Douglas Rusch The Center for Genomics and Bioinformatics, Indiana University, USA
1 protocol

Ram Podicheti The Center for Genomics and Bioinformatics, Indiana University, USA
1 protocol

Jie Huang The Center for Genomics and Bioinformatics, Indiana University, USA
1 protocol

James Ford The Center for Genomics and Bioinformatics, Indiana University, USA
1 protocol

C. Cheng Kao
  • Department of Molecular & Cellular Biochemistry, Indiana University, USA
Research focus
  • Microbiology
  • 1 Author merit


Ph.D, Michigan State University, USA, 1988

Current position

Professor, Molecular & Cellular Biochemistry, Indiana University, USA

Publications (since 2013)

  1. Deng, X., Hackbart, M., Mettelman, R. C., O'Brien, A., Mielech, A. M., Yi, G., Kao, C. C. and Baker, S. C. (2017). Coronavirus nonstructural protein 15 mediates evasion of dsRNA sensors and limits apoptosis in macrophages. Proc Natl Acad Sci U S A 114(21): E4251-E4260.
  2. Zhao, B., Yi, G., Du, F., Chuang, Y. C., Vaughan, R. C., Sankaran, B., Kao, C. C. and Li, P. (2017). Structure and function of the Zika virus full-length NS5 protein. Nat Commun 8: 14762.
  3. Deval, J., Jin, Z., Chuang, Y. C. and Kao, C. C. (2017). Structure(s), function(s), and inhibition of the RNA-dependent RNA polymerase of noroviruses. Virus Res 234: 21-33.
  4. Hoover, H. and Kao, C. C. (2016). Phosphorylation of the viral coat protein regulates infection. Virus Adaptation and Treatment 8: 13-20.
  5. Kao, C., Lin, X., Yi, G., Zhang, Y., Rowe-Magnus, D. A. and Bush, K. (2016). Cathelicidin Antimicrobial Peptides with Reduced Activation of Toll-Like Receptor Signaling Have Potent Bactericidal Activity against Colistin-Resistant Bacteria. MBio 7(5).
  6. Hoover, H., Vaughan, R., Wang, J., Middleton, S., Ni, P. and Kao, C. C. (2016). Phosphorylation regulates brome mosaic virus RNA encapsidation and infection. J. Virol. 90: 7748-7760.
  7. Yi, G., Ybe, J. A., Saha, S. S., Caviness, G., Raymond, E., Ganesan, R., Mbow, M. L. and Kao, C. C. (2016). Structural and Functional Attributes of the Interleukin-36 Receptor. J Biol Chem 291(32): 16597-16609.
  8. Kao, C. C., Yi, G. and Huang, H. C. (2016). The core of hepatitis C virus pathogenesis. Curr Opin Virol 17: 66-73.
  9. Rolfsson, O., Middleton, S., Manfield, I. W., White, S. J., Fan, B., Vaughan, R., Ranson, N. A., Dykeman, E., Twarock, R., Ford, J., Kao, C. C. and Stockley, P. G. (2016). Direct Evidence for Packaging Signal-Mediated Assembly of Bacteriophage MS2. J Mol Biol 428(2 Pt B): 431-448.
  10. Hu, Z., Hu, X., He, S., Yim, H. J., Xiao, J., Swaroop, M., Tanega, C., Zhang, Y. Q., Yi, G., Kao, C. C., Marugan, J., Ferrer, M., Zheng, W., Southall, N. and Liang, T. J. (2015). Identification of novel anti-hepatitis C virus agents by a quantitative high throughput screen in a cell-based infection assay. Antiviral Res 124: 20-29.
  11. Yi, G., Wen, Y., Shu, C., Han, Q., Konan, K. V., Li, P. and Kao, C. C. (2015). Genotype-specific inhibition of hepatitis C virus replication by cyclic GMP-AMP that activates STING-mediated immune responses. J. Virol. 90:254-265.
  12. Tsvetkova, I. B., Yi, G., Yi, Y., Kao, C. C. and Dragnea, B. G. (2015). Segmented GFP-like aptamer probes for functional imaging of viral genome trafficking. Virus Res 210: 291-297.
  13. Jin, Z., Tucker, K., Lin, X., Kao, C. C., Shaw, K., Tan, H., Symons, J., Behera, I., Rajwanshi, V. K., Dyatkina, N., Wang, G., Beigelman, L. and Deval, J. (2015). Biochemical Evaluation of the Inhibition Properties of Favipiravir and 2'-C-Methyl-Cytidine Triphosphates against Human and Mouse Norovirus RNA Polymerases. Antimicrob Agents Chemother 59(12): 7504-7516.
  14. Fan, B., Sutandy, F. X., Syu, G. D., Middleton, S., Yi, G., Lu, K. Y., Chen, C. S. and Kao, C. C. (2015). Heterogeneous Ribonucleoprotein K (hnRNP K) Binds miR-122, a Mature Liver-Specific MicroRNA Required for Hepatitis C Virus Replication. Mol Cell Proteomics 14(11): 2878-2886.
  15. Saha, S. S., Singh, D., Raymond, E. L., Ganesan, R., Caviness, G., Grimaldi, C., Woska, J. R., Jr., Mennerich, D., Brown, S. E., Mbow, M. L. and Kao, C. C. (2015). Signal Transduction and Intracellular Trafficking by the Interleukin 36 Receptor. J Biol Chem 290(39): 23997-24006.
  16. Kitayama, M., Hoover, H., Middleton, S. and Kao, C. C. (2015). Brome mosaic virus Infection of Rice Results in Decreased Accumulation of RNA1. Mol Plant Microbe Interact 28(5): 626-632.
  17. Wen, Y., Lin, X., Fan, B., Ranjith-Kumar, C. T. and Kao, C. C. (2015). The juxtamembrane sequence of the Hepatitis C virus polymerase can affect RNA synthesis and inhibition by allosteric polymerase inhibitors. Virus Genes 51(1): 1-11.
  18. Vaughan, R. C. and Kao, C. C. (2015). Mapping protein-RNA interactions by RCAP, RNA-cross-linking and peptide fingerprinting. Methods Mol Biol 1297: 225-236.
  19. Fan, B., Ni, P. and Kao, C. C. (2015). Mapping RNA interactions to proteins in virions using CLIP-Seq. Methods Mol Biol 1297: 213-224.
  20. Rao, A. L. and Cheng Kao, C. (2015). The brome mosaic virus 3' untranslated sequence regulates RNA replication, recombination, and virion assembly. Virus Res 206: 46-52.
  21. Lin, X., Thorne, L., Jin, Z., Hammad, L. A., Li, S., Deval, J., Goodfellow, I. G. and Kao, C. C. (2015). Subgenomic promoter recognition by the norovirus RNA-dependent RNA polymerases. Nucleic Acids Res 43(1): 446-460.
  22. Kao, C. and Peerson, O. (2014). Replication of plant and animal viruses. Curr. Opin. Virol. Special biennial issue, Elservier Press.
  23. Kao, C. and Peersen, O. (2014). Editorial overview: Replication of plant and animal viruses.  Curr. Opin. Virol. 1-2.
  24. Yunus, M. A., Lin, X., Bailey, D., Karakasiliotis, I., Chaudhry, Y., Zhang, G., Thorne, L., Kao, C. and Goodfellow, I. (2014). Characterization of the murine norovirus subgenomic RNA promoter. J. Virol. 89: 1218-1229.
  25. Singh, D., Vaughan, R. and Kao, C. C. (2014). LL-37 peptide enhancement of signal transduction by Toll-like receptor 3 is regulated by pH: identification of a peptide antagonist of LL-37. J Biol Chem 289(40): 27614-27624.
  26. Wang, Z., Hryc, C. F., Bammes, B., Afonine, P. V., Jakana, J., Chen, D. H., Liu, X., Baker, M. L., Kao, C., Ludtke, S. J., Schmid, M. F., Adams, P. D. and Chiu, W. (2014). An atomic model of brome mosaic virus using direct electron detection and real-space optimization. Nat Commun 5: 4808.
  27. Perez-Vargas, J., Vaughan, R. C., Houser, C., Hastie, K. M., Kao, C. C. and Nemerow, G. R. (2014). Isolation and characterization of the DNA and protein binding activities of adenovirus core protein V. J Virol 88(16): 9287-9296.
  28. Yamane, D., McGivern, D. R., Wauthier, E., Ping, L., Yi, M., Madden, V. J., Wen, Y., Chugh, P. E., McGee, C. E., Widman, D. G., Kim, S., Shimakami, T., Welsch, C., Oikawa, T., Heise, M. T., Dittmer, D. P., Kao, C. C., Pitson, S. M., Merrill, Jr A. H., Reid, L. M. and Lemon, S. M. (2014). Regulation of hepatitis C virus replication by sphingosine kinase 2-mediated endogenous lipid peroxidation. Nat Med 20: 927-935.
  29. Wen, Y. and Cheng Kao, C. (2014). The hepatitis C virus core protein can modulate RNA-dependent RNA synthesis by the 2a polymerase. Virus Res 189: 165-176.
  30. Li, W., Zhang, Y. and Kao, C. C. (2014). The classic swine fever virus (CSFV) core protein can enhance de novo-initiated RNA synthesis by the CSFV polymerase NS5B. Virus Genes 49(1): 106-115.
  31. Vaughan, R., Tragesser, B., Ni, P., Ma, X., Dragnea, B. and Kao, C. C. (2014). The tripartite virions of the brome mosaic virus have distinct physical properties that affect the timing of the infection process. J Virol 88(11): 6483-6491.
  32. Ni, P., Vaughan, R. C., Tragesser, B., Hoover, H. and Kao, C. C. (2014). The plant host can affect the encapsidation of brome mosaic virus (BMV) RNA: BMV virions are surprisingly heterogeneous. J Mol Biol 426(5): 1061-1076.
  33. Fan, B., Lu, K. Y., Reymond Sutandy, F. X., Chen, Y. W., Konan, K., Zhu, H., Kao, C. C. and Chen, C. H. (2014). A human proteome microarray identified that the heterogeneous Ribonucleoprotein K (hnRNP K) recognizes the 5’ terminal sequence of the hepatitis C virus.  Molec. Cell. Proteomics 13(1):84-92.
  34. Li, X., Shu, C., Yi, G., Chaton, C. T., Shelton, C. K., Diao, J., Zuo, X., Cheng Kao, C., Herr, A. B. and P. Li. (2013). Cyclic GMP-AMP synthase is activated by double-strand DNA-induced oligomerization. Immunity 39: 1019-1031.
  35. Park, I. W., Ndjomou, J., Wen, Y., Liu, Z., Ridgway, N. D., Kao, C. C. and He, J. J. (2013). Inhibition of HCV replication by oxysterol-binding protein-related protein 4 (ORP4) through interaction with HCV NS5B and alteration of lipid droplet formation. PLoS One 8(9): e75648.
  36. Yi, G., Brendel, V., Shu, C., Li, P. and Kao, C. C. (2013). Single nucleotide polymorphisms of human STING can affect innate immune response to cyclic dinucleotides. PLoS ONE 8(10): e77846.
  37. Ni, P. and Cheng Kao, C. (2013). Non-encapsidation activities of the capsid proteins of positive-strand RNA viruses. Virology 446(1-2): 123-132.
  38. Zhao, H., Y. Yang, Y., Janga, S. C., Kao, C. C. and Zhou, Y. (2013). Charting the unexplored RNA-binding protein atlas of the human genome by combining structure and binding predictions. Proteins 82: 640-647.
  39. Singh, D., Qi, R., Jordan, J. L., San Mateo, L. and Kao, C. C. (2013). The human antimicrobial peptide LL-37, but not the mouse ortholog, mCRAMP, can stimulate signaling by poly(I:C) through a FPRL1-dependent pathway. J Biol Chem 288(12): 8258-8268.
  40. Leen, E., Kwok, R., Birtley, J. B., Simpson, P. J., Subba-Reddy, Ch. V., Chaudry, Y., Sosnovtsev, S. V., Green, K. Y., Prater, S., Young, J., Chung, L. M., Marchant, J., Roberts, L. O., Kao, C. C., Matthews, S., Goodfellow, I. G. and Curry, S. (2013). Structures of the compact helical core domains of the mouse norovirus and the feline calicivirus VPg proteins. J. Virol. 87: 5318-5330
1 Protocol published
Mapping RNA Sequences that Contact Viral Capsid Proteins in Virions
Authors:  C. Cheng Kao, Ella Chuang, James Ford, Jie Huang, Ram Podicheti and Doug B. Rusch, date: 07/20/2017, view: 5810, Q&A: 0
We have adapted the methodology of CLIP-seq (Crosslinking-Immunoprecipitation and DNA Sequencing) to map the segments of encapsidated RNAs that contact the protein shells of virions. Results from the protocol report on the RNA sequences that contact ...
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