Publications - Universit盲t Ulm

Publications SPP2141

Liao C, Sharma S, Svensson SL, Kibe A, Weinberg Z, Alkhnbashi OS, Bischler T, Backofen R, Caliskan N, Sharma CM, Beisel CL (2022) Spacer prioritization in CRISPR-Cas9 immunity is enabled by the leader RNA. Nature Microbiology 7 (4): 530-541

Wimmer F, Mougiakos I, Englert F, Beisel CL (2022) Rapid cell-free characterization of multi-subunit CRISPR effectors and transposons. Molecular Cell 82 (6): 1210-1224

Collias D, Beisel CL (2021) CRISPR technologies and the search for the PAM-free nuclease. Nat Commun, 12, 555. DOI: 10.1038/s41467-020-20633-y

Collins SP, Rostain W, Liao C, Beisel CL (2021) Sequence-independent RNA sensing and DNA targeting by a split domain CRISPR-Cas12a gRNA switch. Nucleic Acids Res, 49, 2985-2999. DOI: 10.1093/nar/gkab100

Donati S, Kuntz M, Pahl V, Farke N, Beuter D, Glatter T, Gomes-Filho JV, Randau L, Wang C-Y, Link H (2021) Multi-omics analysis of CRISPRi-knockdowns identifies mechanisms that buffer decreases of enzymes in E. coli metabolism. Cell Syst, 12, 56-67. DOI: 10.1016/j.cels.2020.10.011.

Jiao C, Sharma S, Dugar G, Peeck NL, Bischler T, Wimmer F, Yu Y, Barquist L, Schoen C, Kurzai O, Sharma CM, Beisel CL (2021) Noncanonical crRNAs derived from host transcripts enable multiplexable RNA detection by Cas9. Science, Epub ahead of print. DOI: 10.1126/science.abe7106.

Lu W-T, Trost CN, M眉ller-Esparza H, Randau L, Davidson AR (2021) Anti-CRISPR AcrIF9 functions by inducing the CRISPR-Cas complex to bind DNA non-specifically. Nucleic Acids Res, 49, 3381-3393. DOI: 10.1093/nar/gkab092.

M盲rkle P, Maier LK, Maa脽 S, Hirschfeld C, Bartel J, Becher D, 痴辞脽 B, Marchfelder A (2021) A Small RNA Is Linking CRISPR鈥揅as and Zinc Transport. Front Mol Biosci, 8:640440. DOI: 10.3389/fmolb.2021.640440

Mitrofanov A, Alkhnbashi OS, Shmakov SA, Makarova KS, Koonin EV, Backofen R (2021) CRISPRidentify: identification of CRISPR arrays using machine learning approach. Nucleic Acids Res, 49, e20. DOI: 10.1093/nar/gkaa1158.

Mougiakos I, Beisel CL (2021) CRISPR transposons on the move. Cell Host Microbe, 29,675-677. DOI: 10.1016/j.chom.2021.04.012.

M眉nch PC, Franzosa EA, Stecher B, McHardy AC, Huttenhower C (2021) Identification of Natural CRISPR Systems and Targets in the Human Microbiome. Cell Host Microbe, 29, 94-106.e4. DOI: 10.1016/j.chom.2020.10.010.

Riediger M, Sp盲t P, Bilger R, Voigt K, Macek B, Hess WR (2021) Analysis of a photosynthetic cyanobacterium rich in internal membrane systems via gradient profiling by sequencing (Grad-seq). Plant Cell, Epub ahead of press. DOI: 10.1093/plcell/koaa017

Sharma, S and Sharma, CM (2021) Identification of RNA binding partners of CRISPR-Cas proteins in prokaryotes using RIP-seq. Post-transcriptional Gene Regulation, 3rd Edition - Methods in Molecular Biology, Springer, (in press).

Taxiarchi C, Beaghton A, Don NI, Kyrou K, Gribble M, Shittu D, Collins SP, Beisel CL, Galizi R, Crisanti A (2021) A genetically encoded anti-CRISPR protein constrains gene drive spread and prevents population suppression. Nature Communications 12 (1): 3977

W枚rle E, Jakob L, Schmidbauer A, Zinner G, Grohmann D (2021) Decoupling the bridge helix of Cas12a results in a reduced trimming activity, increased mismatch sensitivity and impaired conformational transitions. Nucleic Acids Research,

Alkhnbashi OS, Meier T, Mitrofanov A, Backofen R, 痴辞脽 B. (2020) CRISPR-Cas bioinformatics. Methods. 172:3-11. doi: 10.1016/j.ymeth.2019.07.013.

Alzheimer M, Svensson SL, K枚nig F, Schweinlin M, Metzger M, Walles H, Sharma CM. (2020) A three-dimensional intestinal tissue model reveals factors and small regulatory RNAs important for colonization with Campylobacter jejuni. PLoS Pathog. 16:e1008304. doi: 10.1371/journal.ppat.1008304. eCollection 2020 Feb.

Baumdicker F, Sester-Huss E, Pfaffelhuber P (2020). Modifiers of mutation rate in selectively fluctuating environments. Stochastic Processes and Their Applications 130, 6843鈥�6862.

Beisel CL. (2020) Methods for characterizing, applying, and teaching CRISPR-Cas systems. Methods. 172:1-2. doi: 10.1016/j.ymeth.2020.01.004.

Behler J, Hess WR. (2020) Approaches to study CRISPR RNA biogenesis and the key players involved. Methods. 172:12-26. doi: 10.1016/j.ymeth.2019.07.015.

Collias D, Leenay RT, Slotkowski RA, Zuo Z, Collins SP, McGirr BA, Liu J, Beisel CL. (2020) A positive, growth-based PAM screen identifies noncanonical motifs recognized by the S. pyogenes Cas9. Sci Adv. 6:eabb4054. doi: 10.1126/sciadv.abb4054.

Collins SP, Beisel CL. (2020) Your Base Editor Might Be Flirting with Single (Stranded) DNA: Faithful On-Target CRISPR Base Editing without Promiscuous Deamination. Mol Cell. 79:703-704. doi:0.1016/j.molcel.2020.07.030.

Donati S, Kuntz M, Pahl V, Farke N, Beuter D, Glatter T, Gomes-Filho JV, Randau L, Wang CY, Link H. (2020) Multi-omics Analysis of CRISPRi-Knockdowns Identifies Mechanisms that Buffer Decreases of Enzymes in E. coli Metabolism. Cell Syst. S2405-4712(20)30418-X. doi: 10.1016/j.cels.2020.10.011.

Jacobsen T, Ttofali F, Liao C, Manchalu S, Gray BN, Beisel CL. (2020) Characterization of Cas12a nucleases reveals diverse PAM profiles between closely-related orthologs. Nucleic Acids Res. pii: gkaa272. doi: 10.1093/nar/gkaa272.

Maier LK, Marchfelder A, Randau L (2020). Meeting Report: German Genetics Society-Genome Editing with CRISPR. Bioessays. 42:e1900223. doi: 10.1002/bies.201900223.

Makarova KS, Wolf YI, Iranzo J, Shmakov SA, Alkhnbashi OS, Brouns SJJ, Charpentier E, Cheng D, Haft DH, Horvath P, Moineau S, Mojica FJM, Scott D, Shah SA, Siksnys V, Terns MP, Venclovas 膶, White MF, Yakunin AF, Yan W, Zhang F, Garrett RA, Backofen R, van der Oost J, Barrangou R, Koonin EV. (2020) Evolutionary classification of CRISPR-Cas systems: a burst of class 2 and derived variants. Nat Rev Microbiol. 18:67-83. doi: 10.1038/s41579-019-0299-x.

Marchfelder A. (2020) CRISPR-Cas: In Rekordzeit von der Grundlagenforschung zur Anwendung. Biospektrum (Heidelb). 26:806. German. doi:10.1007/s12268-020-1500-5.

Marshall R, Beisel CL, Noireaux V. (2020) Rapid Testing of CRISPR Nucleases and Guide RNAs in an E. coli Cell-Free Transcription-Translation System. STAR Protoc. 1:100003. doi: 10.1016/j.xpro.2019.100003.

Mitrofanov A, Alkhnbashi OS, Shmakov SA, Makarova KS, Koonin EV, Backofen R. (2020) CRISPRidentify: identification of CRISPR arrays using machine learning approach. Nucleic Acids Res. gkaa1158. doi: 10.1093/nar/gkaa1158.

M眉ller-Esparza H, Osorio-Valeriano M, Steube N, Thanbichler M, Randau L. (2020) Bio-Layer Interferometry Analysis of the Target Binding Activity of CRISPR-Cas Effector Complexes. Front Mol Biosci. 7:98. doi:10.3389/fmolb.2020.00098.

Padilha VA, Alkhnbashi OS, Tran VD, Shah SA, L F Carvalho ACP, Backofen R. (2020)

Casboundary: Automated definition of integral Cas cassettes. Bioinformatics. btaa984. doi: 10.1093/bioinformatics/btaa984.

Padilha VA, Alkhnbashi OS, Shah SA, de Carvalho ACPLF, Backofen R. (2020) CRISPRcasIdentifier: Machine learning for accurate identification and classification of CRISPR-Cas systems. Gigascience. 9:giaa062. doi:10.1093/gigascience/giaa062.

Pinilla-Redondo R, Mayo-Mu帽oz D, Russel J, Garrett RA, Randau L, S酶rensen SJ, Shah SA. (2020) Type IV CRISPR-Cas systems are highly diverse and involved in competition between plasmids. Nucleic Acids Res. 48:2000-2012. doi: 10.1093/nar/gkz1197.

Reimann V, Ziemann M, Li H, Zhu T, Behler J, Lu X, Hess WR. (2020) Specificities and functional coordination between the two Cas6 maturation endonucleases in Anabaena sp. PCC 7120 assign orphan CRISPR arrays to three groups. RNA Biol. 17:1442-1453. doi: 10.1080/15476286.2020.1774197.

Stachler AE, Schwarz TS, Schreiber S, Marchfelder A. (2020) CRISPRi as an efficient tool for gene repression in archaea. Methods. 172:76-85. doi: 10.1016/j.ymeth.2019.05.023.

Stachler AE, W枚rtz J, Alkhnbashi OS, Turgeman-Grott I, Smith R, Allers T, Backofen R, Gophna U, Marchfelder A. (2020) Adaptation induced by self-targeting in a type I-B CRISPR-Cas system. J Biol Chem. 295:13502-13515. doi:10.1074/jbc.RA120.014030.

Turkowyd B, Schreiber S, W枚rtz J, Segal ES, Mevarech M, Duggin IG, Marchfelder A, Endesfelder U. (2020) Establishing Live-Cell Single-Molecule Localization Microscopy Imaging and Single-Particle Tracking in the Archaeon Haloferax volcanii. Front Microbiol. 11:583010. doi:10.3389/fmicb.2020.583010.

Ulbricht A, Nickel L, Weidenbach K, Vargas Gebauer H, Kie脽ling C, F枚rstner KU, Schmitz RA. (2020) The CARF Protein MM_0565 Affects Transcription of the Casposon- Encoded cas1-solo Gene in Methanosarcina mazei G枚1. Biomolecules. 10:1161. doi: 10.3390/biom10081161.

Wandera KG, Collins SP, Wimmer F, Marshall R, Noireaux V, Beisel CL. (2020) An enhanced assay to characterize anti-CRISPR proteins using a cell-free transcription-translation system. Methods. 172:42-50. doi: 10.1016/j.ymeth.2019.05.014.

Wimmer F, Beisel CL. (2020) CRISPR-Cas Systems and the Paradox of Self-Targeting Spacers. Front Microbiol. 10:3078. doi: 10.3389/fmicb.2019.03078. eCollection 2019.

Ziegler H, Nellen W. (2020) CRISPR-Cas experiments for schools and the public. Methods. 172:86-94. doi: 10.1016/j.ymeth.2019.08.009.

Alkhnbashi OS, Meier T, Mitrofanov A, Backofen R and 痴辞脽 B. (2019). CRISPR-Cas bioinformatics. Methods. 172:3-11. doi: 10.1016/j.ymeth.2019.07.013. Epub 2019 Jul 19.

Charpentier E, Elsholz A, Marchfelder A. (2019) CRISPR-Cas: more than ten years and still full of mysteries. RNA Biol. 16: 377-379. doi: 10.1080/15476286.2019.1591659.

Collias D, Marshall R, Collins SP, Beisel CL, Noireaux V. (2019) An educational module to explore CRISPR technologies with a cell-free transcription-translation system. Synth Biol (Oxf). 4:ysz005. doi: 10.1093/synbio/ysz005.

Gleditzsch D, Pausch P, M眉ller-Esparza H, 脰zcan A, Guo X, Bange G, Randau L. (2019) PAM identification by CRISPR-Cas effector complexes: diversified mechanisms and structures. RNA Biol. 16:504-517. doi: 10.1080/15476286.2018.1504546.

Heidrich N, Bauriedl S, Schoen C. (2019). Investigating RNA-Protein Interactions in Neisseria meningitidis by RIP-Seq Analysis. Methods Mol Biol. 1969: 33-49. doi: 10.1007/978-1-4939-9202-7_3.

Heidrich N, Hagmann A, Bauriedl S, Vogel J, Schoen C. (2019). The CRISPR/Cas system in Neisseria meningitidis affects bacterial adhesion to human nasopharyngeal epithelial cells. RNA Biol. 16: 390-396. doi: 10.1080/15476286.2018.1486660.

Hou S, Brenes-脕lvarez M, Reimann V, Alkhnbashi OS, Backofen R, Muro-Pastor AM, Hess WR. (2019) CRISPR-Cas systems in multicellular cyanobacteria. RNA Biol. 16:518-529. doi: 10.1080/15476286.2018.1493330.

Jacobsen T, Liao C, Beisel CL. (2019) The Acidaminococcus sp. Cas12a nuclease recognizes GTTV and GCTV as non-canonical PAMs. FEMS Microbiol Lett. 366. pii: fnz085. doi: 10.1093/femsle/fnz085.

Jesser R, Behler J, Benda C, Reimann V, Hess WR. (2019) Biochemical analysis of the Cas6-1 RNA endonuclease associated with the subtype I-D CRISPR-Cas system in Synechocystis sp. PCC 6803. RNA Biol. 16:481-491. doi: 10.1080/15476286.2018.1447742.

Leenay RT, Vento JM, Shah M, Martino ME, Leulier F, Beisel CL. (2019) Genome Editing with CRISPR-Cas9 in Lactobacillus plantarum Revealed That Editing Outcomes Can Vary Across Strains and Between Methods. Biotechnol J. 14:e1700583. doi: 10.1002/biot.201700583.

Liao C, Ttofali F, Slotkowski RA, Denny SR, Cecil TD, Leenay RT, Keung AJ, Beisel CL. (2019) Modular one-pot assembly of CRISPR arrays enables library generation and reveals factors influencing crRNA biogenesis. Nat Commun. 10:2948. doi: 10.1038/s41467-019-10747-3.

Liao C, Slotkowski RA, Achmedov T, Beisel CL. (2019) The Francisella novicida Cas12a is sensitive to the structure downstream of the terminal repeat in CRISPR arrays. RNA Biol. 16: 404-412. doi: 10.1080/15476286.2018.1526537.

Liao C, Slotkowski RA, Beisel CL. (2019) CRATES: A one-step assembly method for Class 2 CRISPR arrays. Methods Enzymol. 629:493-511. doi: 10.1016/bs.mie.2019.04.011.

Maier LK, Stachler AE, Brendel J, Stoll B, Fischer S, Haas KA, Schwarz TS, Alkhnbashi OS, Sharma K, Urlaub H, Backofen R, Gophna U, Marchfelder A. (2019) The nuts and bolts of the Haloferax CRISPR-Cas system I-B. RNA Biol. 16:469-480. doi: 10.1080/15476286.2018.1460994.

Makarova, KS, Wolf, YI, Iranzo, J, Shmakov, SA, Alkhnbashi, OS, Brouns, SJJ, Charpentier, E, Cheng, D, Haft, DH, Horvath, P, Moineau, S, Mojica, FJM, Scott, D, Shah, SA, Siksnys, V, MP, Venclovas, C, White, MF, Yakunin, AF, Yan, W, Zhang, F, Garrett, RA, Backofen, R, Oost, J, Barrangou, R, Koonin, EV. (2019). Evolutionary classification of CRISPR鈥揅as systems: a burst of class 2 and derived variants. Nat Rev Microbiol. 18:67-83. doi: 10.1038/s41579-019-0299-x

Nickel L, Ulbricht A, Alkhnbashi OS, F枚rstner KU, Cassidy L, Weidenbach K, Backofen R, Schmitz RA. (2019) Cross-cleavage activity of Cas6b in crRNA processing of two different CRISPR-Cas systems in Methanosarcina mazei G枚1. RNA Biol. 16: 492-503. doi: 10.1080/15476286.2018.1514234.

脰zcan A, Pausch P, Linden A, Wulf A, Sch眉hle K, Heider J, Urlaub H, Heimerl T, Bange G, Randau L. (2019) Type IV CRISPR RNA processing and effector complex formation in Aromatoleum aromaticum. Nat Microbiol. 4:89-96. doi: 10.1038/s41564-018-0274-8.

Papathanasiou P, Erdmann S, Leon-Sobrino C, Sharma K, Urlaub H, Garrett RA, Peng X. (2019) Stable maintenance of the rudivirus SIRV3 in a carrier state in Sulfolobus islandicus despite activation of the CRISPR-Cas immune response by a second virus SMV1. RNA Biol. 16: 557-565. doi: 10.1080/15476286.2018.1511674.

Pickar-Oliver A, Black JB, Lewis MM, Mutchnick KJ, Klann TS, Gilcrest KA, Sitton MJ, Nelson CE, Barrera A, Bartelt LC, Reddy TE, Beisel CL, Barrangou R, Gersbach CA. (2019) Targeted transcriptional modulation with type I CRISPR-Cas systems in human cells. Nat Biotechnol. 37:1493-1501. doi: 10.1038/s41587-019-0235-7.

Scholz I, Lott SC, Behler J, G盲rtner K, Hagemann M, Hess WR. (2019) Divergent methylation of CRISPR repeats and cas genes in a subtype I-D CRISPR-Cas-system. BMC Microbiol. 19:147. doi: 10.1186/s12866-019-1526-3.

Shah SA, Alkhnbashi OS, Behler J, Han W, She Q, Hess WR, Garrett RA, Backofen R. (2019) Comprehensive search for accessory proteins encoded with archaeal and bacterial type III CRISPR-cas gene cassettes reveals 39 new cas gene families. RNA Biol. 16: 530-542. doi: 10.1080/15476286.2018.1483685.

Songailiene I, Rutkauskas M, Sinkunas T, Manakova E, Wittig S, Schmidt C, Siksnys V, Seidel R. (2019) Decision-Making in Cascade Complexes Harboring crRNAs of Altered Length. Cell Rep. 28:3157-3166.e4. doi: 10.1016/j.celrep.2019.08.033.

Turgeman-Grott, I, Joseph, S, Marton, S, Eizenshtein, K, Naor, A, Soucy, S, Stachler, A-E, Shalev, Y, Zarkor, M, Reshef, L, Altman-Price, N, Marchfelder, A, and Gophna, U (2019) Pervasive acquisition of CRISPR memory driven by inter-species mating of archaea can limit gene transfer and influence speciation, Nat Microbiol. 4:177-186. doi: 10.1038/s41564-018-0302-8.

Turkowyd B, M眉ller-Esparza H, Climenti V, Steube N, Endesfelder U, Randau L. (2019) Live-cell single-particle tracking photoactivated localization microscopy of Cascade-mediated DNA surveillance. Methods Enzymol. 616:133-171. doi: 10.1016/bs.mie.2018.11.001.

Vento JM, Crook N, Beisel CL. (2019) Barriers to genome editing with CRISPR in bacteria. J Ind Microbiol Biotechnol. 46:1327-1341. doi: 10.1007/s10295-019-02195-1.

Wolf S, Fischer MA, Kupczok A, Reetz J, Kern T, Schmitz RA, Rother M. (2019) Characterization of the lytic archaeal virus Drs3 infecting Methanobacterium formicicum. Arch Virol. 164:667-674. doi: 10.1007/s00705-018-04120-w.

Yair Y, Gophna U. (2019) Repeat modularity as a beneficial property of multiple CRISPR-Cas systems. RNA Biol. 16: 585-587. doi: 10.1080/15476286.2018.1474073.