The main goal of the proposed research is to understand the architecture, dynamics, and function of complex assemblies involved in transcriptional activation of human immunodeficiency virus type-1 (HIV-1) gene expression. HIV-1 encodes a transcriptional transactivator protein called Tat, which is expressed early in the viral life cycle and is absolutely required for viral replication and progression to disease. A regulatory element between +1 and +60 in the HIV-1 long terminal repeat which is capable of forming a stable stem-loop structure, designated TAR, is critical for Tat function. Tat interacts with cyclinT1 (CycT1), a regulatory partner of CDK9 in the positive transcription elongation factor b (P-TEFb) complex, and binds cooperatively with CycT1 to TAR RNA. Recruitment of P-TEFb to TAR promotes transcription elongation. P-TEFb is a key enzyme in the control of transcription elongation by RNA polymerase II and there are two pools of P-TEFb, active and inactive, present in the cell. P-TEFb is inactivated by sequestration into a large ribonucleoprotein (RNP) complex containing the small nuclear RNA, 7SK, and the Hexim1 protein. Therefore, there are two RNP complexes, TAR-Tat-P-TEFb and 7SK-Hexim1-P-TEFb, which are important in HIV-1 gene expression, however, it is not known how the equilibrium between these two RNPs is modulated. We have developed innovative chemical and physical approaches to probe RNA-protein and protein-protein interactions. The proposed work addresses the structure, dynamics, and function of TAR-Tat-P-TEFb and 7SK-Hexim1-P-TEFb complexes by revealing the molecular network of RNA-RNA and RNA-protein interactions that govern assembly and stability of the RNP complexes.

Public Health Relevance

Results of these studies would contribute to understanding the mechanisms of assembly and stability of RNA- protein complexes under physiological conditions and will improve our understanding of HIV-1 gene regulation by Tat. Since P-TEFb is a key enzyme regulating cellular gene expression, understanding the mechanism of P- TEFb activation would provide fundamental insight into a number of regulatory processes involved in the development of diseases such as cardiac hypertrophy, cancer, inflammation, and autoimmunity. These results would also be valuable in developing new strategies for blocking the expression of retroviral or other disease- related genes.

Agency
National Institute of Health (NIH)
Institute
National Institute of Allergy and Infectious Diseases (NIAID)
Type
Research Project (R01)
Project #
5R01AI041404-14
Application #
8287578
Study Section
AIDS Molecular and Cellular Biology Study Section (AMCB)
Program Officer
Sharma, Opendra K
Project Start
1997-09-01
Project End
2014-06-30
Budget Start
2012-07-01
Budget End
2013-06-30
Support Year
14
Fiscal Year
2012
Total Cost
$472,725
Indirect Cost
$225,225
Name
Sanford-Burnham Medical Research Institute
Department
Type
DUNS #
020520466
City
La Jolla
State
CA
Country
United States
Zip Code
92037
Sakurai, Kumi; Talukdar, Indrani; Patil, Veena S et al. (2014) Kinome-wide functional analysis highlights the role of cytoskeletal remodeling in somatic cell reprogramming. Cell Stem Cell 14:523-34
Lin, Nianwei; Chang, Kung-Yen; Li, Zhonghan et al. (2014) An evolutionarily conserved long noncoding RNA TUNA controls pluripotency and neural lineage commitment. Mol Cell 53:1005-19
Patil, Veena S; Zhou, Rui; Rana, Tariq M (2014) Gene regulation by non-coding RNAs. Crit Rev Biochem Mol Biol 49:16-32
Yang, Chao-Shun; Chang, Kung-Yen; Rana, Tariq M (2014) Genome-wide functional analysis reveals factors needed at the transition steps of induced reprogramming. Cell Rep 8:327-37
Xiong, Xiao-Peng; Kurthkoti, Krishna; Chang, Kung-Yen et al. (2013) Core small nuclear ribonucleoprotein particle splicing factor SmD1 modulates RNA interference in Drosophila. Proc Natl Acad Sci U S A 110:16520-5
Zhou, Rui; Rana, Tariq M (2013) RNA-based mechanisms regulating host-virus interactions. Immunol Rev 253:97-111
Shen, Yang; Altman, Michael D; Ali, Akbar et al. (2013) Testing the substrate-envelope hypothesis with designed pairs of compounds. ACS Chem Biol 8:2433-41
Nalam, Madhavi N L; Ali, Akbar; Reddy, G S Kiran Kumar et al. (2013) Substrate envelope-designed potent HIV-1 protease inhibitors to avoid drug resistance. Chem Biol 20:1116-24
Silver, Nathaniel W; King, Bracken M; Nalam, Madhavi N L et al. (2013) Efficient Computation of Small-Molecule Configurational Binding Entropy and Free Energy Changes by Ensemble Enumeration. J Chem Theory Comput 9:5098-5115
Baigude, Huricha; Su, Jie; McCarroll, Joshua et al. (2013) In Vivo Delivery of RNAi by Reducible Interfering Nanoparticles (iNOPs). ACS Med Chem Lett 4:720-723

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