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Tariq Rana

Title(s)Professor, Pediatrics
SchoolHealth Sciences
Phone858-246-1100
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    Collapse Overview 
    Collapse Overview
    RNA Biology and Immunobiology

    We are a multidisciplinary laboratory focused on discovering fundamental mechanisms of RNA biology that regulate the immune response to viral infections and cancer, and the host response to immunotherapy. We are located in the School of Medicine at the University of California, San Diego, La Jolla, California. The lab is also associated with the Department of Pediatrics, Division of Genetics, Institute for Genomic Medicine, Moores Cancer Center, Center for Drug Discovery Innovation, and the Biomedical Sciences Program of UCSD.

    We are investigating the structure and function of RNA-associated cellular machineries involved in immune regulation during the host response to viral infection and cancer, as well as to immunotherapy. Our team has helped to uncover numerous functions of regulatory RNA assemblies in gene silencing, stem cell biology, cancer, immunity, and host–pathogen interactions. In addition, our reports describing genome-wide dynamics of m6A modification of both human and viral RNA during infection with HIV and Zika virus pioneered the new field of epitranscriptomics in virology and immunology. We employ multidisciplinary approaches involving chemistry and biology and, as part of our commitment to translational research, we routinely collaborate with clinicians. Several of the technologies invented and developed by our group have launched biotech companies and have been used to develop small molecule and biologic therapeutics currently in clinical trials.

    Here are some examples of three distinct yet interconnected projects currently being pursued in our laboratory:
    (1) The recent success of immune checkpoint therapies has transformed our approach to cancer treatment and has galvanized hopes that cures for many types of cancer and, potentially, other diseases are on the horizon. Despite the success of FDA-approved biological therapies targeting CTLA-4 and the PD-L1/PD-1 checkpoints in some cancers, many patients do not respond and the tumors are able to escape therapy. Therefore, we are investigating the fundamental mechanisms that determine whether the host immune system undergoes immune exhaustion leading to tumor evasion or mounts a durable immune response during immunotherapy to various cancers.
    (2) One key aspect of the development of AIDS in HIV-infected individuals is exhaustion of the immune system, resulting in an inability to clear infection. However, it is not clear how HIV induces the reprogramming of immune cell populations that culminates in exhaustion. We are currently deciphering the molecular events underlying T cell exhaustion in diverse subsets of HIV-infected individuals.
    (3) RNA epigenetics or epitranscriptomics is an emerging field focused on nucleotide modifications in RNA. One such modification is N6-methylation of adenosine (m6A), which plays important roles in regulating RNA metabolism and gene expression. We are interested in understanding how RNA modifications affect the immune system during viral infections and in the development of cancer, primarily glioblastoma.

    As a translational research lab, a crucially important aspect of our work is to design and develop novel therapies based on our research findings. The projects outlined above will undoubtedly identify fundamental processes that regulate the immune system in physiological and pathological situations. The knowledge gained and technologies generated during these studies could provide new opportunities to develop novel ‘personalized medicines’ such as disease-specific rejuvenated T cells, as well as therapies with broader uses such as small molecule and biological therapies and vaccines. Our goal is to develop interventions that enable the patient’s immune system to mount durable responses to viral infections and cancer, thereby helping to transform the fields of oncology and virology.

    We and our collaborators currently have projects ongoing in glioblastoma, HIV/AIDS, Zika virus, neurodegenerative disease, drug addiction, cancer immunotherapy, and regenerative medicine.

    Collapse Research 
    Collapse Research Activities and Funding
    Identification and Regulation of RNA Modification by HIV infection and Methamphetamine
    NIH/NIDA R01DA046171Apr 1, 2018 - Jan 31, 2023
    Role: Principal Investigator
    Regulation of HIV-1 Replication by Cellular IncRNAs
    NIH/NIAID R21AI125103Aug 5, 2016 - Jul 31, 2018
    Role: Principal Investigator
    Modeling HIV/AIDS Associated Neurological Disorders with Human Pluripotent Cells
    NIH/NIDA DP1DA039562Mar 1, 2015 - Jan 31, 2020
    Role: Principal Investigator
    Innate Immune Responses and Vaccines Against Tumor-Associated Herpesviruses
    NIH/NCI P01CA177322Sep 19, 2014 - Aug 31, 2019
    Role: Co-Investigator
    Preclinical Development of HIV-1 Vif Antagonists
    NIH P01MH100942Aug 19, 2013 - Jul 31, 2018
    Role: Co-Investigator
    Regulation of HIV infection by Methamphetamine and non-coding RNAs
    NIH/NIDA R01DA030199Jul 15, 2010 - Feb 28, 2015
    Role: Principal Investigator
    RNAi-Based Therapy of ALS
    NIH/NINDS R01NS060856Aug 5, 2009 - Jul 31, 2012
    Role: Principal Investigator
    Preclinical Development of HIV-1 Vif Antagonists
    NIH U19MH081836Apr 16, 2007 - Mar 31, 2013
    Role: Co-Investigator
    TARGETING HIV VIF PROTEIN
    NIH/NIAID R21AI054181Sep 30, 2002 - Aug 31, 2004
    Role: Principal Investigator
    Targeting Ensembles of Drug Resistant HIV-Protease
    NIH P01GM066524Aug 20, 2002 - Aug 31, 2013
    Role: Co-Investigator
    INHIBITION OF HIV REPLICATION
    NIH/NIAID R01AI045466Jul 1, 2000 - Jun 30, 2004
    Role: Principal Investigator
    INHIBITION OF HIV REPLICATION
    NIH/NIAID R21AI045466Sep 30, 1999 - Sep 30, 2000
    Role: Principal Investigator
    Mechanisms of innate immunity against HIV
    NIH/NIAID R01AI043198Jun 1, 1998 - Jan 31, 2015
    Role: Principal Investigator
    Structure and Function of Ribonucleoprotein Complexes Modulating HIV Replication
    NIH/NIAID R01AI041404Sep 1, 1997 - Jun 30, 2016
    Role: Principal Investigator
    Structure and Function of Ribonucleoprotein Complexes Modulating HIV Replication
    NIH/NIAID R56AI041404Sep 1, 1997 - Aug 31, 2010
    Role: Principal Investigator
    STRUCTURE OF CHEMICALLY MODIFIED TAT-TAR COMPLEX
    NIH/FIC R03TW000702Jul 1, 1996 - Jun 30, 1999
    Role: Principal Investigator
    PROBING TAT TAR INTERACTIONS IN HIV BY CHEMICAL METHODS
    NIH/NIAID K02AI001369Apr 1, 1996 - Mar 31, 2001
    Role: Principal Investigator
    TAT-TAR INTERACTIONS IN HIV PROBED BY CHEMICAL METHODS
    NIH/NIAID R29AI034785Jul 15, 1993 - Jun 30, 1998
    Role: Principal Investigator
    Cancer Center Support Grant (CCSG)
    NIH/NCI P30CA030199Jul 1, 1981 - Apr 30, 2020
    Role: Co-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.
    List All   |   Timeline
    1. Dang JW, Tiwari SK, Qin Y, Rana TM. Genome-wide Integrative Analysis of Zika-Virus-Infected Neuronal Stem Cells Reveals Roles for MicroRNAs in Cell Cycle and Stemness. Cell Rep. 2019 Jun 18; 27(12):3618-3628.e5. PMID: 31216479.
      View in: PubMed
    2. Zhang Q, Chao TC, Patil VS, Qin Y, Tiwari SK, Chiou J, Dobin A, Tsai CM, Li Z, Dang J, Gupta S, Urdahl K, Nizet V, Gingeras TR, Gaulton KJ, Rana TM. The long noncoding RNA ROCKI regulates inflammatory gene expression. EMBO J. 2019 Apr 15; 38(8). PMID: 30918008.
      View in: PubMed
    3. Sharkey M, Sharova N, Mohammed I, Huff SE, Kummetha IR, Singh G, Rana TM, Stevenson M. HIV-1 Escape from Small-Molecule Antagonism of Vif. MBio. 2019 02 26; 10(1). PMID: 30808702.
      View in: PubMed
    4. Lichinchi G, Rana TM. Profiling of N6-Methyladenosine in Zika Virus RNA and Host Cellular mRNA. Methods Mol Biol. 2019; 1870:209-218. PMID: 30539558.
      View in: PubMed
    5. Liu C, Han T, Stachura DL, Wang H, Vaisman BL, Kim J, Klemke RL, Remaley AT, Rana TM, Traver D, Miller YI. Lipoprotein lipase regulates hematopoietic stem progenitor cell maintenance through DHA supply. Nat Commun. 2018 04 03; 9(1):1310. PMID: 29615667.
      View in: PubMed
    6. Yau EH, Rana TM. Next-Generation Sequencing of Genome-Wide CRISPR Screens. Methods Mol Biol. 2018; 1712:203-216. PMID: 29224076.
      View in: PubMed
    7. Yau EH, Kummetha IR, Lichinchi G, Tang R, Zhang Y, Rana TM. Genome-Wide CRISPR Screen for Essential Cell Growth Mediators in Mutant KRAS Colorectal Cancers. Cancer Res. 2017 11 15; 77(22):6330-6339. PMID: 28954733.
      View in: PubMed
    8. Tiwari SK, Dang J, Qin Y, Lichinchi G, Bansal V, Rana TM. Zika virus infection reprograms global transcription of host cells to allow sustained infection. Emerg Microbes Infect. 2017 Apr 26; 6(4):e24. PMID: 28442752.
      View in: PubMed
    9. Xiong XP, Kurthkoti K, Chang KY, Li JL, Ren X, Ni JQ, Rana TM, Zhou R. miR-34 Modulates Innate Immunity and Ecdysone Signaling in Drosophila. PLoS Pathog. 2016 Nov; 12(11):e1006034. PMID: 27893816.
      View in: PubMed
    10. Gong D, Kim YH, Xiao Y, Du Y, Xie Y, Lee KK, Feng J, Farhat N, Zhao D, Shu S, Dai X, Chanda SK, Rana TM, Krogan NJ, Sun R, Wu TT. A Herpesvirus Protein Selectively Inhibits Cellular mRNA Nuclear Export. Cell Host Microbe. 2016 Nov 09; 20(5):642-653. PMID: 27832591.
      View in: PubMed
    11. Han T, Yang CS, Chang KY, Zhang D, Imam FB, Rana TM. Identification of novel genes and networks governing hematopoietic stem cell development. EMBO Rep. 2016 12; 17(12):1814-1828. PMID: 27797851.
      View in: PubMed
    12. Lichinchi G, Zhao BS, Wu Y, Lu Z, Qin Y, He C, Rana TM. Dynamics of Human and Viral RNA Methylation during Zika Virus Infection. Cell Host Microbe. 2016 Nov 09; 20(5):666-673. PMID: 27773536.
      View in: PubMed
    13. Zhou Y, Dang J, Chang KY, Yau E, Aza-Blanc P, Moscat J, Rana TM. miR-1298 Inhibits Mutant KRAS-Driven Tumor Growth by Repressing FAK and LAMB3. Cancer Res. 2016 10 01; 76(19):5777-5787. PMID: 27698189.
      View in: PubMed
    14. Mohammed I, Kummetha IR, Singh G, Sharova N, Lichinchi G, Dang J, Stevenson M, Rana TM. 1,2,3-Triazoles as Amide Bioisosteres: Discovery of a New Class of Potent HIV-1 Vif Antagonists. J Med Chem. 2016 08 25; 59(16):7677-82. PMID: 27509004.
      View in: PubMed
    15. Yang CS, Chang KY, Dang J, Rana TM. Polycomb Group Protein Pcgf6 Acts as a Master Regulator to Maintain Embryonic Stem Cell Identity. Sci Rep. 2016 06 01; 6:26899. PMID: 27247273.
      View in: PubMed
    16. Dang J, Tiwari SK, Lichinchi G, Qin Y, Patil VS, Eroshkin AM, Rana TM. Zika Virus Depletes Neural Progenitors in Human Cerebral Organoids through Activation of the Innate Immune Receptor TLR3. Cell Stem Cell. 2016 08 04; 19(2):258-265. PMID: 27162029.
      View in: PubMed
    17. Johnson TC, Chin MR, Han T, Shen JP, Rana T, Siegel D. Synthesis of Eupalinilide E, a Promoter of Human Hematopoietic Stem and Progenitor Cell Expansion. J Am Chem Soc. 2016 05 11; 138(18):6068-73. PMID: 27096704.
      View in: PubMed
    18. Lichinchi G, Gao S, Saletore Y, Gonzalez GM, Bansal V, Wang Y, Mason CE, Rana TM. Dynamics of the human and viral m(6)A RNA methylomes during HIV-1 infection of T cells. Nat Microbiol. 2016 Feb 22; 1:16011. PMID: 27572442.
      View in: PubMed
    19. Dang J, Rana TM. Enhancing Induced Pluripotent Stem Cell Generation by MicroRNA. Methods Mol Biol. 2016; 1357:71-84. PMID: 25687299.
      View in: PubMed
    20. Sansó M, Levin RS, Lipp JJ, Wang VY, Greifenberg AK, Quezada EM, Ali A, Ghosh A, Larochelle S, Rana TM, Geyer M, Tong L, Shokat KM, Fisher RP. P-TEFb regulation of transcription termination factor Xrn2 revealed by a chemical genetic screen for Cdk9 substrates. Genes Dev. 2016 Jan 01; 30(1):117-31. PMID: 26728557; PMCID: PMC4701974.
    21. McCarroll JA, Dwarte T, Baigude H, Dang J, Yang L, Erlich RB, Kimpton K, Teo J, Sagnella SM, Akerfeldt MC, Liu J, Phillips PA, Rana TM, Kavallaris M. Therapeutic targeting of polo-like kinase 1 using RNA-interfering nanoparticles (iNOPs) for the treatment of non-small cell lung cancer. Oncotarget. 2015 May 20; 6(14):12020-34. PMID: 25557168; PMCID: PMC4494920.
    22. Lin N, Dang J, Rana TM. Haunting the HOXA Locus: Two Faces of lncRNA Regulation. Cell Stem Cell. 2015 May 07; 16(5):449-50. PMID: 25957895.
      View in: PubMed
    23. Baigude H, Rana TM. Strategies to antagonize miRNA functions in vitro and in vivo. Nanomedicine (Lond). 2014 Nov; 9(16):2545-55. PMID: 25490425.
      View in: PubMed
    24. Li Z, Rana TM. Decoding the noncoding: prospective of lncRNA-mediated innate immune regulation. RNA Biol. 2014; 11(8):979-85. PMID: 25482890; PMCID: PMC4615744.
    25. Li Z, Dang J, Chang KY, Rana TM. MicroRNA-mediated regulation of extracellular matrix formation modulates somatic cell reprogramming. RNA. 2014 Dec; 20(12):1900-15. PMID: 25336587.
      View in: PubMed
    26. Han J, Cai J, Borjihan W, Ganbold T, Rana TM, Baigude H. Preparation of novel curdlan nanoparticles for intracellular siRNA delivery. Carbohydr Polym. 2015 Mar 06; 117:324-30. PMID: 25498642; PMCID: PMC4268549.
    27. Yang CS, Chang KY, Rana TM. Genome-wide functional analysis reveals factors needed at the transition steps of induced reprogramming. Cell Rep. 2014 Jul 24; 8(2):327-37. PMID: 25043178.
      View in: PubMed
    28. Li Z, Rana TM. Therapeutic targeting of microRNAs: current status and future challenges. Nat Rev Drug Discov. 2014 Aug; 13(8):622-38. PMID: 25011539.
      View in: PubMed
    29. Sakurai K, Talukdar I, Patil VS, Dang J, Li Z, Chang KY, Lu CC, Delorme-Walker V, Dermardirossian C, Anderson K, Hanein D, Yang CS, Wu D, Liu Y, Rana TM. Kinome-wide functional analysis highlights the role of cytoskeletal remodeling in somatic cell reprogramming. Cell Stem Cell. 2014 Apr 03; 14(4):523-34. PMID: 24702998.
      View in: PubMed
    30. Lin N, Chang KY, Li Z, Gates K, Rana ZA, Dang J, Zhang D, Han T, Yang CS, Cunningham TJ, Head SR, Duester G, Dong PD, Rana TM. An evolutionarily conserved long noncoding RNA TUNA controls pluripotency and neural lineage commitment. Mol Cell. 2014 Mar 20; 53(6):1005-19. PMID: 24530304; PMCID: PMC4010157.
    31. Henzler CM, Li Z, Dang J, Arcila ML, Zhou H, Liu J, Chang KY, Bassett DS, Rana TM, Kosik KS. Staged miRNA re-regulation patterns during reprogramming. Genome Biol. 2013 Dec 31; 14(12):R149. PMID: 24380417; PMCID: PMC4053856.
    32. Li Z, Chao TC, Chang KY, Lin N, Patil VS, Shimizu C, Head SR, Burns JC, Rana TM. The long noncoding RNA THRIL regulates TNFa expression through its interaction with hnRNPL. Proc Natl Acad Sci U S A. 2014 Jan 21; 111(3):1002-7. PMID: 24371310.
      View in: PubMed
    33. Patil VS, Zhou R, Rana TM. Gene regulation by non-coding RNAs. Crit Rev Biochem Mol Biol. 2014 Jan-Feb; 49(1):16-32. PMID: 24164576; PMCID: PMC4721600.
    34. Shen Y, Altman MD, Ali A, Nalam MN, Cao H, Rana TM, Schiffer CA, Tidor B. Testing the substrate-envelope hypothesis with designed pairs of compounds. ACS Chem Biol. 2013 Nov 15; 8(11):2433-41. PMID: 23952265; PMCID: PMC3833293.
    35. Xiong XP, Kurthkoti K, Chang KY, Lichinchi G, De N, Schneemann A, MacRae IJ, Rana TM, Perrimon N, Zhou R. Core small nuclear ribonucleoprotein particle splicing factor SmD1 modulates RNA interference in Drosophila. Proc Natl Acad Sci U S A. 2013 Oct 08; 110(41):16520-5. PMID: 24067655; PMCID: PMC3799365.
    36. Nalam MN, Ali A, Reddy GS, Cao H, Anjum SG, Altman MD, Yilmaz NK, Tidor B, Rana TM, Schiffer CA. Substrate envelope-designed potent HIV-1 protease inhibitors to avoid drug resistance. Chem Biol. 2013 Sep 19; 20(9):1116-24. PMID: 24012370.
      View in: PubMed
    37. Silver NW, King BM, Nalam MN, Cao H, Ali A, Kiran Kumar Reddy GS, Rana TM, Schiffer CA, Tidor B. Efficient Computation of Small-Molecule Configurational Binding Entropy and Free Energy Changes by Ensemble Enumeration. J Chem Theory Comput. 2013 Nov 12; 9(11):5098-5115. PMID: 24250277.
      View in: PubMed
    38. Baigude H, Su J, McCarroll J, Rana TM. In Vivo Delivery of RNAi by Reducible Interfering Nanoparticles (iNOPs). ACS Med Chem Lett. 2013 Aug 08; 4(8):720-723. PMID: 24319542.
      View in: PubMed
    39. Zhou R, Rana TM. RNA-based mechanisms regulating host-virus interactions. Immunol Rev. 2013 May; 253(1):97-111. PMID: 23550641; PMCID: PMC3695692.
    40. Yang CS, Rana TM. Learning the molecular mechanisms of the reprogramming factors: let's start from microRNAs. Mol Biosyst. 2013 Jan 27; 9(1):10-7. PMID: 23037570; PMCID: PMC3933261.
    41. Parai MK, Huggins DJ, Cao H, Nalam MN, Ali A, Schiffer CA, Tidor B, Rana TM. Design, synthesis, and biological and structural evaluations of novel HIV-1 protease inhibitors to combat drug resistance. J Med Chem. 2012 Jul 26; 55(14):6328-41. PMID: 22708897.
      View in: PubMed
    42. Mohammed I, Parai MK, Jiang X, Sharova N, Singh G, Stevenson M, Rana TM. SAR and Lead Optimization of an HIV-1 Vif-APOBEC3G Axis Inhibitor. ACS Med Chem Lett. 2012 Jun 14; 3(6):465-469. PMID: 24533175.
      View in: PubMed
    43. Baigude H, Li Z, Zhou Y, Rana TM. miR-TRAP: a benchtop chemical biology strategy to identify microRNA targets. Angew Chem Int Ed Engl. 2012 Jun 11; 51(24):5880-3. PMID: 22566243; PMCID: PMC3501383.
    44. Ali A, Wang J, Nathans RS, Cao H, Sharova N, Stevenson M, Rana TM. Synthesis and structure-activity relationship studies of HIV-1 virion infectivity factor (Vif) inhibitors that block viral replication. ChemMedChem. 2012 Jul; 7(7):1217-29. PMID: 22555953; PMCID: PMC3517065.
    45. Zhou H, Arcila ML, Li Z, Lee EJ, Henzler C, Liu J, Rana TM, Kosik KS. Deep annotation of mouse iso-miR and iso-moR variation. Nucleic Acids Res. 2012 Jul; 40(13):5864-75. PMID: 22434881; PMCID: PMC3401436.
    46. Li Z, Rana TM. Molecular mechanisms of RNA-triggered gene silencing machineries. Acc Chem Res. 2012 Jul 17; 45(7):1122-31. PMID: 22304792; PMCID: PMC3398549.
    47. O'Brien SK, Knight KL, Rana TM. Phosphorylation of histone H1 by P-TEFb is a necessary step in skeletal muscle differentiation. J Cell Physiol. 2012 Jan; 227(1):383-9. PMID: 21503884; PMCID: PMC3562545.
    48. Li Z, Rana TM. Using microRNAs to enhance the generation of induced pluripotent stem cells. Curr Protoc Stem Cell Biol. 2012; Chapter 4:Unit 4A.4. PMID: 22415842.
      View in: PubMed
    49. Baigude H, Rana TM. Interfering nanoparticles for silencing microRNAs. Methods Enzymol. 2012; 509:339-53. PMID: 22568914; PMCID: PMC3933207.
    50. Li Z, Rana TM. A kinase inhibitor screen identifies small-molecule enhancers of reprogramming and iPS cell generation. Nat Commun. 2012; 3:1085. PMID: 23011139.
      View in: PubMed
    51. Yang CS, Lopez CG, Rana TM. Discovery of nonsteroidal anti-inflammatory drug and anticancer drug enhancing reprogramming and induced pluripotent stem cell generation. Stem Cells. 2011 Oct; 29(10):1528-36. PMID: 21898684; PMCID: PMC3419601.
    52. Yang CS, Li Z, Rana TM. microRNAs modulate iPS cell generation. RNA. 2011 Aug; 17(8):1451-60. PMID: 21693621; PMCID: PMC3153970.
    53. Li Z, Yang CS, Nakashima K, Rana TM. Small RNA-mediated regulation of iPS cell generation. EMBO J. 2011 Mar 02; 30(5):823-34. PMID: 21285944; PMCID: PMC3049216.
    54. Su J, Baigude H, McCarroll J, Rana TM. Silencing microRNA by interfering nanoparticles in mice. Nucleic Acids Res. 2011 Mar; 39(6):e38. PMID: 21212128; PMCID: PMC3064800.
    55. Ali A, Reddy GS, Nalam MN, Anjum SG, Cao H, Schiffer CA, Rana TM. Structure-based design, synthesis, and structure-activity relationship studies of HIV-1 protease inhibitors incorporating phenyloxazolidinones. J Med Chem. 2010 Nov 11; 53(21):7699-708. PMID: 20958050.
      View in: PubMed
    56. Lu CC, Li Z, Chu CY, Feng J, Feng J, Sun R, Rana TM. MicroRNAs encoded by Kaposi's sarcoma-associated herpesvirus regulate viral life cycle. EMBO Rep. 2010 Oct; 11(10):784-90. PMID: 20847741; PMCID: PMC2948186.
    57. Ghosh A, Mukherjee K, Jiang X, Zhou Y, McCarroll J, Qu J, Swain PM, Baigude H, Rana TM. Design and assembly of new nonviral RNAi delivery agents by microwave-assisted quaternization (MAQ) of tertiary amines. Bioconjug Chem. 2010 Sep 15; 21(9):1581-7. PMID: 20722369; PMCID: PMC3012264.
    58. James V, Zhang Y, Foxler DE, de Moor CH, Kong YW, Webb TM, Self TJ, Feng Y, Lagos D, Chu CY, Rana TM, Morley SJ, Longmore GD, Bushell M, Sharp TV. LIM-domain proteins, LIMD1, Ajuba, and WTIP are required for microRNA-mediated gene silencing. Proc Natl Acad Sci U S A. 2010 Jul 13; 107(28):12499-504. PMID: 20616046; PMCID: PMC2906597.
    59. O'Brien SK, Cao H, Nathans R, Ali A, Rana TM. P-TEFb kinase complex phosphorylates histone H1 to regulate expression of cellular and HIV-1 genes. J Biol Chem. 2010 Sep 24; 285(39):29713-20. PMID: 20551309; PMCID: PMC2943301.
    60. Nalam MN, Ali A, Altman MD, Reddy GS, Chellappan S, Kairys V, Ozen A, Cao H, Gilson MK, Tidor B, Rana TM, Schiffer CA. Evaluating the substrate-envelope hypothesis: structural analysis of novel HIV-1 protease inhibitors designed to be robust against drug resistance. J Virol. 2010 May; 84(10):5368-78. PMID: 20237088; PMCID: PMC2863851.
    61. McCarroll J, Baigude H, Yang CS, Rana TM. Nanotubes functionalized with lipids and natural amino acid dendrimers: a new strategy to create nanomaterials for delivering systemic RNAi. Bioconjug Chem. 2010 Jan; 21(1):56-63. PMID: 19957956; PMCID: PMC2814541.
    62. Das S, Pan D, Bera AK, Rana T, Bandyopadhyay S, De S, Das SK, Bhattacharya D, Bandyopadhyay SK. Stress inducible heat shock protein 70: a potent molecular and toxicological signature in arsenic exposed broiler chickens. Mol Biol Rep. 2010 Oct; 37(7):3151-5. PMID: 19826909.
      View in: PubMed
    63. Baigude H, Rana TM. Delivery of therapeutic RNAi by nanovehicles. Chembiochem. 2009 Oct 12; 10(15):2449-54. PMID: 19688785.
      View in: PubMed
    64. Pan D, Bera AK, Das S, Bandyopadhyay S, Rana T, Bandyopadhyay S, Das SK, Bhattacharya D. Use of zinc chloride as alternative stimulant for in vitro study of nitric oxide production pathway in avian splenocyte culture. Mol Biol Rep. 2010 Jun; 37(5):2223-6. PMID: 19690983.
      View in: PubMed
    65. Ali A, Ghosh A, Nathans RS, Sharova N, O'Brien S, Cao H, Stevenson M, Rana TM. Identification of flavopiridol analogues that selectively inhibit positive transcription elongation factor (P-TEFb) and block HIV-1 replication. Chembiochem. 2009 Aug 17; 10(12):2072-80. PMID: 19603446; PMCID: PMC2754223.
    66. Nathans R, Chu CY, Serquina AK, Lu CC, Cao H, Rana TM. Cellular microRNA and P bodies modulate host-HIV-1 interactions. Mol Cell. 2009 Jun 26; 34(6):696-709. PMID: 19560422.
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    67. Bélanger F, Baigude H, Rana TM. U30 of 7SK RNA forms a specific photo-cross-link with Hexim1 in the context of both a minimal RNA-binding site and a fully reconstituted 7SK/Hexim1/P-TEFb ribonucleoprotein complex. J Mol Biol. 2009 Mar 06; 386(4):1094-107. PMID: 19244621; PMCID: PMC2754221.
    68. Jorissen RN, Reddy GS, Ali A, Altman MD, Chellappan S, Anjum SG, Tidor B, Schiffer CA, Rana TM, Gilson MK. Additivity in the analysis and design of HIV protease inhibitors. J Med Chem. 2009 Feb 12; 52(3):737-54. PMID: 19193159; PMCID: PMC2715819.
    69. Nathans R, Cao H, Sharova N, Ali A, Sharkey M, Stranska R, Stevenson M, Rana TM. Small-molecule inhibition of HIV-1 Vif. Nat Biotechnol. 2008 Oct; 26(10):1187-92. PMID: 18806783.
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    70. Cao H, Yang CS, Rana TM. Evolutionary emergence of microRNAs in human embryonic stem cells. PLoS One. 2008 Jul 30; 3(7):e2820. PMID: 18665260; PMCID: PMC2474702.
    71. Chu CY, Rana TM. Potent RNAi by short RNA triggers. RNA. 2008 Sep; 14(9):1714-9. PMID: 18658119.
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    72. Altman MD, Ali A, Reddy GS, Nalam MN, Anjum SG, Cao H, Chellappan S, Kairys V, Fernandes MX, Gilson MK, Schiffer CA, Rana TM, Tidor B. HIV-1 protease inhibitors from inverse design in the substrate envelope exhibit subnanomolar binding to drug-resistant variants. J Am Chem Soc. 2008 May 14; 130(19):6099-113. PMID: 18412349.
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    73. Wang H, Ghosh A, Baigude H, Yang CS, Qiu L, Xia X, Zhou H, Rana TM, Xu Z. Therapeutic gene silencing delivered by a chemically modified small interfering RNA against mutant SOD1 slows amyotrophic lateral sclerosis progression. J Biol Chem. 2008 Jun 06; 283(23):15845-52. PMID: 18367449; PMCID: PMC2414310.
    74. Chu CY, Rana TM. Small RNAs: regulators and guardians of the genome. J Cell Physiol. 2007 Nov; 213(2):412-9. PMID: 17674365.
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    75. Reddy GS, Ali A, Nalam MN, Anjum SG, Cao H, Nathans RS, Schiffer CA, Rana TM. Design and synthesis of HIV-1 protease inhibitors incorporating oxazolidinones as P2/P2' ligands in pseudosymmetric dipeptide isosteres. J Med Chem. 2007 Sep 06; 50(18):4316-28. PMID: 17696512.
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    76. Robb GB, Rana TM. RNA helicase A interacts with RISC in human cells and functions in RISC loading. Mol Cell. 2007 May 25; 26(4):523-37. PMID: 17531811.
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    77. Chellappan S, Kiran Kumar Reddy GS, Ali A, Nalam MN, Anjum SG, Cao H, Kairys V, Fernandes MX, Altman MD, Tidor B, Rana TM, Schiffer CA, Gilson MK. Design of mutation-resistant HIV protease inhibitors with the substrate envelope hypothesis. Chem Biol Drug Des. 2007 May; 69(5):298-313. PMID: 17539822.
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    78. Baigude H, McCarroll J, Yang CS, Swain PM, Rana TM. Design and creation of new nanomaterials for therapeutic RNAi. ACS Chem Biol. 2007 Apr 24; 2(4):237-41. PMID: 17432823.
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    79. Chiu YL, Cao H, Rana TM. Quantitative analysis of RNA-mediated protein-protein interactions in living cells by FRET. Chem Biol Drug Des. 2007 Apr; 69(4):233-9. PMID: 17461970.
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    80. Rana TM. Illuminating the silence: understanding the structure and function of small RNAs. Nat Rev Mol Cell Biol. 2007 Jan; 8(1):23-36. PMID: 17183358.
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    81. Ali A, Reddy GS, Cao H, Anjum SG, Nalam MN, Schiffer CA, Rana TM. Discovery of HIV-1 protease inhibitors with picomolar affinities incorporating N-aryl-oxazolidinone-5-carboxamides as novel P2 ligands. J Med Chem. 2006 Dec 14; 49(25):7342-56. PMID: 17149864.
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    82. Richter SN, Bélanger F, Zheng P, Rana TM. Dynamics of nascent mRNA folding and RNA-protein interactions: an alternative TAR RNA structure is involved in the control of HIV-1 mRNA transcription. Nucleic Acids Res. 2006; 34(15):4278-92. PMID: 16920743; PMCID: PMC1616951.
    83. Chu CY, Rana TM. Translation repression in human cells by microRNA-induced gene silencing requires RCK/p54. PLoS Biol. 2006 Jul; 4(7):e210. PMID: 16756390; PMCID: PMC1475773.
    84. Wichroski MJ, Robb GB, Rana TM. Human retroviral host restriction factors APOBEC3G and APOBEC3F localize to mRNA processing bodies. PLoS Pathog. 2006 May; 2(5):e41. PMID: 16699599; PMCID: PMC1458959.
    85. Cao H, Tamilarasu N, Rana TM. Orientation and affinity of HIV-1 Tat fragments in Tat-TAR complex determined by fluorescence resonance energy transfer. Bioconjug Chem. 2006 Mar-Apr; 17(2):352-8. PMID: 16536465.
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    86. Lee CW, Cao H, Ichiyama K, Rana TM. Design and synthesis of a novel peptidomimetic inhibitor of HIV-1 Tat-TAR interactions: squaryldiamide as a new potential bioisostere of unsubstituted guanidine. Bioorg Med Chem Lett. 2005 Oct 01; 15(19):4243-6. PMID: 16054360.
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    87. Chiu YL, Dinesh CU, Chu CY, Ali A, Brown KM, Cao H, Rana TM. Dissecting RNA-interference pathway with small molecules. Chem Biol. 2005 Jun; 12(6):643-8. PMID: 15975509.
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    88. Brown KM, Chu CY, Rana TM. Target accessibility dictates the potency of human RISC. Nat Struct Mol Biol. 2005 May; 12(5):469-70. PMID: 15852021.
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    89. Lee HK, Cao H, Rana TM. Design, microwave-assisted synthesis, and photophysical properties of small molecule organic antennas for luminescence resonance energy transfer. J Comb Chem. 2005 Mar-Apr; 7(2):279-84. PMID: 15762757.
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    90. Ping YH, Rana TM. Mechanism of site-specific psoralen photoadducts formation in triplex DNA directed by psoralen-conjugated oligonucleotides. Biochemistry. 2005 Feb 22; 44(7):2501-9. PMID: 15709762.
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    91. Robb GB, Brown KM, Khurana J, Rana TM. Specific and potent RNAi in the nucleus of human cells. Nat Struct Mol Biol. 2005 Feb; 12(2):133-7. PMID: 15643423.
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    92. Ping YH, Chu CY, Cao H, Jacque JM, Stevenson M, Rana TM. Modulating HIV-1 replication by RNA interference directed against human transcription elongation factor SPT5. Retrovirology. 2004 Dec 27; 1:46. PMID: 15620346; PMCID: PMC545048.
    93. Wichroski MJ, Ichiyama K, Rana TM. Analysis of HIV-1 viral infectivity factor-mediated proteasome-dependent depletion of APOBEC3G: correlating function and subcellular localization. J Biol Chem. 2005 Mar 04; 280(9):8387-96. PMID: 15537645.
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    94. Chiu YL, Ali A, Chu CY, Cao H, Rana TM. Visualizing a correlation between siRNA localization, cellular uptake, and RNAi in living cells. Chem Biol. 2004 Aug; 11(8):1165-75. PMID: 15324818.
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    95. Zhang L, Rana TM. Solid-phase synthesis of alpha-(2-(benzylthio)-1,4-dihydro-6-methyl-4-p-tolylpyrimidine-5-carboxamido) acids: a new strategy to create diversity in heterocyclic scaffolds. J Comb Chem. 2004 Jul-Aug; 6(4):457-9. PMID: 15244403.
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    96. Lee HK, Rana TM. Microwave-assisted parallel synthesis of a 4,6-diamino-2,2-dimethyl-1,2-dihydro-1-phenyl-s-triazine library. J Comb Chem. 2004 Jul-Aug; 6(4):504-8. PMID: 15244411.
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    97. Chiu YL, Cao H, Jacque JM, Stevenson M, Rana TM. Inhibition of human immunodeficiency virus type 1 replication by RNA interference directed against human transcription elongation factor P-TEFb (CDK9/CyclinT1). J Virol. 2004 Mar; 78(5):2517-29. PMID: 14963154; PMCID: PMC369228.
    98. Gelman MA, Richter S, Cao H, Umezawa N, Gellman SH, Rana TM. Selective binding of TAR RNA by a Tat-derived beta-peptide. Org Lett. 2003 Oct 02; 5(20):3563-5. PMID: 14507173.
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    99. Chiu YL, Rana TM. siRNA function in RNAi: a chemical modification analysis. RNA. 2003 Sep; 9(9):1034-48. PMID: 12923253; PMCID: PMC1370469.
    100. Hwang S, Tamilarasu N, Kibler K, Cao H, Ali A, Ping YH, Jeang KT, Rana TM. Discovery of a small molecule Tat-trans-activation-responsive RNA antagonist that potently inhibits human immunodeficiency virus-1 replication. J Biol Chem. 2003 Oct 03; 278(40):39092-103. PMID: 12857725.
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    101. Hamma T, Saleh A, Huq I, Rana TM, Miller PS. Inhibition of HIV tat-TAR interactions by an antisense oligo-2'-O-methylribonucleoside methylphosphonate. Bioorg Med Chem Lett. 2003 Jun 02; 13(11):1845-8. PMID: 12749881.
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    102. Kesavan V, Tamilarasu N, Cao H, Rana TM. A new class of RNA-binding oligomers: peptoid amide and ester analogues. Bioconjug Chem. 2002 Nov-Dec; 13(6):1171-5. PMID: 12440849.
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    103. Chiu YL, Rana TM. RNAi in human cells: basic structural and functional features of small interfering RNA. Mol Cell. 2002 Sep; 10(3):549-61. PMID: 12408823.
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    104. Chiu YL, Ho CK, Saha N, Schwer B, Shuman S, Rana TM. Tat stimulates cotranscriptional capping of HIV mRNA. Mol Cell. 2002 Sep; 10(3):585-97. PMID: 12408826.
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    105. Zhou C, Rana TM. A bimolecular mechanism of HIV-1 Tat protein interaction with RNA polymerase II transcription elongation complexes. J Mol Biol. 2002 Jul 26; 320(5):925-42. PMID: 12126615.
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    106. Richter S, Ping YH, Rana TM. TAR RNA loop: a scaffold for the assembly of a regulatory switch in HIV replication. Proc Natl Acad Sci U S A. 2002 Jun 11; 99(12):7928-33. PMID: 12048247.
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    107. Richter S, Cao H, Rana TM. Specific HIV-1 TAR RNA loop sequence and functional groups are required for human cyclin T1-Tat-TAR ternary complex formation. Biochemistry. 2002 May 21; 41(20):6391-7. PMID: 12009901.
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    108. Dinman JD, Richter S, Plant EP, Taylor RC, Hammell AB, Rana TM. The frameshift signal of HIV-1 involves a potential intramolecular triplex RNA structure. Proc Natl Acad Sci U S A. 2002 Apr 16; 99(8):5331-6. PMID: 11959986; PMCID: PMC122769.
    109. Wang Z, Shah K, Rana TM. Probing Tat peptide-TAR RNA interactions by psoralen photo-cross-linking. Biochemistry. 2001 May 29; 40(21):6458-64. PMID: 11371209.
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    110. O'Brien TP, Li QJ, Sauerburger F, Reviglio VE, Rana T, Ashraf MF. The role of matrix metalloproteinases in ulcerative keratolysis associated with perioperative diclofenac use. Ophthalmology. 2001 Apr; 108(4):656-9. PMID: 11297478.
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    111. Tamilarasu N, Zhang J, Hwang S, Rana TM. A new strategy for site-specific protein modification: analysis of a Tat peptide-TAR RNA interaction. Bioconjug Chem. 2001 Mar-Apr; 12(2):135-8. PMID: 11312672.
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    112. Tamilarasu N, Huq I, Rana TM. Targeting RNA with peptidomimetic oligomers in human cells. Bioorg Med Chem Lett. 2001 Feb 26; 11(4):505-7. PMID: 11229758.
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    113. Chiu YL, Coronel E, Ho CK, Shuman S, Rana TM. HIV-1 Tat protein interacts with mammalian capping enzyme and stimulates capping of TAR RNA. J Biol Chem. 2001 Apr 20; 276(16):12959-66. PMID: 11278368.
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    114. Ping YH, Rana TM. DSIF and NELF interact with RNA polymerase II elongation complex and HIV-1 Tat stimulates P-TEFb-mediated phosphorylation of RNA polymerase II and DSIF during transcription elongation. J Biol Chem. 2001 Apr 20; 276(16):12951-8. PMID: 11112772.
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    115. Zhang J, Tamilarasu N, Hwang S, Garber ME, Huq I, Jones KA, Rana TM. HIV-1 TAR RNA enhances the interaction between Tat and cyclin T1. J Biol Chem. 2000 Nov 03; 275(44):34314-9. PMID: 10944537.
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    116. Tamilarasu N, Huq I, Rana TM. Design, synthesis, and biological activity of a cyclic peptide: an inhibitor of HIV-1 tat-TAR interactions in human cells. Bioorg Med Chem Lett. 2000 May 01; 10(9):971-4. PMID: 10853671.
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    117. Hwang S, Tamilarasu N, Rana TM. Selection of HIV replication inhibitors: chemistry and biology. Adv Pharmacol. 2000; 49:167-97. PMID: 11013764.
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    118. Hwang S, Tamilarasu N, Ryan K, Huq I, Richter S, Still WC, Rana TM. Inhibition of gene expression in human cells through small molecule-RNA interactions. Proc Natl Acad Sci U S A. 1999 Nov 09; 96(23):12997-3002. PMID: 10557261.
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    119. Rana TM, Jeang KT. Biochemical and functional interactions between HIV-1 Tat protein and TAR RNA. Arch Biochem Biophys. 1999 May 15; 365(2):175-85. PMID: 10328810.
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    120. Wang Z, Huq I, Rana TM. Proximity of a Tat peptide to the HIV-1 TAR RNA loop region determined by site-specific photo-cross-linking. Bioconjug Chem. 1999 May-Jun; 10(3):512-9. PMID: 10346885.
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    121. Huq I, Ping YH, Tamilarasu N, Rana TM. Controlling human immunodeficiency virus type 1 gene expression by unnatural peptides. Biochemistry. 1999 Apr 20; 38(16):5172-7. PMID: 10213623.
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    122. Ping YH, Rana TM. Tat-associated kinase (P-TEFb): a component of transcription preinitiation and elongation complexes. J Biol Chem. 1999 Mar 12; 274(11):7399-404. PMID: 10066804.
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    123. Huq I, Tamilarasu N, Rana TM. Visualizing tertiary folding of RNA and RNA-protein interactions by a tethered iron chelate: analysis ofHIV-1 Tat-TAR complex. Nucleic Acids Res. 1999 Feb 15; 27(4):1084-93. PMID: 9927743.
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    124. Wang Z, Rana TM. Probing RNA-protein interactions by psoralen photocrosslinking. Methods Mol Biol. 1999; 118:49-62. PMID: 10549514.
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    125. Wang Z, Rana TM. RNA-protein interactions in the Tat-trans-activation response element complex determined by site-specific photo-cross-linking. Biochemistry. 1998 Mar 24; 37(12):4235-43. PMID: 9521746.
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    126. Huq I, Wang X, Rana TM. Specific recognition of HIV-1 TAR RNA by a D-Tat peptide. Nat Struct Biol. 1997 Nov; 4(11):881-2. PMID: 9360598.
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    127. Huq I, Rana TM. Probing the proximity of the core domain of an HIV-1 Tat fragment in a Tat-TAR complex by affinity cleaving. Biochemistry. 1997 Oct 14; 36(41):12592-9. PMID: 9376365.
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    128. Ping YH, Liu Y, Wang X, Neenhold HR, Rana TM. Dynamics of RNA-protein interactions in the HIV-1 Rev-RRE complex visualized by 6-thioguanosine-mediated photocrosslinking. RNA. 1997 Aug; 3(8):850-60. PMID: 9257644.
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    129. Wang Z, Rana TM. DNA damage-dependent transcriptional arrest and termination of RNA polymerase II elongation complexes in DNA template containing HIV-1 promoter. Proc Natl Acad Sci U S A. 1997 Jun 24; 94(13):6688-93. PMID: 9192626.
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    130. Song AI, Rana TM. Synthesis of an amino acid analogue to incorporate p-aminobenzyl-EDTA in peptides. Bioconjug Chem. 1997 Mar-Apr; 8(2):249-52. PMID: 9095368.
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    131. Wang Z, Wang X, Rana TM. Protein orientation in the Tat-TAR complex determined by psoralen photocross-linking. J Biol Chem. 1996 Jul 19; 271(29):16995-8. PMID: 8663586.
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    132. Wang Z, Rana TM. RNA conformation in the Tat-TAR complex determined by site-specific photo-cross-linking. Biochemistry. 1996 May 21; 35(20):6491-9. PMID: 8639596.
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    133. Shah K, Neenhold H, Wang Z, Rana TM. Incorporation of an artificial protease and nuclease at the HIV-1 Tat binding site of trans-activation responsive RNA. Bioconjug Chem. 1996 May-Jun; 7(3):283-9. PMID: 8816949.
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    134. Liu Y, Wang Z, Rana TM. Visualizing a specific contact in the HIV-1 Tat protein fragment and trans-activation responsive region RNA complex by photocross-linking. J Biol Chem. 1996 Apr 26; 271(17):10391-6. PMID: 8626612.
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    135. Neenhold HR, Rana TM. Major groove opening at the HIV-1 Tat binding site of TAR RNA evidenced by a rhodium probe. Biochemistry. 1995 May 16; 34(19):6303-9. PMID: 7756257.
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    136. Shah K, Wu H, Rana TM. Synthesis of uridine phosphoramidite analogs: reagents for site-specific incorporation of photoreactive sites into RNA sequences. Bioconjug Chem. 1994 Nov-Dec; 5(6):508-12. PMID: 7533002.
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    137. Rana TM, Meares CF. N-terminal modification of immunoglobulin polypeptide chains tagged with isothiocyanato chelates. Bioconjug Chem. 1990 Sep-Oct; 1(5):357-62. PMID: 2129106.
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