Publikationen

Publikationen aus dem DFG-Schwerpunktprogramm (SPP2141)

Nachfolgend aufgelistet sind Publikationen, die bislang im Rahmen des SPP2141 entstanden sind.

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2021

Collias D, Beisel CL (2021) CRISPR technologies and the search for the PAM-free nuclease. Nature Communications 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 Research 49(5): 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 Systems 12(1): 56–67.e6. 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 372(6545): 941–948. doi:10.1126/science.abe7106.

Lu W-T, Trost CN, Müller-Esparza H, Randau L, Davidson AR (2021) Anti-CRISPR AcrIF9 functions by inducing the CRISPR-Cas complex to bind DNA non-specifically. Nucleic Acids Research 49(1): 3381–3393. doi:10.1093/nar/gkab092.

Märkle P, Maier LK, Maaß S, Hirschfeld C, Bartel J, Becher D, Voß B, Marchfelder A (2021) A small RNA is linking CRISPR–Cas and zinc transport. Frontiers in Molecular Biosciences 8(1): 1–13. 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 Research 49(4): e20. doi:10.1093/nar/gkaa1158.

Mougiakos I, Beisel CL (2021) CRISPR transposons on the move. Cell Host & Microbe 29(1): 675–677. doi:10.1016/j.chom.2021.04.012.

Münch 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(1): 94–106e4. doi:10.1016/j.chom.2020.10.01.

Riediger M, Spät 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). The Plant Cell 33(2): 248–269. doi:10.1093/plcell/koaa017.

2020

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

Alzheimer M, Svensson SL, König 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 Pathogens 16(2): e1008304. doi: 10.1371/journal.ppat.1008304.

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.

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

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 Research 48(10): 5624–5638. doi: 10.1093/nar/gkaa272.

Maier LK, Marchfelder A, Randau L (2020). Meeting Report: German Genetics Society–Genome Editing with CRISPR. Bioessays 42(2): 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 Č, 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. Nature Reviews Microbiology 18(2): 67–83. doi: 10.1038/s41579-019-0299-x.

Pfeiffer F, Losensky G, Marchfelder A, Habermann B, Dyall-Smith M (2020) Whole-genome comparison between the type strain of Halobacterium salinarum (DSM 3754(T) ) and the laboratory strains R1 and NRC-1. MicrobiologyOpen 9(2): e974. doi: 10.1002/mbo3.974.

Pinilla-Redondo R, Mayo-Muñoz D, Russel J, Garrett RA, Randau L, Sørensen SJ, Shah SA (2020) Type IV CRISPR-Cas systems are highly diverse and involved in competition between plasmids. Nucleic Acids Research 48(4): 2000–2012. doi: 10.1093/nar/gkz1197.

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.

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. Frontiers in Microbiology 10: 3078. doi: 10.3389/fmicb.2019.03078.

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.

2019

Charpentier E, Elsholz A, Marchfelder A (2019) CRISPR-Cas: more than ten years and still full of mysteries. RNA Biology 16(4): 377–379. doi: 10.1080/15476286.2019.1591659.

Gleditzsch D, Pausch P, Müller-Esparza H, Özcan A, Guo X, Bange G, Randau L (2019) PAM identification by CRISPR-Cas effector complexes: diversified mechanisms and structures. RNA Biology 16(4): 504–517. doi: 10.1080/15476286.2018.1504546.

Gomes-Filho JV, Randau L (2019) RNA stabilization in hyperthermophilic archaea. Annals of the New York Academy of Sciences 1447(1): 88–96. doi: 10.1111/nyas.14060.

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 Biology 16(4): 390–396. doi: 10.1080/15476286.2018.1486660.

Hou S, Brenes-Álvarez M, Reimann V, Alkhnbashi OS, Backofen R, Muro-Pastor AM, Hess WR (2019) CRISPR-Cas systems in multicellular cyanobacteria. RNA Biology 16(4): 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 Microbiology Letters 366(8): 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 Biology 16(4): 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. Biotechnology Journal 14(3): e1700583. doi: 10.1002/biot.201700583.

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

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 Biology 16(4): 404–412. doi: 10.1080/15476286.2018.1526537.

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. Nature Communications 10(1): 2948. doi: 10.1038/s41467-019-10747-3.

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 Biology 16(4): 469–480. doi: 10.1080/15476286.2018.1460994.

Nickel L, Ulbricht A, Alkhnbashi OS, Förstner 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 Gö1. RNA Biology 16(4): 492–503. doi: 10.1080/15476286.2018.1514234.

Özcan A, Pausch P, Linden A, Wulf A, Schühle K, Heider J,Urlaub H, Heimerl T, Bange G, Randau L (2019) Type IV CRISPR RNA processing and effector complex formation in Aromatoleum aromaticum. Nature Microbiology 4(1): 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 Biology 16(4): 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. Nature Biotechnology 37(12): 1493–1501. doi: 10.1038/s41587-019-0235-7.

Scholz I, Lott SC, Behler J, Gärtner K, Hagemann M, Hess WR (2019) Divergent methylation of CRISPR repeats and cas genes in a subtype I-D CRISPR-Cas-system. BMC Microbiology 19(1): 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 Biology 16(4): 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 Reports 28(12): 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, Gophna U (2019) Pervasive acquisition of CRISPR memory driven by inter-species mating of archaea can limit gene transfer and influence speciation. Nature Microbiology 4(1): 177–186. doi: 10.1038/s41564-018-0302-8.

Turkowyd B, Müller-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 in Enzymology 616 (1): 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. Journal of Industrial Microbiology and Biotechnology 46(9–10): 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. Archives of Virology 164(3): 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 Biology 16(4): 585–587. doi: 10.1080/15476286.2018.1474073.

2018

Alper HS, Beisel CL (2018) Advances in CRISPR technologies for microbial strain engineering. Biotechnology Journal 13(9): e1800460. doi: 10.1002/biot.201800460.

Baumdicker F, Huebner AMI, Pfaffelhuber P (2018) The independent loss model with ordered insertions for the evolution of CRISPR spacers. Theoretical Population Biology 119(1): 72–82. doi: 10.1016/j.tpb.2017.11.001.

Behler J, Vijay D, Hess WR, Akhtar MK (2018) CRISPR-based technologies for metabolic engineering in Cyanobacteria. Trends in Biotechnology 36(10): 996–1010. doi: 10.1016/j.tibtech.2018.05.011.

Behler J, Sharma K, Reimann V, Wilde A, Urlaub H, Hess WR (2018) The host-encoded RNase E endonuclease as the crRNA maturation enzyme in a CRISPR-Cas subtype III-Bv system. Nature Microbiology 3(3): 367–377. doi: 10.1038/s41564-017-0103-5.

Beisel CL (2018) CRISPR tool puts RNA on the record. Nature 562(7727): 347–349. doi: 10.1038/d41586-018-06869-1.

Beuter D, Gomes-Filho JV, Randau L, Díaz-Pascual F, Drescher K, Link H (2018) Selective enrichment of slow-growing bacteria in a metabolism-wide CRISPRi library with a TIMER protein. ACS Synthetic Biology 7(12): 2775–2782. doi: 10.1021/acssynbio.8b00379.

Clouet-d’Orval B, Batista M, Bouvier M, Quentin Y, Fichant G, Marchfelder A, Maier LK (2018) Insights into RNA-processing pathways and associated RNA-degrading enzymes in Archaea. FEMS Microbiology Reviews 42(5): 579–613. doi: 10.1093/femsre/fuy016.

Dugar G, Leenay RT, Eisenbart SK, Bischler T, Aul BU, Beisel CL, Sharma CM (2018)CRISPR RNA-dependent binding and cleavage of endogenous RNAs by the Campylobacter jejuni Cas9. Molecular Cell 69(5): 893–905. doi: 10.1016/j.molcel.2018.01.032.

Kieper SN, Almendros C, Behler J, McKenzie RE, Nobrega FL, Haagsma AC, Vink JNA, Hess WR, Brouns SJJ (2018) Cas4 facilitates PAM-compatible spacer selection during CRISPR adaptation. Cell Reports 22(13): 3377–3384. doi: 10.1016/j.celrep.2018.02.103.

Krivoy A, Rutkauskas M, Kuznedelov K, Musharova O, Rouillon C, Severinov K, Seidel R (2018) Primed CRISPR adaptation in Escherichia coli cells does not depend on conformational changes in the Cascade effector complex detected in Vitro. Nucleic Acids Research 46(8): 4087–4098. doi: 10.1093/nar/gky219.

Marshall R, Maxwell CS, Collins SP, Jacobsen T, Luo ML, Begemann MB, Gray BN, January E, Singer A, He Y, Beisel CL, Noireaux V (2018) Rapid and scalable characterization of CRISPR technologies using an E. coli cell-free transcription-translation system. Molecular Cell 69(1): 146–157.e3. doi: 10.1016/j.molcel.2017.12.007.

Maxwell CS, Jacobsen T, Marshall R, Noireaux V, Beisel CL (2018) A detailed cell-free transcription-translation-based assay to decipher CRISPR protospacer-adjacent motifs. Methods 143(1): 48–57. doi: 10.1016/j.ymeth.2018.02.016.