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at the Weill Cornell Medical College of Cornell University

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SELECTED PUBLICATIONS

For a more complete list, check Pubmed

Grozhik, A.V., Jaffrey S.R.  Shrinking maps of RNA modifications.  Nature, 551:174-176, 2017.  Read this online here.

Patil, D.P., Pickering, B.F., Jaffrey S.R.  Reading m6A in the transcriptome: m6A-binding proteins.  Trends in Cell Biology, in press, 2017.  Read this online here.

Dumelie, J., Jaffrey S.R.  Defining the location of promoter-associated R-loops at near-nucleotide resolution using bisDRIP-seq. eLIFE, in press, 2017.  Read this online here.

Meyer K.D., Jaffrey S.R.  Rethinking m6A Readers, Writers, and Erasers.  Annual Review of Cell and Developmental Biology, 33:319-342, 2017. Read this online here.

Vu, L.P., Pickering, B.F., Cheng, Y., Zaccara, S., Nguyen, D., Minuesa, G., Chou, T., Chow, A., Saletore, Y., MacKay, M., Schulman, J., Famulare, C., Patel, M., Klimek, V. M., Garrett-Bakelman, F.E., Melnick, A., Carroll, M., Mason, C. E., Jaffrey, S.R.*, and Kharas, M.G.* The N6-methyladenosine (m6A)-forming enzyme METTL3 controls myeloid differentiation of normal hematopoietic and leukemia cells. Nature Medicine, 23:1369-1376, 2017.  Read this online here.  Read the News and Views on this article here.

Song, W., Filonov, G.S., Kim, H., Hirsch, M., Li, X., Moon, J. D., Jaffrey, S. R. Imaging RNA polymerase III transcription using a photostable RNA-fluorophore complex. Nature Chemical Biology, 13:1187-1194, 2017.  Read this online here.  Read the News and Views on this article here.

Warner, K.D., Sjekloća, L., Song, W., Filonov, G.S., Jaffrey, S.R., Ferré-D’Amaré, A.R.  A homodimer interface without base pairs in an RNA mimic of red fluorescent protein. Nature Chemical Biology, 13:1195-1201, 2017.  Read this online here.  Read the News and Views on this article here.

Kan, L., Grozhik, A.V., Vedanayagam, J., Patil, D.P., Pang, N., Lim, K.-S., Huang, Y.-C., Joseph, B., Lin, C.-J., Despic, V., Guo, J., Yan, D., Kondo, S., Deng, W.-M., Dedon, P.C., Jaffrey, S.R., Lai, E.C.  The m6A pathway facilitates sex determination in Drosophila. Nature Communications, 8:15737, 2017.  Read this online here.

Grozhik A.V., Linder B., Olarerin-George A.O., Jaffrey S.R. Mapping m6A at Individual-Nucleotide Resolution Using Crosslinking and Immunoprecipitation (miCLIP). Methods Molecular Biology, 1562:55-78, 2017.  Read this online here.

Olarerin-George A.O., Jaffrey S.R. MetaPlotR: a Perl/R pipeline for plotting metagenes of nucleotide modifications and other transcriptomic sites. Bioinformatics, 33:1563-1564, 2017.  Read this online here.

Jaffrey, S.R.*, and Kharas, M.G.* Emerging links between m6A and misregulated mRNA methylation in cancer. Genome Medicine, 9:2, 2017.  Read this online here.

Mauer, J., Luo, X., Blanjoie, A., Jiao, X., Grozhik, A.V., Patil, D.P., Vasseur, J.-J., Chen, Q., Gross, S.S., Elemento, O., Debart, F., Kiledjian, M., Jaffrey, S.R.  Reversible methylation of m6Am in the 5’ cap controls mRNA stability.  Nature, 541:371-375, 2017.  Read this online here.  Read the News and Views on this article here.

Patil, D.P., Chen, C.-K., Pickering, B.F., Chow A., Jackson C., Guttman, M., Jaffrey, S.R.  m6A RNA methylation promotes XIST-mediated transcriptional repression. Nature, 537:369-73, 2016. Read this online here.

Litke J.L., You M., Jaffrey S.R., Developing Fluorogenic Riboswitches for Imaging Metabolite Concentration Dynamics in Bacterial Cells. Methods in Enzymology, 572:315-33, 2016. Read this online here.

Laptenok, S.P., Conyard J., Bulman Page, P.C., Chan Y., You, M., Jaffrey, S.R., Meech, S.R. Photoacid Behaviour in a Fluorinated Green Fluorescent Protein Chromophore: Ultrafast Formation of Anion and Zwitterion States, Chemical Science, 7:5747-5752, 2016. Read this online here.

Svensen, N., Jaffrey, S.R.  Fluorescent RNA aptamers as a tool to study RNA-modifying enzymes.  Cell Chemical Biology, 23:415-25, 2016.  Read this online here. Read a commentary on this article here.
 
Meyer, K.D., Patil, D.P., Zhou, J., Zinoviev, A., Skabkin, M.A., Elemento, O., Pestova, T.V., Qian, S.-B., Jaffrey, S.R.  5'UTR m6A promotes cap-independent translation.  Cell, 163:999-1010, 2015. Read this online here.  Read a commentary on this paper here.

Zhou, J., Wan, J., Gao, X., Zhang, X., Jaffrey, S.R., Qian, S.-B.  Dynamic m6A mRNA methylation directs translational control of heat shock response.  Nature, 526:591-4, 2015. Read this online here.

Miyawaki, A., Jaffrey, S.R.  Editorial overview: Molecular imaging: Cellular imaging approaches.  Current Opinion in Chemical Biology, 27:v-vi, 2015.

Liu, Y., Huang, X., He, X., Zhou, Y., Jiang X., Chen-Kiang, S., Jaffrey, S.R., Xu, G. A novel effect of thalidomide and its analogs: suppression of cereblon ubiquitination enhances ubiquitin ligase function.  FASEB J., 29:4829-39, 2015.

You, M., Jaffrey, S.R.  Structure and Mechanism of RNA Mimics of Green Fluorescent Protein.  Annual Review of Biophysics, 44:187-206, 2015.  Read this online here.

Lu, Z., Filonov, G.S., Noto, J.J., Schmidt, C.A., Hatkevich-O’Donnell, T., Wen, Y., Jaffrey, S.R., Matera, A.G.  Metazoan tRNA introns generate stable circular RNAs. RNA, in press.  Read this online here.

Linder, B., Grozhik, A.V., Olarerin-George, A.O., Meydan, C., Mason, C.E., Jaffrey, SR. Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome.  Nature Methods, 12:767-772, 2015.  Read this online here.

You, M., Litke, J.L., Jaffrey, S.R.  Imaging metabolite dynamics in living cells using a Spinach-based riboswitch.  Proc. Natl. Acad. Sci. USA., 112:E2756-65, 2015.  Read this online here.

Filonov, G.S. Kam, C.W., Song, W., Jaffrey, S.R.  In-gel imaging of RNA processing using Broccoli reveals optimal aptamer expression strategies.  Chemistry & Biology, 22:649-60, 2015.  Read this online here.

Deglincerti, A., Liu, Y., Colak, D., Hengst, U., Xu, G., Jaffrey, S.R.  Coupled local translation and degradation regulate growth cone collapse.  Nature Communications, 6:6888, doi: 10.1038/ncomms7888, 2015.  Read this online here.

You, M., Jaffrey, S.R. Designing optogenetically controlled RNA for regulating biological systems. Ann. N.Y. Acad. Sci., in press.  Read this online here.

Strack, R.L., Jaffrey, S.R. Live-cell imaging of mammalian RNAs with Spinach2. Methods in Enzymology, 550:129-46, 2015.  Read this online here.

Witkin K.L., Hanlon S.E., Strasburger J.A., Coffin J.M., Jaffrey S.R., Howcroft T.K., Dedon P.C., Steitz J.A., Daschner P.J., Read-Connole E.  RNA editing, epitranscriptomics, and processing in cancer progression.  Cancer Biol Ther. 16:21-7, 2015.  

Brown, K.D., Maqsood, S., Huang, J.-Y., Pan, Y., Harkcom, W., Li, W., Sauve, A., Verdin, E., Jaffrey, S.R.  Activation of SIRT3 by the NAD+ precursor nicotinamide riboside protects from noise-induced hearing loss, Cell Metabolism, 20:1059-1068, 2014.  Read this online here.

Jaffrey, S.R.  An expanding universe of mRNA modifications. Nature Struct. Mol. Biol., 21:945-946, 2014.  Read this online here.

Filonov, G.S., Moon, J.D., Svensen, N, Jaffrey, S.R.  Broccoli: Rapid selection of an RNA mimic of green fluorescent protein by fluorescence-based selection and directed evolution. Journal of the American Chemical Society, 136:16299-16308, 2014.  Read this online here.

Warner, K.D., Chen, M.C., Song, W., Strack, R.L., Thorn, A., Jaffrey, S.R., Ferré-D’Amaré, A.R.  Structural basis for activity of highly efficient RNA mimics of green fluorescent protein. Nature Struct. Mol. Biol., 21:658-663, 2014.  Read this online here.

Harkcom, W.T., Ghosh, A.K., Sung, M.S., Matov, A., Brown, K.D., Giannakakou, P., Jaffrey, S.R. NAD+ and SIRT3 control microtubule dynamics and reduce susceptibility to anti-microtubule agents. Proc. Natl. Acad. Sci. USA., 111:E2443-52, 2014.  Read this online here.

Meyer, K.D., Jaffrey, S.R. The dynamic epitranscriptome: N6-methyladenosine and gene expression control. Nature Reviews Molecular Cell Biology, 15:313-26, 2014.  Read this online here.

Colak, D., Zaninovic, N., Cohen, M.S., Rosenwaks, Z., Yang, W.-Y., Gerhardt, J., Disney, M.D., Jaffrey, S.R. Promoter-bound trinucleotide repeat mRNA drives epigenetic silencing in Fragile X syndrome. Science, 343:1002-1005, 2014. Read this online here.  Read a commentary on this paper here.

Lundquist, M.R., Storaska, A., Liu, T.-C., Larsen, S.D., Evans, T., Neubig, R.R., Jaffrey, S.R. Redox modification of nuclear actin by MICAL-2 regulates SRF signaling. Cell, 156:563-576, 2014.  Read this online here.

Song, W., Strack, R.L., Svensen, N., Jaffrey, S.R. Plug-and-play fluorophores extend the spectral properties of Spinach. Journal of the American Chemical Society, in press, 2014.  Read this online here.  Read what people are saying about this article here.

Gerhardt, J., Tomishima, M.J., Zaninovic, N., Colak, D., Yan, Z., Zhan, Q., Rosenwaks, Z., Jaffrey, S.R., and Schildkraut, C.L. The DNA replication program is altered at the FMR1 locus in fragile X embryonic stem cells. Molecular Cell, 53:19-31, 2014. Read this online here.

Strack, R.L., Song, W., Jaffrey, S.R.  Using Spinach-based sensors for fluorescence imaging of intracellular metabolites and proteins in living bacteria. Nature Protocols, Nature Protocols, 9:146-55, 2014.  Read this online here.

Strack, R.L., Disney, M.D., Jaffrey, S.R. A superfolding Spinach2 reveals the dynamic nature of trinucleotide repeat RNA. Nature Methods, 10:1219-1224, 2013.  Read this online here.

Xu, G., Jiang, X. Jaffrey, S.R. A mental retardation-linked nonsense mutation in cereblon is rescued by proteasome inhibition. Journal of Biological Chemistry, 288:29573-29585, 2013.

Curanovic, D., Cohen, M., Slagle, C.E., Singh, I., Leslie, C.S., Jaffrey, S.R. Transcriptome-wide profiling of stimulus-induced polyadenylation in living cells using a poly(A) trap. Nature Chemical Biology, 9:671-3, 2013.  Read this online here.

Ji, S.-J., Jaffrey, S.R. Axonal transcription factors: Novel regulators of growth cone-to-nucleus signaling. Developmental Neurobiology, in press, 2013.

Xu, G., Jaffrey, S.R. Proteomic Identification of Protein Ubiquitination Events. Biotechnology and Genetic Engineering Reviews, in press, 2013.

Song, W., Strack, R.L., Jaffrey, S.R. Imaging bacterial protein expression using genetically encoded RNA sensors. Nature Methods, 10:873-5, 2013.  Read this online here.

Hess, M.E., Hess, S., Meyer, K.D., Verhagen, L.A.W., Koch, L., Brönneke, H.S., Dietrich, M.O., Jordan, S.D., Saletore, Y., Elemento, O., Belgardt, B.F., Franz, T., Horvath, T.L., Rüther, U., Jaffrey, S.R., Kloppenburg, P., Brüning, J.C.  The Fat Mass and Obesity Associated (Fto) Gene Regulates Activity of the Dopaminergic Midbrain Circuitry.  Nature Neuroscience, 16:1042-1048, 2013.  Read this online here.

Strack, R.L., Jaffrey, S.R. New approaches for sensing metabolites and proteins in live cells using RNA. Current Opinion in Chemical Biology, 17:651-655, 2013.

Colak, D., Ji, S.-J., Porse, B.T., Jaffrey, S.R.  Regulation of axon guidance by compartmentalized nonsense mediated mRNA decay. Cell, 6:1252-1265, 2013.  Read this online here.

Xu, G., Jaffrey, S.R. Comprehensive Profiling of Protein Ubiquitination for Drug Discovery. Current Pharmaceutical Design, 19:3315-28. 2013.

Walker, B.A., Ji., S.-J., Jaffrey, S.R. Intra-axonal translation of RhoA promotes axon growth inhibition by CSPG. Journal of Neuroscience, 32:14442-7, 2012.

Deglincerti A., Jaffrey, S.R. Insights into the roles of local translation from the axonal transcriptome. Open Biology, 2:120079, 2012.

Meyer, K.D., Saletore, Y., Zumbo, P., Elemento, O., Mason, C.E., Jaffrey, S.R.  Comprehensive analysis of mRNA methylation reveals enrichment in 3' UTRs and near stop codons. Cell, 149:1635-1646, 2012.  Read this online here.

     Read what people are saying about this manuscript in Biotechniques, The New Scientist, and Science Daily.


Ji, S.-J., Jaffrey, S.R. Intra-axonal translation of SMAD1/5/8 mediates retrograde regulation of trigeminal ganglia subtype specification, Neuron,74:95-107, 2012.  Read this online here.

     Read the Preview Article for this article here.


Paige, J.S., Ngyuen-Duc, T., Song, W., Jaffrey, S.R. Fluorescence imaging of cellular metabolites with RNA, Science, 335:1194, 2012.  Read this online here.

     Read news about this paper in Biotechniques and Chemical & Engineering News.


Walker, B.A., Hengst, U., Kim, H.J., Jeon, N.L., Schmidt, E.F., Heintz, N., Milner, T.A., Jaffrey, S.R., Reprogramming axonal behavior by axon-specific viral transduction, Gene Therapy, in press.  Read this online here.

Cohen, M.S., Ghosh, A.K., Kim, H.J., Jeon, N.L., Jaffrey, S.R. Chemical genetic-mediated spatial regulation of protein expression in neurons reveals an axonal function for WldS, Chemistry & Biology, 19:179-187, 2012.  Read this online here.

Baeza, J.L., de la Torre, B.G., Santiveri, C.M., Almeida, R.D., García-López, M.T., Gerona-Navarro, G., Jaffrey, S.R., Jiménez, M.A., Andreu, D., González-Muñiz, R., Martín-Martínez, M. Cyclic amino acid linkers stabilizing key loops of brain derived neurotrophic factor, Bioorg. Chem. Med. Lett., 22:444-448, 2012.

Xu, G., Jaffrey, S.R. The new landscape of protein ubiquitination, Nature Biotechnology, 29:1098-1100, 2011.  Read this online here.

Xu, G., Shin, S.Y., Jaffrey, S.R. Chemoenzymatic labeling of protein C-termini for positive selection of C-terminal peptides, ACS Chem Biol, 6:1015-1020, 2011.  Read this online here.

Paige, J.S., Wu, K.Y., Jaffrey, S.R. RNA mimics of green fluorescent protein, Science, 333:642-646, 2011.  Read this online here.



Cohen, M.S., Bas Orth, C., Kim, H.J. Jeon, N.L., Jaffrey, S.R. Neurotrophin-mediated dendrite-to-nucleus signaling revealed by microfluidic compartmentalization of dendrites, Proc. Natl. Acad. Sci. USA., 108:11246-11251, 2011.  Read this online here.

Xu, G., Jaffrey, S.R. N-CLAP: Global Profiling of N-Termini by Chemoselective Labeling of the α-Amine of Proteins, Cold Spring Harbor Protocols, doi:10.1101/pdb.prot5528, 2010.  Read this online here.

Shin, S.Y., Almeida, R.D., Gerona-Navarro, G., Bracken, C., Jaffrey, S.R. Assembling ligands in situ using bioorthogonal boronate ester synthesis, Chemistry & Biology, 17: 1171-1176, 2010.  Read this online here.

Xu, G., Paige, J.S., Jaffrey, S.R. Global analysis of lysine ubiquitination by ubiquitin remnant immunoaffinity profiling, Nature Biotechnology, 28:868-873, 2010.  Read this online here.

Xu, G., Shin, S.Y., Jaffrey, S.R. Global profiling of protease cleavage sites by chemoselective labeling of protein N-termini. Proc. Natl. Acad. Sci. USA., 46:19310-19315, 2009.  Read this online here.

Rivieccio, M.A., Brochier, C., Willis, D.E., Walker, B.A., D’Annibale, M.A., McLaughlin, K., Siddiq, A., Kozikowski, A.P., Jaffrey, S.R, Twiss, J.L., Ratan, R.R., Langley, B. HDAC6 is a target for protection and regeneration following injury in the nervous system. Proc. Natl. Acad. Sci. USA., 46:19599-19604, 2009.  Read this online here.

Hengst, U., Deglincerti, A., Kim, H.J., Jeon, N.L., Jaffrey, S.R. Axonal elongation triggered by stimulus-induced local translation of a polarity complex protein. Nature Cell Biology, 11:1024-30, 2009.  Read this online here.

     Read the News and Views on this article here.


Paige, J.S., Xu, G., Stancevic, B., Jaffrey, S.R.  Nitrosothiol reactivity profiling identifies S-nitrosylated proteins with unexpected stability, Chemistry & Biology, 15:1307-1316, 2008.  Read this online here.

Cox, L.J., Hengst, U., Gurskaya, N.G., Lukyanov, K.A., Jaffrey, S.R. Intra-axonal translation and retrograde trafficking of CREB promotes neuronal survival, Nature Cell Biology, 10:149-159, 2008.  Read this online here.

     Read the News and Views on this article here.


Hengst, U.H., Jaffrey, S.R.  Regulation of mRNA translation during axonal development, Semin. Cell & Dev. Biol. 18:209-15, 2007.

Paige, J.S., Jaffrey, S.R. Pharmacologic manipulation of nitric oxide signaling: Targeting NOS dimerization and protein-protein interactions, Curr. Topics Med. Chem. 7:97-114, 2007.

Wu, K. Stessin, A., Kaminetsky, M., Hengst, U., Zippin, J., Buck, J., Levin, L.R., Jaffrey, S.R.  Soluble adenylyl cyclase is required for netrin-1 signaling in nerve growth cones. Nature Neuroscience, 9:1257-1264, 2006.

Hengst, U., Cox, L.J., Macosko, E.Z., Jaffrey, S.R. Functional and selective RNA interference in developing axons and growth cones.  Journal of Neuroscience, 26:5727-32, 2006.

Wu, K., Hengst, U, Cox, L.J., Macosko, E.Z., Jeromin, A., Urquhart, E.R., Jaffrey, S.R.  Local translation of RhoA regulates growth cone collapse. Nature, 436:1020-1024, 2005.

Jaffrey, S.R. Detection and quantification of protein nitrosothiols. Methods in Enzymology, 396:105-118, 2005.

He, X., Gerona-Navarro, G., Jaffrey, S.R., Ligand discovery using small-molecule microarrrays. J. Pharm. Exp. Therap., 313:1-7, 2005.

Jaffrey, S.R., Fang, M., Snyder, S.H.  Nitrosopeptide mapping: A novel methodology reveals S-nitrosylation of Dexras1 on a single cysteine residue. Chem. & Biol., 9:1329-1335, 2002.

Jaffrey, S.R., Benfenati, F, Snowman, A.S., Snyder, S.H.  Neuronal nitric oxide synthase localization mediated by a ternary complex with synapsin and CAPON.  Proc. Natl. Acad. Sci. U.S.A., 99:3199-3204, 2002.

Jaffrey, S.R., Snyder, S.H.  The biotin switch method for the detection of S-nitrosylated proteins.  Science STKE, www.stke.org/cgi/content/full/OC_sigtrans;2001/86, 2001.

Jaffrey, S.R., Erdjument-Bromage, H., Ferris, C.D., Tempst, P., Snyder, S.H.  Protein S-nitrosylation: A physiologic signal for neuronal nitric oxide.  Nature Cell Biology, 3:193-197, 2001.

Fang, M., Jaffrey, S.R.*, Sawa, A., Ye, K., Snyder, S.H.  Dexras1: A G-protein coupled to neuronal nitric oxide synthase via CAPON.  Neuron, 28:183-193, 2000.

Watkins, C.C., Sawa, A., Jaffrey, S.R., Blackshaw, S., Barrow, R.K., Snyder, S.H., Ferris, C.D.  Insulin restores neuronal nitric oxide synthase expression and function that is lost in diabetic gastropathy.  J. Clin. Invest., 106:373-384, 2000.

Snyder, S.H., Jaffrey, S.R.  Vessels vivified by Akt acting on NO synthase.  Nature Cell Biology, 1:E95-E96, 1999.

Ferris, C.D., Jaffrey, S.R., Sawa, A., Takahashi, M., Brady, S.D., Barrow, R.K., Tysoe, S.A., Wolosker, H, Baranano, D, Dore, S, Snyder, S.H.  Heme oxygenase-1 prevents cell death by regulating cellular iron.  Nature Cell Biology, 1:152-157, 1999.

Liang, J, Jaffrey, S.R., Guo, W., Snyder, S.H., Clardy, J.  Structure of PIN/LC8 dimer with a bound peptide.  Nature Structural Biology, 6:735-740, 1999.

Snyder, S.H., Jaffrey, S.R., Zakhary, R.  Nitric oxide and carbon monoxide: parallel roles as neural messengers.  Brain Research Reviews, 26:167-175, 1998.

Jaffrey, S.R., Snowman, A.M., Eliasson, M.J.L., Cohen, N.A., Snyder, S.H.  CAPON: A protein associated with neuronal nitric oxide synthase that regulates its interactions with PSD95.  Neuron, 20:115-24, 1998.

Zakhary, R., Poss, K.D., Jaffrey, S.R., Ferris, C.D., Tonegawa, S, Snyder, S.H.  Targeted deletion of heme oxygenase-2 reveals neural role for carbon monoxide.  Proc. Natl. Acad. Sci. U.S.A., 94:14848-53, 1997.

Jaffrey, S.R., Snyder, S.H.  PIN: An associated protein inhibitor of neuronal nitric oxide synthase. Science, 274:774-7, 1996.

Jaffrey, S.R., Snyder, S.H.  Nitric oxide: A neural messenger. Annu. Rev. Cell and Dev. Biol., 11:471-40, 1995.

Jaffrey, S.R., Cohen, N.A., Rouault, T.A., Klausner, R.D., Snyder, S.H.  The iron-responsive element binding protein: A target for synaptic actions of nitric oxide.  Proc. Natl. Acad. Sci. USA., 91:12994-8, 1994.

Jaffrey, S.R., Haile, D.J., Klausner, R.D., Harford, J.B.  The interaction between the iron-responsive element binding protein and its cognate RNA is highly dependent upon both RNA sequence and structure.  Nucl. Acids Res., 21:4627-4631, 1993.