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Department of Biochemistry

Calendar of Events

Publications of the Jinek Group (in alphabetical order)

Brandmann, T., Fakim, H., Padamsi, Z., Youn, JY., Gingras, AC., Fabian, MR. & Jinek, M. Molecular architecture of LSM14 interactions involved in the assembly of mRNA silencing complexes. EMBO J. 37(7) e97869 (2018). PMID: 29510985.

Clerici, M., Faini, M., Muckenfuss, LM., Aebersold, R. &  Jinek, M. Author correction: Structural basis of AAUAAA polyadenylation signal recognition by the human CPSF complex. Nat Struct Mol Biol. 25, 355 (2018). PMID: 29540792.

Clerici, M., Faini, M., Muckenfuss, LM., Aebersold, R. & Jinek, M. Structural basis of AAUAAA polyadenylation signal recognition by the human CPSF complex. Nat Struct Mol Biol. 25, 135-138 (2018). PMID: 29358758.

Nishimura, T., Fakim, H., Brandmann, T., Youn, JY., Gingras, AC., Jinek, M. & Fabian, MR. Human MARF1 is an endoribonuclease that interacts with the DCP1:2 decapping complex and degrades target mRNAs. Nucleic Acids Res. 46, 12008-12021 (2018). PMID: 30364987.

Palermo, G., Chen, JS., Ricci, CG., Rivalta, I., Jinek, M., Batista, VS., Doudna, JA. & McCammon, JA. Key role of the REC lobe during CRISPR-Cas9 activation by 'sensing', 'regulating', and 'locking' the catalytic HNH domain. Q. Rev. Biophys. 51, (2018). PMID: 30555184.

Savic, N., Ringnalda, FC., Lindsay, H., Berk, C., Bargsten, K., Li, Y., Neri, D., Robinson, MD., Ciaudo, C., Hall, J., Jinek, M. &  Schwank, G. Covalent linkage of the DNA repair template to the CRISPR-Cas9 nuclease enhances homology-directed repair. Elife 7. pii: e33761 (2018). PMID: 29809142.

Swarts, D. & Jinek. M. Cas9 versus Cas12a/Cpf1: Structure-function comparisons and implications for genome editing. Wiley Interdiscip Rev RNA 9, e1481 (2018). PMID: 29790280.

Vlot, M., Houkes, J., Lochs, SJA., Swarts, DC., Zheng, P., Kunne, T., Mohanraju, P., Anders, C., Jinek, M., van der Oost, J.,  Dickman, MJ. & Brouns, SJJ. Bacteriophage DNA glucosylation impairs target DNA binding by type I and II but not type V CRISPR-Cas effector complexes. Nucleic Acids Res. 46, 873-885 (2018). PMID: 29253268.

Clerici, M., Faini, M., Aebersold, R. & Jinek, M. Structural insights into the assembly and polyA signal recognition mechanism of the human CPSF complex. Elife e33111 (2017). PMID: 29274231.

Garcia-Doval, C. & Jinek, M. Molecular architectures and mechanisms of Class 2 CRISPR-associated nucleases. Curr. Opin. Struct. Biol. [Epub ahead of print] (2017). PMID: 29107822.

Niewoehner, O. & Jinek, M. Specialized Weaponry: How a Type III-A CRISPR-Cas System Excels at Combating Phages. Cell Host Microbe 22, 258-259 (2017). PMID: 28910631.

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., Ricci, CG., Fernando, A., Basak, R., Jinek, M., Rivalta, I., Batista, VS. & McCammon, JA. Protospacer Adjacent Motif-Induced Allostery Activates CRISPR-Cas9. J. Am. Chem. Soc. 139, 16028-16031 (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

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.

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.

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.

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).

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).

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).

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).

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).

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).

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

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).

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).