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  • 1
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    Genome-wide analysis reveals positional-nucleosome-oriented binding pattern of pioneer factor FOXA1 (2016)
    Oxford University Press
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    Publication Date: 2016-09-20
    Description: The compaction of nucleosomal structures creates a barrier for DNA-binding transcription factors (TFs) to access their cognate cis -regulatory elements. Pioneer factors (PFs) such as FOXA1 are able to directly access these cis -targets within compact chromatin. However, how these PFs interplay with nucleosomes remains to be elucidated, and is critical for us to understand the underlying mechanism of gene regulation. Here, we have conducted a computational analysis on a strand-specific paired-end ChIP-exo (termed as ChIP-ePENS) data of FOXA1 in LNCaP cells by our novel algorithm ePEST. We find that FOXA1 chromatin binding occurs via four distinct border modes (or footprint boundary patterns), with a preferential footprint boundary patterns relative to FOXA1 motif orientation. In addition, from this analysis three fundamental nucleotide positions ( oG, oS and oH ) emerged as major determinants for blocking exo-digestion and forming these four distinct border modes. By integrating histone MNase-seq data, we found an astonishingly consistent, ‘well-positioned’ configuration occurs between FOXA1 motifs and dyads of nucleosomes genome-wide. We further performed ChIP-seq of eight chromatin remodelers and found an increased occupancy of these remodelers on FOXA1 motifs for all four border modes (or footprint boundary patterns), indicating the full occupancy of FOXA1 complex on the three blocking sites ( oG, oS and oH ) likely produces an active regulatory status with well-positioned phasing for protein binding events. Together, our results suggest a positional-nucleosome-oriented accessing model for PFs seeking target motifs, in which FOXA1 can examine each underlying DNA nucleotide and is able to sense all potential motifs regardless of whether they face inward or outward from histone octamers along the DNA helix axis.
    Keywords: Protein-nucleic acid interaction, Computational Methods, Chromatin and Epigenetics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    Selectively Constrained RNA Editing Regulation Crosstalks with piRNA Biogenesis in Primates (2015)
    Oxford University Press
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    Publication Date: 2015-11-20
    Description: Although millions of RNA editing events have been reported to modify hereditary information across the primate transcriptome, evidence for their functional significance remains largely elusive, particularly for the vast majority of editing sites in noncoding regions. Here, we report a new mechanism for the functionality of RNA editing—a crosstalk with PIWI-interacting RNA (piRNA) biogenesis. Exploiting rhesus macaque as an emerging model organism closely related to human, in combination with extensive genome and transcriptome sequencing in seven tissues of the same animal, we deciphered accurate RNA editome across both long transcripts and the piRNA species. Superimposing and comparing these two distinct RNA editome profiles revealed 4,170 editing-bearing piRNA variants, or epiRNAs, that primarily derived from edited long transcripts. These epiRNAs represent distinct entities that evidence an intersection between RNA editing regulations and piRNA biogenesis. Population genetics analyses in a macaque population of 31 independent animals further demonstrated that the epiRNA-associated RNA editing is maintained by purifying selection, lending support to the functional significance of this crosstalk in rhesus macaque. Correspondingly, these findings are consistent in human, supporting the conservation of this mechanism during the primate evolution. Overall, our study reports the earliest lines of evidence for a crosstalk between selectively constrained RNA editing regulation and piRNA biogenesis, and further illustrates that such an interaction may contribute substantially to the diversification of the piRNA repertoire in primates.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    A Study of Semantic Web Services Network (2015)
    Oxford University Press
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    Publication Date: 2015-06-02
    Description: Loosely coupled and cross-platform features make Web services accessible and increasingly popular on the Internet. However, efficient service discovery and automated service composition are still challenges under the conventional practice where services are organized into categories. In this paper, we propose a graph-based method to organize Web services into a service ecosystem interlaced with service relationships at the semantic level. First, Web services are modelled as a set of interfaces, whose input and output parameters are annotated with well-defined ontologies. Secondly, semantic associations and interactions between Web services are mined, and services are constructed into a Web services network (SN), a variant of bipartite graph, by projecting the functional aspects of concrete Web services onto the abstract service layer. Thirdly, from the complex network perspective, the services relations are investigated and the structure of SN is analysed. To demonstrate the basic topological properties of SN, an empirical study is conducted on two data sets for comparative purposes, 10 000+ Web services collected from the Internet and 1231 Web services provided by Titan system of Zhejiang University. The experimental results reveal that SNs, which are built by different data sets on the semantic level, exhibit the same features such as small-world and scale-free. In addition, our results yield valuable insight for developing service discovery and automated composition algorithms, and characterizing the evolution of the entire Web service ecosystem.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
    Published by Oxford University Press
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  • 4
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    Simultaneous denoising and reconstruction of 5-D seismic data via damped rank-reduction method (2016)
    Oxford University Press
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    Publication Date: 2016-07-20
    Description: The Cadzow rank-reduction method can be effectively utilized in simultaneously denoising and reconstructing 5-D seismic data that depend on four spatial dimensions. The classic version of Cadzow rank-reduction method arranges the 4-D spatial data into a level-four block Hankel/Toeplitz matrix and then applies truncated singular value decomposition (TSVD) for rank reduction. When the observed data are extremely noisy, which is often the feature of real seismic data, traditional TSVD cannot be adequate for attenuating the noise and reconstructing the signals. The reconstructed data tend to contain a significant amount of residual noise using the traditional TSVD method, which can be explained by the fact that the reconstructed data space is a mixture of both signal subspace and noise subspace. In order to better decompose the block Hankel matrix into signal and noise components, we introduced a damping operator into the traditional TSVD formula, which we call the damped rank-reduction method. The damped rank-reduction method can obtain a perfect reconstruction performance even when the observed data have extremely low signal-to-noise ratio. The feasibility of the improved 5-D seismic data reconstruction method was validated via both 5-D synthetic and field data examples. We presented comprehensive analysis of the data examples and obtained valuable experience and guidelines in better utilizing the proposed method in practice. Since the proposed method is convenient to implement and can achieve immediate improvement, we suggest its wide application in the industry.
    Keywords: Seismology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 5
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    De novo deciphering three-dimensional chromatin interaction and topological domains by wavelet transformation of epigenetic profiles (2016)
    Oxford University Press
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    Publication Date: 2016-06-21
    Description: Defining chromatin interaction frequencies and topological domains is a great challenge for the annotations of genome structures. Although the chromosome conformation capture (3C) and its derivative methods have been developed for exploring the global interactome, they are limited by high experimental complexity and costs. Here we describe a novel computational method, called CITD, for de novo prediction of the chromatin interaction map by integrating histone modification data. We used the public epigenomic data from human fibroblast IMR90 cell and embryonic stem cell (H1) to develop and test CITD, which can not only successfully reconstruct the chromatin interaction frequencies discovered by the Hi-C technology, but also provide additional novel details of chromosomal organizations. We predicted the chromatin interaction frequencies, topological domains and their states (e.g. active or repressive) for 98 additional cell types from Roadmap Epigenomics and ENCODE projects. A total of 131 protein-coding genes located near 78 preserved boundaries among 100 cell types are found to be significantly enriched in functional categories of the nucleosome organization and chromatin assembly. CITD and its predicted results can be used for complementing the topological domains derived from limited Hi-C data and facilitating the understanding of spatial principles underlying the chromosomal organization.
    Keywords: Chromatin and Epigenetics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 6
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    ISL1 and JMJD3 synergistically control cardiac differentiation of embryonic stem cells (2016)
    Oxford University Press
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    Publication Date: 2016-08-20
    Description: ISL1 is expressed in cardiac progenitor cells and plays critical roles in cardiac lineage differentiation and heart development. Cardiac progenitor cells hold great potential for clinical and translational applications. However, the mechanisms underlying ISL1 function in cardiac progenitor cells have not been fully elucidated. Here we uncover a hierarchical role of ISL1 in cardiac progenitor cells, showing that ISL1 directly regulates hundreds of potential downstream target genes that are implicated in cardiac differentiation, through an epigenetic mechanism. Specifically, ISL1 promotes the demethylation of tri-methylation of histone H3K27 (H3K27me3) at the enhancers of key downstream target genes, including Myocd and Mef2c , which are core cardiac transcription factors. ISL1 physically interacts with JMJD3, a H3K27me3 demethylase, and conditional depletion of JMJD3 leads to impaired cardiac progenitor cell differentiation, phenocopying that of ISL1 depletion. Interestingly, ISL1 is not only responsible for the recruitment of JMJD3 to specific target loci during cardiac progenitor differentiation, but also modulates its demethylase activity. In conclusion, ISL1 and JMJD3 partner to alter the cardiac epigenome, instructing gene expression changes that drive cardiac differentiation.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 7
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    Heating load and COP optimization of a double resonance energy selective electron (ESE) heat pump (2016)
    Oxford University Press
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    Publication Date: 2016-08-26
    Description: A model of a double resonance energy selective electron (ESE) heat pump in one-dimensional system with two idealized energy filters is established in this paper. The analytical expressions of heating load and coefficient of performance (COP) for the ESE heat pump are derived. The optimum heating load and COP performances of the double resonance ESE heat pump are analyzed by using the theory of finite time thermodynamics. The effective regions of central energy level and heating load are obtained. The influences of energy space as well as resonance width of the two resonances on the performance of the ESE heat pump are discussed by detailed numerical examples. The values of some important performance parameters are also obtained by numerical calculations. The performance of the double resonance device is compared with that of the single resonance device. It is found that the maximum heating load decreases with the increase of energy space or the decrease of resonance width, while the maximum COP decreases with the increase of energy space or resonance width. By reasonable choices of the first resonance energy level, the energy space and the resonance width, the heat pump can be controlled to operate under the maximum COP condition. The results obtained herein can provide some theoretical guidelines for the design of practical multi-barrier nanostructured devices.
    Print ISSN: 1748-1317
    Electronic ISSN: 1748-1325
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Published by Oxford University Press
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  • 8
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    A possible formation channel for blue hook stars in globular clusters (2015)
    Oxford University Press
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    Publication Date: 2015-04-04
    Description: The formation mechanism for blue hook (BHk) stars in globular clusters (GCs) is still unclear. Following one of the possible scenarios, called the late hot flash scenario, we propose that a tidally enhanced stellar wind in binary evolution might provide the huge mass loss on the red giant branch (RGB) and produce BHk stars. Employing the detailed stellar evolution code mesa (Modules for Experiments in Stellar Astrophysics), we have investigated the contributions of tidally enhanced stellar wind as a possible formation channel for BHk stars in GCs. We evolved the primary stars with different initial orbital periods using the binary module in mesa (version 6208) from the zero-age main-sequence (ZAMS) to the post-horizontal branch (HB) stage, and obtained their evolution parameters, which are compared with the observation. The results are consistent with observations in the colour–magnitude diagram and the log g – T eff plane for NGC 2808, which is an example GC hosting BHk stars. However, the helium abundance in the surface for our models is higher than the one obtained in BHk stars. This discrepancy between our models and observations is possibly due to the fact that gravitational settling and radiative levitation, which are common processes in hot HB stars, are not considered in the models as well as the fact that the flash mixing efficiency might be overestimated in the calculations. Our results suggest that tidally enhanced stellar wind in binary evolution is able to naturally provide the huge mass loss on the RGB needed for the late hot flash scenario, and it is a possible and reasonable formation channel for BHk stars in GCs.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 9
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    Elastic wave finite-difference simulation using discontinuous curvilinear grid with non-uniform time step: two-dimensional case (2015)
    Oxford University Press
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    Publication Date: 2015-04-24
    Description: A discontinuous grid finite-difference (FD) method with non-uniform time step Runge–Kutta scheme on curvilinear collocated-grid is developed for seismic wave simulation. We introduce two transition zones: a spatial transition zone and a temporal transition zone, to exchange wavefield across the spatial and temporal discontinuous interfaces. A Gaussian filter is applied to suppress artificial numerical noise caused by down-sampling the wavefield from the finer grid to the coarser grid. We adapt the non-uniform time step Runge–Kutta scheme to a discontinuous grid FD method for further increasing the computational efficiency without losing the accuracy of time marching through the whole simulation region. When the topography is included in the modelling, we carry out the discontinuous grid method on a curvilinear collocated-grid to obtain a sufficiently accurate free-surface boundary condition implementation. Numerical tests show that the proposed method can sufficiently accurately simulate the seismic wave propagation on such grids and significantly reduce the computational resources consumption with respect to regular grids.
    Keywords: Seismology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 10
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    Large-scale exploration and analysis of drug combinations (2015)
    Oxford University Press
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    Publication Date: 2015-06-14
    Description: Motivation: Drug combinations are a promising strategy for combating complex diseases by improving the efficacy and reducing corresponding side effects. Currently, a widely studied problem in pharmacology is to predict effective drug combinations, either through empirically screening in clinic or pure experimental trials. However, the large-scale prediction of drug combination by a systems method is rarely considered. Results: We report a systems pharmacology framework to predict drug combinations (PreDCs) on a computational model, termed probability ensemble approach (PEA), for analysis of both the efficacy and adverse effects of drug combinations. First, a Bayesian network integrating with a similarity algorithm is developed to model the combinations from drug molecular and pharmacological phenotypes, and the predictions are then assessed with both clinical efficacy and adverse effects. It is illustrated that PEA can predict the combination efficacy of drugs spanning different therapeutic classes with high specificity and sensitivity (AUC = 0.90), which was further validated by independent data or new experimental assays. PEA also evaluates the adverse effects (AUC = 0.95) quantitatively and detects the therapeutic indications for drug combinations. Finally, the PreDC database includes 1571 known and 3269 predicted optimal combinations as well as their potential side effects and therapeutic indications. Availability and implementation: The PreDC database is available at http://sm.nwsuaf.edu.cn/lsp/predc.php . Contact: yh_wang@nwsuaf.edu.cn Supplementary Information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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