Human artificial chromosomes generated by modification of a yeast artificial chromosome containing both human alpha satellite and single-copy DNA sequences

A human artificial chromosome (HAC) vector was constructed from a 1-Mb yeast artificial chromosome (YAC) that was selected based on its size from among several YACs identified by screening a randomly chosen subset of the Centre d'Etude du Polymorphisme Humain (CEPH) (Paris) YAC library with a degenerate alpha satellite probe. This YAC, which also included non-alpha satellite DNA, was modified to contain human telomeric DNA and a putative origin of replication from the human beta-globin locus. The resultant HAC vector was introduced into human cells by lipid-mediated DNA transfection, and HACs were identified that bound the active kinetochore protein CENP-E and were mitotically stable in the absence of selection for at least 100 generations. Microdissected HACs used as fluorescence in situ hybridization probes localized to the HAC itself and not to the arms of any endogenous human chromosomes, suggesting that the HAC was not formed by telomere fragmentation. Our ability to manipulate the HAC vector by recombinant genetic methods should allow us to further define the elements necessary for mammalian chromosome function.     

Isolation of yeast artificial chromosomes free of endogenous yeast chromosomes: construction of alternate hosts with defined karyotypic alterations

An intrinsic feature of yeast artificial chromosomes (YACs) is that the cloned DNA is generally in the same size range (i.e., approximately 200-2000 kb) as the endogenous yeast chromosomes. As a result, the isolation of YAC DNA, which typically involves separation by pulsed-field gel electrophoresis, is frequently confounded by the presence of a comigrating or closely migrating endogenous yeast chromosome(s). We have developed a strategy that reliably allows the isolation of any YAC free of endogenous yeast chromosomes. Using recombination-mediated chromosome fragmentation, a set of Saccharomyces cerevisiae host strains was systematically constructed. Each strain contains defined alterations in its electrophoretic karyotype, which provide a large-size interval devoid of endogenous chromosomes (i.e., a karyotypic "window"). All of the constructed strains contain the kar1-delta 15 mutation, thereby allowing the efficient transfer of a YAC from its original host into an appropriately selected window strain using the kar1-transfer procedure. This approach provides a robust and efficient means to obtain relatively pure YAC DNA regardless of YAC size.     

Amplified c-MYC sequences localized by fluorescence in-situ hybridization on double minute chromosomes in acute myeloid leukemias

Double minute chromosomes (dmin) are small acentric fragments frequently observed when karyotyping human tumor cells. They are considered the cytogenetic manifestation of gene amplification. The finding of dmin in leukemia is a rare event usually associated with progression of the disease and unfavorable prognosis. We present four patients affected by myeloid disorders with an abnormal karyotype and a variable number of dmin. In an attempt to clarify the origin of the dmin and the amplified gene, we utilized a fluorescent in-situ hybridization (FISH) technique and a panel of specific probes. The results of the analysis indicate that, although chromosomes 8 are apparently uninvolved, dmin retained c-MYC sequencs in three cases. By observing previously reported cases, we found that the majority of patients with myeloid disorders and dmin showed an amplified c-MYC gene, regardless of the chromosomal abnormalities. The FISH technique proved to be informative in demonstrating gene amplification in both metaphase and interphase cells. Finally, in the one patient carrying a 20q deletion, FISH allowed the detection of a previously unreported translocation between a 16p and the 20q-, confirming the ability of the technique to understand complex karyotypes.     

Rapid cloning of mouse DNA as yeast artificial chromosomes by transformation-associated recombination (TAR)

The purpose of this study is to investigate the count-characteristics of wrist actigraphy in basic human activities and to discuss the agreement of sleep-wake identification between polysomnography (PSG) and wrist actigraphy during nocturnal sleep. There was a distinct distribution of actigraphy counts over the studied activities. The evaluation of sleep-wake scoring using the wrist actigraphy agreed 96.9% with the polysomnographic scoring during nocturnal sleep.     

GAA trinucleotide repeat expansion in variant Friedreich's ataxia families

Phenotypic variants in Friedreich's ataxia include late onset, preservation of the lower limbs tendon reflexes, and slow progression. We describe clinical and electrophysiological features from three families with Friedreichlike phenotypes. Friedreich's ataxia diagnosis was confirmed by finding two allelic expansions of the GAA trinucleotide repeat at the X25 gene. In family 1 both patients had a late-onset phenotype with preservation of knee and ankle jerks, lack of cardiomyopathy, and preserved H reflex. One of them did not have electrophysiologic evidence of sensory axonal neuropathy. Patients from family 2 showed variability in the age of onset, and 2 out of 3 affected children had hyperactive lower limbs reflexes with preserved H reflex. Disease progression in a patient from family 3 was very slow after onset at the age of 21. The finding of two expanded alleles in these families confirms the wide variability of the clinical spectrum of Friedreich's ataxia.     

Brain glyceraldehyde-3-phosphate dehydrogenase activity in human trinucleotide repeat disorders

BACKGROUND: Although the abnormal gene products responsible for several hereditary neurodegenerative disorders caused by repeat CAG trinucleotides have been identified, the mechanism by which the proteins containing the expanded polyglutamine domains cause cell death is unknown. The observation that several of the mutant proteins interact in vitro with the key glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH) suggests that interaction between the different gene products and GAPDH might damage brain neurons. OBJECTIVE: To measure the activity of GAPDH in postmortem brain of patients with CAG repeat disorders. PATIENTS AND METHODS: Activity of GAPDH was measured in morphologically affected and unaffected brain areas of patients with 4 different CAG repeat disorders (Huntington disease, spinocerebellar ataxia 1 [SCA1], SCA2, and SCA3-Machado-Joseph disease), in brains of patients with Friedreich ataxia (a GAA repeat disorder) and Alzheimer disease, and in brains of matched control subjects. RESULTS: Brain GAPDH activity was normal in all groups with the exception of a slight but statistically significant region-specific reduction in the patients with Huntington disease (caudate nucleus, -12%) and Alzheimer disease (temporal cortex, -19%). CONCLUSION: The presence of the polyglutamine-containing proteins in CAG repeat disorders does not result in substantial irreversible inactivation or in increased activity of GAPDH in human brain.     

Identification of complex chromosome rearrangements in the gibbon by fluorescent in situ hybridization (FISH) of a human chromosome 2q specific microlibrary, yeast artificial chromosomes, and reciprocal chromosome painting

Chromosome painting has revealed that the human chromosome homologs in lesser apes are often fragmented and translocated to a number of different hylobatid chromosomes. We investigated the fragmented human chromosome 2 homologs in gibbons to illustrate a new strategy in mapping regional and band-specific chromosomal homologies between species. Previous research showed that the DNA library specific to human chromosome 2 paints parts of four gibbon (lar species group) chromosomes (viz., 1, 10, 12, and 16) and yields five distinct hybridization signals (including two on gibbon chromosome 16). However, the exact segments of human chromosome 2 that were translocated to the various gibbon chromosomes could not be distinguished. To determine the origin of the human chromosome 2 signals, we hybridized a microlibrary for the long arm of human chromosome 2, as well as YACs specific for most of the major bands on this chromosome, to metaphases of the gibbon. For reciprocal chromosome painting, we hybridized flow-sorted gibbon chromosome probes to human chromosome 2. Each method added additional insights that helped clarify the shuffling of human chromosome 2 material in the highly reorganized gibbon genome. There was an excellent correspondence between these complementary techniques. YAC 958d2 identified the breakpoint between human chromosome 2 material present on gibbon chromosomes 10 and 16. The reciprocal chromosome painting permitted a more complete and regional assignment of homology between segments on various gibbon chromosomes to human chromosome 2. The results show that a combination of reciprocal chromosome painting, subregional microlibraries, and band-specific probes (such as YACs) can be used to identify homologies between species and to rapidly construct detailed comparative chromosome maps, especially when the karyotypes are highly rearranged.     

Correlation between left ventricular hypertrophy and GAA trinucleotide repeat length in Friedreich's ataxia

BACKGROUND: Friedreich's ataxia (FA), the most common inherited ataxia, is associated frequently with cardiac hypertrophy, and death is often cardiac related. Recently, the disease has been associated with a mutation that consists of an unstable expansion of GAA repeats in the first intron of the gene encoding frataxin on chromosome 9. METHODS AND RESULTS: We studied 44 consecutive patients with FA, determined the size of GAA expansions in the frataxin gene, and examined the relation between the genotype and cardiac phenotype assessed by M-mode and two-dimensional echocardiography. All the patients were homozygous for the mutation. The size of the GAA expansion on the smaller allele varied from 270 to 1200. We found a correlation between the size of GAA expansion and the left ventricular wall thickness (r = .51, P < .001) and the left ventricular mass index (r = .45, P = .002). Left ventricular hypertrophy was observed in 81% of patients with a number of GAA repeats above the median value of 770 compared with only 14% in the other group (P = .002). CONCLUSIONS: These data demonstrate that in FA, the severity of left ventricular hypertrophy is related to the number of GAA repeats. These results suggest that abnormalities of the gene encoding frataxin, a protein of unknown function highly expressed in the normal heart, may play an important role in the modulation of cardiac hypertrophy.     

Generalized chorea in two patients harboring the Friedreich''s ataxia gene trinucleotide repeat expansion

Recently, a trinucleotide repeat expansion in intron 1 of the frataxin gene on chromosome 9p13 has been identified as the genetic defect in Friedreich's ataxia (FA). We have identified two patients exhibiting generalized chorea in the absence of cerebellar signs who were homozygous for this intron 1 expansion. Chorea as a rare manifestation of FA has previously been controversial. This is the first report of chorea in patients confirmed to have the FA genetic abnormality and broadens further the clinical phenotype associated with the FA genotype.     

Detection of the leghemoglobin gene on two chromosomes of Phaseolus vulgaris by in situ PCR linked-fluorescent in situ hybridization (FISH)

OBJECTIVE: To investigate the effect of phentolamine, a sympathetic blocking agent, on the spontaneous electrical activity (SEA) recorded from a locus of a myofascial trigger spot (MTrS), equivalent to a human trigger point, in rabbit skeletal muscle. DESIGN: Randomized control trial. SETTING: A university medical laboratory. PATIENTS OR OTHER PARTICIPANTS: Nine adult New Zealand rabbits. INTERVENTION: In the experimental group phentolamine mesylate (1mg/kg) was injected into the external iliac artery, followed by flushing with normal saline. The control group was treated with normal saline instead of phentolamine using the same procedure. MAIN OUTCOME MEASURES: SEA was recorded from multiple active loci of MTrSs in the biceps femoris muscle: initially SEA in the same locus was recorded before and immediately after phentolamine (or normal saline) injection; then SEA was recorded from 25 different active loci. The mean of the average integrated signal (AIS) of SEA was analyzed, comparing the effects of phentolamine and normal saline on SEA. RESULTS: In the same active locus, the AIS of SEA showed statistically a linear decay with time after phentolamine injection, with a correlation coefficient of .56 at p < .05. However, no statistical relationship could be derived for the control group data with time by using regression analysis, probably because of large variations among the rabbits and movement artifacts during the experiment. In 25 different loci in the phentolamine group, the mean of the AIS of SEA (7.92 microV) was significantly lower than that of the control group (9.89 microV) at p < .05. CONCLUSIONS: The results support the hypothesis that the autonomic nervous system is involved in the pathogenesis of myofascial trigger points. The application of the AIS as an evaluation index seems to be feasible in the quantitative measurement of SEA.     

Relationship between parental trinucleotide GCT repeat length and severity of myotonic dystrophy in offspring

OBJECTIVE: To assess the relationship between the GCT repeat number in the myotonic dystrophy gene and the clinical phenotype and examine its predictive utility in prenatal testing. DESIGN: DNA from patients was examined for the length of the myotonic dystrophy GCT repeat region, using both Southern blot analysis and polymerase chain reaction. The results were compared with the clinical onset of disease, as well as with pregnancy outcomes. SETTING: Patient samples were referred to the Kleberg DNA Diagnostic Laboratory at the Baylor College of Medicine for DNA analysis by geneticists and genetic counselors (84%), neurologists (10%), and obstetricians and other specialists (6%). Clinical features including onset of disease and family pedigrees were determined by the referring centers. PATIENTS: A total of 241 patient samples from 118 families referred from primarily genetic or neurological centers for genetic linkage analysis or mutation analysis for myotonic dystrophy. This included 44 families referred for prenatal diagnosis. MAIN OUTCOME MEASURES: A relationship between myotonic dystrophy disease onset and length of the GCT repeat allele, parental origin of the disease allele, and results of prenatal diagnosis predictions of disease status were measured. RESULTS: There is a relationship between increasing repeat length and earlier clinical onset of disease. Essentially all (> 99%) myotonic mutations causing myotonic dystrophy are accounted for by GCT repeat amplification. Congenital myotonic dystrophy occurs with as few as 730 GCT repeats but only with alleles of maternal origin. Maternal GCT repeats were found as low as 75 (asymptomatic) that were amplified to result in a child with congenital myotonic dystrophy. Application of DNA diagnosis to 32 pregnancies provided an accurate method for identification of at-risk fetuses and allele enlargement. CONCLUSIONS: The GCT repeat in myotonic dystrophy is highly mutable. The triplet repeat amplification is highly specific for mutations involving the myotonin protein kinase gene accounting for myotonic dystrophy. The quantitation of triplet repeats can be more sensitive than physical, ophthalmologic, and electromyography examinations since the mutation can be detected in patients without evidence of myotonic dystrophy clinical findings. The length of the triplet expansion is influenced by the sex of the transmitting parent and is related to the clinical onset of disease features. Prenatal measurement of the GCT triplet repeat has utility for families with myotonic dystrophy risk since mutant and normal repeats are distinguishable and the length of mutant repeat alleles is associated with clinical severity. Thus, GCT triplet measurement provides a highly accurate means of detecting the myotonic dystrophy mutation in patients and offers a new reproductive option for families at risk for myotonic dystrophy.     

2个Huntington病家系临床特征及CAG重复性分析

目的:探讨Huntington病(Huntington disease,HD)的临床和遗传特征.方法:对收集的2个中国汉族HD家系患者的临床资料进行综合分析,应用聚合酶链式反应及基因扫描方法对其中9例家系成员的IT15基因的三核苷酸重复序列进行分析.结果:在两个家系中确诊了6例患者(男女均有发病),患者IT15基因的基因型均为杂合子,致病CAG重复拷贝数介于40～78次.两个家系中子代较父代发病年龄提前,家系2中可见发病年龄与CAG重复拷贝数呈负相关.6例患者中有1例为少年型HD,其临床表现明显不同于成人型,以肌张力障碍为主要表现.结论:HD是一种由CAG重复序列异常扩增所致的神经变性病,存在遗传早现现象;少年型HD的临床表现不同于成人型,CAG重复拷贝数与发病年龄及疾病严重程度有关.     

Importance of the number of trinucleotide repeat expansions in the clinical manifestations of Huntington's chorea

INTRODUCTION: In 1993 the gene responsible for Huntington's disease (IT15) was isolated [5]. It was mapped to the tip of the short arm of chromosome 4 and within its coding sequence, near the 5' end, it contained a certain number of trinicleotide (CAG)n (cytosine-adenine-guanine) repeats (Figure 1). This gene codes for a protein (348 kd) called "huntington" that is widely expressed, and its sequence is not related to any protein [6]. The normal range of (CAG)n repeat numbers within IT15 was reported to be between 6 and 37 [6]. Mutation responsible for Huntington's disease implied expansion of (CAG)n repeats: in patients with Huntington's disease the pathologic range was determined to be between 35 and 121 repeats [7-10]. PATIENTS AND METHODS: In this study we correlated the age at onset, rate of progression and initial symptoms of Huntington's disease with the number of trinucleotide (CAG)n repeats in IT15. DNA was isolated from peripheral blood leukocytes of patients fulfilling clinical criteria for definite and probable Huntington's disease [2]. Genetic verification of Huntington's disease was made by the previously described and modified PRC (polymerase chain reaction) technique [17, 18]. In our laboratory a gene with 40 or more repeats was considered as a marker of Huntington's disease. RESULTS: The study comprised 26 patients (11 women and 15 men). At the onset of Huntington's disease they were between 19 and 66 years old (36.6 12.8 years), with the duration of the disease between 1 and 15 years (5.8 4.3 years). The number of (CAG)n, repeats in IT15 ranged between 40 and 95 (49.9 14.1). The negative correlation between the (CAG)n, count in the expanded allele and the age at onset of the disease has been confirmed. Regression analysis showed the correlation coefficient of -0.54 (p = 0.012). The effect of trinucleotide (CAG)n, repeats on the initial clinical manifestations and rate of progression of Huntington's disease is only one of the growing group of "CAG-repeat" disorders that also include entities such as spinocerebellar ataxia-type 1 and 3, spinobulbar muscular atrophy and dentato-rubo-pallidoluysian atrophy [6].     

Characterization of Alu repeats that are associated with trinucleotide and tetranucleotide repeat microsatellites

The association of subclasses of Alu repetitive elements with various classes of trinucleotide and tetranucleotide microsatellites was characterized as a first step toward advancing our understanding of the evolution of microsatellite repeats. In addition, information regarding the association of specific classes of microsatellites with families of Alu elements was used to facilitate the development of genetic markers. Sequences containing Alu repeats were eliminated because unique primers could not be designed. Various classes of microsatellites are associated with different classes of Alu repeats. Very abundant and poly(A)-rich microsatellite classes (ATA, AATA) are frequently associated with an evolutionarily older subclass of Alu repeats, AluSx, whereas most of GATA and CA microsatellites are associated with a recent Alu subfamily, AluY. Our observations support all three possible mechanisms for the association of Alu repeats to microsatellites. Primers designed using a set of sequences from a particular microsatellite class showed higher homology with more sequences of that class than probes designed for other classes. We developed an efficient method of prescreening GGAA and ATA microsatellite clones for Alu repeats with probes designed in this study. We also showed that Alu probes labeled in a single reaction (multiplex labeling) could be used efficiently for prescreening of GGAA clones. Sequencing of these prescreened GGAA microsatellites revealed only 5% Alu repeats. Prescreening with primers designed for ATA microsatellite class resulted in the reduction of the loss of markers from approximately 50% to 10%. The new Alu probes that were designed have also proved to be useful in Alu-Alu fingerprinting.     

Lack of association of trinucleotide repeat polymorphisms in very-low-density lipoprotein receptor gene with Alzheimer''s disease

Inheritance of the apolipoprotein E epsilon 4 allele is a risk factor for Alzheimer's disease (AD). A recent report studying Japanese patients suggested that a polymorphism of a trinucleotide repeat in the 5' untranslated region of an apolipoprotein E receptor, the very-low-density lipoprotein receptor, is genetically associated with AD, with overrepresentation of the allele containing five copies of the repeat. We determined the allele frequencies of the very-low-density lipoprotein receptor in 3 white populations totaling 469 individuals. In contrast to the previous report, we found no differences in allele frequencies between case patients and control subjects. The discrepancy could be due to differences in Japanese and white populations. Nonetheless, these data weaken the likelihood that this polymorphism in the very-low-density lipoprotein receptor gene is strongly associated with AD.     

Enhanced discrimination of single nucleotide polymorphisms by artificial mismatch hybridization

A 53-year-old patient had a complex ventricular arrhythmia, which most likely was an intermittent pure (nonmodulated) parasystole, due to protection limited to the first part of the cycle coexisting with exit block. However, other interpretations of the observations were possible. Foremost among these was modulated parasystole with partial protection or with an attenuated or nondetectable early delaying phase, with exit block. Interestingly, the parasystole appeared to have fulfilled the dynamic rules regarding the number of sinus beats interposed between manifest parasystolic beats, as has been reported for pure or weakly modulated parasystole. This case corroborates unusual manifestations of an arrhythmia, which because of its newly found complexities and various possible interpretations seems to be discussed with decreasing frequency in most textbooks on general cardiology.     

Mitotic stability of fragile X mutations in differentiated cells indicates early post-conceptional trinucleotide repeat expansion

We demonstrate here that somatic variation of CGG repeat length is based on a mosaic of cells with different but stable FMR-1 alleles and does not reflect permanent mitotic instability. The length of a particular allele in an individual cell was maintained in progeny cells establishing a clone. The mutation patterns of multiple repeats in the DNA of fetal tissues were identical and did not significantly change during proliferation in vitro. It is proposed that genotype mosaicism and expansion to full mutation are generated post-conceptionally by the same molecular mechanism in a particular window of early development.