Publications

2024

The CRISPR-associated adenosine deaminase Cad1 converts ATP to ITP to provide antiviral immunity.

Baca CF, Majumder P, Hickling JH, Ye L, Teplova M, Brady SF, Patel DJ, Marraffini LA. Cell. 2024 Oct 28;S0092-8674(24)01150-4.

Cas9 interaction with the tracrRNA nexus modulates the repression of type II-A CRISPR-cas genes.

Kim H, Marraffini LA. Nuclei Acids Res. 2024 Jul 12;52(17):10595-10606.

DNA glycosylases provide antiviral defence in prokaryotes.

Hossain AA, Pigli YZ, Baca CF, Heissel S, Thomas A, Libis VK, Burian J, Chappie JS, Brady SF, Rice PA, Marraffini LA. Nature. 2024 Apr 17;629(8011):410-416.

The CRISPR effector Cam1 mediates membrane depolarization for phage defence.

Baca CF, Yu Y, Rostøl JT, Majumder P, Patel DJ, Marraffini LA. Nature. 2024 Jan 10;625(7996):797-804.

Type III CRISPR-Cas: beyond the Cas10 effector complex.

Stella G, Marraffini LA. Trends Biochem Sci. 2024 Jan;49(1):28-37.

2023

Bacterial cGAS senses a viral RNA to initiate immunity.

Banh DV, Roberts CG, Morales-Amador A, Berryhill BA, Chaudhry W, Levin BR, Brady SF, Marraffini LA. Nature. 2023 Nov;623(7989):1001-1008.

Rarely acquired type II-A CRISPR-Cas spacers mediate anti-viral immunity through the targeting of a non-canonical PAM sequence.

Kenney CT, Marraffini LA. Nuclei Acids Res. 2023 Aug 11;51(14):7438-7450.

2022

CRISPR-assisted transposition: TnsC finds (and threads) the needle in the haystack.

Hossain AA, Marraffini LA. Mol Cell. 2022 Nov 3;82(21):3968-3969.

Cleavage of viral DNA by restriction endonucleases stimulates the type II CRISPR-Cas immune response.

Maguin P, Varble A, Modell JW, Marraffini LA. Mol Cell. 2022 Mar 3;82(5):907-919.e7.

Different modes of spacer acquisition by the Staphylococcus epidermidis type III-A CRISPR-Cas system.

Aviram N, Thornal AN, Zeevi D, Marraffini LA. Nucleic Acids Res. 2022 Feb 22;50(3):1661-1672.

2021

Prophage integration into CRISPR loci enables evasion of antiviral immunity in Streptococcus pyogenes.

Varble A, Campisi E, Euler CW, Maguin P, Kozlova A, Fyodorova J, Rostøl JT, Fischetti VA, Marraffini LA. Nat Microbiol. 2021 Dec;6(12):1516-1525.

Viral recombination systems limit CRISPR-Cas targeting through the generation of escape mutations.

Hossain AA, McGinn J, Meeske AJ, Modell JW, Marraffini LA. Cell Host Microbe. 2021 Oct 13;29(10):1482-1495.e12.

Type III-A CRISPR immunity promotes mutagenesis of staphylococci.

Mo CY, Mathai J, Rostøl JT, Varble A, Banh DV, Marraffini LA. Nature. 2021 Apr;592(7855):611-615.

From the discovery of DNA to current tools for DNA editing.

Maguin P, Marraffini LA. J Exp Med. 2021 Apr 5;218(4):e20201791.

A CRISPR-Cas9-integrase complex generates precise DNA fragments for genome integration.

Jakhanwal S, Cress BF, Maguin P, Lobba MJ, Marraffini LA, Doudna JA. Nucleic Acids Res. 2021 Apr 6;49(6):3546-3556.

The Card1 nuclease provides defence during type-III CRISPR immunity.

Rostøl JT, Xie W, Kuryavyi V, Maguin P, Kao K, Froom R, Patel DJ, Marraffini LA. Nature. 2021 Feb;590(7847):624-629.

2020

Molecular Mechanisms of CRISPR-Cas Immunity in Bacteria.

Nussenzweig PM, Marraffini LA. Annu Rev Genet. 2020 Nov 23;54:93-120.

A phage-encoded anti-CRISPR enables complete evasion of type VI-A CRISPR-Cas immunity.

Meeske AJ, Jia N, Cassel AK, Kozlova A, Liao J, Wiedmann M, Patel DJ, Marraffini LA. Science. 2020 Jul 3;369(6499):54-59.

Co-evolution within structured bacterial communities results in multiple expansion of CRISPR loci and enhanced immunity.

Pyenson NC, Marraffini LA. Elife. 2020 Mar 30;9:e53078.

Activation and self-inactivation mechanisms of the cyclic oligoadenylate-dependent CRISPR ribonuclease Csm6.

Garcia-Doval C, Schwede F, Berk C, Rostøl JT, Niewoehner O, Tejero O, Hall J, Marraffini LA, Jinek M. Nat Commun. 2020 Mar 27;11(1):1596.

2019

Cas9 Cleavage of Viral Genomes Primes the Acquisition of New Immunological Memories.

Nussenzweig PM, McGinn J, Marraffini LA. Cell Host Microbe. 2019 Oct 9;26(4):515-526.

Cas13-induced cellular dormancy prevents the rise of CRISPR-resistant bacteriophage.

Meeske AJ, Nakandakari-Higa S, Marraffini LA. Nature. 2019 Jun;570(7760):241-245.

A High-Throughput Platform to Identify Small-Molecule Inhibitors of CRISPR-Cas9.

Maji B, Gangopadhyay SA, Lee M, Shi M, Wu P, Heler R, Mok B, Lim D, Siriwardena SU, Paul B, Dančík V, Vetere A, Mesleh MF, Marraffini LA, Liu DR, Clemons PA, Wagner BK, Choudhary A. Cell. 2019 May 2;177(4):1067-1079.

Three New Cs for CRISPR: Collateral, Communicate, Cooperate.

Varble A, Marraffini LA. Trends Genet. 2019 Jun;35(6):446-456.

Recombination between phages and CRISPR-cas loci facilitates horizontal gene transfer in staphylococci.

Varble A, Meaden S, Barrangou R, Westra ER, Marraffini LA. Nat Microbiol. 2019 Jun;4(6):956-963.

Non-specific degradation of transcripts promotes plasmid clearance during type III-A CRISPR-Cas immunity.

Rostøl JT, Marraffini LA. Nat Microbiol. 2019 Apr;4(4):656-662.

Spacer Acquisition Rates Determine the Immunological Diversity of the Type II CRISPR-Cas Immune Response.

Heler R, Wright AV, Vucelja M, Doudna JA, Marraffini LA. Cell Host Microbe. 2019 Feb 13;25(2):242-249.

(Ph)ighting Phages: How Bacteria Resist Their Parasites.

Rostøl JT, Marraffini L. Cell Host Microbe. 2019 Feb 13;25(2):184-194.

Dynamics of Cas10 Govern Discrimination between Self and Non-self in Type III CRISPR-Cas Immunity.

Wang L, Mo CY, Wasserman MR, Rostøl JT, Marraffini LA, Liu S. Mol Cell. 2019 Jan 17;73(2):278-290.

Type III-A CRISPR-Cas Csm Complexes: Assembly, Periodic RNA Cleavage, DNase Activity Regulation, and Autoimmunity.

Jia N, Mo CY, Wang C, Eng ET, Marraffini LA, Patel DJ. Mol Cell. 2019 Jan 17;73(2):264-277.

2018

Molecular mechanisms of CRISPR-Cas spacer acquisition.

McGinn J, Marraffini LA. Nat Rev Microbiol. 2019 Jan;17(1):7-12.

RNA Guide Complementarity Prevents Self-Targeting in Type VI CRISPR Systems.

Meeske AJ, Marraffini LA. Mol Cell. 2018 Sep 6;71(5):791-801.

Enhanced Bacterial Immunity and Mammalian Genome Editing via RNA-Polymerase-Mediated Dislodging of Cas9 from Double-Strand DNA Breaks.

Clarke R, Heler R, MacDougall MS, Yeo NC, Chavez A, Regan M, Hanakahi L, Church GM, Marraffini LA, Merrill BJ. Mol Cell. 2018 Jul 5;71(1):42-55.

Incomplete prophage tolerance by type III-A CRISPR-Cas systems reduces the fitness of lysogenic hosts.

Goldberg GW, McMillan EA, Varble A, Modell JW, Samai P, Jiang W, Marraffini LA. Nat Commun. 2018 Jan 4;9(1):61.

2017

Type III CRISPR-Cas systems: when DNA cleavage just isn't enough.

Pyenson NC, Marraffini LA. Curr Opin Microbiol. 2017 Jun;37:150-154.

Broad Targeting Specificity during Bacterial Type III CRISPR-Cas Immunity Constrains Viral Escape.

Pyenson NC, Gayvert K, Varble A, Elemento O, Marraffini LA. Cell Host Microbe. 2017 Sep 13;22(3):343-353.

Type III CRISPR-Cas systems produce cyclic oligoadenylate second messengers.

Niewoehner O, Garcia-Doval C, Rostøl JT, Berk C, Schwede F, Bigler L, Hall J, Marraffini LA, Jinek M. Nature. 2017 Aug 31;548(7669):543-548.

CRISPR-Cas systems exploit viral DNA injection to establish and maintain adaptive immunity.

Modell JW, Jiang W, Marraffini LA. Nature. 2017 Apr 6;544(7648):101-104.

Mutations in Cas9 Enhance the Rate of Acquisition of Viral Spacer Sequences during the CRISPR-Cas Immune Response.

Heler R, Wright AV, Vucelja M, Bikard D, Doudna JA, Marraffini LA. Mol Cell. 2017 Jan 5;65(1):168-175.

2016

CRISPR-Cas Systems Optimize Their Immune Response by Specifying the Site of Spacer Integration.

McGinn J, Marraffini LA. Mol Cell. 2016 Nov 3;64(3):616-623.

Degradation of Phage Transcripts by CRISPR-Associated RNases Enables Type III CRISPR-Cas Immunity.

Jiang W, Samai P, Marraffini LA. Cell. 2016 Feb 11;164(4):710-21.

Impact of Different Target Sequences on Type III CRISPR-Cas Immunity.

Maniv I, Jiang W, Bikard D, Marraffini LA. J Bacteriol. 2016 Jan 11;198(6):941-50.

The CRISPR-Cas system of Streptococcus pyogenes: function and applications.

Marraffini LA. Streptococcus pyogenes: Basic Biology to Clinical Manifestations. Oklahoma City (OK): University of Oklahoma Health Sciences Center; 2016 Apr 7.

2015

Resistance and tolerance to foreign elements by prokaryotic immune systems - curating the genome.

Goldberg GW, Marraffini LA. Nat Rev Immunol. 2015 Nov;15(11):717-24. Review.

CRISPR-Cas immunity in prokaryotes.

Marraffini LA. Nature. 2015 Oct 1;526(7571):55-61. Review.

Co-transcriptional DNA and RNA Cleavage during Type III CRISPR-Cas Immunity.

Samai P, Pyenson N, Jiang W, Goldberg GW, Hatoum-Aslan A, Marraffini LA. Cell. 2015 May 21;161(5):1164-74.

Cas9 specifies functional viral targets during CRISPR-Cas adaptation.

Heler R, Samai P, Modell JW, Weiner C, Goldberg GW, Bikard D, Marraffini LA. Nature. 2015 Mar 12;519(7542):199-202.

2014

Exploiting CRISPR-Cas nucleases to produce sequence-specific antimicrobials.

Bikard D, Euler CW, Jiang W, Nussenzweig PM, Goldberg GW, Duportet X, Fischetti VA, Marraffini LA. Nat Biotechnol. 2014 Nov;32(11):1146-50.

Conditional tolerance of temperate phages via transcription-dependent CRISPR-Cas targeting.

Goldberg GW, Jiang W, Bikard D, Marraffini LA. Nature. 2014 Oct 30;514(7524):633-7.

Harnessing CRISPR-Cas9 immunity for genetic engineering.

Charpentier E, Marraffini LA. Curr Opin Microbiol. 2014 Jun;19:114-9. Review.

Editorial overview: Novel technologies in microbiology: Recent advances in techniques in microbiology.

Charpentier E, Marraffini LA. Curr Opin Microbiol. 2014 Jul 10. Review.

Adapting to new threats: the generation of memory by CRISPR-Cas immune systems.

Heler R, Marraffini LA, Bikard D. Mol Microbiol. 2014 Jul. Review.

CRISPR-Cas systems: Prokaryotes upgrade to adaptive immunity.

Barrangou R, Marraffini LA. Mol Cell. 2014 Apr 24. Review.

Impact of CRISPR immunity on the emergence and virulence of bacterial pathogens.

Hatoum-Aslan A, Marraffini LA. Curr Opin Microbiol. 2014 Feb. Review.

2013

CRISPR-Cas immunity against phages: its effects on the evolution and survival of bacterial pathogens.

Marraffini LA. PLoS Pathog. 2013 Dec. Review.

Control of gene expression by CRISPR-Cas systems.

Bikard D, Marraffini LA. F1000Prime Rep. 2013 Nov 1. Review.

Genetic characterization of antiplasmid immunity through a type III-A CRISPR-Cas system.

Hatoum-Aslan A, Maniv I, Samai P, Marraffini LA. J Bacteriol. 2014 Jan.

Dealing with the evolutionary downside of CRISPR immunity: bacteria and beneficial plasmids.

Jiang W, Maniv I, Arain F, Wang Y, Levin BR, Marraffini LA. PLoS Genet. 2013.

A ruler protein in a complex for antiviral defense determines the length of small interfering CRISPR RNAs.

Hatoum-Aslan A, Samai P, Maniv I, Jiang W, Marraffini LA. J Biol Chem. 2013 Sep 27.

DNA targeting specificity of RNA-guided Cas9 nucleases.

Hsu PD, Scott DA, Weinstein JA, Ran FA, Konermann S, Agarwala V, Li Y, Fine EJ, Wu X, Shalem O, Cradick TJ, Marraffini LA, Bao G, Zhang F. Nat Biotechnol. 2013 Sep.

Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system.

Bikard D, Jiang W, Samai P, Hochschild A, Zhang F, Marraffini LA. Nucleic Acids Res. 2013 Aug.

CRISPR decoys: competitive inhibitors of CRISPR immunity.

Maniv I, Hatoum-Aslan A, Marraffini LA. RNA Biol. 2013 May.

RNA-guided editing of bacterial genomes using CRISPR-Cas systems.

Jiang W, Bikard D, Cox D, Zhang F, Marraffini LA. Nat Biotechnol. 2013 Mar.

Multiplex genome engineering using CRISPR/Cas systems.

Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA, Zhang F. Science. 2013 Feb 15.