Biomedical subjects

J J Hayes

Publications and source records attributed to J J Hayes.

At least 37 records · Page 2Linked to original sources

PubMed1998

Linker DNA and H1-dependent reorganization of histone-DNA interactions within the nucleosome.

We have employed a site-directed photochemical cross-linking procedure to precisely map interactions between nucleosomal DNA and the C-terminal tail of core histone H2A. We find that this tail has the potential to contact multiple sites within the nucleosome and that these contacts are dependent upon the configuration of the complex. This tail contacts DNA near the dyad axis within nucleosome core particles but rearranges to a site near the edge of the nucleosomal DNA when linker DNA is present. Moreover, in the presence of linker histone H1 the contacts near the edge of the nucleosome but not at the dyad are further rearranged. In addition, we present further evidence for the suggestion that the binding of linker histone causes a subtle but global change in core histone-DNA interactions within the nucleosome [Usachenko, S. I., Gavin, I. M., and Bavykin, S. G. (1996) J. Biol. Chem. 271, 3831-3836].

Animals↗

PubMed1998

(1,4,7-trimethyl-1,4,7-triazacyclononane)iron (III)-mediated cleavage of DNA: detection of selected protein-DNA interactions.

A new reagent for the oxidative cleavage of DNA, (1,4,7-trimethyl-1, 4,7-triazacyclononane)iron(III) chloride was recently introduced. We have determined the utility of this reagent for detecting protein-DNA interactions within two types of complexes. Interestingly, we find that the rates of DNA cleavage by this reagent are differentially affected by the two classes of protein-DNA interactons studied. We find that the rate of DNA cleavage by this reagent is relatively unaffected by the non-sequence-specific histone-DNA interactions within a nucleosome complex. Conversely, a clear footprint pattern is obtained with two different DNA sequence-specific protein-DNA complexes. The results suggest that (1,4,7-trimethyl-1,4,7-triazacyclononane)iron(III) chloride will be a useful reagent to probe trans -acting-factor-DNA interactions within a chromatin environment. Differences between these two types of protein-DNA interactions, which might account for this observation, are discussed.

Bacterial Proteins↗

PubMed1998

Paroxysmal supraventricular tachycardia in the general population.

OBJECTIVES: We sought to determine the epidemiology and clinical significance of paroxysmal supraventricular tachycardia (PSVT) in the general population. BACKGROUND: Current knowledge of PSVT has been derived primarily from otherwise healthy patients referred to specialized centers. METHODS: We used the resources of the Marshfield Epidemiologic Study Area, a region covering practically all medical care received by its 50,000 residents. A review of 1,763 records identified prevalent cases as of July 1, 1991 and all new cases of PSVT diagnosed from that day until June 30, 1993. A mean follow-up period of 2 years was completed in all incident patients. Patients without other cardiovascular disease were labeled as having "lone PSVT." RESULTS: The prevalence was 2.25/1,000 persons and the incidence was 35/100,000 person-years (95% confidence interval, 23 to 47/100,000). Other cardiovascular disease was present in 90% of males and 48% of females (p = 0.0495). Compared with patients with other cardiovascular disease, those with lone PSVT were younger (mean 37 vs. 69 years, p = 0.0002), had a faster PSVT heart rate (mean 186 vs. 155 beats/min, p = 0.0006) and were more likely to have their condition first documented in the emergency room (69% vs. 30%, p = 0.0377). The onset of symptoms occurred during the childbearing years in 58% of females with lone PSVT versus 9% of females with other cardiovascular disease (p = 0.0272). CONCLUSIONS: There are approximately 89,000 new cases/year and 570,000 persons with PSVT in the United States. In the general population, there are two distinct subsets of patients with PSVT: those with other cardiovascular disease and those with lone PSVT. Our data suggest etiologic heterogeneity in the pathogenesis of PSVT and the need for more population-based research on this common condition.

Adolescent↗

PubMed1998

Infections with nonthoracotomy implantable cardioverter defibrillators: can these be prevented? Endotak Lead Clinical Investigators.

Nonthoracotomy ICDs are believed to be the best therapeutic modality for treatment of life-threatening ventricular arrhythmias. Little is known about the risk of infection with initial implantation of these devices. We studied the incidence, clinical characteristics, and risk factors associated with infections in 1,831 patients with nonthoracotomy ICD from the Endotak-C nonthoracotomy lead registry of Cardiac Pacemakers, Inc. A transvenous lead was implanted in 950 patients (51.9%) and a combination transvenous plus subcutaneous patch was used in 881 patients (48.1%). Nine preselected data variables were studied, and all investigators identified as having patients with infections were personally contacted. Infections occurred in 22 (1.2%) of 1,831 patients receiving this nonthoracotomy ICD system. The mean time to infection was 5.7 +/- 6.5 months (range 1-25 months). Staphylococci were isolated in 58% of patients with reported infection. The presence of a subcutaneous defibrillator patch system was associated with the development of infection. Six of 950 patients (0.63%) with a totally transvenous lead system developed infection versus 16 of 838 (1.9%) patients with a transvenous lead plus subcutaneous patch system configuration (P = 0.015, Chi-square test), with an unadjusted estimated odds ratio of 3.06 (CI 1.19-7.86). The risk of infection encountered with the nonthoracotomy ICD is low, estimated from our data to be 1.2%. Placement of a subcutaneous defibrillator patch appears to be an independent risk factor for development of infection.

Adolescent↗

PubMed1998

The Bacillus subtilis DinR binding site: redefinition of the consensus sequence.

Recently, the DinR protein was established as the cellular repressor of the SOS response in the bacterium Bacillus subtilis. It is believed that DinR functions as the repressor by binding to a consensus sequence located in the promoter region of each SOS gene. The binding site for DinR is believed to be synonymous with the formerly identified Cheo box, a region of 12 bp displaying dyad symmetry (GAAC-N4-GTTC). Electrophoretic mobility shift assays revealed that highly purified DinR does bind to such sites located upstream of the dinA, dinB, dinC, and dinR genes. Furthermore, detailed mutational analysis of the B. subtilis recA operator indicates that some nucleotides are more important than others for maintaining efficient DinR binding. For example, nucleotide substitutions immediately 5' and 3' of the Cheo box as well as those in the N4 region appear to affect DinR binding. This data, combined with computational analyses of potential binding sites in other gram-positive organisms, yields a new consensus (DinR box) of 5'-CGAACRNRYGTTYC-3'. DNA footprint analysis of the B. subtilis dinR and recA DinR boxes revealed that the DinR box is centrally located within a DNA region of 31 bp that is protected from hydroxyl radical cleavage in the presence of DinR. Furthermore, while DinR is predominantly monomeric in solution, it apparently binds to the DinR box in a dimeric state.

Amino Acid Sequence↗

PubMed1997

The N-terminal tail of histone H2A binds to two distinct sites within the nucleosome core.

Each of the core histone proteins within the nucleosome has a central "structured" domain that comprises the spool onto which the DNA superhelix is wrapped and an N-terminal "tail" domain in which the structure and molecular interactions have not been rigorously defined. Recent studies have shown that the N-terminal domains of core histones probably contact both DNA and proteins within the nucleus and that these interactions play key roles in the regulation of nuclear processes (such as transcription and replication) and are critical in the formation of the chromatin fiber. An understanding of these complex mechanisms awaits identification of the DNA or protein sites within chromatin contacted by the tail domains. To this end, we have developed a site-specific histone protein-DNA photocross-linking method to identify the DNA binding sites of the N-terminal domains within chromatin complexes. With this approach, we demonstrate that the N-terminal tail of H2A binds DNA at two defined locations within isolated nucleosome cores centered around a position approximately 40 bp from the nucleosomal dyad and that this tail probably adopts a defined structure when bound to DNA.

Animals↗

PubMed1997

Antisera directed against anti-histone H4 antibodies recognize linker histones. Novel immunological probes to detect histone interactions.

We introduce a novel immunological approach to detect structural interactions between chromosomal proteins. Antigenically pure core histone H4 was prepared from chicken erythrocytes and used to produce anti-histone H4 antisera. IgG fractions were isolated from purified anti-H4 antibodies and used as antigens to produce "second generation" antisera. Epitopes cross-reacting with the second generation antisera were then identified within chromosomal proteins. These epitopes were presumed to mimic the complementary molecular surface of the original anti-H4 antibodies, and thus proteins containing these epitopes were putatively identified as specific ligands of H4 in chromatin. Surprisingly, we found this immunoreactivity was predominantly directed against H1 compared with H5 from chicken erythrocytes. Further, the immunoreactive epitopes were located within the C-terminal tail domain of the linker histones. These results suggest similar complementary interactions occur between H4 and the C-terminal tail domain of H1s in native chromatin. This could occur either within a single nucleosome as suggested by a previous report (Banères, J.-L., Essalouh, L., Jariel-Encontre, I., Mesnier, D., Garrod, S., and Parello, J. (1994) J. Mol. Biol., 243, 48-59) or between neighboring nucleosomes within the condensed chromatin fiber. The implications of these results with regard to the structure of the chromatin fiber and the future utility of this technique are discussed.

Animals↗

PubMed1997

In vitro reconstitution and analysis of mononucleosomes containing defined DNAs and proteins.

Increasingly, biochemical analyses of processes that occur within eukaryotic nuclei such as transcription and replication require the construction of specific chromatin substrates. Nucleosome complexes reconstituted in vitro have been key elements in a variety of recent studies of polymerase progression and trans-acting factor binding activities. Reconstituted complexes can be easily constructed from purified components in quantities suitable for biochemical and biophysical studies. In addition, reconstituted mononucleosome complexes exhibit native biochemical and biophysical properties but necessarily contain much less heterogeneity with regard to both protein and DNA components than bulk complexes isolated from natural sources. This review details the protocols for reconstitution of model mononucleosome complexes that contain unique DNA sequences and specifically tailored core histone proteins and describes common pitfalls associated with these procedures.

Animals↗

PubMed1996

A putative DNA binding surface in the globular domain of a linker histone is not essential for specific binding to the nucleosome.

A fundamental step in the assembly of native chromatin is the specific recognition and binding of linker histones to the nucleoprotein subunit known as the nucleosome. A first step in defining this important interaction is the determination of residues within linker histones that are important for the structure-specific recognition of the nucleosome core. By combining in vitro assays for the native binding activity of linker histones and site-directed mutagenesis, we have examined a cluster of basic residues within the globular domain of H1(0), a somatic linker histone variant from Xenopus laevis. We show that these residues, which comprise a putative DNA binding surface within the globular domain, do not play an essential role in the structure-specific binding of a linker histone to the nucleosome.

Animals↗

PubMed1996

Site-directed cleavage of DNA by a linker histone--Fe(II) EDTA conjugate: localization of a globular domain binding site within a nucleosome.

The globular domain of linker histones specifically recognizes and binds to the nucleosome core. However, the exact location of the binding site of the globular domain has not been definitively elucidated. To address this issue, a linker histone has been specifically modified at a site adjacent to the globular domain with a radical-based DNA cleavage reagent. The linker histone-Fe(II) EDTA conjugate was bound to reconstituted nucleosomes containing a Xenopus 5S RNA gene, and the resulting cleavage of DNA was used to precisely map the location of the linker histone binding site. The results indicate that the binding site is located on the inside of the superhelical gyre of DNA, just inside the periphery of the nucleosome core region. The implications of these results for the binding of linker histones within native chromatin complexes are discussed.

Animals↗

PubMed1995

A positive role for nucleosome mobility in the transcriptional activity of chromatin templates: restriction by linker histones.

Nucleosome mobility facilitates the transcription of chromatin templates containing only histone octamers. Inclusion of linker histones in chromatin inhibits nucleosome mobility, directs nucleosome positioning and represses transcription. Transcriptional repression by linker histone occurs preferentially on templates associated with histone octamers relative to naked DNA. Mobile nucleosomes and the restriction of mobility by linker histones might be expected to exert a major influence on the accessibility of chromatin to regulatory molecules.

Animals↗

PubMed1995

DNA binding specificity of the Mu Ner protein.

Binding of purified phage Mu Ner protein to a series of DNA fragments was investigated in order to determine the length requirements for tight specific binding. Gel retardation experiments with wild-type 307 base pair (bp) Mu DNA and shorter, synthetic oligonucleotides were performed, and apparent dissociation constants (KappD) were determined from the half-saturation point. While Ner formed four complexes with the 307 bp DNA fragment, only one complex was observed with the shorter DNAs. The 50 and 30 bp fragments had KappD values of 5 and 20 nM, respectively. Ner binding was progressively weaker with decreasing size of the DNA fragments, with no binding observed for 12mers. The shortest DNA fragments which bound well were two 18 bp fragments for which KappD values were in the range of 50-100 nM. The stoichiometry of Ner complexes with the 30 and 18 bp fragments was determined using a modified Ferguson method. Ner was found to form a tetramer on the 30 bp DNA and a dimer on the 18 bp DNA, which makes the latter a good candidate for the study of a Ner-DNA complex by NMR. In order to clarify which DNA regions were important for Ner-DNA binding, hydroxyl radical footprinting was performed for a range of Ner concentrations from 30 to 500 nM. The footprint revealed that Ner contacts the DNA backbone every 12-13 bp, on both strands of the DNA. The order in which protected regions appeared with increasing protein concentration indicated that two Ner monomers bound to DNA simultaneously. A model of Ner binding to DNA is proposed on the basis of these results.

Bacteriophage mu↗

PubMed1995

Nucleosomal anatomy--where are the histones?

The recent surge of discoveries concerning the structural organization of nucleosomes, together with genetic evidence of highly specialized roles for the histones in gene regulation, have brought a renewed need for a detailed understanding of nucleosomal anatomy. Here we review recent structural advances leading to a new level of understanding of the nucleosome and chromatin fibre structure. We discuss the problems and challenges for existing models of chromatin structure and, in particular, consider how linker histones may bind within the nucleosome, together with the implications of their association for the structure of the chromatin fibre.

Animals↗

PubMed1995

Chemical probes of DNA structure in chromatin.

Understanding the way genes work requires detailed knowledge of the organization of DNA in the chromatin complex. The difficulties associated with the study of this large macromolecular assembly present an interesting challenge to both biologists and chemists.

Chromatin↗

PubMed1995

[Advances in the treatment of tachiarrhythmias: role of nonpharmacological methods].

Nonpharmacological methods are a novel therapeutic option for tachiarrhythmias. Transcatheter ablation or surgery can cure many arrhythmias, avoiding the collateral effects of antiarrhythmic drugs. Likewise, implantable defibrillators, have changed life expectancy of patients with high risk arrhythmias or sudden death survivors. However, the high cost and sophistication of these methods, preclude their widespread use, thus limiting the number of patients that can be benefited. This article reviews the main nonpharmacological techniques for treatment of arrhythmias, their results and complications.

Catheter Ablation↗

PubMed1994

Core histone acetylation does not block linker histone binding to a nucleosome including a Xenopus borealis 5 S rRNA gene.

We demonstrate that acetylation of core histone tails does not significantly impair the ability of linker histones to bind preferentially and asymmetrically to a defined sequence mononucleosome core reconstituted in vitro. Thus a simple inhibition mechanism cannot explain models whereby acetylation is causal for the observed reduction in the linker histone content in chromatin. Other models to explain this correlation are discussed.

Acetylation↗

PubMed1994

Contacts of the globular domain of histone H5 and core histones with DNA in a "chromatosome".

The globular domain of histone H5 is found to asymmetrically associate with a nucleosome core including the Xenopus borealis somatic 5S RNA gene. Histones H2A and H2B are required for association of histone H5. Strong crosslinking of the globular domain of histone H5 to the 5S DNA in the nucleosome occurs at a single site to one side of the dyad axis. This site is also in contact with the core histones, and the interactions of the core histones with 5S DNA change as a result of association of the globular domain of histone H5. We discuss evidence for an allosteric change in core histone-5S DNA interactions following the association of the linker histone in the nucleosome.

Animals↗

PubMed1994

Nucleosome structural changes due to acetylation.

We have measured the helical repeat of acetylated nucleosomes reconstituted with HeLa cell histone octamers and the 5 S RNA gene positioning sequence from Xenopus borealis. The hydroxyl radical footprinting experiments show that the helical repeat of nucleosome-bound DNA is unchanged upon acetylation, and that the extent of DNA-protein contacts remains unaltered. These results, combined with previous determinations of the linking number change in minichromosomes as a function of the extent of acetylation, are analyzed with surface linking theory. We demonstrate that the shape of the nucleosome changes upon acetylation, in such a way as to decrease the number of times the DNA winds around the nucleosome central axis.

Acetylation↗