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Department of Biochemistry

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Publications of the Jinek Group (in alphabetical order)

2017
Niewoehner, O., Garcia-Doval, C.,  Rostøl, JT., Berk, C., Schwede, F., Bigler. L., Hall, J., Marraffini, LA. & Jinek, M. Type III CRISPR-Cas systems produce cyclic oligoadenylate second messengers. Nature 548, 543-548 (2017).  28722012.

Palermo, G., Miao, Y., Walker, RC., Jinek, M. & McCammon, JA. CRISPR-Cas9 conformational activation as elucidated from enhanced molecular simulations. Proc. Natl. Acad. Sci. U.S.A. 114, 7260-7265 (2017). PMID: 28652374.

Palermo, G.,G Ricci C., Fernando, A., Basak, R., Jinek, M., Rivalta, I., Batista, VS. & McCammon, JA. PAM-induced allostery activates CRISPR-Cas9. J Am Chem Soc. 2017 Aug 2. [Epub ahead of print] (2017).  PMID: 28764328.

Swarts, DC., van der Oost, J. & Jinek, M. Structural Basis for Guide RNA Processing and Seed-Dependent DNA Targeting by CRISPR-Cas12a. Mol. Cell 66, 221-233.e4 (2017). PMID: 28431230

2016
Anders, C., Bargsten, K. & Jinek, M. Structural Plasticity of PAM Recognition by Engineered Variants of the RNA-Guided Endonuclease Cas9. Mol. Cell 61, 895-902 (2016). PMID: 26990992.

Burger, A., Lindsay, H., Felker, A., Hess, C., Anders, C., Chiavacci, E., Zaugg, J., Weber, LM., Catena, R., Jinek, M., Robinson, MD. & Mosimann, C. Maximizing mutagenesis with solubilized CRISPR-Cas9 ribonucleoprotein complexes. Development 143, 2025-2037 (2016). PMID: 27130213.

Lindsay, H., Burger, A., Biyong, B., Felker, A., Hess, C., Zaugg, J., Chiavacci, E., Anders, C., Jinek, M., Mosimann, C. & Robinson, MD. CrispRVariants charts the mutation spectrum of genome engineering experiments. Nat. Biotechnol. 34, 701-2 (2016). PMID: 27404876.

Niewoehner, O. & Jinek, M. Structural basis for the endoribonuclease activity of the type III-A CRISPR-associated protein Csm6. RNA 22, 318-329 (2016). PMID: 26763118

Olieric, V., Weinert, T., Finke, AD., Anders, C., Li, D., Olieric, N., Borca, CN., Steinmetz, MO., Caffrey, M., Jinek, M. & Wang, M. Data-collection strategy for challenging native SAD phasing. Acta Crystallogr D Struct Biol 72, 421-9 (2016). PMID: 26960129.

Palermo, G., Miao, Y., Walker, RC., Jinek, M. & McCammon, JA. Striking Plasticity of CRISPR-Cas9 and Key Role of Non-target DNA, as Revealed by Molecular Simulations. ACS Cent Sci 2, 756-763 (2016). PMID: 27800559.

Śledź, P. & Jinek, M. Structural insights into the molecular mechanism of the m(6)A writer complex. Elife 5, (2016). PMID: 27627798.

Reimão-Pinto, M.M., Manzenreither, R.A., Burkard, T.R., Sledz, P., Jinek M, Mechtler K. & Ameres, S.L. Molecular Basis for Cytoplasmic RNA Surveillance by Uridylation-triggered Decay in Drosophila. EMBO J. 35, 2417-2434 (2016). PMID: 27729457.

2015
Anders, C., Niewoehner, O. & Jinek, M. In Vitro Reconstitution and Crystallization of Cas9 Endonuclease Bound to a Guide RNA and a DNA Target. Meth. Enzymol. 558, 515-37 (2015). PMID: 26068752.

Baltimore, D., Berg, P., Botchan, M., Carroll, D., Charo, RA., Church, G., Corn, JE., Daley, GQ., Doudna, JA., Fenner, M., Greely, HT., Jinek, M., Martin, GS., Penhoet, E., Puck, J., Sternberg, SH., Weissman, JS. & Yamamoto, KR. Biotechnology. A prudent path forward for genomic engineering and germline gene modification. Science 348, 36-8 (2015). PMID: 25791083.

Brandmann, T. & Jinek, M. Crystal structure of the C-terminal 2',5'-phosphodiesterase domain of group A rotavirus protein VP3. Proteins 83, 997-1002 (2015). PMID: 25758703.

Zou, J., Tran, D., Baalbaki, M., Tang, LF., Poon, A., Pelonero, A., Titus, EW., Yuan, C., Shi, C., Patchava, S., Halper, E., Garg, J., Movsesyan, I., Yin, C., Wu, R., Wilsbacher, LD., Liu, J., Hager, RL., Coughlin, SR., Jinek, M., Pullinger, CR., Kane, JP., Hart, DO., Kwok, PY. & Deo, RC. An internal promoter underlies the difference in disease severity between N- and C-terminal truncation mutations of Titin in zebrafish. Elife 4, (2015). PMID: 26473617.

2014
Anders, C. & Jinek, M. In vitro enzymology of cas9. Meth. Enzymol. 546, 1-20 (2014). PMID: 25398333.

Anders, C., Niewoehner, O., Duerst, A. & Jinek, M. Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease. Nature 513, 569-73 (2014). PMID: 25079318.

Jinek, M., Jiang, F., Taylor, DW., Sternberg, SH., Kaya, E., Ma, E., Anders, C., Hauer, M., Zhou, K., Lin, S., Kaplan, M., Iavarone, AT., Charpentier, E., Nogales, E. & Doudna, JA. Structures of Cas9 endonucleases reveal RNA-mediated conformational activation. Science 343, 1247997 (2014). PMID: 24505130.

Niewoehner, O., Jinek, M. & Doudna, JA. Evolution of CRISPR RNA recognition and processing by Cas6 endonucleases. Nucleic Acids Res. 42, 1341-53 (2014). PMID: 24150936.

Sternberg, SH., Redding, S., Jinek, M., Greene, EC. & Doudna, JA. DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature 507, 62-7 (2014). PMID: 24476820.

2013
Jinek, M., East, A., Cheng, A., Lin, S., Ma, E. & Doudna, J. RNA-programmed genome editing in human cells. elife. 2:e00471 (2013).

Kassube, SA., Jinek, M., Fang, J., Tsutakawa, S. & Nogales, E. Structural mimicry in transcription regulation of human RNA polymerase II by the DNA helicase RECQL5. Nat Struct Mol Biol. 20, 892-899 (2013).

2012
Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, JA. & Charpentier, E. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816-821 (2012).

2011
Sashital, D., Jinek, M. & Doudna, JA. An RNA induced conformational change required for CRISPR RNA cleavage by the endonuclease CasE. Nat Struct Mol Biol. 18, 680-87 (2011).

Jinek, M., Coyle, SM. & Doudna, JA. Coupled 5’ nucleotide recognition and processivity in Xrn1-mediated mRNA decay. Mol Cell. 41, 600-608 (2011).

2010
Haurwitz, RE.*, Jinek, M.*, Wiedenheft, B., Zhou, K. & Doudna, JA. Sequence- and structure-specific RNA processing by a CRISPR endonuclease. Science 329, 1355-1358 (2010) *Equal contribution

Weeks, AM., Coyle, SM., Jinek, M., Doudna, JA. & Chang, MC. Structural and biochemical studies of fluoroacetyl-CoA-specific thioesterase reveal a molecular basis for fluorine selectivity. Biochemistry 49, 9269-9279 (2010).

Leung, AK., Kambach, C., Kondo, Y., Kampmann, M., Jinek, M. & Nagai, K. Use of RNA tertiary interaction modules for the crystallisation of the spliceosomal snRNP core domain. J Mol Biol. 402, 154-64 (2010).

Jinek, M., Fabian, MR., Coyle, SM., Sonenberg, N. & Doudna, JA. Structural insights into the human GW182-PABC interaction in microRNA-mediated deadenylation. Nat Struct Mol Biol. 17, 238-240 (2010).

2009
Jinek, M. &  Doudna, JA. A three-dimenstional view of the molecular machinery of RNA interference. Nature  457, 405-412 (2009).

Fabian, MR., Mathonnet, G., Sundermeier, T., Mathys, H., Zipprich, JT., Svitkin ,YV., Rivas, F., Jinek, M., Wohlschlegel, J., Doudna, JA., Chen, CY., Shyu, AB., Yates ,JR. 3rd, Hannon, GJ., Filipowicz, W., Duchaine, TF. & Sonenberg, N. Mammalian miRNA RISC recruits CAF1 and PABP to affect PABPdependent deadenylation. Mol Cell. 35, 868-880 (2009).

Cook, AG., Fukuhara, N., Jinek, M. & Conti, E. Structures of the tRNA export factor in the nuclear and cytosolic states. Nature 461, 60-85 (2009).

Wiedenheft, B., Zhou, K., Jinek, M., Coyle, SM., Ma, W. & Doudna, JA. Structural basis for DNase activity of a conserved protein implicated in CRISPR-mediated genome defense. Structure 17, 904-912 (2009).

2008
Jinek, M., Eulalio, A., Lingel, A., Helms, S., Conti, E. & Izaurralde, E. The C-terminal region of Ge-1presents conserved structural features required for P-body localization. RNA 14, 1991-1998 (2008).

2007
Cook, A., Bono, F., Jinek, M. & Conti, E. Structural biology of nucleocytoplasmic transport. Annu Rev Biochem. 76, 647-71 (2007).

2006
Jinek, M., Chen, YW., Clausen, H., Cohen, SM. & Conti, E. Structural insights into the Notchmodifying glycosyltransferase Fringe. Nature Struct Mol Biol. 13, 945-946 (2006).

Jinek, M. & Conti, E. Eukaryotic expression, purification, crystallization and preliminary X-ray analysis of murine Manic Fringe. Acta Crystallographica  F62, 774-777 (2006).

2004
Jinek, M., Rehwinkel, J., Lazarus, BD., Izaurralde, E., Hanover, JA. & Conti, E. The superhelical TPRrepeat domain of O-linked GlcNAc transferase exhibits structural similarities to importin alpha. Nature Struct Mol Biol. 11, 1001-1007 (2004).