High-throughput sequencing reveals a simple model of nucleosome energetics

We use nucleosome maps obtained by high-throughput sequencing to study sequence specificity of intrinsic histone-DNA interactions. In contrast with previous approaches, we employ an analogy between a classical one-dimensional fluid of finite-size particles in an arbitrary external potential and arrays of DNA-bound histone octamers. We derive an analytical solution to infer free energies of nucleosome formation directly from nucleosome occupancies measured in high-throughput experiments. The sequence-specific part of free energies is then captured by fitting them to a sum of energies assigned to individual nucleotide motifs. We have developed hierarchical models of increasing complexity and spatial resolution, establishing that nucleosome occupancies can be explained by systematic differences in mono- and dinucleotide content between nucleosomal and linker DNA sequences, with periodic dinucleotide distributions and longer sequence motifs playing a secondary role. Furthermore, similar sequence signatures are exhibited by control experiments in which genomic DNA is either sonicated or digested with micrococcal nuclease in the absence of nucleosomes, making it possible that current predictions based on high-throughput nucleosome positioning maps are biased by experimental artifacts.Comment: 36 pages, 13 figure

Back-to-back emission of the electrons in double photoionization of helium

We calculate the double differential distributions and distributions in recoil momenta for the high energy non-relativistic double photoionization of helium. We show that the results of recent experiments is the pioneering experimental manifestation of the quasifree mechanism for the double photoionization, predicted long ago in our papers. This mechanism provides a surplus in distribution over the recoil momenta at small values of the latter, corresponding to nearly "back-to-back" emission of the electrons. Also in agreement with previous analysis the surplus is due to the quadrupole terms of the photon-electron interaction. We present the characteristic angular distribution for the "back-to-back" electron emission. The confirmation of the quasifree mechanism opens a new area of exiting experiments, which are expected to increase our understanding of the electron dynamics and of the bound states structure. The results of this Letter along with the recent experiments open a new field for studies of two-electron ionization not only by photons but by other projectiles, e.g. by fast electrons or heavy ions.Comment: 10 pages, 2 figure

Utilization of a deoxynucleoside diphosphate substrate by HIV reverse transcriptase

Background: Deoxynucleoside triphosphates (dNTPs) are the normal substrates for DNA sysnthesis is catalyzed by polymerases such as HIV-1 reverse transcriptase (RT). However, substantial amounts of deoxynucleoside diphosphates (dNDPs) are also present in the cell. Use of dNDPs in HIV-1 DNA sysnthesis could have significant implications for the efficacy of nucleoside RT inhibitors such as AZT which are first line therapeutics fro treatment of HIV infection. Our earlier work on HIV-1 reverse transcriptase (RT) suggested that the interaction between the γ phosphate of the incoming dNTP and RT residue K65 in the active site is not essential for dNTP insertion, implying that this polymerase may be able to insert dNPs in addition to dNTPs. Methodology/Principal Findings: We examined the ability of recombinant wild type (wt) and mutant RTs with substitutions at residue K65 to utilize a dNDP substrate in primer extension reactions. We found that wild type HIV-1 RT indeed catalyzes incorporation of dNDP substrates whereas RT with mutations of residue K645 were unable to catalyze this reaction. Wild type HIV-1 RT also catalyzed the reverse reaction, inorganic phosphate-dependent phosphorolysis. Nucleotide-mediated phosphorolytic removal of chain-terminating 3′-terminal nucleoside inhibitors such as AZT forms the basis of HIV-1 resistance to such drugs, and this removal is enhanced by thymidine analog mutations (TAMs). We found that both wt and TAM-containing RTs were able to catalyze Pi-mediated phosphorolysis of 3′-terminal AZT at physiological levels of Pi with an efficacy similar to that for ATP-dependent AZT-excision. Conclusion: We have identified two new catalytic function of HIV-1 RT, the use of dNDPs as substrates for DNA synthesis, and the use of Pi as substrate for phosphorolytic removal of primer 3′-terminal nucleotides. The ability to insert dNDPs has been documented for only one other DNA polymerase The RB69 DNA polymerase and the reverse reaction employing inorganic phosphate has not been documented for any DNA polymerase. Importantly, our results show that Pi-mediated phosphorolysis can contribute to AZT resistance and indicates that factors that influence HIV resistance to AZT are more complex than previously appreciated. © 2008 Garforth et al

Cross Priming Amplification: Mechanism and Optimization for Isothermal DNA Amplification

CPA is a class of isothermal amplification reactions that is carried out by a strand displacement DNA polymerase and does not require an initial denaturation step or the addition of a nicking enzyme. At the assay temperature of 63°C, the formation of a primer-template hybrid at transient, spontaneous denaturation bubbles in the DNA template is favored over re-annealing of the template strands by the high concentration of primer relative to template DNA. Strand displacement is encouraged by the annealing of cross primers with 5′ ends that are not complementary to the template strand and the binding of a displacement primer upstream of the crossing primer. The resulting exponential amplification of target DNA is highly specific and highly sensitive, producing amplicons from as few as four bacterial cells. Here we report on the basic CPA mechanism – single crossing CPA – and provide details on alternative mechanisms

Genome prediction of PhoB regulated promoters in Sinorhizobium meliloti and twelve proteobacteria

In proteobacteria, genes whose expression is modulated in response to the external concentration of inorganic phosphate are often regulated by the PhoB protein which binds to a conserved motif (Pho box) within their promoter regions. Using a position weight matrix algorithm derived from known Pho box sequences, we identified 96 putative Pho regulon members whose promoter regions contained one or more Pho boxs in the Sinorhizobium meliloti genome. Expression of these genes was examined through assays of reporter gene fusions and through comparison with published microarray data. Of 96 genes, 31 were induced and 3 were repressed by Pi starvation in a PhoB dependent manner. Novel Pho regulon members included several genes of unknown function. Comparative analysis across 12 proteobacterial genomes revealed highly conserved Pho regulon members including genes involved in Pi metabolism (pstS, phnC and ppdK). Genes with no obvious association with Pi metabolism were predicted to be Pho regulon members in S.meliloti and multiple organisms. These included smc01605 and smc04317 which are annotated as substrate binding proteins of iron transporters and katA encoding catalase. This data suggests that the Pho regulon overlaps and interacts with several other control circuits, such as the oxidative stress response and iron homeostasis

The Role of the Novel Exopolyphosphatase MT0516 in Mycobacterium tuberculosis Drug Tolerance and Persistence

Inorganic polyphosphate (poly P) has been postulated to play a regulatory role in the transition to bacterial persistence. In bacteria, poly P balance in the cell is maintained by the hydrolysis activity of the exopolyphosphatase PPX. However, the Mycobacterium tuberculosis PPX has not been characterized previously. Here we show that recombinant MT0516 hydrolyzes poly P, and an MT0516-deficient M. tuberculosis mutant exhibits elevated intracellular levels of poly P and increased expression of the genes mprB, sigE, and rel relative to the isogenic wild-type strain, indicating poly P-mediated signaling. Deficiency of MT0516 resulted in decelerated growth during logarithmic-phase in axenic cultures, and tolerance to the cell wall-active drug isoniazid. The MT0516-deficient mutant showed a significant survival defect in activated human macrophages and reduced persistence in the lungs of guinea pigs. We conclude that exopolyphosphatase is required for long-term survival of M. tuberculosis in necrotic lung lesions

RNA Is an Integral Component of Chromatin that Contributes to Its Structural Organization

Chromatin structure is influenced by multiples factors, such as pH, temperature, nature and concentration of counterions, post-translational modifications of histones and binding of structural non-histone proteins. RNA is also known to contribute to the regulation of chromatin structure as chromatin-induced gene silencing was shown to depend on the RNAi machinery in S. pombe, plants and Drosophila. Moreover, both in Drosophila and mammals, dosage compensation requires the contribution of specific non-coding RNAs. However, whether RNA itself plays a direct structural role in chromatin is not known. Here, we report results that indicate a general structural role for RNA in eukaryotic chromatin. RNA is found associated to purified chromatin prepared from chicken liver, or cultured Drosophila S2 cells, and treatment with RNase A alters the structural properties of chromatin. Our results indicate that chromatin-associated RNAs, which account for 2%–5% of total chromatin-associated nucleic acids, are polyA− and show a size similar to that of the DNA contained in the corresponding chromatin fragments. Chromatin-associated RNA(s) are not likely to correspond to nascent transcripts as they are also found bound to chromatin when cells are treated with α-amanitin. After treatment with RNase A, chromatin fragments of molecular weight >3.000 bp of DNA showed reduced sedimentation through sucrose gradients and increased sensitivity to micrococcal nuclease digestion. This structural transition, which is observed both at euchromatic and heterochromatic regions, proceeds without loss of histone H1 or any significant change in core-histone composition and integrity

Lipidna peroksidacija i aktivnost antioksidativnih enzima u eritrocitima radnika profesionalno izloženih aluminiju

Current research indicates that lipid peroxidation could have a role in aluminium toxicity. The aim of this study was to asses lipid peroxidation and antioxidative enzyme activity in erythrocytes of workers occupationally exposed to aluminium. We investigated a group of 59 workers (Al group) exposed to aluminium fumes (contamination factor F=8.07 to 13.47, national maximal allowed concentration value is 2 mg m-3). The control group (C group) consisted of 75 subjects employed in lime production who had not been occupationally exposed to aluminium or any known toxic substance. Erythrocyte aluminium concentrations were significantly higher in the exposed group than controls [Al group (8.41±3.66) µg L-1, C group (5.60±0.86) µg L-1, p<0.001]. In the Al group, erythrocyte malondialdehyde concentration was also significantly higher [Al group (189.59±81.27) µmol L-1, C group (105.21±49.62) µmol L-1, p<0.001] and antioxidative enzyme activity reduced for glucoso-6-phosphatedehydrogenase [Al group (5.05±1.70) IU g-1 Hb, C group (12.53±4.12) IU g-1 Hb, p<0.001], glutathione reductase [Al group (1.41±0.56) IU g-1 Hb, C group (1.89±0.57) IU g-1 Hb, p<0.001], glutathione peroxidase [Al group (12.37±5.76) IU g-1 Hb, C group (15.54±4.85) IU g-1 Hb, p<0.001], catalase [Al group (116.76±26.60) IU g-1 Hb, C group (158.81±71.85) IU g-1 Hb, p<0.001] and superoxide dismutase [Al group (1175.8±149.9) IU mg-1 Hb, C group (1377.9±207.5) IU mg-1 Hb, p<0.001].Rezultati suvremenih istraživanja pokazuju da lipidna peroksidacija može imati važnu ulogu u toksičnosti aluminija. Cilj istraživanja bio je da se ispita lipidna peroksidacija i aktivnost antioksidativnih enzima u eritrocitima kod radnika profesionalno izloženih aluminiju. Ispitivanjem je obuhvaćena skupina od 59 radnika (Al skupina) profesionalno izloženih aluminiju (faktor onečišćenja F=8,07 do 13,47, nacionalna maksimalno dopuštena koncentracija je 2 mg m-3). Kontrolna skupina sastojala se od 75 osoba zaposlenih u proizvodnji vapna koje nikada nisu bile profesionalno izložene aluminiju ni drugim toksičnim tvarima. U skupini izloženoj aluminiju utvrđene su statistički signifikantno više koncentracije aluminija u eritrocitima nego u kontrolnoj skupini [Al skupina (8,41±3,66) µg L-1, kontrolna skupina (5,60±0,86) µg L-1, p<0,001]. U Al skupini utvrđene su statistički značajno više koncentracije malondialdehida u eritrocitima [Al skupina (189,59±81,27) µmol L-1, kontrolna skupina (105,21±49,62) µmol L-1, p<0,001]. Također, u Al skupini utvrđene su i statistički značajno niže aktivnosti antioksidativnih enzima u eritrocitima: glukozo- 6-fosfatdehidrogenaza [Al skupina (5,05±1,70) IU g-1 Hb, kontrolna skupina (12,53±4,12) IU g-1 Hb, p<0,001], glutationreduktaza [Al skupina (1,41±0,56) IU g-1 Hb, kontrolna skupina (1,89±0,57) IU g-1 Hb, p<0,001], glutationperoksidaza [Al skupina (12,37±5,76) IU g-1 Hb, kontrolna skupina (15,54±4,85) IU g-1 Hb, p<0,001], katalaza [Al skupina (116,76±26,60) IU g-1 Hb, kontrolna skupina (158,81±71,85) IU g-1 Hb, p<0,001] i superoksiddizmutaza [Al skupina (1175,8±149,9) IU mg-1 Hb, kontrolna skupina (1377,9±207,5) IU mg-1 Hb, p<0,001]

PDNAsite:identification of DNA-binding site from protein sequence by incorporating spatial and sequence context

Protein-DNA interactions are involved in many fundamental biological processes essential for cellular function. Most of the existing computational approaches employed only the sequence context of the target residue for its prediction. In the present study, for each target residue, we applied both the spatial context and the sequence context to construct the feature space. Subsequently, Latent Semantic Analysis (LSA) was applied to remove the redundancies in the feature space. Finally, a predictor (PDNAsite) was developed through the integration of the support vector machines (SVM) classifier and ensemble learning. Results on the PDNA-62 and the PDNA-224 datasets demonstrate that features extracted from spatial context provide more information than those from sequence context and the combination of them gives more performance gain. An analysis of the number of binding sites in the spatial context of the target site indicates that the interactions between binding sites next to each other are important for protein-DNA recognition and their binding ability. The comparison between our proposed PDNAsite method and the existing methods indicate that PDNAsite outperforms most of the existing methods and is a useful tool for DNA-binding site identification. A web-server of our predictor (http://hlt.hitsz.edu.cn:8080/PDNAsite/) is made available for free public accessible to the biological research community