Publications of the Jinek Group

2023

Pacesa, M., Loeff, L., Querques, I., Muckenfuss, LM., Sawicka, M. & Jinek, M. Publisher Correction: R-loop formation and conformational activation mechanisms of Cas9. Nature [Epub ahead of print] (2023). PMID: 37903882.

Schmidheini, L., Mathis, N., Marquart, KF., Rothgangl, T., Kissling, L., Böck, D., Chanez, C., Wang, JP., Jinek, M. & Schwank, G. Continuous directed evolution of a compact CjCas9 variant with broad PAM compatibility. Nat Chem Biol [Epub ahead of print] (2023). PMID: 37735239.

Zhao, L., Koseki, SRT., Silverstein, RA., Amrani, N., Peng, C., Kramme, C., Savic, N., Pacesa, M., Rodríguez, TC., Stan, T., Tysinger, E., Hong, L., Yudistyra, V., Ponnapati, MR., Jacobson, JM., Church, GM., Jakimo, N., Truant, R., Jinek, M., Kleinstiver, BP., Sontheimer, EJ. & Chatterjee, P. PAM-flexible genome editing with an engineered chimeric Cas9. Nat Commun 14, 6175 (2023). PMID: 37794046.

2022

Muckenfuss, LM., Migenda Herranz, AC., Boneberg, FM., Clerici, M. & Jinek, M. Fip1 is a multivalent interaction scaffold for processing factors in human mRNA 3' end biogenesis. Elife 11, (2022). PMID: 36073787.

Nierzwicki, Ł., East, KW., Binz, JM., Hsu, RV., Ahsan, M., Arantes, PR., Skeens, E., Pacesa, M., Jinek, M., Lisi, GP. & Palermo, G. Principles of target DNA cleavage and the role of Mg2+ in the catalysis of CRISPR-Cas9. Nat Catal 5, 912-922 (2022). PMID: 36778082.

Pacesa, M., Lin, CH., Cléry, A., Saha, A., Arantes, PR., Bargsten, K., Irby, MJ., Allain, FH., Palermo, G., Cameron, P., Donohoue, PD. & Jinek, M. Structural basis for Cas9 off-target activity. Cell 185, 4067-4081.e21 (2022). PMID: 36306733.

Pacesa, M., Loeff, L., Querques, I., Muckenfuss, LM., Sawicka, M. & Jinek, M. R-loop formation and conformational activation mechanisms of Cas9. Nature 609, 191-196 (2022). PMID: 36002571.

Schmitz, M., Querques, I., Oberli, S., Chanez, C. & Jinek, M. Structural basis for the assembly of the type V CRISPR-associated transposon complex. Cell 185, 4999-5010 (2022). PMID: 36435179.

2021
Asanović, I., Strandback, E., Kroupova, A., Pasajlic, D., Meinhart, A., Tsung-Pin, P., Djokovic, N., Anrather, D., Schuetz, T., Suskiewicz, MJ., Sillamaa, S., Köcher, T., Beveridge, R., Nikolic, K., Schleiffer, A., Jinek, M., Hartl, M., Clausen, T., Penninger, J., Macheroux, P., Weitzer, S. & Martinez, J. + as an antioxidant to sustain tRNA ligase activity in pre-tRNA splicing and unfolded protein response. Mol Cell 81, 2520-2532.e16 (2021).PMID: 33930333

Bawankar, P., Lence, T., Paolantoni, C., Haussmann, IU., Kazlauskiene, M., Jacob, D., Heidelberger, JB., Richter, FM., Nallasivan, MP., Morin, V., Kreim, N., Beli, P., Helm, M., Jinek, M., Soller, M. & Roignant, JY. 6A mRNA methylation machinery. Nat Commun 12, 3778 (2021). PMID: 34145251.

Donohoue, PD., Pacesa, M., Lau, E., Vidal, B., Irby, MJ., Nyer, DB., Rotstein, T., Banh, L., Toh, MS., Gibson, J., Kohrs, B., Baek, K., Owen, ALG., Slorach, EM., van Overbeek, M., Fuller, CK., May, AP., Jinek, M. & Cameron, P. Conformational control of Cas9 by CRISPR hybrid RNA-DNA guides mitigates off-target activity in T cells. Mol Cell 81, 3637-3649.e5 (2021). PMID: 34478654.

Kroupova, A., Ackle, F., Asanović, I., Weitzer, S., Boneberg, FM., Faini, M., Leitner, A., Chui, A., Aebersold, R., Martinez, J. & Jinek, M. Molecular architecture of the human tRNA ligase complex. Elife 10, (2021). PMID: 34854379.
 
Makasheva, K., Bryan, LC., Anders, C., Panikulam, S., Jinek, M. & Fierz, B. Multiplexed Single-Molecule Experiments Reveal Nucleosome Invasion Dynamics of the Cas9 Genome Editor. J Am Chem Soc 143, 16313-16319 (2021). PMID: 34597515.

Querques, I., Schmitz, M., Oberli, S., Chanez, C. & Jinek, M. Target site selection and remodelling by type V CRISPR-transposon systems. Nature 599, 497-502 (2021). PMID: 34759315.

Rothgangl, T., Dennis, MK., Lin, PJC., Oka, R., Witzigmann, D., Villiger, L., Qi, W., Hruzova, M., Kissling, L., Lenggenhager, D., Borrelli, C., Egli, S., Frey, N., Bakker, N., Walker, JA., Kadina, AP., Victorov, DV., Pacesa, M., Kreutzer, S., Kontarakis, Z., Moor, A., Jinek, M., Weissman, D., Stoffel, M., van Boxtel, R., Holden, K., Pardi, N., Thöny, B., Häberle, J., Tam, YK., Semple, SC. & Schwank, G. In vivo adenine base editing of PCSK9 in macaques reduces LDL cholesterol levels. Nat Biotechnol [Epub ahead of print] (2021). PMID: 34012094.

2020
Casalino, L., Nierzwicki, Ł., Jinek, M. & Palermo, G. Ab Initio Molecular Dynamics. ACS Catal 10, 13596-13605 (2020). PMID: 33520346.

Davies, K. & Jínek, M. The CRISPR-RNA World: An Interview with Martin Jínek. CRISPR J 3, 68-72 (2020). PMID: 32315230.

Garcia-Doval, C., Schwede, F., Berk, C., Rostøl, JT., Niewoehner, O., Tejero, O., Hall, J., Marraffini, LA. & Jinek, M. Activation and self-inactivation mechanisms of the cyclic oligoadenylate-dependent CRISPR ribonuclease Csm6. Nat Commun 11, 1596 (2020). PMID: 32221291.

Pinto, PH., Kroupova, A., Schleiffer, A., Mechtler, K., Jinek, M., Weitzer, S. & Martinez, J. ANGEL2 is a member of the CCR4 family of deadenylases with 2',3'-cyclic phosphatase activity. Science 369, 524-530 (2020). PMID: 32732418.

Saha, A., Arantes, PR., Hsu, RV., Narkhede, YB., Jinek, M. & Palermo, G. Molecular Dynamics Reveals a DNA-Induced Dynamic Switch Triggering Activation of CRISPR-Cas12a.  J Chem Inf Model 60, 6427-6437 (2020). PMID: 33107304.

Wrona, D., Pastukhov, O., Pritchard, RS., Raimondi, F., Tchinda, J., Jinek, M., Siler, U. & Reichenbach, J. NCF1 Locus Is Challenged by Frequent Incidence of Chromosomal Deletions. Mol Ther Methods Clin Dev 17, 936-943 (2020). PMID: 32420407.

2019
Allain, FH. & Jinek, M. Editorial overview: Protein-nucleic acid interactions - cryo-EM, what else?. Curr. Opin. Struct. Biol. 59, vi-viii (2019). PMID: 31635992.

Boneberg, FM., Brandmann, T., Kobel, L., van den Heuvel, J., Bargsten, K., Bammert, L., Kutay, U. & Jinek, M. Molecular mechanism of the RNA helicase DHX37 and its activation by UTP14A in ribosome biogenesis. RNA 25, 685-701 (2019). PMID: 30910870.

Boneberg, FM., Brandmann, T., Kobel, L., van den Heuvel, J., Bargsten, K., Bammert, L., Kutay, U. & Jinek, M. Corrigendum: Molecular mechanism of the RNA helicase DHX37 and its activation by UTP14A in ribosome biogenesis. RNA 25, 1576 (2019). PMID: 31619564.

Dumeau, CE., Monfort, A., Kissling, L., Swarts, DC., Jinek, M. & Wutz, A. Introducing gene deletions by mouse zygote electroporation of Cas12a/Cpf1. Transgenic Res. 28, 525-535 (2019). PMID: 31482512.

Hegge, JW., Swarts, DC., Chandradoss, SD., Cui, TJ., Kneppers, J., Jinek, M., Joo, C. & van der Oost, J. DNA-guided DNA cleavage at moderate temperatures by Clostridium butyricum Argonaute. Nucleic Acids Res. 47, 5809-5821 (2019). PMID: 31069393.

Jínek, M. Uncut but Primed for Change. CRISPR J 2, 352-354 (2019). PMID: 31860347.

Kissling, L., Monfort, A., Swarts, DC., Wutz, A. & Jinek, M. Preparation and electroporation of Cas12a/Cpf1-guide RNA complexes for introducing large gene deletions in mouse embryonic stem cells. Meth. Enzymol. 616, 241-263 (2019). PMID: 30691645.

Kroupova, A., Ivascu, A., Reimão-Pinto, MM., Ameres, SL. & Jinek, M. Structural basis for acceptor RNA substrate selectivity of the 3' terminal uridylyl transferase Tailor. Nucleic Acids Res. 47, 1030-1042 (2019). PMID: 30462292.

Kumar, A., Clerici, M., Muckenfuss, LM., Passmore, LA. & Jinek, M. Mechanistic insights into mRNA 3'-end processing. Curr. Opin. Struct. Biol. 59, 143-150 (2019). PMID: 31499460.

Ricci, CG., Chen, JS., Miao, Y., Jinek, M., Doudna, JA., McCammon, JA. & Palermo, G. Deciphering Off-Target Effects in CRISPR-Cas9 through Accelerated Molecular Dynamics. ACS Cent Sci 5, 651-662 (2019). PMID: 31041385.

Savić, N., Ringnalda, FC., Berk, C., Bargsten, K., Hall, J., Jinek, M. & Schwank, G. In vitro Generation of CRISPR-Cas9 Complexes with Covalently Bound Repair Templates for Genome Editing in Mammalian Cells. Bio Protoc 9, (2019). PMID: 30675496.

Swarts, DC. & Jinek, M. Mechanistic Insights into the cis- and trans-Acting DNase Activities of Cas12a. Mol. Cell 73, 589-600.e4 (2019). PMID: 30639240.

2018
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.

2017
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. 

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).