Selected Papers (2003 to Present)


Oh, Y-S., Gao, P., Lee, K., Ceglia, I., Zhang, X., Ahn, J-H., Chait, B. T., Patel, D. J., Kim, Y. & Greengard, P. (2013). SMARCA3, a chromatin-remodeling factor, is required for p11-dependent antidepressant action. Cell 152, 831-843.

Shen, J., Xia, Y., Khotskaya, Y. B., Huo, L., Nakanishi, K., Lim, S-O., Du, Y., Wang, Y., Chang, W-C., Chen, C-H., Hsu, J. L., Lam, Y. C., James, B. P., Liu, C-G., Liu, X., Patel, D. J. & Hung, M. C. (2013). EGFR modulates miRNA maturation in response to hypoxia through phosphorylation of Ago2. Nature 497, 383-387.

Law, J. A., Du, J., Hale, C. J., Feng, S., Krajewski, K., Strahl, B. D., Patel, D. J. & Jacobsen, S. E. (2013). Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1. Nature 498, 385-389.

Sun, X-J., Wang, Z., Wang, L., Jiang, Y., Chen, W-Y., Melnick, A., Patel, D. J., Nimer, S. D. & Roeder, R. G. (2013). A stable transcription factor complex nucleated by oligomeric AML1-ETO controls leukaemogenesis. Nature 500, 93-97.

Simanshu, D. K., Kamlekar, R. K., Wijesinghe, D. S., Zou, X., Zhai, X., Mishra, S. K., Molotkovsky, J. G., Malinina, L., Hincliffe, E. H., Chalfant, C. E., Brown, R. E. & Patel, D. J. (2013). Non-vesicular trafficking by a ceramide-1-phosphate transfer protein regulates eicosanoids. Nature 500, 463-467.

Gao, P., Ascano, M., Wu, Y., Barchet, W., Gaffney, B. L., Zillinger, T., Serganov, A., Jones, R. A., Hartmann, G., Tuschl, T. and Patel, D. J. (2013). Cyclic [G(2',5')pA(3',5')p] is the metazoan second messenger produced by DNA-activated cyclic GMP-AMP synthase. Cell 153, 1094-1107.

Gao, P., Ascano, M., Zillinger, T., Wang, Y., Dai, P., Serganov, A. A., Gaffney, B. L., Shuman, S., Jones, R., Deng, L., Hartmann, G., Barchet, W., Tuschl, T. and Patel, D.J. (2013). Structure-function analysis of STING activation by c[G(2',5')pA(3',5')p] and targeting by antiviral DMXAA. Cell 154, 748-762.

Cai, L., Rothbart, S. B., Lu, R., Xu, B., Tripathy, A., Chen, W-Y., Zheng, D., Patel, D. J., Allis, C. D., Strahl, B. D., Song, J. & Wang, G. (2013). An H3K36 methylation-engaging Tudor motif of polycomb-like proteins mediates PRC2 complex targeting. Mol. Cell 49, 571-582.

Dai, Q., Ren, A., Westholm, J. O., Serganov, A., Patel, D. J. & Lai, E. C. (2013). The BEN domain is a novel sequence-specific DNA-binding domain conserved in neural transcriptional repressors. Genes Dev. 27, 602-614.

Teplova, M., Hafner, M., Teplov, D., Essig, K., Tuschl, T. and Patel, D. J. (2013). Structure-function studies of STAR family Quaking proteins bound to their in vivo RNA target sites. Genes Dev. 27, 928-940.

Nakanishi, K., Ascano, M., Gogakos, T., Ishibi-Murakami, S., Serganov, A. A., Briskin, D., Morozov, P., Tuschl, T. and Patel, D. J. (2013). Eukaryote-specific insertion elements control human ARGONAUTE slicer activity. Cell Reports 3, 1893-1900.


Song, J., Teplova, M., Ishibe-Murakami, S. & Patel, D. J. (2012). Structure-based mechanistic insights into DNMT1-mediated maintenance DNA methylation. Science 335, 709-712.

Kuo, A. J., Song, J., Cheung, P., Ishibe-Murakami, S., Yamazoe, S., Chen, J., Patel, D. J. & Gozani, O. (2012). ORC1 BAH domain links dimethylation of H4K20 to DNA replication licensing and Meier-Gorlin syndrome. Nature 484, 115-119.

Ren, A., Rajashankar, K. & Patel, D. J. (2012). Fluoride ion encapsulation by Mg2+ and phosphates in a fluoride riboswitch. Nature 486, 85-89.

Nakanishi, K., Weinberg, D., Bartel, D. P. & Patel, D. J. (2012). Structure of yeast Argonaute with guide RNA. Nature 486, 368-374.

Kruidenier, L., Chung, C., Cheng, Z., Liddle, J., Bantscheff, M., Bountra, C., Bridges, A., Che, K., Diallo, H., Eberhard, D., Hutchinson, S., Joberty, G., Jones, E., Katso, R., Leveridge, M., Mosley, J., Rowland, P., Ramirez-Molina, C., Schofield, C. J., Sheppard, R., Smith, J. E., Swales, C., Tanner, R., Thomas, P., Tumber, A., Drewes, G., Oppermann, U., Patel, D. J., Lee, K., & Wilson, W. (2012). A selective jumonji H3K27 demethylase inhibitor modulates the proinflammatory macrophage response. Nature 488, 404-408.

Du, J., Zhong, X., Barnatavichute, Y. V., Stroud, H., Feng, S., Caro, E., Vashisht, A. A., Terragni, J., Chin, H. G., Tu, J., Hetzel, J., Wohlschlegel, J. A., Pradhan, S., Patel, D. J. & Jacobsen, S. E. (2012). Dual binding of chromomethylase domains to H3K9me2-containing nucleosomes directs DNA methylation in plants. Cell 151,167-180.

Elsasser, S. J., Huang, H., Lewis, P. W., Allis, C. D. & Patel, D. J. (2012). DAXX histone chaperone envelops an H3.3/H4 dimer for H3.3-specific recognition. Nature 491, 560-565.


Song, J., Rechkoblit, O., Bestor, T. H. & Patel, D. J. (2011). Structure of DNMT1-DNA complex reveals a role for autoinhibition in maintenance DNA methylation. Science 331, 1036-1040.

Ruthenburg, A., Li, H., Milne, T., Dou, Y., McGinty, R. K., Yuen, M., Muir, T. W., Patel, D. J. & Allis, C. D. (2011). Recognition of a mononucleosomal histone modification pattern by BPTF via multivalent interactions. Cell 145, 692-706.

Weinberg, D., Nakanishi, K., Patel, D. J. & Bartel, D. P. (2011). The inside-out mechanism of Dicers from budding yeasts. Cell 146, 262-276.

Park, J. E., Heo, I., Tian, Y., Shimanshu, D., Chang, H., Jee, D., Patel, D. J. & Kim, V. N. (2011). Human Dicer recognizes the 5'-phosphorylated end of RNA for efficient and accurate cleavage. Nature 475, 201-205.

Eerappa R., Law, J. A., Shimanshu, D. K., Voigt, P., Johnson, L. M., Reinberg, D., Patel, D. J. & Jacobsen, S. E. (2011). A dual flip out mechanism for 5mC recognition by the Arabidopsis SUVH5 SRA domain and its impact on DNA methylation and H3K9 dimethylation in vivo. Genes Dev. 25, 137-152.

Tian, Y., Simanshu, D. K., Ascano, M., Daiz-Avalos, R., Park, A. Y., Juranek, S. A., Rice, W. J., Yin, Q., Robinson, C. C., Tuechl, T. & Patel, D. J. (2011). Multimeric assembly and biochemical characterization of the Trax-translin endonuclease complex. Nat. Struct. Mol. Biol. 18, 658-664.

Iwase, S., Xiang, B., Ghosh, S., Ren, T., Lewis, P. W., Cochrane, J. C., Allis, C. D., Picketts, D. J., Patel, D. J., Li, H. & Shi, Y. (2011). ATRX links atypical histone methylation recognition mechanisms to human brain function. Nat. Struct. Mol. Biol. 18, 769-776.

Phan, A. T., Kuryavyi, V., Darnell, J. C., Serganov, A., Majumdar, A., Raslin, T., Polonskaia, A., Chen, C., Clain, D., Darnell, R. B. & Patel, D. J. (2011). Structure-function studies of FMRP RGG peptide recognition of an RNA duplex-quadruplex junction. Nat. Struct. Mol. Biol. 18, 769-804.

Teplova, M., Wohlbold, L., Kim, N. Y., Izaurralde, E. & Patel, D. J. (2011). Structure-function studies of nucleocytoplasmic transport of retroviral genomic RNA by mRNA export factor TAP. Nat. Struct. Mol. Biol. 18, 990-998.


Wang, Z., Song, J., Milne, T. A., Wang, G. G., Li, H., Allis, C. D. & Patel, D. J. (2010). Pro isomerization in MLL1 PHD3-Bromo cassette connects H3K4me3 readout to CyP33 and HDAC-mediated repression. Cell 141, 1183-1194.

Tsai, W-W., Wang, Z., Yiu, T. T., Akdemir, K. C., Xia, W., Winter, S., Tsai, C-Y., Shi, X., Schwarzer, D., Plunkett, W., Aronow, B., Gozani, O., Fischle, W., Hung, M. C., Patel, D. J. & Barton, M. C. (2010). TRIM24 links recognition of a non-canonical histone signature to breast cancer. Nature 468, 927-932.

Rechkoblit, O., Kolbanovskiy, A., Malinina, L., Geacintov, N. E., Broyde, S. & Patel, D. J. (2010). Y-family polymerase-facilitated mechanism of error-free bypass and semi-targeted mutagenic processing of an aromatic amine lesion. Nat. Struct. Mol. Biol. 17, 379-388.

Wang, Y., Ludwig, J., Schuberth, C., Goldeck, M., Schlee, M., Li, H., Juranek, S., Sheng, G., Micura, R., Tuschl, T., Hartmann, G. & Patel, D. J. (2010). Structural and functional insights into 5'-ppp-RNA pattern recognition by the innate immune receptor RIG-I. Nat. Struct. Mol. Biol. 17, 781-787.

Huang, L., Serganov, A. & Patel, D. J. (2010). Structural insights into ligand recognition by a sensing domain of the cooperative glycine riboswitch. Mol. Cell 40, 774-786.


Wang, Y., Juranek, S., Li, H., Sheng, G., Wardle, G. S., Tuschl, T. Patel, D. J. (2009). Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes. Nature 461, 754-761.

Wang, G. G., Song, J., Wang, Z., Dormann, H. L., Casadio, F., Li, H., Luo, J., Patel, D. J. & Allis, C. D. (2009). Haematopoietic malignancies initiated by dysregulation of a chromatin-binding PHD fineger. Nature 459, 847-851.

Serganov, A., Huang, L. & Patel, D. J. (2009). Coenzyme recognition and gene regulation by a FMN riboswitch. Nature 458, 233-237.

Xiao, A., Li, H., Shechter, D., Ahn, S. H., Fabrizio, L., Erajument-Bromage, H., Murakami-Ishibe, S., Wang, B., Tempst, P., Hofmann, K., Patel, D. J., Elledge, S. J. & Allis, C. D. (2009). WSTF regulates the DNA damage response of H2A.X via a novel tyrosine kinase activity. Nature 457, 57-62.

Li, H., Motamedi, M., Wang, Z., Patel, D. J. & Moazed, D. (2009), An alpha motif of Tas3 C-terminus mediated RITS cis-spreading and promotes heterochromatin gene silencing. Mol. Cell 34, 155-167.

Zhao, Q., Rank, G., Tan, Y. T., Li, H., Moritz, R. L., Simpson, R. J., Cerruti, L., Curtis, D. J., Patel, D. J., Allis, C. D., Cunningham, J. M. & Jane, S. M. (2009). PRMT5-mediated methylation of histone H4R3 recruits DNMT3A coupling histone and DNA methylation in gene silencing. Nat. Struct. Mol. Biol.16, 304-311.


Wang, Y., Li, H., Juranek, S., Sheng, G., Tuschl, T. & Patel, D. J. (2008). Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex. Nature 456, 921-926.

Wang, Y., Sheng, G., Juranek, S., Tuschl, T. & Patel, D. J. (2008). Structure of the guide-strand-containing argonaute silencing complex. Nature 456, 209-213.

Serganov, A., Huang, L. & Patel, D. J. (2008). Structural insights into ligand binding and gene control by a lysine riboswitch. Nature 455, 1263-1267.

Teplova, M. & Patel, D. J. (2008). Structural insights into RNA recognition by the alternate splicing regulator muscleblind-like MBNL1. Nat. Struct. Mol. Biol. 15, 1343-1351.


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.

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. Nature Protocols, 2, 1536-1546.


Li, H., Ilin, S., Wang, W. K., Wysocka, J., Allis, C. D. & Patel, D. J. (2006). Molecular basis for site- and state-specific readout of histone H3 lysine 4 trimethylation by NURF BPTF PHD finger. Nature 442, 91-95.

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.

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.

Ruthenberg, A. J., Wang, W., Graybosch, D. M., Li, H., Allis, C. D., Patel, D. J. & Verdine, G. (2006). Histone H3 recognition and presentation by the WDR5 module of the MLL1 complex. Nat. 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 Biology 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 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 Argonautel cleavage activity to counter plant defense. Genes Dev. 20, 3255-3268.


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. fulgidus PIWI protein. Nature 434, 666-670.

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.

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. Nat. Struct. Mol. Biol. 12, 218-224.

Phan, A. T., Kuryavyi, V., Gaw, H. Y. & Patel, D. J. (2005). Targeting anticancer drugs to a parallel-stranded snap-back G-quadruplex formed by five-guanine tracts of the human c-myc promotor. Nat. Chem. Biol. 1, 167-173.


Malinina, L., Malakhova, M. L., Teplov, A., Brown, R. E. & Patel, D. J. (2004). Structural basis for glycosphingolipid transfer specificity. Nature 430, 1048-1053.

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.


Ye, K., Malinina, L. & Patel, D. J. (2003). Recognition of siRNA by a viral suppressor of RNA silencing. Nature 426, 874-878.

Reviews (2006 to Present)


Patel, D. J. and Wang, Z. (2013). Readout of epigenetic modifications. Ann. Rev. Biochem. 82, 81-118.

Wang, Z. and Patel, D. J. (2013). Small molecule epigenetic inhibitors targeted to histone lysine methyltransferases and demethylases. Quart. Rev. Biophys. 46, 349-373.


Serganov, A. & Patel, D. J. (2012). Metabolite recognition principles and molecular mechanisms underlying riboswitch function. Ann. Rev. Biophys. 41, 343-370.

Serganov, A. & Patel, D. J. (2012). Molecular recognition and function of riboswitches. Curr. Opin. Struct. Biol. 22, 279-286.


Wang, Z. & Patel, D. J. (2011). Combinatorial readout of dual histone modifications by paired chromatin-associated modules. J. Biol. Chem. 286, 8363-18368.


Serganov, A. & Patel, D. J. (2009). Amino acid recognition and gene regulation by riboswitches. Biochem. Biophys. Acta. 1789, 592-611.


Broyde, S., Wang, L., Rechkoblit, O., Geacintov, N. E. & Patel, D. J. (2008). Lesion processing by replicative versus bypass polymerases. Trends Biochem. Scis. 33, 209-219.

Serganov, S. & Patel, D. J. (2008). Towards deciphering the principles underlying a mRNA recognition code. Curr. Opin. Struct. Biol. 18, 120-129.


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.

Serganov, A. & Patel, D. J. (2007). Ribozymes, riboswitches and beyond: regulation of gene expression without proteins. Nat. Rev. Genetics 8, 776-790.

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.

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. Cold Spring Harbor Laboratory Symposium on Regulatory RNAs, 71, 81-93.

Patel, D. J., Phan, A. T. & Kuryavyi, V. (2007). Human telomere, oncogenic promotor and 5'-UTR G-quadruplexes: Diverse higher-order DNA and RNA targets for cancer therapeutics. Nucleic Acids Research 22, 7249-7255.


Phan, A. T., Kuryavyi, V. & Patel, D. J. (2006). DNA architecture: from G to Z. Curr. Opin. Struct. Biol. 16, 288-298.