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  • 1
    Publication Date: 2012-06-28
    Description: DNA mimic proteins occupy the DNA binding sites of DNA-binding proteins, and prevent these sites from being accessed by DNA. We show here that the Neisseria conserved hypothetical protein DMP19 acts as a DNA mimic. The crystal structure of DMP19 shows a dsDNA-like negative charge distribution on the surface, suggesting that this protein should be added to the short list of known DNA mimic proteins. The crystal structure of another related protein, NHTF ( Neisseria hypothetical transcription factor), provides evidence that it is a member of the xenobiotic-response element (XRE) family of transcriptional factors. NHTF binds to a palindromic DNA sequence containing a 5'-TGTNAN 11 TNACA-3' recognition box that controls the expression of an NHTF-related operon in which the conserved nitrogen-response protein [i.e. (Protein-PII) uridylyltransferase] is encoded. The complementary surface charges between DMP19 and NHTF suggest specific charge–charge interaction. In a DNA-binding assay, we found that DMP19 can prevent NHTF from binding to its DNA-binding sites. Finally, we used an in situ gene regulation assay to provide evidence that NHTF is a repressor of its down-stream genes and that DMP19 can neutralize this effect. We therefore conclude that the interaction of DMP19 and NHTF provides a novel gene regulation mechanism in Neisseria spps.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 2
    Publication Date: 2016-03-31
    Description: It has been widely accepted that 5-methylcytosine is the only form of DNA methylation in mammalian genomes. Here we identify N(6)-methyladenine as another form of DNA modification in mouse embryonic stem cells. Alkbh1 encodes a demethylase for N(6)-methyladenine. An increase of N(6)-methyladenine levels in Alkbh1-deficient cells leads to transcriptional silencing. N(6)-methyladenine deposition is inversely correlated with the evolutionary age of LINE-1 transposons; its deposition is strongly enriched at young (〈1.5 million years old) but not old (〉6 million years old) L1 elements. The deposition of N(6)-methyladenine correlates with epigenetic silencing of such LINE-1 transposons, together with their neighbouring enhancers and genes, thereby resisting the gene activation signals during embryonic stem cell differentiation. As young full-length LINE-1 transposons are strongly enriched on the X chromosome, genes located on the X chromosome are also silenced. Thus, N(6)-methyladenine developed a new role in epigenetic silencing in mammalian evolution distinct from its role in gene activation in other organisms. Our results demonstrate that N(6)-methyladenine constitutes a crucial component of the epigenetic regulation repertoire in mammalian genomes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wu, Tao P -- Wang, Tao -- Seetin, Matthew G -- Lai, Yongquan -- Zhu, Shijia -- Lin, Kaixuan -- Liu, Yifei -- Byrum, Stephanie D -- Mackintosh, Samuel G -- Zhong, Mei -- Tackett, Alan -- Wang, Guilin -- Hon, Lawrence S -- Fang, Gang -- Swenberg, James A -- Xiao, Andrew Z -- P20GM103429/GM/NIGMS NIH HHS/ -- P30 ES010126/ES/NIEHS NIH HHS/ -- P42 ES005948/ES/NIEHS NIH HHS/ -- R01 GM114472-01/GM/NIGMS NIH HHS/ -- R01GM106024/GM/NIGMS NIH HHS/ -- R01GM114205-01/GM/NIGMS NIH HHS/ -- S10OD018445/OD/NIH HHS/ -- England -- Nature. 2016 Apr 21;532(7599):329-33. doi: 10.1038/nature17640. Epub 2016 Mar 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics and Yale Stem Cell Center, Yale School of Medicine, New Haven, Connecticut 06520, USA. ; Pacific Biosciences, 1380 Willow Road, Menlo Park, California 94025, USA. ; Environmental Sciences &Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA. ; Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York 10029, USA. ; Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA. ; Yale Stem Cell Center and Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA. ; Department of Molecular Biophysics &Biochemistry, Yale Center for Genome Analysis, Yale School of Medicine, New Haven, Connecticut 06520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/27027282" target="_blank"〉PubMed〈/a〉
    Keywords: Adenine/*analogs & derivatives/metabolism ; Animals ; Cell Differentiation/genetics ; *DNA Methylation ; DNA Transposable Elements/genetics ; DNA-(Apurinic or Apyrimidinic Site) Lyase/deficiency/genetics/metabolism ; Enhancer Elements, Genetic/genetics ; Epigenesis, Genetic/*genetics ; Evolution, Molecular ; Gene Silencing ; Long Interspersed Nucleotide Elements/genetics ; Mammals/genetics ; Mice ; Mouse Embryonic Stem Cells/cytology/*metabolism ; Up-Regulation/genetics ; X Chromosome/genetics/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2015-07-22
    Description: Myocardial mitochondrial Ca2+ entry enables physiological stress responses but in excess promotes injury and death. However, tissue-specific in vivo systems for testing the role of mitochondrial Ca2+ are lacking. We developed a mouse model with myocardial delimited transgenic expression of a dominant negative (DN) form of the mitochondrial Ca2+ uniporter...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 4
    Electronic Resource
    Electronic Resource
    Amsterdam : Elsevier
    Chemistry and Physics of Lipids 67-68 (1994), S. 59-66 
    ISSN: 0009-3084
    Keywords: Fragment 2 ; Prothrombin kringle 2 ; Thrombin complex ; α-Thrombin
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Biology , Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
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  • 5
    Publication Date: 2015-03-19
    Description: Author(s): S. F. Jin, Q. Huang, Z. P. Lin, Z. L. Li, X. Z. Wu, T. P. Ying, G. Wang, and X. L. Chen We report the results on the structure, transport, and magnetic properties of a layered oxysulfide CaOFeS with a stacked triangle lattice of Fe ions. The susceptibility data show a broad maximum near 120 K, indicating the existence of two-dimensional (2D) short-range ordering in this compound. Featu... [Phys. Rev. B 91, 094420] Published Wed Mar 18, 2015
    Keywords: Magnetism
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
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