Nucleosome assembly on telomeric sequences

The organization of telomeric chromatin differs from that of bulk chromatin in some peculiar features, such as the unusually short nucleosomal spacing found in vertebrates. Telomeric DNAs are straight, since they consist mostly of 6-8-bp repeated sequences, therefore out of phase with the B DNA period. This feature should be of relevance in nucleosome formation, suggesting the usefulness of studying simple model systems of nucleosome assembly. We reconstituted nucleosomes in vitro, by using purified histone octamers and/or by octamer transfer from chicken erythrocyte nucleosomes, onto telomeric sequences from human, Arabidopsis thaliana, and Saccharomyces cerevisiae. All of these telomeres contain GGG and GGT triplets but are characterized by different repeat lengths (6, 7, and 8 bp). The free energies involved in the association process are the highest among the biological sequences so far assayed, suggesting a main role of DNA flexibility in the assembly of telomeric chromatin. Digestion studies with DNase I, hydroxyl radicals, exonuclease III, and lambda exonuclease indicate that telomeric nucleosomes are characterized by multiple translational positioning without rotational phasing, whereas the telomeric DNA folding around the histone octamer shows the canonical periodicity of about 10.2 bp. The experimental results and a theoretical simulation of DNase I digestion indicate a multiple nucleosome positioning with the periodicity of telomeric DNA. This suggests a main role of local chemical recognition between telomeric sequences and the histone octamer in nucleosome assembly.     

Archaeal nucleosome positioning by CTG repeats

DNA shape recognition determines the preferred binding sites for sequence-independent DNA binding proteins, and here we document that archaeal histones assemble archaeal nucleosomes in vitro centered preferentially within (CTG)6 and (CTG)8 repeats, close to junctions with flanking mixed-sequence DNA. Archaeal nucleosomes were not positioned by (CTG)4-, (CTG)5-, or (CTG)3AA(CTG)3-containing DNA sequences. The features of CTG repeat-containing sequences that direct eucaryal nucleosome positioning may also be similarly recognized by archaeal histones.     

Long CAG/CTG repeats in mice

BACKGROUND: Accommodation-convergence spasm (spasm of the near reflex) is usually bilateral, resulting in increased myopia, convergence, and miosis. Unilateral spasm of accommodation has rarely been reported. PATIENTS: We investigated three females (age range 10-19 years) referred for investigations of retrobulbar optic neuritis (2 cases) and decompensated esophoria (1 case). RESULTS: They all presented unilateral spasm of accommodation with visual loss due to increased myopia (-3.5 to -11.75 diopters). Apart from that, results of neuro-ophthalmological examination were normal. CONCLUSIONS: Unilateral accommodation spasm is rare and can mimic retrobulbar optic neuritis and convergent strabismus. The three components of the accommodation-convergence spasm may not always be present simultaneously. Recognizing such an entity is important to prevent the patient from useless, costful and potentially harmful investigations.     

Expansion and length-dependent fragility of CTG repeats in yeast

Expansion of DNA trinucleotide repeats (TNRs) is the causative mutation in a growing number of human genetic diseases. Large expansions of a CTG tract were obtained and shown by genetic and physical assays to be length-dependent sites of chromosome breakage in Saccharomyces cerevisiae. Deletion of RAD27, which encodes a nuclease involved in Okazaki fragment processing, caused length-dependent destabilization of CTG tracts and a substantial increase in expansion frequency. The genetic assay described here can be used to evaluate other factors that induce TNR expansion or chromosome fragility in humans.     

Proton spectroscopy in myotonic dystrophy: correlations with CTG repeats

We have previously reported inhibition of cell-free activation of the neutrophil superoxide-generating NADPH oxidase by a soluble cationic protein of neutrophil granules and by low concentrations of human defensin. Subcellular fractionation carried out in the current study indicated that the inhibitory substance was derived from azurophilic granules, was released into the medium on cell stimulation, and was resistant to phenylmethylsulfonyl fluoride (PMSF). Phorbol ester was the most effective stimulus for the release of the blocking activity. The possibility was raised that granule protein(s) act in vivo as negative modulators of superoxide production. Gel filtration of granule extract revealed a markedly retarded protein peak exhibiting oxidase-blocking activity and containing lysozyme as the main protein. Because lysozyme did not exert inhibitory effects on oxidase activation, association of the inhibitory protein with lysozyme was assumed. Indeed a column of immobilized lysozyme retained a fraction of the granule extract's oxidase-blocking activity. Elution with a low-pH buffer recovered a component capable of inhibition of the NADPH oxidase in stimulated neutrophils and in the cell-free system. The main 29-kDa protein band in the eluted fraction was identified as proteinase 3, a serine protease of azurophilic granules. Enzymatically active as well as PMSF-blocked conventionally purified proteinase 3 interfered with phorbol myristate acetate-induced superoxide release. These findings support the hypothesis that exocytosed granule constituents may prevent excessive activation of the NADPH oxidase.     

Exclusion of expansion of 50 CAG/CTG trinucleotide repeats in bipolar disorder

OBJECTIVE: The purpose of this study was to identify the specific expanded CAG/CTG trinucleotide repeat associated with bipolar disorder. METHOD: The study employed an efficient multistage approach for using a genomic CAG/CTG screening set. RESULTS: The authors found no evidence of expanded repeats at 43 polymorphic autosomal loci and seven X chromosomal loci. Secondary screening was pursued at the only locus that contained a large allele (37 repeats) in the primary screening. No association was found between allele size and diagnostic status. CONCLUSIONS: It is highly unlikely that expansions in repeat size at any of the 50 candidate trinucleotide repeat loci examined are responsible for the association between expanded CAG/ CTG repeats and bipolar disorder. However, although the authors prioritized the repeats that were a priori most likely to be involved, the study does not reject the more general hypothesis that expanded CAG/CTG repeats are implicated in the pathogenesis of bipolar disorder.     

Identification and mapping of 26 human testis mRNAs containing CAG/CTG repeats

Postoperative mediastinitis is a rare but life-threatening complication after cardiac surgery. We successfully managed three infants with postoperative mediastinitis. When the postoperative mediastinitis was suspected, intravenous infusion of antibiotics (Vancomycin) and local irrigation were performed. The reoperation for closure was planned when the value of c-reactive protein decreased to 1.0-2.0. An application of a pectoral musculocutaneous flap was effective when the sternum was destroyed by infection.     

Nucleosome assembly during complementary DNA strand synthesis in extracts from mammalian cells

Circular single-stranded phage M13 DNA is used as a template for complementary strand synthesis in cytosolic extracts from proliferating HeLa cells. DNA synthesis is initiated by one or maximally two priming events and typically leads to covalently closed double-stranded reaction products. When carried out in the presence of the nuclear chromatin assembly factor CAF-1, complementary strand synthesis is accompanied by nucleosome assembly. This novel system is very useful for the study of basic biochemical aspects concerning the assembly of nucleosomes. The activity of CAF-1 completely depends on complementary strand synthesis and acts stoichiometrically to promote the assembly of nucleosomes in a noncooperative manner. Apparently, CAF-1 activity is coupled to DNA synthesis via a structural feature of replicating DNA, most likely its partial single strandedness.     

NGG-triplet repeats form similar intrastrand structures: implications for the triplet expansion diseases

Tandem repeats of certain trinucleotides show extensive intergenerational instability in humans that is associated with a class of genetic disorders known as the Triplet Expansion Diseases. This instability is thought to be a consequence of the formation of intrastrand structures, including hairpins, triplexes and tetraplexes, by the tandem repeats. I show here that CGG-repeats which are associated with this group of diseases, and AGG- and TGG-repeats which are not currently known to be, form several intrastrand structures including tetraplexes. In all cases the tetraplexes have the same overall conformation in which all the G residues are involved in G4-tetrads. CGG-repeats also form stable hairpins, but AGG- and TGG-repeats do not form hairpins of comparable stability. However, since tetraplexes can be thought of as folded hairpins, many of the properties ascribed to disease-associated triplets that form hairpins, may apply to these sequences as well. The fact that AGG- and TGG-repeats are not currently associated with any triplet expansion disease suggests either that the ability to adopt an intrastrand folded structure is not sufficient for expansion, or that other diseases associated with such triplets might remain to be identified.     

Detection of polymorphic triplet repeats in the genomes of patients suffering from bipolar affective disorder

P2X receptors are a family of ion channels gated by extracellular ATP. Each member of the family can form functional homomeric channels, but only P2X2 and P2X3 have been shown to combine to form a unique heteromeric channel. Data from in situ hybridization studies suggest that P2X1 and P2X5 may also co-assemble. In this study, we tested this hypothesis by expressing recombinant P2X1 and P2X5 receptor subunits either individually or together in human embryonic kidney 293 cells. In cells expressing the homomeric P2X1 receptor, 30 microM alpha,beta-methylene ATP (alpha,beta-me-ATP) evoked robust currents that completely desensitized in less than 1 sec, whereas alpha,beta-me-ATP failed to evoke current in cells expressing the homomeric P2X5 receptor. By contrast, alpha, beta-me-ATP evoked biphasic currents with a pronounced nondesensitizing plateau phase in cells that co-expressed both subunits. Further, the EC50 for alpha,beta-me-ATP was greater in cells expressing both P2X1 and P2X5 than in cells expressing P2X1 alone (5 and 1.6 microM, respectively). Heteromeric assembly was confirmed using a co-immunoprecipitation assay of epitope-tagged P2X1 and P2X5 subunits. In summary, this study provides biochemical and functional evidence of a novel channel formed by P2X subunit heteropolymerization. This finding suggests that heteromeric subunit assembly constitutes an important mechanism for generating functional diversity of ATP-mediated responses.     

Computer simulation of expansions of DNA triplet repeats in the fragile X syndrome and Huntington''s disease

The use of high capacity micron-sized non-porous magnetic metal chelator adsorbents for the direct recovery of a recombinant metal-binding protein from crude liquors is described. Selectivity and interaction strength of magnetic chelator particles were assessed using a set of native proteins with known behaviour towards commercially available immobilised metal chelate adsorbents. Particles charged with Cu2+ were highly effective in recovering a recombinant histidine-tailed T4 lysozyme fusion protein directly from crude E. coli extracts in a single step. Levels of recovery and purity were high and compared favourably with those achieved by chromatography of pre-clarified extracts on Cu(2+)-IDA Sepharose. The magnetic approach offers advantages such as the avoidance of clarification to prevent fouling of chromatography columns, steps that become especially significant at large scale. By detailed characterisation of the magnetic chelators the practical use of tailed T4 lysozyme for repeated production of periplasmic products is a realistic prospect.     

Abnormal calcium metabolism in myotonic dystrophy as shown by the Ellsworth-Howard test and its relation to CTG triplet repeat length

Myotonic dystrophy (DM) is an autosomal dominant disorder characterized by peculiar clinical features. Its molecular basis is the unstable expansion of a CTG triplet repeat in the gene encoding myotonin protein kinase (Mt-PK), the nucleotide sequence of which has extensive homology to the cyclic AMP (cAMP)-dependent protein kinase gene. Extensive efforts have been made to clarify the signal transduction pathway in which the responsible gene operates, but confirming evidence has yet to be obtained. Because some symptoms in DM are similar to those in hypoparathyroidism, we divided 24 DM patients into two groups on the basis of their serum calcium levels; Group 1, those with normocalcemia (11 patients), and group 2, those with hypocalcemia (13 patients). The highly sensitive parathyroid hormone (HS-PTH) plasma levels in group 1 were within normal limits, whereas those in group 2 were abnormally high. Laboratory findings for the group 2 patients resembled those for pseudohypoparathyroidism (PHP), whereas those for group 1 patients were normal. The Ellsworth-Howard (EH) test was used to determine which type of PHP the group 2 patients belonged to. Both the phosphaturic (delta P) and urinary cAMP (UcAMP) responses were estimated. The delta P responses in group 2 were significantly lower than those in group 1, but their UcAMP responses did not differ. This is evidence that group 2 patients had PHP type II, whereas group 1 patients were normal. We also investigated whether the disease severity differed between the groups. Cataracts, ectopic calcifications, and ossifications, which are associated with PHP, were more frequent in group 2. In addition, the mean IQ in that group was significantly lower. Clinically, the group 2 signs agreed well with those of PHP, whereas for group 1 there was only a slight similarity. These results are additional evidence that the patients in group 2 have abnormal calcium metabolism, the abnormality being in the postadenylate cyclase-cAMP pathway in the renal tubular cells. The degree of (CTG)n expansion, the so-called expanded DNA fragment (EF) size, was determined by standard Southern blot analysis. The allelic EF sizes in both groups were greater than in the healthy controls. Moreover, those in group 2 were significantly longer than those in group 1. We therefore investigated whether EF size is correlated with the serum calcium and plasma PTH levels, the delta P responses in the EH test, and IQ. All these items were significantly correlated with EF size. Our findings show that the expanded DNA fragment size in DM is correlated with the degree of abnormal calcium metabolism.     

CAG/CTG and CGG/GCC repeats in human brain reference cDNAs: outcome in searching for new dynamic mutations

The cysteine-rich region (CRR) of the beta2 integrin subunit was replaced by that of beta1 to give the chimera beta2NV1. Beta2NV1 can combine with alphaL to form a variant leukocyte-function-associated antigen (LFA)-1 on COS cell surface, suggesting that the specificity of the beta2 interaction with alphaL does not lie in the CRR. Unlike those expressing wild-type LFA-1, COS cells expressing alphaL beta2NV1 are constitutively active in intercellular adhesion molecule (ICAM)-1 adhesion. These results suggest that activation of LFA-1 involves the release of an intramolecular constraint, which is maintained, in part, by the authentic beta2 CRR.     

Expansion of CTG repeats from human disease genes is dependent upon replication mechanisms in Escherichia coli: the effect of long patch mismatch repair revisited

OBJECTIVE: New techniques for minimally invasive coronary artery bypass grafting have recently emerged. The purpose of this study was to determine the safety and efficacy of Port-Access (Heartport, Inc., Redwood City, Calif.) coronary revascularization and to evaluate with angiography the early graft patency rate with this new approach. METHODS: From October 1996 to May 1997, 31 patients underwent Port-Access coronary artery bypass grafting with an anterior minithoracotomy and endovascular-occlusion cardiopulmonary bypass. There were 26 men and 5 women with a mean age of 62 years (range 42 to 82 years). Fifteen patients underwent single bypass; 12 patients underwent double bypass, and 4 patients underwent triple bypass. Bypass conduits included the left internal thoracic artery (n = 30), right internal thoracic artery (n = 2), radial artery (n = 10), and saphenous vein (n = 6). Three sequential grafts were used. Angiographic studies of the bypass grafts were performed in 27 of 31 patients (87%). RESULTS: There were no deaths, neurologic deficits, myocardial infarctions, or aortic dissections. Conversion to sternotomy was not required in any case. There were two reoperations for bleeding, one reoperation for tamponade, and one reoperation for pulmonary embolus. Postoperative angiography revealed anastomotic patency of the left internal thoracic artery to left anterior descending artery in 26 of 26 grafts (100%) with overall anastomotic patency in 43 of 44 grafts (97.7%). CONCLUSION: These results demonstrate that Port-Access coronary artery bypass can be performed accurately and safely with acceptable morbidity. This approach allows for multivessel revascularization on an arrested, protected heart with excellent anastomotic precision and reproducible early graft patency.     

Unstable triplet repeat diseases

Seven inherited human disorders are now associated with the intragenic expansion of triplet repeat DNA sequences. These repeats demonstrate extreme instability in both germline and somatic tissue, accounting for the unusual genetic inheritance patterns and symptom variability associated with these diseases.     

Myelodysplasia in triplet pregnancy

INTRODUCTION: The myelodysplastic syndromes (MSD) are a group of hematologic disorders that manifest dysplastic hematopoiesis and usually a hypercellular bone marrow. Ineffective hematopoiesis leads to haematologic failure in these syndromes. The MDS are a rare event during pregnancy although the exact incidence is unknown it is likely to be less than that for leukaemia. CLINICAL REPORT: The case, a 29 year old woman, presented during 23rd week of her first, triplet, pregnancy with symptoms of anemia and thrombocytopenia is described. DISCUSSION: The pathogenetic aspect and diagnostic management is discussed, underlined especially under the point of view of the triplet pregnancy. It is suggested that the association of myelodysplastic syndromes during pregnancy is coincidental and that acute leukemia evolves in a majority of these cases. Furthermore, refractory macrocytic anemias in pregnancy need to be carefully evaluated for a primary myelodysplastic state.     

Nucleosome units and hidden periodicities in DNA sequences

The relationship between the hidden periodicities in DNA sequences and the nucleosome units is investigated. It is shown that in the vicinity of lengths of about 200 bases there are statistically significant periodicities which remain approximately universal for exon-intron sequences both in the different genes and the different eukaryotic species. The additional analysis displays, nevertheless, that these approximately coincident universal periodicities can be generated by a variety of mechanisms. The relevance of the features observed to the structure of chromatin is discussed.     

Nucleosome packaging and nucleosome positioning of genomic DNA

The goals of this study were to assess the extent to which bulk genomic DNA sequences contribute to their own packaging in nucleosomes and to reveal the relationship between nucleosome packaging and positioning. Using a competitive nucleosome reconstitution assay, we found that at least 95% of bulk DNA sequences have an affinity for histone octamer in nucleosomes that is similar to that of randomly synthesized DNA; they contribute little to their own packaging at the level of individual nucleosomes. An equation was developed that relates the measured free energy to the fractional occupancy of specific nucleosome positions. Evidently, the bulk of eukaryotic genomic DNA is also not evolved or constrained for significant sequence-directed nucleosome positioning at the level of individual nucleosomes. Implications for gene regulation in vivo are discussed.