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Koh Fujinaga, PhD

Title(s)Assistant Professor, Medicine
SchoolSchool of Medicine
Address533 Parnassus Avenue
San Francisco CA 94117
Phone415-502-9614
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    Collapse Biography 
    Collapse Education and Training
    University of California, San FranciscoPostdoctoral StudiesGraduate Division

    Collapse Overview 
    Collapse Overview
    My main research interest is understanding the regulatory mechanism of eukaryotic gene expression. I have studied HIV transcription as a model system. However, my research topics are not limited to HIV and AIDS. The elongation control of HIV transcritpion which I have been studying during the past two decades is now recognized as a common regulatory mechanism in most cellular gene transcription. Since transcriptional regulation plays a central role in most biological pathways and diseases, I began to study the mechanisms of transcriptional regulation and misregulation in various diseases including cardiac hypertrophy, cancers such as breast cancer, leukemia and lymphoma, and autoimmune and inflammatory diseases.

    Collapse Research 
    Collapse Research Activities and Funding
    Anti-HIV effects by human Piwi proteins
    NIH/NIAID R56AI136683Jul 4, 2018 - Jun 30, 2019
    Role: Principal Investigator
    HIV transcriptome analysis during viral latency
    NIH/NIAID R21AI127274Aug 8, 2016 - Jul 31, 2018
    Role: Principal Investigator
    Roles of NELF on HIV replication and viral latency
    NIH/NIAID R21AI062516Sep 30, 2004 - Aug 31, 2007
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Nucleolar protein NOP2/NSUN1 suppresses HIV-1 transcription and promotes viral latency by competing with Tat for TAR binding and methylation. PLoS Pathog. 2020 03; 16(3):e1008430. Kong W, Biswas A, Zhou D, Fiches G, Fujinaga K, Santoso N, Zhu J. PMID: 32176734.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    2. P-TEFb as A Promising Therapeutic Target. Molecules. 2020 Feb 14; 25(4). Fujinaga K. PMID: 32075058.
      View in: PubMed   Mentions:    Fields:    
    3. Fused in sarcoma silences HIV gene transcription and maintains viral latency through suppressing AFF4 gene activation. Retrovirology. 2019 06 25; 16(1):16. Krasnopolsky S, Marom L, Victor RA, Kuzmina A, Schwartz JC, Fujinaga K, Taube R. PMID: 31238957.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    4. P-TEFb Activation by RBM7 Shapes a Pro-survival Transcriptional Response to Genotoxic Stress. Mol Cell. 2019 04 18; 74(2):254-267.e10. Bugai A, Quaresma AJC, Friedel CC, Lenasi T, Düster R, Sibley CR, Fujinaga K, Kukanja P, Hennig T, Blasius M, Geyer M, Ule J, Dölken L, Barboric M. PMID: 30824372.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    5. HEXIM1-Tat chimera inhibits HIV-1 replication. PLoS Pathog. 2018 11; 14(11):e1007402. Leoz M, Kukanja P, Luo Z, Huang F, Cary DC, Peterlin BM, Fujinaga K. PMID: 30395647.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    6. HIV Tat/P-TEFb Interaction: A Potential Target for Novel Anti-HIV Therapies. Molecules. 2018 Apr 17; 23(4). Asamitsu K, Fujinaga K, Okamoto T. PMID: 29673219.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    7. Bromodomain-containing protein 4-independent transcriptional activation by autoimmune regulator (AIRE) and NF-?B. J Biol Chem. 2018 04 06; 293(14):4993-5004. Huang F, Shao W, Fujinaga K, Peterlin BM. PMID: 29463681.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    8. Susceptibility of Human Endogenous Retrovirus Type K to Reverse Transcriptase Inhibitors. J Virol. 2017 12 01; 91(23). Contreras-Galindo R, Dube D, Fujinaga K, Kaplan MH, Markovitz DM. PMID: 28931682.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    9. Hili Inhibits HIV Replication in Activated T Cells. J Virol. 2017 06 01; 91(11). Peterlin BM, Liu P, Wang X, Cary D, Shao W, Leoz M, Hong T, Pan T, Fujinaga K. PMID: 28331090.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    10. Euphorbia Kansui Reactivates Latent HIV. PLoS One. 2016; 11(12):e0168027. Cary DC, Fujinaga K, Peterlin BM. PMID: 27977742.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimalsCells
    11. FBXO3 Protein Promotes Ubiquitylation and Transcriptional Activity of AIRE (Autoimmune Regulator). J Biol Chem. 2016 08 19; 291(34):17953-63. Shao W, Zumer K, Fujinaga K, Peterlin BM. PMID: 27365398.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansAnimalsCells
    12. Stress from Nucleotide Depletion Activates the Transcriptional Regulator HEXIM1 to Suppress Melanoma. Mol Cell. 2016 Apr 07; 62(1):34-46. Tan JL, Fogley RD, Flynn RA, Ablain J, Yang S, Saint-André V, Fan ZP, Do BT, Laga AC, Fujinaga K, Santoriello C, Greer CB, Kim YJ, Clohessy JG, Bothmer A, Pandell N, Avagyan S, Brogie JE, van Rooijen E, Hagedorn EJ, Shyh-Chang N, White RM, Price DH, Pandolfi PP, Peterlin BM, Zhou Y, Kim TH, Asara JM, Chang HY, Young RA, Zon LI. PMID: 27058786.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansAnimalsCells
    13. The two sides of Tat. Elife. 2016 Jan 19; 5:e12686. Barboric M, Fujinaga K. PMID: 26783762.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    14. Molecular mechanisms of HIV latency. J Clin Invest. 2016 Feb; 126(2):448-54. Cary DC, Fujinaga K, Peterlin BM. PMID: 26731470.
      View in: PubMed   Mentions: 32     Fields:    Translation:HumansAnimalsCells
    15. CDK11 in TREX/THOC Regulates HIV mRNA 3' End Processing. Cell Host Microbe. 2015 Nov 11; 18(5):560-70. Pak V, Eifler TT, Jäger S, Krogan NJ, Fujinaga K, Peterlin BM. PMID: 26567509.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansCells
    16. An In-Depth Comparison of Latency-Reversing Agent Combinations in Various In Vitro and Ex Vivo HIV-1 Latency Models Identified Bryostatin-1+JQ1 and Ingenol-B+JQ1 to Potently Reactivate Viral Gene Expression. PLoS Pathog. 2015 Jul; 11(7):e1005063. Darcis G, Kula A, Bouchat S, Fujinaga K, Corazza F, Ait-Ammar A, Delacourt N, Melard A, Kabeya K, Vanhulle C, Van Driessche B, Gatot JS, Cherrier T, Pianowski LF, Gama L, Schwartz C, Vila J, Burny A, Clumeck N, Moutschen M, De Wit S, Peterlin BM, Rouzioux C, Rohr O, Van Lint C. PMID: 26225566.
      View in: PubMed   Mentions: 85     Fields:    Translation:HumansCells
    17. Visualization of positive transcription elongation factor b (P-TEFb) activation in living cells. J Biol Chem. 2015 Jan 16; 290(3):1829-36. Fujinaga K, Luo Z, Schaufele F, Peterlin BM. PMID: 25492871.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    18. Cyclin-dependent kinase 12 increases 3' end processing of growth factor-induced c-FOS transcripts. Mol Cell Biol. 2015 Jan; 35(2):468-78. Eifler TT, Shao W, Bartholomeeusen K, Fujinaga K, Jäger S, Johnson JR, Luo Z, Krogan NJ, Peterlin BM. PMID: 25384976.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansCells
    19. Genetic analysis of the structure and function of 7SK small nuclear ribonucleoprotein (snRNP) in cells. J Biol Chem. 2014 Jul 25; 289(30):21181-90. Fujinaga K, Luo Z, Peterlin BM. PMID: 24917669.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCells
    20. Negative elongation factor is required for the maintenance of proviral latency but does not induce promoter-proximal pausing of RNA polymerase II on the HIV long terminal repeat. Mol Cell Biol. 2014 Jun; 34(11):1911-28. Jadlowsky JK, Wong JY, Graham AC, Dobrowolski C, Devor RL, Adams MD, Fujinaga K, Karn J. PMID: 24636995.
      View in: PubMed   Mentions: 39     Fields:    Translation:HumansCells
    21. Release of positive transcription elongation factor b (P-TEFb) from 7SK small nuclear ribonucleoprotein (snRNP) activates hexamethylene bisacetamide-inducible protein (HEXIM1) transcription. J Biol Chem. 2014 Apr 04; 289(14):9918-25. Liu P, Xiang Y, Fujinaga K, Bartholomeeusen K, Nilson KA, Price DH, Peterlin BM. PMID: 24515107.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansCells
    22. Bromodomain and extra-terminal (BET) bromodomain inhibition activate transcription via transient release of positive transcription elongation factor b (P-TEFb) from 7SK small nuclear ribonucleoprotein. Journal of Biological Chemistry. 2013 Apr 26; 288(17):12214-12214. Koen Bartholomeeusen, Yanhui Xiang, Koh Fujinaga, B. Matija Peterlin. .
      View in: Publisher Site   Mentions:
    23. Histone deacetylase inhibitors (HDACis) that release the positive transcription elongation factor b (P-TEFb) from its inhibitory complex also activate HIV transcription. J Biol Chem. 2013 May 17; 288(20):14400-7. Bartholomeeusen K, Fujinaga K, Xiang Y, Peterlin BM. PMID: 23539624.
      View in: PubMed   Mentions: 40     Fields:    Translation:HumansCells
    24. Bromodomain and extra-terminal (BET) bromodomain inhibition activate transcription via transient release of positive transcription elongation factor b (P-TEFb) from 7SK small nuclear ribonucleoprotein. J Biol Chem. 2012 Oct 19; 287(43):36609-16. Bartholomeeusen K, Xiang Y, Fujinaga K, Peterlin BM. PMID: 22952229.
      View in: PubMed   Mentions: 85     Fields:    Translation:HumansCells
    25. PKC phosphorylates HEXIM1 and regulates P-TEFb activity. Nucleic Acids Res. 2012 Oct; 40(18):9160-70. Fujinaga K, Barboric M, Li Q, Luo Z, Price DH, Peterlin BM. PMID: 22821562.
      View in: PubMed   Mentions: 26     Fields:    Translation:HumansCells
    26. Functional characterization of a human cyclin T1 mutant reveals a different binding surface for Tat and HEXIM1. Virology. 2012 May 10; 426(2):152-61. Kuzmina A, Hadad U, Fujinaga K, Taube R. PMID: 22342181.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    27. Activation of P-TEFb at sites of dual HIV/TB infection, and inhibition of MTB-induced HIV transcriptional activation by the inhibitor of CDK9, Indirubin-3'-monoxime. AIDS Res Hum Retroviruses. 2012 Feb; 28(2):182-7. Toossi Z, Wu M, Hirsch CS, Mayanja-Kizza H, Baseke J, Aung H, Canaday DH, Fujinaga K. PMID: 21453127.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    28. HIV-1 inhibits autophagy in bystander macrophage/monocytic cells through Src-Akt and STAT3. PLoS One. 2010 Jul 22; 5(7):e11733. Van Grol J, Subauste C, Andrade RM, Fujinaga K, Nelson J, Subauste CS. PMID: 20661303.
      View in: PubMed   Mentions: 49     Fields:    Translation:HumansAnimalsCells
    29. Cyclin T1 stabilizes expression levels of HIV-1 Tat in cells. FEBS J. 2009 Dec; 276(23):7124-33. Imai K, Asamitsu K, Victoriano AF, Cueno ME, Fujinaga K, Okamoto T. PMID: 20064163.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    30. Dominant negative mutant cyclin T1 proteins that inhibit HIV transcription by forming a kinase inactive complex with Tat. J Gen Virol. 2008 Nov; 89(Pt 11):2783-2787. Jadlowsky JK, Nojima M, Okamoto T, Fujinaga K. PMID: 18931076.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    31. HEXIM1 regulates 17beta-estradiol/estrogen receptor-alpha-mediated expression of cyclin D1 in mammary cells via modulation of P-TEFb. Cancer Res. 2008 Sep 01; 68(17):7015-24. Ogba N, Chaplin LJ, Doughman YQ, Fujinaga K, Montano MM. PMID: 18757415.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansAnimalsCells
    32. The positive transcription elongation factor b is an essential cofactor for the activation of transcription by myocyte enhancer factor 2. J Mol Biol. 2008 Oct 03; 382(2):275-87. Nojima M, Huang Y, Tyagi M, Kao HY, Fujinaga K. PMID: 18662700.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansAnimalsCells
    33. Dominant negative mutant cyclin T1 proteins inhibit HIV transcription by specifically degrading Tat. Retrovirology. 2008 Jul 11; 5:63. Jadlowsky JK, Nojima M, Schulte A, Geyer M, Okamoto T, Fujinaga K. PMID: 18620576.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansAnimalsCells
    34. Cyclin box structure of the P-TEFb subunit cyclin T1 derived from a fusion complex with EIAV tat. J Mol Biol. 2007 Jul 27; 370(5):826-36. Anand K, Schulte A, Fujinaga K, Scheffzek K, Geyer M. PMID: 17540406.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimalsCells
    35. The breast cell growth inhibitor, estrogen down regulated gene 1, modulates a novel functional interaction between estrogen receptor alpha and transcriptional elongation factor cyclin T1. Oncogene. 2005 Aug 25; 24(36):5576-88. Wittmann BM, Fujinaga K, Deng H, Ogba N, Montano MM. PMID: 15940264.
      View in: PubMed   Mentions: 45     Fields:    Translation:HumansAnimalsCells
    36. Dynamics of human immunodeficiency virus transcription: P-TEFb phosphorylates RD and dissociates negative effectors from the transactivation response element. Mol Cell Biol. 2004 Jan; 24(2):787-95. Fujinaga K, Irwin D, Huang Y, Taube R, Kurosu T, Peterlin BM. PMID: 14701750.
      View in: PubMed   Mentions: 131     Fields:    Translation:HumansCells
    37. A minimal chimera of human cyclin T1 and tat binds TAR and activates human immunodeficiency virus transcription in murine cells. J Virol. 2002 Dec; 76(24):12934-9. Fujinaga K, Irwin D, Taube R, Zhang F, Geyer M, Peterlin BM. PMID: 12438619.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansAnimalsCells
    38. Optimized chimeras between kinase-inactive mutant Cdk9 and truncated cyclin T1 proteins efficiently inhibit Tat transactivation and human immunodeficiency virus gene expression. J Virol. 2002 Nov; 76(21):10873-81. Fujinaga K, Irwin D, Geyer M, Peterlin BM. PMID: 12368330.
      View in: PubMed   Mentions: 12     Fields:    Translation:AnimalsCells
    39. Extracellular Nef protein activates signal transduction pathway from Ras to mitogen-activated protein kinase cascades that leads to activation of human immunodeficiency virus from latency. AIDS Res Hum Retroviruses. 2002 Apr 10; 18(6):461-7. Tobiume M, Fujinaga K, Suzuki S, Komoto S, Mukai T, Ikuta K. PMID: 11958689.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    40. P-TEFb containing cyclin K and Cdk9 can activate transcription via RNA. J Biol Chem. 2002 May 10; 277(19):16873-8. Lin X, Taube R, Fujinaga K, Peterlin BM. PMID: 11884399.
      View in: PubMed   Mentions: 26     Fields:    Translation:HumansCells
    41. Structure-based computational database screening, in vitro assay, and NMR assessment of compounds that target TAR RNA. Chem Biol. 2002 Feb; 9(2):185-93. Lind KE, Du Z, Fujinaga K, Peterlin BM, James TL. PMID: 11880033.
      View in: PubMed   Mentions: 36     Fields:    Translation:HumansCells
    42. Interaction between P-TEFb and the C-terminal domain of RNA polymerase II activates transcriptional elongation from sites upstream or downstream of target genes. Mol Cell Biol. 2002 Jan; 22(1):321-31. Taube R, Lin X, Irwin D, Fujinaga K, Peterlin BM. PMID: 11739744.
      View in: PubMed   Mentions: 50     Fields:    Translation:HumansAnimalsCells
    43. Binding of Tat to TAR and recruitment of positive transcription elongation factor b occur independently in bovine immunodeficiency virus. J Virol. 2000 Jul; 74(13):6039-44. Barboric M, Taube R, Nekrep N, Fujinaga K, Peterlin BM. PMID: 10846086.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansAnimalsCells
    44. Interactions between equine cyclin T1, Tat, and TAR are disrupted by a leucine-to-valine substitution found in human cyclin T1. J Virol. 2000 Jan; 74(2):892-8. Taube R, Fujinaga K, Irwin D, Wimmer J, Geyer M, Peterlin BM. PMID: 10623752.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansAnimalsCells
    45. Tat transactivation: a model for the regulation of eukaryotic transcriptional elongation. Virology. 1999 Nov 25; 264(2):245-53. Taube R, Fujinaga K, Wimmer J, Barboric M, Peterlin BM. PMID: 10562489.
      View in: PubMed   Mentions: 51     Fields:    Translation:HumansAnimalsCells
    46. Interactions between Tat and TAR and human immunodeficiency virus replication are facilitated by human cyclin T1 but not cyclins T2a or T2b. Virology. 1999 Mar 01; 255(1):182-9. Wimmer J, Fujinaga K, Taube R, Cujec TP, Zhu Y, Peng J, Price DH, Peterlin BM. PMID: 10049833.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansAnimalsCells
    47. Interactions between human cyclin T, Tat, and the transactivation response element (TAR) are disrupted by a cysteine to tyrosine substitution found in mouse cyclin T. Proc Natl Acad Sci U S A. 1999 Feb 16; 96(4):1285-90. Fujinaga K, Taube R, Wimmer J, Cujec TP, Peterlin BM. PMID: 9990016.
      View in: PubMed   Mentions: 57     Fields:    Translation:HumansAnimalsCells
    48. The ability of positive transcription elongation factor B to transactivate human immunodeficiency virus transcription depends on a functional kinase domain, cyclin T1, and Tat. J Virol. 1998 Sep; 72(9):7154-9. Fujinaga K, Cujec TP, Peng J, Garriga J, Price DH, Graña X, Peterlin BM. PMID: 9696809.
      View in: PubMed   Mentions: 73     Fields:    Translation:HumansCells
    49. The HIV transactivator TAT binds to the CDK-activating kinase and activates the phosphorylation of the carboxy-terminal domain of RNA polymerase II. Genes Dev. 1997 Oct 15; 11(20):2645-57. Cujec TP, Okamoto H, Fujinaga K, Meyer J, Chamberlin H, Morgan DO, Peterlin BM. PMID: 9334327.
      View in: PubMed   Mentions: 80     Fields:    Translation:HumansAnimalsCells