Roopa Thapar, Ph.D.
Assistant Professor, Department of Biochemistry & Biophysics and Program in Molecular Biology and Biotechnology (PMBB), University of North Carolina, Chapel Hill, NC;
Visiting Scientist, Hauptman-Woodward Institute, Buffalo, NY

EDUCATION
B.S. Pharmacy, C.U. Shah College of Pharmacy, Mumbai, INDIA, 1988
Ph.D., Biochemistry (NMR, Structural Biology) Merck Fellow,
University of Washington, Seattle, 1992-1997
Postdoctoral Fellow (Biomolecular NMR), UNC, Chapel Hill, 1997-2000.

Research Interests:

My interests lie in understanding molecular recognition and assembly of large multi-protein and protein-RNA complexes (RNPs) that play important roles in post-transcriptional regulation of gene expression and in cell signaling.  The ultimate goal of these studies is to use the tools of structural biology (NMR and X-ray crystallography), biophysical tools (CD, ITC, DSC, Biacore, fluorescence, and AUC) along with biochemical, molecular biological and proteomics approaches to (i) identify protein-protein and protein-RNA interaction networks important for gene expression, (ii) understand the structural and thermodynamic basis of these interactions, and (iii) to use this information for the design of novel therapeutics that either stimulate or interfere with the assembly of these complexes.   

1.  Protein-Protein and Protein-RNA complexes involved in histone mRNA metabolism.  The steady state levels of eukaryotic mRNAs are determined by their rates of synthesis and degradation.  Post-transcriptional mechanisms therefore play pivotal roles in control of gene expression.  I am interested in characterizing RNP complexes that regulate histone pre-mRNA processing and translation initiation.  Replication-dependent histone mRNAs are unique in that they are the only metazoan mRNAs that are not polyadenylated.  They are regulated post-transcriptionally during the S-phase of the cell cycle by protein-RNA complexes that are specific to histone mRNAs.  Coordinate regulation of histone gene expression and DNA replication is important for correct packaging of DNA into nucleosomes.  There are at least three protein-RNA assemblies that control the level of mature histone message or the level of histone proteins: the histone pre-mRNA processing complex, histone mRNA translation initiation complex, and the histone mRNA degradation complex.  Many trans-acting factors that are involved in regulating histone mRNA processing, translation, and degradation have not yet been identified.  There is also little information currently available on structures of the protein and RNA components, and on the specific interactions that occur between the proteins that form these assemblies.  This information will provide fundamental insight into how genes are controlled, how they are regulated, and how histone protein synthesis is coordinated with DNA replication.  Our recent work is focused on how phosphorylation of Stem-Loop Binding Protein (SLBP) regulates its interaction with the histone message, and the structural basis by which SLIP1, a novel translation initiation factor upregulates histone protein synthesis.  These studies are performed in collaboration with Dr. Bill Marzluff (Dept. of Biochemistry, UNC, Chapel Hill).

2. Structure-Function studies of the structure-specific 3’hExo/ERI-1 family of 3’ to 5’ Exonucleases.  The DnaQ-H family exonuclease Snipper (Snp) is a 33-kDa Drosophila melanogaster homolog of 3'hExo and ERI-1, exoribonucleases implicated in the degradation of histone mRNA in mammals and in the negative regulation of RNA interference (RNAi) in Caenorhabditis elegans, respectively.  In collaboration with Dr. Robert Duronio (Dept of Biology, UNC, Chapel Hill), we recently showed that in metazoans, Snp, Exod1, 3'hExo, ERI-1, and the prpip nucleases define a new subclass of structure-specific 3'-5' exonucleases that bind and degrade double-stranded RNA and/or DNA substrates with 3' overhangs of 2-5 nucleotides (nt) in the presence of Mg2+ with no apparent sequence specificity. These nucleases are also capable of degrading linear substrates. Snp efficiently degrades structured RNA and DNA substrates as long as there exists a minimum 3' overhang of 2 nt to initiate degradation.  Current studies are focused on understanding the function, structure, and the catalytic mechanism of Snipper.   

3. E-Ras as a target for Embryonic Stem Cell Renewal. 

Selected Publications:

Jeremy Kupsco, Ming Jing Wu, William F. Marzluff, Roopa Thapar*, Robert J. Duronio*. Genetic and biochemical characterization of Drosophila Snipper: A promiscuous member of the 3’hExo/Eri-1 family of exonucleases. (2006) RNA, Dec;12(12):2103-17. *co-senior author   [ learn more ]

Christoph H. Borchers, Roopa Thapar, Evgeniy V. Petrochenko, Matthew Torres, J. Paul Speir, Michael Wasterling, Zbigniew Dominski, William F. Marzluff.  (2006) Proteomic identification of a cryptic phosphorylation site in the RNA binding domain of Drosophila and human SLBPs and its implications for histone mRNA recognition. PNAS, 103(9):3094-9. [ learn more ]

Matthew P. Torres, Roopa Thapar, William F. Marzluff, and Christoph H. Borchers.  (2005) Phosphatase-directed phosphorylation-site determination: A synthesis of methods for the detection and identification of phosphopeptides.  J. Proteome Research, 4(5):1628-35   [ learn more ]

Jongyun Heo, Roopa Thapar, and Sharon Campbell.  (2005) Recognition and activation of Rho family GTPases by the guanine nucleotide exchange factors Vav1 and Vav2. Biochemistry, 44(17):6573-85. [ learn more ]

Roopa Thapar, Jason G Williams, and Sharon Campbell. NMR characterization of full length farnesylated and non-farnesylated H-Ras isoforms and its implications for Raf activation. (2004) J. Mol. Biol,343(5):1391-408 [ PubMed ]

Roopa Thapar, William F. Marzluff and Matthew R. Redinbo. Electrostatic contribution of protein phosphorylation to the SLBP-histone mRNA complex, (2004) Biochemistry, Jul 27;43(29):9401-12. [ pdf ]

Roopa Thapar, Geoffrey Mueller, and William F. Marzluff. The N-terminal domain of Stem Loop Binding Protein (SLBP) is intrinsically disordered in solution. (2004) Biochemistry, 43(29):9390-9400  [ learn more ]

Roopa Thapar, Cathy D. Moore, Sharon L Campbell. Backbone 1H, 13C, 15N resonance assignments for the 21 kDa GTPase Rac1 complexed to GDP and Mg2+.(2003) J. Biomol. N.M.R  27 (1), 87-88.