deletional origins. In a third variant these changes were not demonstrable. All three variants showed reductions in amount of cell surface HLA antigens: 40% for the Ia antigens (HLA-DR) and 20-25% for HLA-ABC antigens. The reductions in cell surface antigen in deletion variants have an important implication: in the case of the HLA-A, -B, and -C heterodimer, which consists of a subunit coded for within the major histocompatibility complex and another subunit (beta(2)-microglobulin) coded for on a different chromosome, it is the gene of the major histocompatibility complex that is limiting. The nonmutant haplotype includes A2; binding of an A2 monoclonal antibody in two of the mutants was found to be approximately equal to that in the wild-type cells. Thus, loss of one copy of HLA-ABC genes does not lead to gene dosage compensation-i.e., increased activity by the remaining ABC alleles. The results with the two types of antibodies support a deletional mechanism and are inconsistent with mitotic crossing-over. Of interest with respect to the potential use of deletion variants for purposes of mapping is the fact that each of these variants has distinctive breakpoints. The absence of mitotic crossing-over in 1.2 x 10(7) cells selected suggests that the event is rare in this autosomal region, if it occurs at all.
Cell Line↗
Real-time quantitative PCR analysis of gene dosages reveals gene amplification in low-grade oligodendrogliomas.
Proto-oncogene amplification is an important alteration that is present in about 45% to 50% of high-grade human gliomas. We studied this mechanism in 8 genes (cyclin-dependent kinase-4 [CDK4], MDM2, MDM4, renin-angiotensin system-1, ELF3, GAC1, human epidermal growth factor receptor-2, and platelet-derived growth factor receptor-A gene) in a series of 40 oligodendrogliomas (World Health Organization (WHO) grade II, 21; WHO grade III, 13; and WHO grade II-III oligoastrocytomas, 6) using real-time quantitative polymerase chain reaction. Amplification of at least 1 of these genes was detected in 58% of samples (23/40). By histopathologic grade, 67% of grade II oligodendrogliomas (14/21), 46% of grade III anaplastic oligodendrogliomas (6/13), and 50% of mixed oligoastrocytomas (3/6) were positive for amplification of at least 1 gene. CDK4, MDM2, and GAC1 were the most frequently involved genes (12/40 [30%], 12/40 [30%], and 13/40 [33%], respectively). Our findings demonstrate gene amplification in low-grade samples indicating that it is an important alteration in the early steps of oligodendroglioma development and, therefore, might be considered a molecular mechanism leading to malignant progression toward anaplastic forms.
Biomarkers, Tumor↗
The effect of gene concentration and relative gene dosage on gene output in Escherichia coli.
The differential rate of synthesis of several Escherichia coli gene products was measured under conditions in which the average number of copies of the corresponding chromosomal gene had been changed by altering the replication velocity of the chromosome. The data show that in steady state exponential cultures the output of genes in a fully repressed, fully derepressed, or non-repressible state is proportional to the average number of copies of the gene per unit mass (gene: mass ratio) and does not depend on the number of copies of the gene relative to all other genes (gene: DNA ratio). In contrast, the output of a gene which was under regulation by endogenously generated effectors was independent of such changes in gene frequency. The relationship found between the number of copies of a gene per unit of cell mass and enzyme output provides a new method for determining the location of the chromosome origin and the direction of replication in bacteria.
Alleles↗
Relationship between Gene Dosage and Gene Expression in the Chloroplast of Chlamydomonas reinhardtii.
Expression of three chloroplast genes encoding proteins of different chloroplast complexes and the rRNA gene has been examined in cells having reduced numbers of chloroplast genomes as a result of growth in the presence of the thymidine analog 5-fluorodeoxyuridine. While accumulation of total mRNA for rpl2 (ribosomal protein L-1), rbcL (ribulose bisphosphate carboxylase large subunit) and atpA (alpha-subunit of ATP synthase) declined with gene copy number, the levels of translatable mRNA and rates of synthesis of these three proteins were largely unaffected. Accumulation of rRNA declined less precipitously than mRNA levels for the three proteins in response to the reduction in chloroplast genome number. Chlamydomonas appears to compensate for reductions in the number of chloroplast genomes at several different levels. Populations of cells with only one-fourth the wild-type amount of chloroplast DNA per cell on average have half the normal level of chloroplast ribosomes and nearly normal rates of CO(2) fixation and levels of specific chloroplast encoded proteins. These results suggest that normal cells accumulate a large excess of transcripts for chloroplast genes and that levels of expression of these genes are regulated by posttranscriptional mechanisms.
Journal Article↗
Gene expression profiling of isogenic cells with different TP53 gene dosage reveals numerous genes that are affected by TP53 dosage and identifies CSPG2 as a direct target of p53.
TP53 does not fully comply with the Knudson model [Knudson, A. G., Jr. (1971) Proc. Natl. Acad. Sci. USA 68, 820-823] in that a reduction of constitutional expression of p53 may be sufficient for tumor predisposition. This finding suggests a gene-dosage effect for p53 function. To determine whether TP53 gene dosage affects the transcriptional regulation of target genes, we performed oligonucleotide-array gene expression analysis by using human cells with wild-type p53 (p53 +/+), or with one (p53 +/-), or both (p53 -/-) TP53 alleles disrupted by homologous recombination. We identified 35 genes whose expression is significantly correlated to the dosage of TP53. These genes are involved in a variety of cellular processes including signal transduction, cell adhesion, and transcription regulation. Several of them are involved in neurogenesis and neural crest migration, developmental processes in which p53 is known to play a role. Motif search analysis revealed that of the genes highly expressed in p53 +/+ and +/- cells, several contain a putative p53 consensus binding site (bs), suggesting that they could be directly regulated by p53. Among those genes, we chose CSPG2 (which encodes versican) for further study because it contains a bona fide p53 bs in its first intron and its expression highly correlates with TP53 dosage. By using in vitro and in vivo assays, we showed CSPG2 to be directly transactivated by p53. In conclusion, we developed a strategy to demonstrate that many genes are affected by TP53 gene dosage for their expression. We report several candidate genes as potential downstream targets of p53 in nonstressed cells. Among them, CSPG2 is validated as being directly transactivated by p53. Our method provides a useful tool to elucidate additional mechanisms by which p53 exerts its functions.
Adenocarcinoma↗
Use of microsatellite markers and gene dosage to quantify gene copy numbers in Candida albicans.
With microsatellite marker typing, the number of alleles must be known for calculation of allelic frequencies in the diploid Candida albicans for a given locus. We describe a gene dosage with a double real-time PCR. Such a dosage should also be useful in exploring the loss of heterozygosity in C. albicans.
Candida albicans↗
Gene dosage as a regulatory factor for gene expression. I. In lambda plac5-infected cells.
To study the effect of gene dosage on gene expression, lambda plac5cI857O29P3, a replication defective lambda phage carrying part of the lac operon (containing the lac promotor, operator and z gene) in the b2 region was studied in Escherichia coli strain JC6256 where the lac operon is deleted and at a temperature where the lambda repressor is inactive. In measuring the synthesis of beta-galactosidase, it was possible to separate the effects of the lac promoter from those of the phage promoter. When the synthesis of beta-galactosidase was initiated from the inserted lac promoter in JC6256(lambda +) in the presence of additional cyclic AMP, the rate and level of beta-galactosidase synthesis were directly proportional to the multiplicity of infection (gene dosage). Furthermore, beta-galactosidase synthesis was initiated about 5 min after infection, just as with isopropyl-beta-D-thiogalactoside (IPTG) induction. When the synthesis of beta-galactosidase was initiated from the phage promoter in JC6256 in the absence of additional cyclic AMP, the rate and level of beta-galactosidase synthesis were again linearly proportional to gene dosage. On the other hand, initiation of beta-galactosidase synthesis was delayed until 10 to 20 min after infection. These results suggest that: (i) in the absence of negative controlling factors, the extent of gene expression is proportional to gene dosage; (ii) varying the gene dosage can be used to regulate gene expression.
Bacteriophage lambda↗
Confirmation of regional assignment of nucleoside phosphorylase (NP) on chromosome 14 by gene dosage studies.
Gene dosage studies yielded results consistent with assignment of the locus for nucleoside phosphorylase to band 14q13. The red blood cells from a patient with the karyotype 47,XX,+der(14),t(8;14)(8qter leads to 8q24::14q21 leads to 14pter)pat had enzyme activity 50% higher than red cells from 47 normal controls, two trisomies involving chromosomes other than 14, and five balanced translocations involving chromosome 14. On the other hand, the red cells of a case with a karyotype 45,XX,-14,-22+der(22),t(14;22)(14qter leads to 14q11 or 14q12::22p11 leads to 22qter)mat and a case with a a karyotype 47,XX,+der(14),t(14;16)(14pter leads to 14q11::16q24 leads to 16qter)mat had normal activity
Child, Preschool↗
Down syndrome--a gene dosage disease caused by trisomy of genes within a small segment of the long arm of chromosome 21, exemplified by the study of effects from the superoxide-dismutase type 1 (SOD-1) gene.
Down syndrome (DS), the most common postnatally viable human autosomal chromosomal abnormality is caused by trisomy for chromosome 21. The mechanism whereby the supernumerary chromosome 21 contributes to the pathology of DS remains elusive. There are, however, several evidences that DS is a gene dosage disease. This means that overproduction of certain proteins, encoded by normal genes on the extra chromosome, distorts the delicate balance of some biochemical pathways that are important for proper development and function of the organs affected in DS. It has been shown that only the distal segment of the long arm of chromosome 21 is involved in the pathogenesis of DS. Great efforts to define this "DS specific" segment are made today, with the aim to find the "DS responsible" genes. It is suggested that as few as 10-20 genes might be responsible for the DS phenotype. We will report from a world-wide collaboration study and especially the result from one single patient. It is a woman with a characteristic phenotype of DS, but with microscopically normal karyotype. She had a sister with DS, who is dead. The parents were related, why an autosomal recessive disorder is suspected. Autoradiograms of quantitative Southern blots of DNAs from the patient and her parents were analyzed after hybridization with unique DNA sequences regionally mapped on chromosome 21. The patient seems to have three alleles at the VTNR-polymorphism in the Col6A1 gene, one copy from the father and two copies from the mother. The Col6A1 gene is mapped at the very distal segment of the long arm of chromosome 21 (21q22.3). She has only two alleles of all loci analyzed proximal to Col6A1. This might indicate that she has trisomy only for the very distal part of band 21q22.3. It is, however, not enough to find the genes within the "DS specific" segment. The metabolic gene dosage effects from these genes must be evaluated. Although several genes have been mapped on chromosome 21, not one single feature of DS has been proved to be an effect of any single gene. As an example of the difficulties to assign features of DS to chromosome 21 specific genes the gene dosage effects of the superoxide dismutase type I (SOD-1) will be presented.
Adult↗
Modeling del(17)(p11.2p11.2) and dup(17)(p11.2p11.2) contiguous gene syndromes by chromosome engineering in mice: phenotypic consequences of gene dosage imbalance.
Contiguous gene syndromes (CGS) are a group of disorders associated with chromosomal rearrangements of which the phenotype is thought to result from altered copy numbers of physically linked dosage-sensitive genes. Smith-Magenis syndrome (SMS) is a CGS associated with a deletion within band p11.2 of chromosome 17. Recently, patients harboring the predicted reciprocal duplication product [dup(17)(p11.2p11.2)] have been described as having a relatively mild phenotype. By chromosomal engineering, we created rearranged chromosomes carrying the deletion [Df(11)17] or duplication [Dp(11)17] of the syntenic region on mouse chromosome 11 that spans the genomic interval commonly deleted in SMS patients. Df(11)17/+ mice exhibit craniofacial abnormalities, seizures, marked obesity, and male-specific reduced fertility. Dp(11)17/+ animals are underweight and do not have seizures, craniofacial abnormalities, or reduced fertility. Examination of Df(11)17/Dp(11)17 animals suggests that most of the observed phenotypes result from gene dosage effects. Our murine models represent a powerful tool to analyze the consequences of gene dosage imbalance in this genomic interval and to investigate the molecular genetic bases of both SMS and dup(17)(p11.2p11.2).
Animals↗
The importance of gene dosage studies: mutational analysis of the parkin gene in early-onset parkinsonism.
Early-onset parkinsonism (EOP) may be associated with different mutations in the parkin gene, including exon deletions and duplications. To test for gene dosage alterations, we developed a new method of quantitative duplex PCR using the fluorescence resonance energy transfer technique on the LightCycler (Roche Diagnostics). In 21 patients with EOP, three mutations (a single base pair substitution in exon 3 and small deletions in exon 9) were detected by conventional mutational screening (single-strand conformation polymorphism and sequence analysis), while alterations of gene dosage were found in seven patients. We identified heterozygous and compound heterozygous deletions of exons 2, 3, 5 and 7. The latter was also found in the homozygous state. In addition, two heterozygous duplications of exon 4 were observed. Remarkably, two patients carried more than two parkin mutations. This is the first study systematically screening all 12 exons of parkin by real-time, kinetic quantification and clearly shows that mutational analysis of the parkin gene should include gene dosage studies. Furthermore, our method of quantitative PCR is easily applicable to any other gene to be screened for deletions or duplications of whole exons.
Age of Onset↗
Gene dosage effects of the structural gene for a lipoprotein of the Escherichia coli outer membrane.
The gene dosage effects of the structural gene (lpp) for the lipoprotein of the Escherichia coli outer membrane were examined. A novel F-prime factor containing the lpp gene was constructed. The amount of the free-form lipoprotein in the merodiploid strain carrying the F-prime factor was found to be about two times as great as that in the corresponding haploid strain. On the other hand, the amount of the bound-form lipoprotein, which is vovalently linked to the peptidoglycan, was not significantly different in the merodiploid strain as compared with the corresponding haploid strain. The present results suggest that the lpp gene is expressed constitutively in contrast to another major protein of the E. coli outer membrane, tolG protein (protein II, D. B. Datta et al., J. Bacteriol. 128:834-841, 1976). The F-prime factor isolated may include a portion of the E. coli chromosome (located between 33 and 36 min on the genetic map) that is not covered by any other F-prime factor.
Bacterial Proteins↗
Tandem repeats of the 5' non-transcribed spacer of Tetrahymena rDNA function as high copy number autonomous replicons in the macronucleus but do not prevent rRNA gene dosage regulation.
The rRNA genes in the somatic macronucleus of Tetrahymena thermophila are normally on 21 kb linear palindromic molecules (rDNA). We examined the effect on rRNA gene dosage of transforming T.thermophila macronuclei with plasmid constructs containing a pair of tandemly repeated rDNA replication origin regions unlinked to the rRNA gene. A significant proportion of the plasmid sequences were maintained as high copy circular molecules, eventually consisting solely of tandem arrays of origin regions. As reported previously for cells transformed by a construct in which the same tandem rDNA origins were linked to the rRNA gene [Yu, G.-L. and Blackburn, E. H. (1990) Mol. Cell. Biol., 10, 2070-2080], origin sequences recombined to form linear molecules bearing several tandem repeats of the origin region, as well as rRNA genes. The total number of rDNA origin sequences eventually exceeded rRNA gene copies by approximately 20- to 40-fold and the number of circular replicons carrying only rDNA origin sequences exceeded rRNA gene copies by 2- to 3-fold. However, the rRNA gene dosage was unchanged. Hence, simply monitoring the total number of rDNA origin regions is not sufficient to regulate rRNA gene copy number.
Animals↗
CNS myelination and PLP gene dosage.
The phenomenon of gene dosage effects demonstrates that the mechanisms of some genetic diseases are best recognised at the genomic level. Classical gene mutation screening approaches utilising PCR are unsuccessful in unravelling the basis of disease because the gene sequence is unaltered and only the copy number is different. Techniques for detecting DNA dosage are required. Examples of haploinsufficiency and gene deletions are well documented, but increased gene dosage is also an important genetic mechanism in disorders involving myelin proteins in the central (CNS) and peripheral nervous system (PNS). Here we review the dosage effects and mutations of the proteolipid protein (PLP) gene that causes Pelizaeus-Merzbacher disease (PMD) and spastic paraplegia Type 2 (SPG2) disorders of CNS myelination. Similarities are drawn with the peripheral neuropathies Charcot-Marie-Tooth disease Type 1 (CMT1A) and hereditary neuropathy with liability to pressure palsies (HNPP) that are also caused by dosage effects and mutations in a single myelin protein gene (peripheral myelin protein 22, PMP-22). We compare the different mutational mechanisms in man and analogous mouse models that suggest a function for PLP beyond its structural role in myelin. We focus on the increased dosage of the PLP gene that is the major cause of PMD and results from a submicroscopic duplication of Xq22. Other clinical phenotypes may arise from gene dosage imbalance with the potential effect of submicroscopic duplications and deletions of the genome being underestimated. Genome sequencing may identify intrinsic structural properties of the DNA with greater susceptibility to these rearrangements and thereby reflect structural changes in the genome.
Animals↗
Differential polymerase chain reaction in the analysis of gene dosage.
Abnormalities of gene dosage are important in human disease. We have developed the differential polymerase chain reaction (PCR) to detect gene amplification and deletion in small amounts of tissues whose DNA may be degraded. The current utility of differential PCR required optimization of DNA isolation procedures, of primer selection approaches, and of PCR conditions. From this experience, we have formulated a theoretical framework for the technique, and describe appropriate applications and potential improvements based on emerging PCR technologies. Special emphasis is placed on the analysis of formalin fixed and paraffin embedded, archived specimens.
Base Sequence↗
Charcot-Marie-Tooth disease type 1A: molecular mechanisms of gene dosage and point mutation underlying a common inherited peripheral neuropathy.
Charcot-Marie-Tooth disease type 1A is a demyelinating, inherited peripheral neuropathy which is associated with a DNA duplication in chromosome 17p11.2-p12 in over 70% of patients with CMT1A. The CMT1A duplication is not detected cytogenetically, and constitutes a tandem duplication of a 1.5-Mb region of DNA flanked by homologous sequences designated as CMT1A-REP. Detection of the CMT1A duplication by molecular methods is a valuable diagnostic test for the majority of CMT1A cases. This duplication mutation shows stable inheritance through multiple generations, and may also arise as a new mutation in sporadic patients. The CMT1A duplication leads to the disease phenotype apparently through increased dosage of a gene(s) within the duplicated segment. A disease gene associated with CMT1A has been identified in the form of PMP22, which maps within the CMT1A duplication region, and encodes a myelin protein of the peripheral nerve. Point mutations in the PMP22 gene have been identified in CMT1A patients, including one case of a new mutation in PMP22 which coincided with the onset of the disease. Thus, two alternative molecular mechanisms are responsible for CMT1A: DNA duplication leading to increased gene dosage, and point mutation of the PMP22 gene.
Charcot-Marie-Tooth Disease↗
[Study on gene-dosage effect of high level expression of the yeast glucoamylase genes].
Diploid strains homozygous for both MAT allele and STA genes (a/a, STA1/STA1 or STA2/STA2 or STA3/STA3) and diploid strains homozygous for MAT allele but intercombinative for STA genes (a/a, STA1/STA2 or STA2/STA3 or STA1/STA3) were constructed by means of the protoplast fusion or the colchicine treatment. According to glucoamylase activity in YPS medium, we studied the gene-dosage effect and their interrelation of these three polymeric genes coding for glucoamylase. The results of the glucoamylase activity determination showed that the gene-dosage effect of glucoamylase is obvious in diploid and triploid strains homozygous for both MAT allele and STA gene, such as the glucoamylase activity of a diploid strain SFY56-6 and a triploid strain SFY56-104 homozygous for both MAT allele and STA genes were respectively 2.35 and 3.18-fold as compared with that of the their parental strain IATA-Y56 that is a haploid Saccharomyces diastaticus. Moreover, the glucoamylase activity of diploid strains homozygous for MAT allele but intercombinative for STA genes also showed the combinative gene-dosage effect to a certain extent.
Gene Dosage↗