Koh Fujinaga, PhD

Associate Adjunct Professor

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.

Education
Postdoctoral Studies, - Graduate Division, University of California, San Francisco
Publications

  1. Kuzmina A, Sadhu L, Hasanuzzaman M, Fujinaga K, Schwartz JC, Fackler OT, Taube R. Direct and indirect effects of CYTOR lncRNA regulate HIV gene expression. PLoS pathogens 2024. PMID: 38662769


  2. Li Y, Liu X, Fujinaga K, Gross JD, Frankel AD. Enhanced NF-κB activation via HIV-1 Tat-TRAF6 cross-talk. Science advances 2024. PMID: 38241362


  3. Fujinaga K, Huang F, Peterlin BM. P-TEFb: The master regulator of transcription elongation. Molecular cell 2023. PMID: 36599353


  4. Huang F, Yao W, Sun B, Fujinaga K. Corrigendum to 'DCAF1 inhibits the NF-?B pathway by targeting p65'[Immunology Letters 249 (2022) 33-42]. Immunology letters 2022. PMID: 36280456


  5. Huang F, Yao W, Sun B, Fujinaga K. DCAF1 inhibits the NF-?B pathway by targeting p65. Immunology letters 2022. PMID: 36055411


  6. Huang F, Feng Y, Peterlin BM, Fujinaga K. P-TEFb is degraded by Siah1/2 in quiescent cells. 2022. PMID: 35524561


  7. Huang F, Nguyen TT, Echeverria I, Ramachandran R, Cary DC, Paculova H, Sali A, Weiss A, Peterlin BM, Fujinaga K. Reversible phosphorylation of cyclin T1 promotes assembly and stability of P-TEFb. 2021. PMID: 34821217


  8. Fujinaga K, Cary DC. Experimental Systems for Measuring HIV Latency and Reactivation. Viruses 2020. PMID: 33182414


  9. Kong W, Biswas A, Zhou D, Fiches G, Fujinaga K, Santoso N, Zhu J. Nucleolar protein NOP2/NSUN1 suppresses HIV-1 transcription and promotes viral latency by competing with Tat for TAR binding and methylation. PLoS pathogens 2020. PMID: 32176734


  10. Fujinaga K. P-TEFb as A Promising Therapeutic Target. Molecules (Basel, Switzerland) 2020. PMID: 32075058


  11. Krasnopolsky S, Marom L, Victor RA, Kuzmina A, Schwartz JC, Fujinaga K, Taube R. Fused in sarcoma silences HIV gene transcription and maintains viral latency through suppressing AFF4 gene activation. Retrovirology 2019. PMID: 31238957


  12. 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. P-TEFb Activation by RBM7 Shapes a Pro-survival Transcriptional Response to Genotoxic Stress. Molecular cell 2019. PMID: 30824372


  13. Leoz M, Kukanja P, Luo Z, Huang F, Cary DC, Peterlin BM, Fujinaga K. HEXIM1-Tat chimera inhibits HIV-1 replication. PLoS pathogens 2018. PMID: 30395647


  14. Asamitsu K, Fujinaga K, Okamoto T. HIV Tat/P-TEFb Interaction: A Potential Target for Novel Anti-HIV Therapies. Molecules (Basel, Switzerland) 2018. PMID: 29673219


  15. Huang F, Shao W, Fujinaga K, Peterlin BM. Bromodomain-containing protein 4-independent transcriptional activation by autoimmune regulator (AIRE) and NF-?B. The Journal of biological chemistry 2018. PMID: 29463681


  16. Contreras-Galindo R, Dube D, Fujinaga K, Kaplan MH, Markovitz DM. Susceptibility of Human Endogenous Retrovirus Type K to Reverse Transcriptase Inhibitors. Journal of virology 2017. PMID: 28931682


  17. Peterlin BM, Liu P, Wang X, Cary D, Shao W, Leoz M, Hong T, Pan T, Fujinaga K. Hili Inhibits HIV Replication in Activated T Cells. Journal of virology 2017. PMID: 28331090


  18. Cary DC, Fujinaga K, Peterlin BM. Euphorbia Kansui Reactivates Latent HIV. PloS one 2016. PMID: 27977742


  19. Shao W, Zumer K, Fujinaga K, Peterlin BM. FBXO3 Protein Promotes Ubiquitylation and Transcriptional Activity of AIRE (Autoimmune Regulator). The Journal of biological chemistry 2016. PMID: 27365398


  20. 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. Stress from Nucleotide Depletion Activates the Transcriptional Regulator HEXIM1 to Suppress Melanoma. Molecular cell 2016. PMID: 27058786


  21. Barboric M, Fujinaga K. The two sides of Tat. eLife 2016. PMID: 26783762


  22. Cary DC, Fujinaga K, Peterlin BM. Molecular mechanisms of HIV latency. The Journal of clinical investigation 2016. PMID: 26731470


  23. Pak V, Eifler TT, Jäger S, Krogan NJ, Fujinaga K, Peterlin BM. CDK11 in TREX/THOC Regulates HIV mRNA 3' End Processing. Cell host & microbe 2015. PMID: 26567509


  24. 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. 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 pathogens 2015. PMID: 26225566


  25. Fujinaga K, Luo Z, Schaufele F, Peterlin BM. Visualization of positive transcription elongation factor b (P-TEFb) activation in living cells. The Journal of biological chemistry 2014. PMID: 25492871


  26. Eifler TT, Shao W, Bartholomeeusen K, Fujinaga K, Jäger S, Johnson JR, Luo Z, Krogan NJ, Peterlin BM. Cyclin-dependent kinase 12 increases 3' end processing of growth factor-induced c-FOS transcripts. Volume 35 of Issue 2. Molecular and cellular biology 2014. PMID: 25384976


  27. Fujinaga K, Luo Z, Peterlin BM. Genetic analysis of the structure and function of 7SK small nuclear ribonucleoprotein (snRNP) in cells. The Journal of biological chemistry 2014. PMID: 24917669


  28. Jadlowsky JK, Wong JY, Graham AC, Dobrowolski C, Devor RL, Adams MD, Fujinaga K, Karn J. 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. Molecular and cellular biology 2014. PMID: 24636995


  29. Liu P, Xiang Y, Fujinaga K, Bartholomeeusen K, Nilson KA, Price DH, Peterlin BM. Release of positive transcription elongation factor b (P-TEFb) from 7SK small nuclear ribonucleoprotein (snRNP) activates hexamethylene bisacetamide-inducible protein (HEXIM1) transcription. The Journal of biological chemistry 2014. PMID: 24515107


  30. Koen Bartholomeeusen, Yanhui Xiang, Koh Fujinaga, B. Matija Peterlin. 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. PMID:


  31. Bartholomeeusen K, Fujinaga K, Xiang Y, Peterlin BM. Histone deacetylase inhibitors (HDACis) that release the positive transcription elongation factor b (P-TEFb) from its inhibitory complex also activate HIV transcription. The Journal of biological chemistry 2013. PMID: 23539624


  32. Bartholomeeusen K, Xiang Y, Fujinaga K, Peterlin BM. 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. The Journal of biological chemistry 2012. PMID: 22952229


  33. Fujinaga K, Barboric M, Li Q, Luo Z, Price DH, Peterlin BM. PKC phosphorylates HEXIM1 and regulates P-TEFb activity. Nucleic acids research 2012. PMID: 22821562


  34. Kuzmina A, Hadad U, Fujinaga K, Taube R. Functional characterization of a human cyclin T1 mutant reveals a different binding surface for Tat and HEXIM1. Virology 2012. PMID: 22342181


  35. Toossi Z, Wu M, Hirsch CS, Mayanja-Kizza H, Baseke J, Aung H, Canaday DH, Fujinaga K. 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 research and human retroviruses 2011. PMID: 21453127


  36. Van Grol J, Subauste C, Andrade RM, Fujinaga K, Nelson J, Subauste CS. HIV-1 inhibits autophagy in bystander macrophage/monocytic cells through Src-Akt and STAT3. PloS one 2010. PMID: 20661303


  37. Imai K, Asamitsu K, Victoriano AF, Cueno ME, Fujinaga K, Okamoto T. Cyclin T1 stabilizes expression levels of HIV-1 Tat in cells. The FEBS journal 2009. PMID: 20064163


  38. Jadlowsky JK, Nojima M, Okamoto T, Fujinaga K. Dominant negative mutant cyclin T1 proteins that inhibit HIV transcription by forming a kinase inactive complex with Tat. The Journal of general virology 2008. PMID: 18931076


  39. Ogba N, Chaplin LJ, Doughman YQ, Fujinaga K, Montano MM. HEXIM1 regulates 17beta-estradiol/estrogen receptor-alpha-mediated expression of cyclin D1 in mammary cells via modulation of P-TEFb. Cancer research 2008. PMID: 18757415


  40. Nojima M, Huang Y, Tyagi M, Kao HY, Fujinaga K. The positive transcription elongation factor b is an essential cofactor for the activation of transcription by myocyte enhancer factor 2. Journal of molecular biology 2008. PMID: 18662700


  41. Jadlowsky JK, Nojima M, Schulte A, Geyer M, Okamoto T, Fujinaga K. Dominant negative mutant cyclin T1 proteins inhibit HIV transcription by specifically degrading Tat. Retrovirology 2008. PMID: 18620576


  42. Anand K, Schulte A, Fujinaga K, Scheffzek K, Geyer M. Cyclin box structure of the P-TEFb subunit cyclin T1 derived from a fusion complex with EIAV tat. Journal of molecular biology 2007. PMID: 17540406


  43. Wittmann BM, Fujinaga K, Deng H, Ogba N, Montano MM. 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. PMID: 15940264


  44. Fujinaga K, Irwin D, Huang Y, Taube R, Kurosu T, Peterlin BM. Dynamics of human immunodeficiency virus transcription: P-TEFb phosphorylates RD and dissociates negative effectors from the transactivation response element. Molecular and cellular biology 2004. PMID: 14701750


  45. Fujinaga K, Irwin D, Taube R, Zhang F, Geyer M, Peterlin BM. A minimal chimera of human cyclin T1 and tat binds TAR and activates human immunodeficiency virus transcription in murine cells. Journal of virology 2002. PMID: 12438619


  46. Fujinaga K, Irwin D, Geyer M, Peterlin BM. Optimized chimeras between kinase-inactive mutant Cdk9 and truncated cyclin T1 proteins efficiently inhibit Tat transactivation and human immunodeficiency virus gene expression. Journal of virology 2002. PMID: 12368330


  47. Tobiume M, Fujinaga K, Suzuki S, Komoto S, Mukai T, Ikuta K. 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 research and human retroviruses 2002. PMID: 11958689


  48. Lin X, Taube R, Fujinaga K, Peterlin BM. P-TEFb containing cyclin K and Cdk9 can activate transcription via RNA. The Journal of biological chemistry 2002. PMID: 11884399


  49. Lind KE, Du Z, Fujinaga K, Peterlin BM, James TL. Structure-based computational database screening, in vitro assay, and NMR assessment of compounds that target TAR RNA. Chemistry & biology 2002. PMID: 11880033


  50. Taube R, Lin X, Irwin D, Fujinaga K, Peterlin BM. Interaction between P-TEFb and the C-terminal domain of RNA polymerase II activates transcriptional elongation from sites upstream or downstream of target genes. Molecular and cellular biology 2002. PMID: 11739744


  51. Barboric M, Taube R, Nekrep N, Fujinaga K, Peterlin BM. Binding of Tat to TAR and recruitment of positive transcription elongation factor b occur independently in bovine immunodeficiency virus. Journal of virology 2000. PMID: 10846086


  52. Taube R, Fujinaga K, Irwin D, Wimmer J, Geyer M, Peterlin BM. Interactions between equine cyclin T1, Tat, and TAR are disrupted by a leucine-to-valine substitution found in human cyclin T1. Journal of virology 2000. PMID: 10623752


  53. Taube R, Fujinaga K, Wimmer J, Barboric M, Peterlin BM. Tat transactivation: a model for the regulation of eukaryotic transcriptional elongation. Virology 1999. PMID: 10562489


  54. Wimmer J, Fujinaga K, Taube R, Cujec TP, Zhu Y, Peng J, Price DH, Peterlin BM. Interactions between Tat and TAR and human immunodeficiency virus replication are facilitated by human cyclin T1 but not cyclins T2a or T2b. Virology 1999. PMID: 10049833


  55. Fujinaga K, Taube R, Wimmer J, Cujec TP, Peterlin BM. 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. Proceedings of the National Academy of Sciences of the United States of America 1999. PMID: 9990016


  56. Fujinaga K, Cujec TP, Peng J, Garriga J, Price DH, Graña X, Peterlin BM. The ability of positive transcription elongation factor B to transactivate human immunodeficiency virus transcription depends on a functional kinase domain, cyclin T1, and Tat. Journal of virology 1998. PMID: 9696809


  57. Cujec TP, Okamoto H, Fujinaga K, Meyer J, Chamberlin H, Morgan DO, Peterlin BM. The HIV transactivator TAT binds to the CDK-activating kinase and activates the phosphorylation of the carboxy-terminal domain of RNA polymerase II. Genes & development 1997. PMID: 9334327