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  • Articles  (735)
  • Other Sources
  • Nucleic Acids Research  (53)
  • Acta Crystallographica Section E  (15)
  • Physical Review Letters  (14)
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  • Articles  (735)
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  • 1
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    PP1{alpha}, PP1{beta} and Wip-1 regulate H4S47 phosphorylation and deposition of histone H3 variant H3.3 (2013)
    Oxford University Press
    Details
    Publication Date: 2013-09-26
    Description: Phosphorylation of histone H4 serine 47 (H4S47ph) is catalyzed by Pak2, a member of the p21-activated serine/threonine protein kinase (Pak) family and regulates the deposition of histone variant H3.3. However, the phosphatase(s) involved in the regulation of H4S47ph levels was unknown. Here, we show that three phosphatases (PP1α, PP1β and Wip1) regulate H4S47ph levels and H3.3 deposition. Depletion of each of the three phosphatases results in increased H4S47ph levels. Moreover, PP1α, PP1β and Wip1 bind H3-H4 in vitro and in vivo , whereas only PP1α and PP1β, but not Wip1, interact with Pak2 in vivo . These results suggest that PP1α, PP1β and Wip1 regulate the levels of H4S47ph through directly acting on H4S47ph, with PP1α and PP1β also likely regulating the activity of Pak2. Finally, depletion of PP1α, PP1β and Wip1 leads to increased H3.3 occupancy at candidate genes tested, elevated H3.3 deposition and enhanced association of H3.3 with its chaperones HIRA and Daxx. These results reveal a novel role of three phosphatases in chromatin dynamics in mammalian cells.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    Liu et al. Reply: (2012)
    American Physical Society (APS)
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    Publication Date: 2012-06-06
    Description: Author(s): X. Q. Liu, X. B. Li, L. Zhang, Y. Q. Cheng, Z. G. Yan, M. Xu, X. D. Han, S. B. Zhang, Z. Zhang, and E. Ma [Phys. Rev. Lett. 108, 239602] Published Tue Jun 05, 2012
    Keywords: Comments
    Print ISSN: 0031-9007
    Electronic ISSN: 1079-7114
    Topics: Physics
    Published by American Physical Society (APS)
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  • 3
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    New Structural Picture of the Ge_{2} Sb_{2} Te_{5} Phase-Change Alloy (2011)
    American Physical Society (APS)
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    Publication Date: 2011-01-14
    Description: Author(s): X. Q. Liu, X. B. Li, L. Zhang, Y. Q. Cheng, Z. G. Yan, M. Xu, X. D. Han, S. B. Zhang, Z. Zhang, and E. Ma Using electron microscopy and diffraction techniques, as well as first-principles calculations, we demonstrate that as much as 35% of the total Ge atoms in the cubic phase of Ge_{2} Sb_{2} Te_{5} locate in tetrahedral environments. The Ge-vacancy interactions play a crucial stabilizing role, leading... [Phys. Rev. Lett. 106, 025501] Published Thu Jan 13, 2011
    Keywords: Condensed Matter: Structure, etc.
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    Electronic ISSN: 1079-7114
    Topics: Physics
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  • 4
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    Tumor-targeted in vivo gene silencing via systemic delivery of cRGD-conjugated siRNA (2014)
    Oxford University Press
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    Publication Date: 2014-10-10
    Description: RNAi technology is taking strong position among the key therapeutic modalities, with dozens of siRNA-based programs entering and successfully progressing through clinical stages of drug development. To further explore potentials of RNAi technology as therapeutics, we engineered and tested VEGFR2 siRNA molecules specifically targeted to tumors through covalently conjugated cyclo(Arg-Gly-Asp- d -Phe-Lys[PEG-MAL]) (cRGD) peptide, known to bind αvβ3 integrin receptors. cRGD-siRNAs were demonstrated to specifically enter and silence targeted genes in cultured αvβ3 positive human cells (HUVEC). Microinjection of zebrafish blastocysts with VEGFR2 cRGD-siRNA resulted in specific inhibition of blood vessel growth. In tumor-bearing mice, intravenously injected cRGD-siRNA molecules generated no innate immune response and bio-distributed to tumor tissues. Continuous systemic delivery of two different VEGFR2 cRGD-siRNAs resulted in down-regulation of corresponding mRNA (55 and 45%) and protein (65 and 45%) in tumors, as well as in overall reduction of tumor volume (90 and 70%). These findings demonstrate strong potential of cRGD-siRNA molecules as anti-tumor therapy.
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    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 5
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    LncRNA loc285194 is a p53-regulated tumor suppressor (2013)
    Oxford University Press
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    Publication Date: 2013-05-04
    Description: Protein-coding genes account for only a small part of the human genome, whereas the vast majority of transcripts make up the non-coding RNAs including long non-coding RNAs (lncRNAs). Accumulating evidence indicates that lncRNAs could play a critical role in regulation of cellular processes such as cell growth and apoptosis as well as cancer progression and metastasis. LncRNA loc285194 was previously shown to be within a tumor suppressor unit in osteosarcoma and to suppress tumor cell growth. However, it is unknown regarding the regulation of loc285194. Moreover, the underlying mechanism by which loc285194 functions as a potential tumor suppressor is elusive. In this study, we show that loc285194 is a p53 transcription target; ectopic expression of loc285194 inhibits tumor cell growth both in vitro and in vivo . Through deletion analysis, we identify an active region responsible for tumor cell growth inhibition within exon 4, which harbors two miR-211 binding sites. Importantly, this loc285194-mediated growth inhibition is in part due to specific suppression of miR-211. We further demonstrate a reciprocal repression between loc285194 and miR-211; in contrast to loc285194, miR-211 promotes cell growth. Finally, we detect downregulation of loc285194 in colon cancer specimens by quantitative PCR arrays and in situ hybridization of tissue microarrays. Together, these results suggest that loc285194 is a p53-regulated tumor suppressor, which acts in part through repression of miR-211.
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    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 6
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    In vivo imaging of protein-protein and RNA-protein interactions using novel far-red fluorescence complementation systems (2014)
    Oxford University Press
    Details
    Publication Date: 2014-08-01
    Description: Imaging of protein–protein and RNA–protein interactions in vivo , especially in live animals, is still challenging. Here we developed far-red mNeptune-based bimolecular fluorescence complementation (BiFC) and trimolecular fluorescence complementation (TriFC) systems with excitation and emission above 600 nm in the ‘tissue optical window’ for imaging of protein–protein and RNA–protein interactions in live cells and mice. The far-red mNeptune BiFC was first built by selecting appropriate split mNeptune fragments, and then the mNeptune-TriFC system was built based on the mNeptune-BiFC system. The newly constructed mNeptune BiFC and TriFC systems were verified as useful tools for imaging protein–protein and mRNA–protein interactions, respectively, in live cells and mice. We then used the new mNeptune-TriFC system to investigate the interactions between human polypyrimidine-tract-binding protein (PTB) and HIV-1 mRNA elements as PTB may participate in HIV mRNA processing in HIV activation from latency. An interaction between PTB and the 3'long terminal repeat region of HIV-1 mRNAs was found and imaged in live cells and mice, implying a role for PTB in regulating HIV-1 mRNA processing. The study provides new tools for in vivo imaging of RNA–protein and protein–protein interactions, and adds new insight into the mechanism of HIV-1 mRNA processing.
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    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 7
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    H3K9me3 demethylase Kdm4d facilitates the formation of pre-initiative complex and regulates DNA replication (2017)
    Oxford University Press
    Details
    Publication Date: 2017-01-10
    Description: DNA replication is tightly regulated to occur once and only once per cell cycle. How chromatin, the physiological substrate of DNA replication machinery, regulates DNA replication remains largely unknown. Here we show that histone H3 lysine 9 demethylase Kdm4d regulates DNA replication in eukaryotic cells. Depletion of Kdm4d results in defects in DNA replication, which can be rescued by the expression of H3K9M, a histone H3 mutant transgene that reverses the effect of Kdm4d on H3K9 methylation. Kdm4d interacts with replication proteins, and its recruitment to DNA replication origins depends on the two pre-replicative complex components (origin recognition complex [ORC] and minichromosome maintenance [MCM] complex). Depletion of Kdm4d impairs the recruitment of Cdc45, proliferating cell nuclear antigen (PCNA), and polymerase , but not ORC and MCM proteins. These results demonstrate a novel mechanism by which Kdm4d regulates DNA replication by reducing the H3K9me3 level to facilitate formation of pre-initiative complex.
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    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 8
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    Engineered Unique Elastic Modes at a BaTiO_{3} /(2×1)−Ge(001) Interface (2016)
    American Physical Society (APS)
    Details
    Publication Date: 2016-03-08
    Description: Author(s): D. P. Kumah, M. Dogan, J. H. Ngai, D. Qiu, Z. Zhang, D. Su, E. D. Specht, S. Ismail-Beigi, C. H. Ahn, and F. J. Walker The strong interaction at an interface between a substrate and thin film leads to epitaxy and provides a means of inducing structural changes in the epitaxial film. These induced material phases often exhibit technologically relevant electronic, magnetic, and functional properties. The 2 × 1 surface o… [Phys. Rev. Lett. 116, 106101] Published Mon Mar 07, 2016
    Keywords: Condensed Matter: Structure, etc.
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    Electronic ISSN: 1079-7114
    Topics: Physics
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  • 9
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    Drastic Pressure Effect on the Extremely Large Magnetoresistance in WTe_{2} : Quantum Oscillation Study (2015)
    American Physical Society (APS)
    Details
    Publication Date: 2015-07-30
    Description: Author(s): P. L. Cai, J. Hu, L. P. He, J. Pan, X. C. Hong, Z. Zhang, J. Zhang, J. Wei, Z. Q. Mao, and S. Y. Li The quantum oscillations of the magnetoresistance under ambient and high pressure have been studied for WTe 2 single crystals, in which extremely large magnetoresistance was discovered recently. By analyzing the Shubnikov–de Haas oscillations, four Fermi surfaces are identified, and two of them are f… [Phys. Rev. Lett. 115, 057202] Published Tue Jul 28, 2015
    Keywords: Condensed Matter: Electronic Properties, etc.
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    Topics: Physics
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  • 10
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    Evolview v2: an online visualization and management tool for customized and annotated phylogenetic trees (2016)
    Oxford University Press
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    Publication Date: 2016-07-06
    Description: Evolview is an online visualization and management tool for customized and annotated phylogenetic trees. It allows users to visualize phylogenetic trees in various formats, customize the trees through built-in functions and user-supplied datasets and export the customization results to publication-ready figures. Its ‘dataset system’ contains not only the data to be visualized on the tree, but also ‘modifiers’ that control various aspects of the graphical annotation. Evolview is a single-page application (like Gmail); its carefully designed interface allows users to upload, visualize, manipulate and manage trees and datasets all in a single webpage. Developments since the last public release include a modern dataset editor with keyword highlighting functionality, seven newly added types of annotation datasets, collaboration support that allows users to share their trees and datasets and various improvements of the web interface and performance. In addition, we included eleven new ‘Demo’ trees to demonstrate the basic functionalities of Evolview, and five new ‘Showcase’ trees inspired by publications to showcase the power of Evolview in producing publication-ready figures. Evolview is freely available at: http://www.evolgenius.info/evolview/ .
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    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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