Center for Gene Regulation in Health and Disease (GRHD)

Girish C. Shukla

My research goal is to better understand molecular mechanisms that control eukaryotic gene expression at the RNA level. Within this framework, I am exploring three issues: (1) noncoding RNAs and their roles in gene expression, (2) nuclear pre-mRNA splicing, and finally, (3) specific RNA:RNA and RNA:Protein interactions. The current emphasis of the lab is on miRNA-mediated regulation of human androgen receptor expression. Androgen receptor is a key modulator that has been implicated in hormonal dependent and independent stages of prostate cancer. Based on computational predictions and phylogenetic analysis I have proposed a miRNA-mediated model of Androgen Receptor regulation. One particularly interesting idea that I would like to investigate further is the critical level of Androgen receptor influences the transition from the hormone-dependent to hormone refractory stage of prostate cancer. Using computational biology tools I have identified a number of miRNAs that have the potential to interact with the 3' untranslated region of the receptor mRNA. This observation gives rise to the hypothesis that androgen receptor expression is tightly regulated by combinatorial control of miRNAs and deregulation of these miRNAs may contribute in the progression of prostate cancer. Using lentiviral expression systems we are overexpressing a number of miRNAs to understand how androgen receptor expression is controlled by these miRNAs in a variety of prostatic carcinoma cells.

The research in my laboratory is also aimed at understanding the nuclear pre-mRNA splicing by using in vitro and in vivo methods. We are currently studying the structure-function of several snRNAs of the minor spliceosome including U11, U12, U4atac and U6atac. Recently we have identified a small RNA element in the U6atac snRNA that functions in the 'guiding' of the specific spliceosomal complexes to the minor class splice sites. We are now pursuing the identification of proteins that may interact with these U6atac snRNA sub-structures to further define their role in the splicing of minor class introns. We are also studying specific RNA-RNA base-pairing interaction involved in the splicing of the minor class intron using biochemical and in vivo genetic approaches. These studies will help us to understand how multiple sequentially interacting snRNAs facilitate the removal of introns from the precursor mRNA of genes.

  1. Kumar, A., Kumar, V., Shukla, G.C., and Rao, K.V., Immunological characteristics of a recombinant Hepatitis B virus derived multiple-epitope polypeptide: a study in polyvalent vaccine design. Vaccine; 1994, 12(3): 259-66.
  2. Shukla, G.C. and Nene, V., Telomeric features of Theileria parva mitochondrial DNA derived from cycle sequence data of total genomic DNA. Mol. Biochem. Parasitol. 1998, 95, 159-163.
  3. Shukla, G.C. and Padgett, R.A. Features of U6atac and U12 snRNA are conserved in plants and higher organisms RNA, 1999, 5:525-538.
  4. Shukla, G.C. and Padgett, R.A. The intramolecular stem-loop of U6 snRNA can functionally replace the U6atac snRNA stem-loop. RNA, 2001, 7:94-105.
  5. Dietrich, R.C., Shukla, G.C., Fuller, J. D., and Padgett, R.A. Alternative splicing of U12-dependent introns in vivo responds to purine-rich enhancers RNA, 2001, 7:1378-1388.
  6. Padgett, R.A. and Shukla, G.C. A revised model for U4atac/U6atac snRNA base pairing. RNA, 2002, 8:1-4.
  7. Shukla, G.C., and Padgett R.A. A catalytically competent group II intron domain 5 can functionally replace the spliceosomal U6atac snRNA stem-loop Mol. Cell 2002, 9:1145-1150.
  8. Shukla, G.C., and Padgett, R.A. U4 small nuclear RNA can function in both the major and minor spliceosomes Proc. Natl. Acad. Sci., 2004, 6, 101 (1): 93-98.
  9. Shukla, G.C., Cole, A. Dietrich, R.A. and Padgett, R.A. Domains of human U4atac snRNA required for U12-dependent splicing in vivo Nucl. Acid Res., 2002, 30, 21: 4650-4657.
  10. Dietrich RC, Padgett RA, Shukla GC*. The conserved 3' end domain of U6atac snRNA can direct U6 snRNA to the minor spliceosome. RNA. 2009 Jun;15(6):1198-207.
  11. Sikand K, Slane SD, Shukla GC*. Intrinsic expression of host genes and intronic miRNAs in prostate carcinoma cells. Cancer Cell Int. 2009 Aug 12;9(1):21.
  12. Sikand K, Shukla GC. Functionally important structural elements of U12 snRNA. Nucleic Acids Res. 2011 Oct;39(19):8531-43. Epub 2011 Jul 6. PubMed PMID: 21737423; PubMed Central PMCID: PMC3201867.
  13. Sikand K, Slaibi JE, Singh R, Slane SD, Shukla GC. miR 488* inhibits androgen receptor expression in prostate carcinoma cells. Int J Cancer. 2011 Aug 5;129(4):810-9. doi: 10.1002/ijc.25753. PubMed PMID: 21710544.
  14. Shukla GC, Haque F, Tor Y, Wilhelmsson LM, Toulmé JJ, Isambert H, Guo P, Rossi JJ, Tenenbaum SA, Shapiro BA. A boost for the emerging field of RNA nanotechnology. ACS Nano. 2011 May 24;5(5):3405-18. PubMed PMID: 21604810; PubMed Central PMCID: PMC3102291.
  15. Sikand K, Barik S, Shukla GC. MicroRNAs and Androgen Receptor 3' Untranslated Region: A Missing Link in Castration-resistant Prostate Cancer? Mol Cell Pharmacol. 2011;3(3):107-113. PubMed PMID: 22468168; PubMed Central PMCID: PMC3315684.
  16. Shukla GC, Singh J, Barik S. MicroRNAs: Processing, Maturation, Target Recognition and Regulatory Functions. Mol Cell Pharmacol. 2011;3(3):83-92. PubMed PMID: 22468167; PubMed Central PMCID: PMC3315687.
  17. Sikand K, Singh J, Ebron JS, Shukla GC. Housekeeping Gene Selection Advisory: Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH) and β-Actin Are Targets of miR-644a. PLoS One. 2012;7(10):e47510. doi: 10.1371/journal.pone.0047510. Epub 2012 Oct 16. PubMed PMID: 23091630; PubMed Central PMCID: PMC3472982.
  18. Ebron JS, Weyman C, Shukla GC. Targeting of Androgen Receptor expression by andro-miRs as novel adjunctive therapeutics in Prostate Cancer, Journal of Cancer Therapy, 2013.
  19. Singh G, Shukla GC, Gupta S. MicroRNA regulating Glutathione S-transferase P1 in Prostate Cancer, Curr Pharmacol Rep, 2015.
  20. Al-Harbi S, Choudhary GS, Ebron JS, Hill BT, Vivekanathan N, Ting AH, Radivoyevitch T, Smith MR, Shukla GC, Almasan A. miR-377-dependent BCL-xL regulation drives chemotherapeutic resistance in B-cell lymphoid malignancies. Mol Cancer. 2015 Nov 4;14(1):185. doi: 10.1186/s12943-015-0460-8. PubMed PMID: 26537004; PubMed Central PMCID: PMC4632834.
  21. Singh S, Zheng Y, Jagadeeswaran G, Ebron JS, Sikand K, Gupta S, Sunker R, Shukla GC. Deep sequencing of small RNA libraries from human prostate epithelial and stromal cells reveal distinct pattern of microRNAs primarily predicted to target growth factors. Cancer Lett. 2016 Feb 28;371(2):262-73. doi:  0.1016/j.canlet.2015.10.038. Epub 2015 Dec 3. PubMed PMID: 26655274.
  22. Ebron JS, Shukla GC. Molecular characterization of a novel androgen receptor transgene responsive to MicroRNA mediated post-transcriptional control exerted via 3'-untranslated region. Prostate. 2016 Mar 14. doi: 10.1002/pros.23174. [Epub ahead of print] PubMed PMID: 26988939.
  23. Shukla GC, Plaga AR, Shankar E, Gupta S. Androgen receptor-related diseases:what do we know? Andrology. 2016 Mar 16. doi: 10.1111/andr.12167. [Epub ahead of print] Review. PubMed PMID: 26991422.
  24. Singh J, Sikand K, Conrad H, Will CL, Komar AA, Shukla GC. U6atac snRNA stem-loop interacts with U12 p65 RNA binding protein and is functionally interchangeable with the U12 apical stem-loop III. Sci Rep. 2016 Aug 11;6:31393.  doi: 10.1038/srep31393. PubMed PMID: 27510544; PubMed Central PMCID: PMC4980772.
  25. Singh S, Plaga A, Shukla GC. Racial disparities: disruptive genes in prostate carcinogenesis. Front Biosci (Schol Ed). 2017 Jun 1;9:244-253. PubMed PMID: 28410117.