Danica Galonic Fujimori, PhD
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Title(s) | Professor, Cellular Molecular Pharmacology |
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School | School of Medicine |
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Address | 600 16th St San Francisco CA 94158
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Phone | 415-514-0147 |
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vCard | Download vCard |
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Biography Harvard Medical School, Boston, MA | Postdoctoral Fellow | | Biochemistry | University of Illinois - Urbana/Champaign, Urbana/Champaign, IL | PhD | | Chemistry | University of Belgrade, Belgrade, Serbia | BSc | | Chemistry |
University of California, San Francisco | 2017 | | Byers Award Lecture in Basic Sciences | University of California, Berkeley | 2015 | | Sackler Sabbatical Exchange Program | University of California, San Francisco | 2015 | | Chauncey D. Leake Lectureship in Cellular and Molecular Pharmacology | University of California, San Francisco | 2014 | | UCSF Haile T. Debas Academy of Medical Educators Excellence in Teaching Award | Kinship Foundation | 2011 | | Searle Scholar Award | National Science Foundation | 2011 | | NSF Career Award | March of Dimes | 2011 | | Basil O'Connor Starter Scholar Research Award | V Foundation | 2010 | | V Foundation Scholar Award | Hellman Family Foundation | 2010 | | Hellman Family Early-Career Faculty Award | Sidney Kimmel Foundation for Cancer Research | 2009 | | Kimmel Scholar Award | National Institutes of Health | 2007 | | NIH Pathway to Independence Award | Damon Runyon Cancer Research Foundation | 2005 | | Postdoctoral Fellowship |
Overview Our group investigates mechanisms, regulation, and biological functions of methyl group addition to proteins and RNA. Methylation, a common post-transcriptional and post-translational modification, has a profound effect on the regulation of fundamental biological processes such as gene expression, cellular localization, and RNA structure and function. Deregulation of methylation is associated with a wide range of diseases. The enzymatic regulation of methyl group addition and removal provides an opportunity for therapeutic intervention. We seek to understand the molecular mechanisms that control methylation, and develop chemical probes to interrogate the pathophysiological function of enzymes that regulate this modification. Specifically, our research focuses on the following areas:
Regulation and Small Molecule Inhibition of Jumonji Histone Demethylases Jumonji histone demethylases, a family of epigenetic “erasers”, catalyze the removal of methyl marks from lysine residues in proteins. Jumonji demethylases are complex proteins that, in addition to the catalytic domain, often contain one or more chromatin “reader” domains. The reader modules commonly interact with chromatin, and this interaction can be modulated by chromatin modifications. We investigate the functional cross-talk between chromatin recognition and demethylation in the jumonji family to understand how chromatin context impacts methyl mark removal, and consequently transcription. Furthermore, we are interested in understanding how additional regulatory inputs, such as metabolism and cellular signaling cascades, influence chromatin methylation and transcriptional regulation. In addition, our lab is actively involved in the development of small molecule inhibitors of the jumonji demethylases that can be used as cellular probes of their function. We use both rational design and high-throughput screening to identify starting scaffolds, and further optimize these scaffolds through iterative cycles of chemical synthesis and testing their potency and selectivity. Our goal is to use these molecules to inhibit aberrant demethylation caused by misregulation of demethylases in disease models.
Mechanisms and Cellular Roles of RNA Methylation Methylation of RNA is the abundant post-transcriptional modification identified in various types of RNAs. Despite its prevalence, the functional role of methylation is poorly understood. We are interested in elucidating the mechanisms responsible for RNA methylation, and understanding the role this modification plays in controlling the cellular function of RNA. We are particularly interested in 2-methyl and 8-methyladenosine modifications, catalyzed by related enzymes that utilize an unusual mechanism to achieve methylation. Incorporation of 2-methyladenosine into RNA has been implicated in the regulation of translational fidelity, although the mechanisms by which this is achieved are yet to be elucidated. In contrast, 8-methyladenosine formation is responsible for resistance to five chemically distinct classes of antibiotics that target the peptidyltransferase center of the bacterial ribosome, including linezolid. We investigate catalytic mechanisms, substrate recognition, and evolution of function in enzymes that carry out these methylations. Our goal is to determine the impact of methylation on the cellular function of substrate RNA.
Research ORNG Applications Bibliographic
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Histone H3 binding to the PHD1 domain of histone demethylase KDM5A enables active site remodeling. Nat Commun. 2019 01 09; 10(1):94.
Longbotham JE, Chio CM, Dharmarajan V, Trnka MJ, Torres IO, Goswami D, Ruiz K, Burlingame AL, Griffin PR, Fujimori DG. PMID: 30626866.
View in: PubMed Mentions: 5 Fields: Translation: AnimalsCells
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miCLIP-MaPseq, a Substrate Identification Approach for Radical SAM RNA Methylating Enzymes. J Am Chem Soc. 2018 06 13; 140(23):7135-7143.
Stojkovic V, Chu T, Therizols G, Weinberg DE, Fujimori DG. PMID: 29782154.
View in: PubMed Mentions: Fields: Translation: Cells
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Mutations in RNA methylating enzymes in disease. Curr Opin Chem Biol. 2017 Dec; 41:20-27.
Stojkovic V, Fujimori DG. PMID: 29059606.
View in: PubMed Mentions: 7 Fields: Translation: HumansAnimalsCells
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Determinants of tRNA Recognition by the Radical SAM Enzyme RlmN. PLoS One. 2016; 11(11):e0167298.
Fitzsimmons CM, Fujimori DG. PMID: 27902775.
View in: PubMed Mentions: Fields: Translation: Cells
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Antibiotic resistance evolved via inactivation of a ribosomal RNA methylating enzyme. Nucleic Acids Res. 2016 Oct 14; 44(18):8897-8907.
Stojkovic V, Noda-Garcia L, Tawfik DS, Fujimori DG. PMID: 27496281.
View in: PubMed Mentions: 11 Fields: Translation: Cells
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Editorial overview: Chemical genetics and epigenetics. Curr Opin Chem Biol. 2016 08; 33:vi-vii.
Fujimori DG, Conway SJ. PMID: 27614207.
View in: PubMed Mentions: Fields:
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Htm1p-Pdi1p is a folding-sensitive mannosidase that marks N-glycoproteins for ER-associated protein degradation. Proc Natl Acad Sci U S A. 2016 07 12; 113(28):E4015-24.
Liu YC, Fujimori DG, Weissman JS. PMID: 27357682.
View in: PubMed Mentions: 6 Fields: Translation: AnimalsCells
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Opposing Chromatin Signals Direct and Regulate the Activity of Lysine Demethylase 4C (KDM4C). J Biol Chem. 2016 Mar 18; 291(12):6060-70.
Pack LR, Yamamoto KR, Fujimori DG. PMID: 26747609.
View in: PubMed Mentions: 9 Fields: Translation: HumansCells
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Docking and Linking of Fragments To Discover Jumonji Histone Demethylase Inhibitors. J Med Chem. 2016 Feb 25; 59(4):1580-98.
Korczynska M, Le DD, Younger N, Gregori-Puigjané E, Tumber A, Krojer T, Velupillai S, Gileadi C, Nowak RP, Iwasa E, Pollock SB, Ortiz Torres I, Oppermann U, Shoichet BK, Fujimori DG. PMID: 26699912.
View in: PubMed Mentions: 9 Fields: Translation: Humans
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Functional coupling between writers, erasers and readers of histone and DNA methylation. Curr Opin Struct Biol. 2015 Dec; 35:68-75.
Torres IO, Fujimori DG. PMID: 26496625.
View in: PubMed Mentions: 29 Fields: Translation: HumansCells
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Improved Peak Detection and Deconvolution of Native Electrospray Mass Spectra from Large Protein Complexes. J Am Soc Mass Spectrom. 2015 Dec; 26(12):2141-51.
Lu J, Trnka MJ, Roh SH, Robinson PJ, Shiau C, Fujimori DG, Chiu W, Burlingame AL, Guan S. PMID: 26323614.
View in: PubMed Mentions: 10 Fields: Translation: HumansAnimalsCells
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Radical SAM-Mediated Methylation of Ribosomal RNA. Methods Enzymol. 2015; 560:355-76.
Stojkovic V, Fujimori DG. PMID: 26253978.
View in: PubMed Mentions: 5 Fields: Translation: Cells
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Histone demethylase KDM5A is regulated by its reader domain through a positive-feedback mechanism. Nat Commun. 2015 Feb 17; 6:6204.
Torres IO, Kuchenbecker KM, Nnadi CI, Fletterick RJ, Kelly MJ, Fujimori DG. PMID: 25686748.
View in: PubMed Mentions: 33 Fields: Translation: HumansAnimalsCells
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Product binding enforces the genomic specificity of a yeast polycomb repressive complex. Cell. 2015 Jan 15; 160(1-2):204-18.
Dumesic PA, Homer CM, Moresco JJ, Pack LR, Shanle EK, Coyle SM, Strahl BD, Fujimori DG, Yates JR, Madhani HD. PMID: 25533783.
View in: PubMed Mentions: 34 Fields: Translation: AnimalsCells
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Radical SAM-mediated methylation reactions. Curr Opin Chem Biol. 2013 Aug; 17(4):597-604.
Fujimori DG. PMID: 23835516.
View in: PubMed Mentions: 14 Fields: Translation: Cells
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Reconstitution of nucleosome demethylation and catalytic properties of a Jumonji histone demethylase. Chem Biol. 2013 Apr 18; 20(4):494-9.
Shiau C, Trnka MJ, Bozicevic A, Ortiz Torres I, Al-Sady B, Burlingame AL, Narlikar GJ, Fujimori DG. PMID: 23601638.
View in: PubMed Mentions: 11 Fields: Translation: HumansCells
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Site-specific and regiospecific installation of methylarginine analogues into recombinant histones and insights into effector protein binding. J Am Chem Soc. 2013 Feb 27; 135(8):2879-82.
Le DD, Cortesi AT, Myers SA, Burlingame AL, Fujimori DG. PMID: 23398247.
View in: PubMed Mentions: 11 Fields: Translation: Cells
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Covalent Intermediate in the Catalytic Mechanism of the Radical S-Adenosyl-l-methionine Methyl Synthase RlmN Trapped by Mutagenesis. J Am Chem Soc. 2012; 134(43):18074-81.
McCusker KP, Medzihradszky KF, Shiver AL, Nichols RJ, Yan F, Maltby DA, Gross CA, Fujimori DG.
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Covalent intermediate in the catalytic mechanism of the radical S-adenosyl-L-methionine methyl synthase RlmN trapped by mutagenesis. J Am Chem Soc. 2012 Oct 31; 134(43):18074-81.
McCusker KP, Medzihradszky KF, Shiver AL, Nichols RJ, Yan F, Maltby DA, Gross CA, Fujimori DG. PMID: 23088750.
View in: PubMed Mentions: 14 Fields: Translation: Cells
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Protein and nucleic acid methylating enzymes: mechanisms and regulation. Curr Opin Chem Biol. 2012 Dec; 16(5-6):507-15.
Le DD, Fujimori DG. PMID: 23085277.
View in: PubMed Mentions: 8 Fields: Translation: HumansAnimalsCells
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The chemistry of peptidyltransferase center-targeted antibiotics: enzymatic resistance and approaches to countering resistance. ACS Chem Biol. 2012 Jan 20; 7(1):64-72.
McCusker KP, Fujimori DG. PMID: 22208312.
View in: PubMed Mentions: 9 Fields: Translation: HumansCells
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RNA methylation by radical SAM enzymes RlmN and Cfr proceeds via methylene transfer and hydride shift. Proc Natl Acad Sci U S A. 2011 Mar 08; 108(10):3930-4.
Yan F, Fujimori DG. PMID: 21368151.
View in: PubMed Mentions: 33 Fields: Translation: Cells
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A novel enzymatic rearrangement. Chem Biol. 2010 Dec 22; 17(12):1269-70.
Fujimori DG. PMID: 21168760.
View in: PubMed Mentions: Fields:
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RlmN and Cfr are radical SAM enzymes involved in methylation of ribosomal RNA. J Am Chem Soc. 2010 Mar 24; 132(11):3953-64.
Yan F, LaMarre JM, Röhrich R, Wiesner J, Jomaa H, Mankin AS, Fujimori DG. PMID: 20184321.
View in: PubMed Mentions: 64 Fields: Translation: Cells
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Structural analysis of an open active site conformation of nonheme iron halogenase CytC3. J Am Chem Soc. 2009 Apr 08; 131(13):4872-9.
Wong C, Fujimori DG, Walsh CT, Drennan CL. PMID: 19281171.
View in: PubMed Mentions: 31 Fields: Translation: Cells
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Hypoxia sensing goes gauche. Nat Chem Biol. 2009 Apr; 5(4):202-3.
Fujimori DG. PMID: 19295524.
View in: PubMed Mentions: Fields: Translation: Cells
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Halogenation strategies in natural product biosynthesis. Chem Biol. 2008 Feb; 15(2):99-109.
Neumann CS, Fujimori DG, Walsh CT. PMID: 18291314.
View in: PubMed Mentions: 84 Fields: Translation: Cells
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CD and MCD of CytC3 and taurine dioxygenase: role of the facial triad in alpha-KG-dependent oxygenases. J Am Chem Soc. 2007 Nov 21; 129(46):14224-31.
Neidig ML, Brown CD, Light KM, Fujimori DG, Nolan EM, Price JC, Barr EW, Bollinger JM, Krebs C, Walsh CT, Solomon EI. PMID: 17967013.
View in: PubMed Mentions: 43 Fields: Translation: Cells
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Spectroscopic evidence for a high-spin Br-Fe(IV)-oxo intermediate in the alpha-ketoglutarate-dependent halogenase CytC3 from Streptomyces. J Am Chem Soc. 2007 Nov 07; 129(44):13408-9.
Fujimori DG, Barr EW, Matthews ML, Koch GM, Yonce JR, Walsh CT, Bollinger JM, Krebs C, Riggs-Gelasco PJ. PMID: 17939667.
View in: PubMed Mentions: 49 Fields: Translation: Cells
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Cloning and characterization of the biosynthetic gene cluster for kutznerides. Proc Natl Acad Sci U S A. 2007 Oct 16; 104(42):16498-503.
Fujimori DG, Hrvatin S, Neumann CS, Strieker M, Marahiel MA, Walsh CT. PMID: 17940045.
View in: PubMed Mentions: 35 Fields: Translation: Cells
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What's new in enzymatic halogenations. Curr Opin Chem Biol. 2007 Oct; 11(5):553-60.
Fujimori DG, Walsh CT. PMID: 17881282.
View in: PubMed Mentions: 15 Fields: Translation: Cells
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Chemical glycosylation in the synthesis of glycoconjugate antitumour vaccines. Nature. 2007 Apr 26; 446(7139):1000-7.
Galonic DP, Gin DY. PMID: 17460660.
View in: PubMed Mentions: 49 Fields: Translation: HumansAnimalsCells
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Characterization of the aminocarboxycyclopropane-forming enzyme CmaC. Biochemistry. 2007 Jan 16; 46(2):359-68.
Kelly WL, Boyne MT, Yeh E, Vosburg DA, Galonic DP, Kelleher NL, Walsh CT. PMID: 17209546.
View in: PubMed Mentions: 16 Fields: Translation: Cells
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Two interconverting Fe(IV) intermediates in aliphatic chlorination by the halogenase CytC3. Nat Chem Biol. 2007 Feb; 3(2):113-6.
Galonic DP, Barr EW, Walsh CT, Bollinger JM, Krebs C. PMID: 17220900.
View in: PubMed Mentions: 99 Fields: Translation: Cells
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Enzymatic generation of the antimetabolite gamma,gamma-dichloroaminobutyrate by NRPS and mononuclear iron halogenase action in a streptomycete. Chem Biol. 2006 Nov; 13(11):1183-91.
Ueki M, Galonic DP, Vaillancourt FH, Garneau-Tsodikova S, Yeh E, Vosburg DA, Schroeder FC, Osada H, Walsh CT. PMID: 17114000.
View in: PubMed Mentions: 23 Fields: Translation: Cells
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Halogenation of unactivated carbon centers in natural product biosynthesis: trichlorination of leucine during barbamide biosynthesis. J Am Chem Soc. 2006 Mar 29; 128(12):3900-1.
Galonic DP, Vaillancourt FH, Walsh CT. PMID: 16551084.
View in: PubMed Mentions: 41 Fields: Translation: Cells
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Aziridine-2-carboxylic acid-containing peptides: application to solution- and solid-phase convergent site-selective peptide modification. J Am Chem Soc. 2005 May 25; 127(20):7359-69.
Galonic DP, Ide ND, van der Donk WA, Gin DY. PMID: 15898784.
View in: PubMed Mentions: 9 Fields:
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Site-selective conjugation of thiols with aziridine-2-carboxylic acid-containing peptides. J Am Chem Soc. 2004 Oct 13; 126(40):12712-3.
Galonic DP, van der Donk WA, Gin DY. PMID: 15469231.
View in: PubMed Mentions: 10 Fields:
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Oligosaccharide-peptide ligation of glycosyl thiolates with dehydropeptides: synthesis of S-linked mucin-related glycopeptide conjugates. Chemistry. 2003 Dec 15; 9(24):5997-6006.
Galonic DP, Van Der Donk WA, Gin DY. PMID: 14679512.
View in: PubMed Mentions: 8 Fields: Translation: Cells
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Selenocysteine derivatives for chemoselective ligations. Chembiochem. 2002 Aug 02; 3(8):709-16.
Gieselman MD, Zhu Y, Zhou H, Galonic D, van der Donk WA. PMID: 12203969.
View in: PubMed Mentions: 5 Fields: Translation: Cells
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J Serb Chem Soc. Model Study of Epothilone Synthesis: An Alternative Synthetic Approach to the C1-C7 fragment. 2002; 67:221-7.
Lalic G, Galonic D, Matovic R, Saicic RN.
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Tetrahedron. Alkylation of Carbonyl Compounds in the TiCl4-promoted Reaction of Trimethylsilyl Enol Ethers with Epoxides. 2001; 57:583-591.
Lalic G, Petrovski Z, Galonic DP, Matovic R, Saicic RN.
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Year | Publications |
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2001 | 1 | 2002 | 2 | 2003 | 1 | 2004 | 1 | 2005 | 1 | 2006 | 2 | 2007 | 7 | 2008 | 1 | 2009 | 2 | 2010 | 2 | 2011 | 2 | 2012 | 3 | 2013 | 3 | 2014 | 1 | 2015 | 5 | 2016 | 5 | 2017 | 1 | 2018 | 1 | 2019 | 1 |
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Note that an individual publication can be assigned to more than one field. As a result, the publication counts in this graph might add up to more than the number of publications the person has written.
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