Selected Papers (2003 to Present)

2014

Johnson, L. M., Du, J., Hale, C. J., Bischof, S., Feng, S., Chodavarapu, R. K., Zhong, X., Marson, G., Pellergrini, M., Segal, D. J., Patel, D. J. and Jacobsen, S. E. (2014). SRA- and SET-domain-containing proteins link RNA polymerase V occupancy to DNA methylation. Nature 507, 124-128.

Swarts, D. C., Jore, M. M., Westra, E. R., Zhu, Y., Janssen, J. H., Snijders, A. P., Wang, Y., Patel, D. J., Berenguer, J., Brouns, S. J. and van der Oost, J. (2014). DNA-guided DNA interference by prokaryotic Argonaute. Nature 507, 258-261.

Zhong, X., Du, J., Hale, C. J., Gallego-Bartolome, J., Feng, S., Vashisht, A. A., Chory, J., Wohlschlegel, J. A., Patel, D. J. and Jacobsen, S. E. (2014). Molecular mechanism of action of plant DRM de novo DNA methyltransferases. Cell 157, 1050-1060.

Stroud, H., Do, T., Du, J., Zhong, X., Feng, S., Johnson, L., Patel, D. J. and Jacobsen, S. E. (2014). Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis. Nat. Struct. Mol. Biol. 21, 64-72.

Swarts, D. C., Makarova, K., Wang, Y., Nakanishi, K., Ketting, R. F., Koonin, E. V., Patel, D. J. and van der Oost, J. (2014). The evolutionary journey of Argonaute proteins. Nat. Struct. Mol. Biol. 21, 743-753.

Tian, Y., Simanshu, D. K., Ma, J. B., Park, J-E, Heo, I., Kim, V. N. & Patel, D. J. (2014). A phosphate-binding pocket within the platform-PAZ-connector helix cassette of human Dicer. Mol. Cell 53, 606-616.

Du, J., Johnson, L. M., Groth, M., Feng, S., Hale, C. J., Li, S., Vashisht, A. A., Gallego-Bartolome, J., Wohlschlegel, J. A., Patel, D. J. and Jacobsen, S. E. (2014). Mechanism of DNA methylation-directed histone methylation by KRYPTONITE. Mol. Cell 55, 495-504.

Ren, A. and Patel, D. J. (2014). c-di-AMP binds the ydaO riboswitch in two pseudo-symmetry-related pockets. Nat. Chem. Biol. 10, 780-786.

Cheng, Z., Cheung, P., Kuo, A. J., Yuki, E. T., Wilmot, C. M., Gozani, O. and Patel, D. J. (2014). A molecular threading mechanism underlies Jumonji lysine demethylase KDM2A regulation of methylated H3K36. Genes Dev. 28, 1758-1771.

Le Thomas, A., Stuwe, E., LI, S., Du, J.,,Marinov, G., Rozhkov, N., Chen, A. Y-C., Luo, Y., Sachidanandam, R., Tot, K. F., Patel, D. J. and Aravin, A.A. (2014). Transgenerationally inherited piRNAs trigger piRNA biogenesis by changing the chromatin of piRNA clusters and inducing precursor processing. Genes Dev. 28, 1667-1680.

Simanshu, D., Zhai, X., Munch, D., Hofius, D., Markham, J. E., Bielawski, J., Bielawski, A., Slotte, J. P., Malinina, L., Molotkovsky, J. G., Mundy, J. E., Patel, D. J. and Brown, R. E. (2014). Arabidopsis accelerated cell death 11, ACD11, is a ceramide-1-phosphate transfer protein and intermediary regulator of phytoceramide levels. Cell Reports 6, 388-399.

Gao, P., Zillinger, T., Wang, W., Ascano, M., Dai, P., Hartmann, G., Tuschl, T., Deng, L., Barchet, W. and Patel, D. J. (2014). Binding-Pocket and Lid-Region Substitutions Render Human STING Sensitive to the Species-Specific Drug DMXAA. Cell Reports 8, 1668-1676.

2013

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.

2012

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.

2011

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.

2010

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.

2009

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.

2008

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.

2007

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.

2006

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.

2005

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.

2004

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.

2003

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)

2013

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.

2012

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.

2011

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

2009

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

2008

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.

2007

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.

2006

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