Center for RNA Biology Publications
Ohio State University has a large concentration of research labs with interests in RNA research. These laboratories constitute an interdisciplinary group focused on the biochemistry, molecular biology, structure and function of RNA. Organizing RNA research in this manner facilitates sharing of reagents and technologies, collaborations and joint research grants, expanded course offerings, and expanded opportunities for trainees to develop their research careers. In 2008, research expenditures for the RNA group totaled over $8 million, resulting in 80 publications. Over the past three years, members of the Center for RNA Biology have published in the most prestigious scientific journals including the following 77 publications:
Nataliya Miropolskaya, Irina Artsimovitch, Saulius Klimasauskas, Vadim Nikiforov, and Andrey Kulbachinskiy
"Allosteric control of catalysis by the F loop of RNA polymerase."
Proc. Natl. Acad. Sci. U.S.A. 106, 18942-7 (2009).Daniel R Schoenberg and Lynne E Maquat
"Re-capping the message."
Trends Biochem. Sci. 34, 435-42 (2009).Stefan Costinean, Sukhinder K Sandhu, Irene M Pedersen, Esmerina Tili, Rossana Trotta, Danilo Perrotti, David Ciarlariello, Paolo Neviani, Jason Harb, Lauren Rachel Kauffman, Aaditya Shidham, and Carlo Maria Croce
"Src homology 2 domain-containing inositol-5-phosphatase and CCAAT enhancer-binding protein beta are targeted by miR-155 in B cells of Emicro-MiR-155 transgenic mice."
Blood 114, 1374-82 (2009).Ramiro Garzon, Shujun Liu, Muller Fabbri, Zhongfa Liu, Catherine E A Heaphy, Elisa Callegari, Sebastian Schwind, Jiuxia Pang, Jianhua Yu, Natarajan Muthusamy, Violaine Havelange, Stefano Volinia, William Blum, Laura J Rush, Danilo Perrotti, Michael Andreeff, Clara D Bloomfield, John C Byrd, Kenneth Chan, Lai-Chu Wu, Carlo M Croce, and Guido Marcucci
"MicroRNA-29b induces global DNA hypomethylation and tumor suppressor gene reexpression in acute myeloid leukemia by targeting directly DNMT3A and 3B and indirectly DNMT1."
Blood 113, 6411-8 (2009).Don M Benson, Jianhua Yu, Brian Becknell, Min Wei, Aharon G Freud, Amy K Ferketich, Rossana Trotta, Danilo Perrotti, Roger Briesewitz, and Michael A Caligiuri
"Stem cell factor and interleukin-2/15 combine to enhance MAPK-mediated proliferation of human natural killer cells."
Blood 113, 2706-14 (2009).Jiqiang Ling, Byung Ran So, Srujana S Yadavalli, Hervé Roy, Shinichiro Shoji, Kurt Fredrick, Karin Musier-Forsyth, and Michael Ibba
"Resampling and editing of mischarged tRNA prior to translation elongation."
Mol. Cell 33, 654-60 (2009).Georgiy A Belogurov, Rachel A Mooney, Vladimir Svetlov, Robert Landick, and Irina Artsimovitch
"Functional specialization of transcription elongation factors."
EMBO J. 28, 112-22 (2009).Georgiy A Belogurov, Marina N Vassylyeva, Anastasiya Sevostyanova, James R Appleman, Alan X Xiang, Ricardo Lira, Stephen E Webber, Sergiy Klyuyev, Evgeny Nudler, Irina Artsimovitch, and Dmitry G Vassylyev
"Transcription inactivation through local refolding of the RNA polymerase structure."
Nature 457, 332-5 (2009).Robin P Wharton
"A splicer that represses translation."
Genes Dev. 23, 133-7 (2009).Shuiming Qian, Xuehua Zhong, Lianbo Yu, Biao Ding, Peter de Haan, and Kathleen Boris-Lawrie
"HIV-1 Tat RNA silencing suppressor activity is conserved across kingdoms and counteracts translational repression of HIV-1."
Proc. Natl. Acad. Sci. U.S.A. 106, 605-10 (2009).Kurt Fredrick and Michael Ibba
"Protein synthesis Errors rectified in retrospect."
Nature 457, 157-8 (2009).Tina M Henkin
"Riboswitch RNAs using RNA to sense cellular metabolism."
Genes Dev. 22, 3383-90 (2008).Srujana S Yadavalli, Karin Musier-Forsyth, and Michael Ibba
"The return of pretransfer editing in protein synthesis."
Proc. Natl. Acad. Sci. U.S.A. 105, 19031-2 (2008).Huating Wang, Ramiro Garzon, Hao Sun, Katherine J Ladner, Ravi Singh, Jason Dahlman, Alfred Cheng, Brett M Hall, Stephen J Qualman, Dawn S Chandler, Carlo M Croce, and Denis C Guttridge
"NF-kappaB-YY1-miR-29 regulatory circuitry in skeletal myogenesis and rhabdomyosarcoma."
Cancer Cell 14, 369-81 (2008).Joshua Arnold, Bevin Zimmerman, Min Li, Michael D Lairmore, and Patrick L Green
"Human T-cell leukemia virus type-1 antisense-encoded gene, Hbz, promotes T-lymphocyte proliferation."
Blood 112, 3788-97 (2008).Changrui Lu, Angela M Smith, Ryan T Fuchs, Fang Ding, Kanagalaghatta Rajashankar, Tina M Henkin, and Ailong Ke
"Crystal structures of the SAM-III/SMK riboswitch reveal the SAM-dependent translation inhibition mechanism."
Nat. Struct. Mol. Biol. 15, 1076-83 (2008).Weimin Gong, Bing Hao, Zhiyi Wei, Donald J Ferguson, Thomas Tallant, Joseph A Krzycki, and Michael K Chan
"Structure of the alpha2epsilon2 Ni-dependent CO dehydrogenase component of the Methanosarcina barkeri acetyl-CoA decarbonylase/synthase complex."
Proc. Natl. Acad. Sci. U.S.A. 105, 9558-63 (2008).Sarah E Walker, Shinichiro Shoji, Dongli Pan, Barry S Cooperman, and Kurt Fredrick
"Role of hybrid tRNA-binding states in ribosomal translocation."
Proc. Natl. Acad. Sci. U.S.A. 105, 9192-7 (2008).Mary Anne T Rubio, Jesse J Rinehart, Bethany Krett, Stéphane Duvezin-Caubet, Andreas S Reichert, Dieter Söll, and Juan D Alfonzo
"Mammalian mitochondria have the innate ability to import tRNAs by a mechanism distinct from protein import."
Proc. Natl. Acad. Sci. U.S.A. 105, 9186-91 (2008).Krystian Jazdzewski, Elizabeth L Murray, Kaarle Franssila, Barbara Jarzab, Daniel R Schoenberg, and Albert de la Chapelle
"Common SNP in pre-miR-146a decreases mature miR expression and predisposes to papillary thyroid carcinoma."
Proc. Natl. Acad. Sci. U.S.A. 105, 7269-74 (2008).Yogesh K Gupta, Deepak T Nair, Robin P Wharton, and Aneel K Aggarwal
"Structures of human Pumilio with noncognate RNAs reveal molecular mechanisms for binding promiscuity."
Structure 16, 549-57 (2008).Hervé Roy and Michael Ibba
"RNA-dependent lipid remodeling by bacterial multiple peptide resistance factors."
Proc. Natl. Acad. Sci. U.S.A. 105, 4667-72 (2008).Anita K Hopper and Hussam H Shaheen
"A decade of surprises for tRNA nuclear-cytoplasmic dynamics."
Trends Cell Biol. 18, 98-104 (2008).Nikhil H Gokhale, Seth Bradford, and J A Cowan
"Catalytic inactivation of human carbonic anhydrase I by a metallopeptide-sulfonamide conjugate is mediated by oxidation of active site residues."
J. Am. Chem. Soc. 130, 2388-9 (2008).Min Guo, Michael Ignatov, Karin Musier-Forsyth, Paul Schimmel, and Xiang-Lei Yang
"Crystal structure of tetrameric form of human lysyl-tRNA synthetase Implications for multisynthetase complex formation."
Proc. Natl. Acad. Sci. U.S.A. 105, 2331-6 (2008).Shujun Liu, Zhongfa Liu, Zhiliang Xie, Jiuxia Pang, Jianhua Yu, Esther Lehmann, Lenguyen Huynh, Tamara Vukosavljevic, Mitsui Takeki, Rebecca B Klisovic, Robert A Baiocchi, William Blum, Pierluigi Porcu, Ramiro Garzon, John C Byrd, Danilo Perrotti, Michael A Caligiuri, Kenneth K Chan, Lai-Chu Wu, and Guido Marcucci
"Bortezomib induces DNA hypomethylation and silenced gene transcription by interfering with Sp1/NF-kappaB-dependent DNA methyltransferase activity in acute myeloid leukemia."
Blood 111, 2364-73 (2008).Anastasiya Sevostyanova, Vladimir Svetlov, Dmitry G Vassylyev, and Irina Artsimovitch
"The elongation factor RfaH and the initiation factor sigma bind to the same site on the transcription elongation complex."
Proc. Natl. Acad. Sci. U.S.A. 105, 865-70 (2008).Anna M Eiring, Paolo Neviani, Ramasamy Santhanam, Joshua J Oaks, Ji Suk Chang, Mario Notari, William Willis, Carlo Gambacorti-Passerini, Stefano Volinia, Guido Marcucci, Michael A Caligiuri, Gustavo W Leone, and Danilo Perrotti
"Identification of novel posttranscriptional targets of the BCR/ABL oncoprotein by ribonomics requirement of E2F3 for BCR/ABL leukemogenesis."
Blood 111, 816-28 (2008).Xuehua Zhong, Anthony J Archual, Amy A Amin, and Biao Ding
"A genomic map of viroid RNA motifs critical for replication and systemic trafficking."
Plant Cell 20, 35-47 (2008).Qing Liu, Xiaobin Zhao, Frank Frissora, Yihui Ma, Ramasamy Santhanam, David Jarjoura, Amy Lehman, Danilo Perrotti, Ching-Shih Chen, James T Dalton, Natarajan Muthusamy, and John C Byrd
"FTY720 demonstrates promising preclinical activity for chronic lymphocytic leukemia and lymphoblastic leukemia/lymphoma."
Blood 111, 275-84 (2008).Irina Artsimovitch and Dmitry G Vassylyev
"Merging the RNA and DNA worlds."
Nat. Struct. Mol. Biol. 14, 1122-3 (2007).Ted Weinert and Anita K Hopper
"tRNA traffic meets a cell-cycle checkpoint."
Cell 131, 838-40 (2007).Steffen Koschmieder, Francesco DAlò, Hanna Radomska, Christine Schöneich, Ji Suk Chang, Marina Konopleva, Susumu Kobayashi, Elena Levantini, Nanjoo Suh, Annalisa Di Ruscio, Maria Teresa Voso, Julie C Watt, Ramasamy Santhanam, Bülent Sargin, Hagop Kantarjian, Michael Andreeff, Michael B Sporn, Danilo Perrotti, Wolfgang E Berdel, Carsten Müller-Tidow, Hubert Serve, and Daniel G Tenen
"CDDO induces granulocytic differentiation of myeloid leukemic blasts through translational up-regulation of p42 CCAAT enhancer binding protein alpha."
Blood 110, 3695-705 (2007).Marina N Vassylyeva, Vladimir Svetlov, Altaira D Dearborn, Sergiy Klyuyev, Irina Artsimovitch, and Dmitry G Vassylyev
"The carboxy-terminal coiled-coil of the RNA polymerase beta-subunit is the main binding site for Gre factors."
EMBO Rep. 8, 1038-43 (2007).Emily K Thomas, Jose A Cancelas, Hee-Don Chae, Adrienne D Cox, Patricia J Keller, Danilo Perrotti, Paolo Neviani, Brian J Druker, Kenneth D R Setchell, Yi Zheng, Chad E Harris, and David A Williams
"Rac guanosine triphosphatases represent integrating molecular therapeutic targets for BCR-ABL-induced myeloproliferative disease."
Cancer Cell 12, 467-78 (2007).Annamaria Galietta, Rosalind H Gunby, Sara Redaelli, Paola Stano, Cristiana Carniti, Angela Bachi, Philip W Tucker, Carmen J Tartari, Ching-Jung Huang, Emanuela Colombo, Karen Pulford, Miriam Puttini, Rocco G Piazza, Holger Ruchatz, Antonello Villa, Arianna Donella-Deana, Oriano Marin, Danilo Perrotti, and Carlo Gambacorti-Passerini
"NPM/ALK binds and phosphorylates the RNA/DNA-binding protein PSF in anaplastic large-cell lymphoma."
Blood 110, 2600-9 (2007).Jiqiang Ling, Hervé Roy, Daoming Qin, Mary Anne T Rubio, Juan D Alfonzo, Kurt Fredrick, and Michael Ibba
"Pathogenic mechanism of a human mitochondrial tRNAPhe mutation associated with myoclonic epilepsy with ragged red fibers syndrome."
Proc. Natl. Acad. Sci. U.S.A. 104, 15299-304 (2007).Daniel R Schoenberg
"The end defines the means in bacterial mRNA decay."
Nat. Chem. Biol. 3, 535-6 (2007).Xuehua Zhong, Xiaorong Tao, Jesse Stombaugh, Neocles Leontis, and Biao Ding
"Tertiary structure and function of an RNA motif required for plant vascular entry to initiate systemic trafficking."
EMBO J. 26, 3836-46 (2007).Christy F Landes, Yining Zeng, Hsiao-Wei Liu, Karin Musier-Forsyth, and Paul F Barbara
"Single-molecule study of the inhibition of HIV-1 transactivation response region DNA/DNA annealing by argininamide."
J. Am. Chem. Soc. 129, 10181-8 (2007).Michael A Caligiuri, Roger Briesewitz, Jianhua Yu, Lisheng Wang, Min Wei, Kristy J Arnoczky, Trent B Marburger, Jing Wen, Danilo Perrotti, Clara D Bloomfield, and Susan P Whitman
"Novel c-CBL and CBL-b ubiquitin ligase mutations in human acute myeloid leukemia."
Blood 110, 1022-4 (2007).Ji Suk Chang, Ramasamy Santhanam, Rossana Trotta, Paolo Neviani, Anna M Eiring, Edward Briercheck, Mattia Ronchetti, Denis C Roy, Bruno Calabretta, Michael A Caligiuri, and Danilo Perrotti
"High levels of the BCR/ABL oncoprotein are required for the MAPK-hnRNP-E2 dependent suppression of C/EBPalpha-driven myeloid differentiation."
Blood 110, 994-1003 (2007).Yining Zeng, Hsiao-Wei Liu, Christy F Landes, Yoen Joo Kim, Xiaojing Ma, Yongjin Zhu, Karin Musier-Forsyth, and Paul F Barbara
"Probing nucleation, reverse annealing, and chaperone function along the reaction path of HIV-1 single-strand transfer."
Proc. Natl. Acad. Sci. U.S.A. 104, 12651-6 (2007).Dmitry G Vassylyev, Marina N Vassylyeva, Anna Perederina, Tahir H Tahirov, and Irina Artsimovitch
"Structural basis for transcription elongation by bacterial RNA polymerase."
Nature 448, 157-62 (2007).Dmitry G Vassylyev, Marina N Vassylyeva, Jinwei Zhang, Murali Palangat, Irina Artsimovitch, and Robert Landick
"Structural basis for substrate loading in bacterial RNA polymerase."
Nature 448, 163-8 (2007).Yan Jin, Mark A Lewis, Nikhil H Gokhale, Eric C Long, and J A Cowan
"Influence of stereochemistry and redox potentials on the single- and double-strand DNA cleavage efficiency of CuII and NiII Lys-Gly-His-derived ATCUN metallopeptides."
J. Am. Chem. Soc. 129, 8353-61 (2007).Hussam H Shaheen, Rick L Horetsky, Scot R Kimball, Athulaprabha Murthi, Leonard S Jefferson, and Anita K Hopper
"Retrograde nuclear accumulation of cytoplasmic tRNA in rat hepatoma cells in response to amino acid deprivation."
Proc. Natl. Acad. Sci. U.S.A. 104, 8845-50 (2007).Mary Anne T Rubio, Irena Pastar, Kirk W Gaston, Frank L Ragone, Christian J Janzen, George A M Cross, F Nina Papavasiliou, and Juan D Alfonzo
"An adenosine-to-inosine tRNA-editing enzyme that can perform C-to-U deamination of DNA."
Proc. Natl. Acad. Sci. U.S.A. 104, 7821-6 (2007).Georgiy A Belogurov, Marina N Vassylyeva, Vladimir Svetlov, Sergiy Klyuyev, Nick V Grishin, Dmitry G Vassylyev, and Irina Artsimovitch
"Structural basis for converting a general transcription factor into an operon-specific virulence regulator."
Mol. Cell 26, 117-29 (2007).Hsiao-Wei Liu, Yining Zeng, Christy F Landes, Yoen Joo Kim, Yongjin Zhu, Xiaojing Ma, My-Nuong Vo, Karin Musier-Forsyth, and Paul F Barbara
"Insights on the role of nucleic acid/protein interactions in chaperoned nucleic acid rearrangements of HIV-1 reverse transcription."
Proc. Natl. Acad. Sci. U.S.A. 104, 5261-7 (2007).Ryan T Fuchs, Frank J Grundy, and Tina M Henkin
"S-adenosylmethionine directly inhibits binding of 30S ribosomal subunits to the SMK box translational riboswitch RNA."
Proc. Natl. Acad. Sci. U.S.A. 104, 4876-80 (2007).Brian Becknell, Tiffany L Hughes, Aharon G Freud, Bradley W Blaser, Jianhua Yu, Rossana Trotta, Hsiaoyin C Mao, Marie L Caligiuri de Jesús, Mohamad Alghothani, Don M Benson, Amy Lehman, David Jarjoura, Danilo Perrotti, Michael D Bates, and Michael A Caligiuri
"Hlx homeobox transcription factor negatively regulates interferon-gamma production in monokine-activated natural killer cells."
Blood 109, 2481-7 (2007).Yong Peng and Daniel R Schoenberg
"c-Src activates endonuclease-mediated mRNA decay."
Mol. Cell 25, 779-87 (2007).Venkat Gopalan
"Uniformity amid diversity in RNase P."
Proc. Natl. Acad. Sci. U.S.A. 104, 2031-2 (2007).Julius SternJohn, Sanchita Hati, Paul G Siliciano, and Karin Musier-Forsyth
"Restoring species-specific posttransfer editing activity to a synthetase with a defunct editing domain."
Proc. Natl. Acad. Sci. U.S.A. 104, 2127-32 (2007).Jean-Claude Twizere, Jean-Yves Springael, Mathieu Boxus, Arsène Burny, Franck Dequiedt, Jean-François Dewulf, Julie Duchateau, Daniel Portetelle, Patrice Urbain, Carine Van Lint, Patrick L Green, Renaud Mahieux, Marc Parmentier, Luc Willems, and Richard Kettmann
"Human T-cell leukemia virus type-1 Tax oncoprotein regulates G-protein signaling."
Blood 109, 1051-60 (2007).David G Longstaff, Ross C Larue, Joseph E Faust, Anirban Mahapatra, Liwen Zhang, Kari B Green-Church, and Joseph A Krzycki
"A natural genetic code expansion cassette enables transmissible biosynthesis and genetic encoding of pyrrolysine."
Proc. Natl. Acad. Sci. U.S.A. 104, 1021-6 (2007).Jiqiang Ling, Hervé Roy, and Michael Ibba
"Mechanism of tRNA-dependent editing in translational quality control."
Proc. Natl. Acad. Sci. U.S.A. 104, 72-7 (2007).Shinichiro Shoji, Sarah E Walker, and Kurt Fredrick
"Reverse translocation of tRNA in the ribosome."
Mol. Cell 24, 931-42 (2006).Amanda J Bird, Mat Gordon, David J Eide, and Dennis R Winge
"Repression of ADH1 and ADH3 during zinc deficiency by Zap1-induced intergenic RNA transcripts."
EMBO J. 25, 5726-34 (2006).Hsin-Yue Tsai, Dileep K Pulukkunat, Walter K Woznick, and Venkat Gopalan
"Functional reconstitution and characterization of Pyrococcus furiosus RNase P."
Proc. Natl. Acad. Sci. U.S.A. 103, 16147-52 (2006).Young-Jin Lee, Letetia C Jones, Nikolai A Timchenko, Danilo Perrotti, Daniel G Tenen, and Scott C Kogan
"CCAAT/enhancer binding proteins alpha and epsilon cooperate with all-trans retinoic acid in therapy but differ in their antileukemic activities."
Blood 108, 2416-9 (2006).Hervé Roy and Michael Ibba
"Molecular biology sticky end in protein synthesis."
Nature 443, 41-2 (2006).Daniel J Battle, Chi-Kong Lau, Lili Wan, Hongying Deng, Francesco Lotti, and Gideon Dreyfuss
"The Gemin5 protein of the SMN complex identifies snRNAs."
Mol. Cell 23, 273-9 (2006).Jane E Jackman and Eric M Phizicky
"tRNAHis guanylyltransferase catalyzes a 3-5 polymerization reaction that is distinct from G-1 addition."
Proc. Natl. Acad. Sci. U.S.A. 103, 8640-5 (2006).Wei Qiao, Michelle Mooney, Amanda J Bird, Dennis R Winge, and David J Eide
"Zinc binding to a regulatory zinc-sensing domain monitored in vivo by using FRET."
Proc. Natl. Acad. Sci. U.S.A. 103, 8674-9 (2006).Tiffiney Roberts Hartman, Shuiming Qian, Cheryl Bolinger, Soledad Fernandez, Daniel R Schoenberg, and Kathleen Boris-Lawrie
"RNA helicase A is necessary for translation of selected messenger RNAs."
Nat. Struct. Mol. Biol. 13, 509-16 (2006).Jianrong Li, Jennifer T Wang, and Sean P J Whelan
"A unique strategy for mRNA cap methylation used by vesicular stomatitis virus."
Proc. Natl. Acad. Sci. U.S.A. 103, 8493-8 (2006).Joshua Arnold, Brenda Yamamoto, Min Li, Andrew J Phipps, Ihab Younis, Michael D Lairmore, and Patrick L Green
"Enhancement of infectivity and persistence in vivo by HBZ, a natural antisense coded protein of HTLV-1."
Blood 107, 3976-82 (2006).Clara Guerzoni, Michela Bardini, Samanta A Mariani, Giovanna Ferrari-Amorotti, Paolo Neviani, Maria Luisa Panno, Ying Zhang, Robert Martinez, Danilo Perrotti, and Bruno Calabretta
"Inducible activation of CEBPB, a gene negatively regulated by BCR/ABL, inhibits proliferation and promotes differentiation of BCR/ABL-expressing cells."
Blood 107, 4080-9 (2006).Cheng-Yu Lee, Brian D Wilkinson, Sarah E Siegrist, Robin P Wharton, and Chris Q Doe
"Brat is a Miranda cargo protein that promotes neuronal differentiation and inhibits neuroblast self-renewal."
Dev. Cell 10, 441-9 (2006).Mario Notari, Paolo Neviani, Ramasamy Santhanam, Bradley W Blaser, Ji-Suk Chang, Annamaria Galietta, Anne E Willis, Denis C Roy, Michael A Caligiuri, Guido Marcucci, and Danilo Perrotti
"A MAPK/HNRPK pathway controls BCR/ABL oncogenic potential by regulating MYC mRNA translation."
Blood 107, 2507-16 (2006).Li Xie, Brenda Yamamoto, Abdelali Haoudi, O John Semmes, and Patrick L Green
"PDZ binding motif of HTLV-1 Tax promotes virus-mediated T-cell proliferation in vitro and persistence in vivo."
Blood 107, 1980-8 (2006).Ryan T Fuchs, Frank J Grundy, and Tina M Henkin
"The SMK box is a new SAM-binding RNA for translational regulation of SAM synthetase."
Nat. Struct. Mol. Biol. 13, 226-33 (2006).Ross C Wilson, Christopher J Bohlen, Mark P Foster, and Charles E Bell
"Structure of Pfu Pop5, an archaeal RNase P protein."
Proc. Natl. Acad. Sci. U.S.A. 103, 873-8 (2006).David R Engelke and Anita K Hopper
"Modified view of tRNA stability amid sequence diversity."
Mol. Cell 21, 144-5 (2006).Yan Jin and J A Cowan
"Targeted cleavage of HIV rev response element RNA by metallopeptide complexes."
J. Am. Chem. Soc. 128, 410-1 (2006).
