Small RNAs: Mediators of Gene Regulation, Catalysis and Silencing

Small RNAs: Mediators of Gene Regulation, Catalysis and Silencing

Speaker: Dinshaw J. Patel

Affiliation: Abby Rockefeller Mauzé Chair in Experimental Therapeutics
Member, Structural Biology Program
Memorial Sloan-Kettering Cancer Center
New York,  USA

Host: Maria Arménia Carrondo

Abstract:

Metabolite-sensing mRNAs, or riboswitches, specifically interact with small ligands and direct expression of genes dictating their metabolism. We have solved the structures of riboswitch aptamer domains containing bound purines and thiamine pyrophosphate, and more recently, lysine and flavin mononucleotide, thereby defining binding pocket architectures, recognition elements, divalent cation coordination and the molecular basis for exquisite selectivity and specificity.
We have solved the structure of a ribozyme that catalyzes enantioselective carbon-carbon bond formation by the Diels-Alder reaction in the free and reaction product-bound states. RNA folding and product binding are dictated by extensive stacking and hydrogen bonding, whereas stereoselection is governed by the shape of the hydrophobic catalytic pocket.
Small interfering RNA (siRNAs), 19-23 bp duplexes containing 5’-phosphates and 2-nt 3’-overhangs, play a key role in RNA silencing. We have solved the structures of the p19-siRNA, PAZ-siRNA and Piwi-siRNA complexes that define how proteins measure siRNA length, and selectively target 2-nt 3’-overhangs and 5’-phosphates, respectively. Our recent structural studies of Argonaute proteins, their guide strand binary complexes, as well as message strand ternary complexes, have provided insights into loading, mRNA nucleation and site-specific cleavage within the RNA-induced silencing complex.

Short CV:

Dinshaw J. Patel

Abby Rockefeller Mauze Chair in Experimental Therapeutics
Structural Biology Program     Phone: 212-639-7207
Memorial Sloan-Kettering Cancer Center   FAX: 212-717-3066
1275 York Avenue      email: pateld@mskcc.org 
New York, NY, 10021, USA     http://www.mskcc.org/mskcc/html/10829.cfm

Education:
1961   B.Sc.  Chemistry     University of Bombay, India 
1963   M.S.  Chemistry     California Institute of Technology
1968   Ph.D.  Chemistry     New York University
Postdoctoral Training: 
1967   Postdoc Biochemistry  New York Univ. Medical School
1968 - 1969  Postdoc Biophysics  AT&T Bell Laboratories

Appointments:
1970 - 1984 Member of Technical Staff, Polymer Chemistry Department,
  AT&T Bell Laboratories, Murray Hill, NJ
1984 - 1992 Professor of Biochemistry & Molecular Biophysics,
  College of Physicians & Surgeons, Columbia University, New York, NY
1992 -  Member, Structural Biology Program
  Memorial Sloan-Kettering Cancer Center (MSKCC), New York, New York
1994 -  Professor, Graduate Program in Biochemistry & Structural Biology,
  Weill School of Medical Sciences, Cornell University, New York, NY

Honors:
1961 - 1963 Jamshetjee N. Tata Fellow
1983  AT&T Bell Laboratories Distinguished Technical Staff Award
1992 -  Abby Rockefeller Mauzé Chair in Experimental Therapeutics (MSKCC)
1997  Distinguished Alumnus Award, New York University
1997 - 1999 Harvey Society (Vice-President 97-98; President 98-99)
Internal Review Committees:
1988 - 1991 Columbia University Health Sciences, New York, NY
  • Member, Committee on Appointments and Promotions (88-91)
1993 -  Memorial Sloan-Kettering Cancer Center (MSKCC), New York, NY
  • Member, Executive Committee, Sloan Kettering Institute (93-04)
   • Member, Committee on Appointments and Promotions, MSKCC (97-04)
  • Member, Executive Committee, Weill Graduate School of Medical Sciences,
    Cornell University and Sloan-Kettering Division (94-05)
 • Member, Executive Committee, Tri-Institutional Program (Sloan-Kettering,
              Rockefeller University, Cornell University and its Medical school) (00-05 )
External Review Committees:
1984 -  National Institutes of Health, Bethesda, MD
  • Member, Molecular and Cellular Biophysics Study Section (84-88)
  • National Cancer Institute, Board of Scientific Counselors-B (00-05)
1989 - 1996 Howard Hughes Medical Institute, Chevy Chase, MD
   • Member, Scientific Review Board - Structural Biology  (89-92)
  • Member, Medical Advisory Board (93-96)
 
Dinshaw Patel has pioneered the application of NMR and crystallographic techniques to investigate protein and nucleic acid architecture, recognition, regulation and catalysis.
His group’s structure-function studies, in collaboration with David Allis, have provided ground-breaking mechanistic insights into the reading of site-specific lysine modification marks on histones and their contribution to the establishment and maintenance of chromatin-mediated epigenetic ON/OFF states. They have jointly introduced the concept of combinatorial readout of epigenetic marks by covalently linked modules centered on the nucleosome as the repeating unit.
His group’s structure-function research has profoundly impacted on the RNA silencing field through definitive structural characterization of recognition events associated with targeting duplex length, 5’-phosphate and 3’-overhang ends of small interfering RNAs. These results provide a mechanistic framework for guide strand alignment and site-specific cleavage of the paired messenger RNA mediated by Argonaute, the key protein exhibiting ‘slicer’ activity, within the RNA-induced silencing complex.
His group’s structure-function studies of aptamer domains of purine and thiamine pyrophosphate riboswitches, and more recently, lysine and flavin mononucleotide riboswitches, metabolite-sensing mRNAs that modulate gene expression and metabolic homeostasis, and ribozymes that catalyze the carbon-carbon bond forming Diels-Alder reaction, highlight how RNAs containing only four nucleotides can generate precisely defined pockets exhibiting exquisite shape-complementarity for metabolite recognition and discrimination, as well as chemical catalysis.
His group’s structural studies on covalent stereoisomeric polycyclic aromatic hydrocarbon-DNA adducts established the link between lesion chirality and the nature and extent of helical perturbations, while structural studies on antitumor drug-DNA complexes identified recognition principles underlying sequence-dependent targeting of the double helix.
 
Selected peer-reviewed publications (over 350 publication)
Ye, K., Malinina, L. & Patel, D. J. (2003). Recognition of siRNA by a viral suppressor of RNA silencing. Nature 426, 874-878.
Ma, J-B., Ye, K. & Patel, D. J. (2004). Structural basis for overhang-specific small interfering RNA recognition by the PAZ domain. Nature 429, 318-322.
Malinina, L., Malakhova, M. L., Teplov, A., Brown, R. E. & Patel, D. J. (2004). Structural basis for glycosphingolipid transfer specificity. Nature 430, 1048-1053.
Serganov, A., Yuan, Y-R., Pikovskaya, O., Polonskaia, A., Malinina, L., Phan, A. T., Hobartner, C., Micura, R., Breaker, R. R. & Patel, D. J. (2004). Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs. Chem. Biol. 11, 1729-1741.
Phan, A. T., Kuryavyi, V., Ma, J. B., Andreola, M. L. & Patel, D. J. (2005). An interlocked dimeric parallel-stranded DNA quadruplex: a potent inhibitor of HIV-1 integrase. Proc. Natl. Acad. Scis. USA  102, 634-639.
Serganov, A., Keiper, S., Malinina, L., Tereschko, V., Skripkin, E., Hobartner, C., Polonskaia, A., Phan, A. T., Wombacher, R., Micura, R., Dauter, Z., Jaschke, A. & Patel, D. J. (2005). Structural basis for Diels-Alder ribozyme catalyzed carbon-carbon bond formation. Nature Struct. & Mol. Biol. 12, 218-224.
Ma, J. B., Yuan, Y. R., Meister, G., Pei, Y., Tuschl, T. & Patel, D. J. (2005). Structural basis for 5’-end-specific recognition of the guide RNA strand by the A. fugidus PIWI protein. Nature 434, 666-670.
Phan, A. T., Kuryavyi, V., Gaw, H. Y. & Patel, D. J. (2005). Targeting anticancer drugs to a parallel-stranded snapback G-quadruplex formed by five-guanine tracts of the human c-myc promotor. Nature Chem. Biol. 1, 167-173.
Yuan, Y. R., Ma, J. B., Kuryavyi, V., Pei, Y., Zhadina, M., Meister, G., Chen, H. Y., Dauter, Z., Tuschl, T. & Patel, D. J. (2005). Crystal structure of Aquifex aeolicus Argonaute provides unique perspectives into the mechanism of guide strand-mediated mRNA cleavage. Mol. Cell 19, 405-419.
Teplova, M., Yuan, Y. R., Phan, A. T., Malinina, L., Ilin, S., Teplov, A. & Patel, D. J. (2006). Structural basis for recognition and sequestration of UUUOH 3’-terminii of nascent mRNA polymerase III transcripts by La autoantigen. Mol. Cell 21, 75-85.
Rechkoblit, O., Malinina, L., Cheng, Y., Kuryavyi, V., Broyde, S., Geacintov, N. & Patel, D. J. (2006). Stepwise translocation of Dpo4 polymerase during error-free bypass of oxoG lesion. PLoS Biology 4, 25-42.
Serganov, A., Polonskaia, A., Phan, A. T., Breaker, R. R. & Patel, D. J. (2006). Structural basis for gene regulation by a riboswitch that senses thiamine pyrophosphate. Nature 441, 1167-1171.
Li, H., Ilin, S., Wang, W. K., Wysocka, J., Allis, C. D. & Patel, D. J. (2006). Molecular basis for site-specific readout of H3 lysine 4 trimethylation by the BPTF PHD finger. Nature 442, 91-95.
Ruthenberg, A. J., Wang, W., Graybosch, D. M., Li, H., Allis, C. D., Patel, D. J. & Verdine, G. L. (2006). Histone H3 lysine 4 methylation state recognition and presentation by the WDR5 module of the MLL1 complex. Nature Struct. Mol. Biol. 13, 704-712. 
Malinina, L., Malakhova, M. L., Kanack, A. T., Brown, R. E. & Patel, D. J. (2006). The liganding mode   of glycolipid transfer protein is controlled by glycolipid acyl structure. PLoS Biol 4, 1996-2011.
Taverna, S. D., Illin, S., Rogers, R. S., Tanny, J. C., Lavender, H., Li, H., Baker, L., Boyle, J., Blair, L. P., Chait, B., Patel, D. J., Aitchison, J. D., Tackett, A. J. & Allis, C. D. (2006). Yng1 PHD finger binding to H3 trimethylated at K4 targets promotes NuA3 HAT activity at K14 of H3 and transcription at a subset of targeted ORFs. Mol. Cell 24, 785-796.
Zhang, X., Yuan, Y-R., Pei, Y., Tuschl, T., Patel, D. J. & Chua, N-H. (2006). Cucumber mosaic virus-encoded 2b suppressor inhibits Arabidopsis AGO1 cleavage activity to counter plant defense. Genes Dev. 20, 3255-3268.
Patel, D. J., Ma, J-B., Yuan, Y-R., Ye, K., Pei, Y., Kuryavyi, V., Malinina, L., Meister, G. & Tuschl, T. (2007). Structural biology of RNA silencing and its functional implications. Regulatory RNAs, 71, 81-93, Cold Spring Harbor Laboratory Press, New York.
Phan, A. T., Kuryavyi, V., Burge, S., Neidle, S. & Patel, D. J. (2007). Structure of an unprecedented G-quadruplex scaffold adopted by the human c-kit promotor. J. Am. Chem. Soc. 129, 4386-4392.
Bailor, M. H., Musselman, C., Hansen, A. L., Gulati, K., Patel, D. J. & Al-Hashimi, H. M. (2007). Characterizing the relative orientation and dynamics of RNA A-form helices using NMR residual dipolar couplings. Nat. Protocols 2, 1536-1546.
Phan, A. T., Kuryavyi, V., Luu. K. N. & Patel, D. J. (2007). Structure of two intramolecular G-quadruplexes formed by natural human telomere sequences in K+ solution. Nuc. Acids Res. 35, 6517-6525.
Phan, A. T., Kuryavyi, V., Burge, S., Neidle, S. & Patel, D. J. (2007). Structure of an unprecedented G-quadruplex scaffold adopted by the human c-kit promotor. J. Am. Chem. Soc. 129, 4386-4392.
Li, H., Wang, W. K., Fischle, W., Duncan, E. M., Liang, L., Allis, C. D. & Patel, D. J. (2007). Structural basis for lower lysine methylation state-specific readout by MBT repeats and an engineered PHD finger module. Mol. Cell 28, 677-691.
Taverna, S. D., Li, H., Ruthenburg, A. J., Allis, C. D. & Patel, D. J. (2007). How chromatin-binding modules interpret histone modifications: Lessons from professional pocket pickers. Nat. Struct. Mol. Biol. 14, 1025-1040.
Serganov, A. & Patel, D. J. (2007). Ribozymes and riboswitches: beyond simple RNA. Nat. Rev. Genetics 8, 776-790.
Ruthenburg, A. J., Li, H., Patel, D. J. & Allis, C. D. (2007). Multivalent engagement of chromatin modifications by linked binding modules. Nat. Rev. Mol. Cell Biol. 8, 983-994.