Interrogating native CRISPR arrays to achieve scalable combinatorial screens and dissect genetic redundancy

Project Information

CRISPRcombo

Grant agreement ID: 865973

DOI

10.3030/865973

EC signature date 19 December 2019

Start date 1 June 2020

End date 31 March 2026

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 2 000 000,00

EU contribution

€ 2 000 000,00

Coordinated by

HELMHOLTZ-ZENTRUM FUR INFEKTIONSFORSCHUNG GMBH
Germany

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Publications

Peer reviewed articles (19)

Improved prediction of bacterial CRISPRi guide efficiency from depletion screens through mixed-effect machine learning and data integration

Author(s): Yanying Yu, Sandra Gawlitt, Lisa Barros de Andrade e Sousa, Erinc Merdivan, Marie Piraud, Chase L. Beisel, Lars Barquist
Published in: Genome Biology, Issue 25, 2024, Page(s) 13, ISSN 1474-760X
Publisher: Springer Nature
DOI: 10.1186/s13059-023-03153-y

Differentially Optimized Cell-Free Buffer Enables Robust Expression from Unprotected Linear DNA in Exonuclease-Deficient Extracts

Author(s): Angelo Cardoso Batista, Antoine Levrier, Paul Soudier, Peter L. Voyvodic, Tatjana Achmedov, Tristan Reif-Trauttmansdorff, Angelique DeVisch, Martin Cohen-Gonsaud, Jean-Loup Faulon, Chase L. Beisel, Jerome Bonnet, Manish Kushwaha
Published in: ACS Synthetic Biology, 2022, Page(s) (in press), ISSN 2161-5063
Publisher: American Chemical Society
DOI: 10.1021/acssynbio.1c00448

Synthetic biology landscape and community in Germany

Author(s): Nicolas Krink, Anne C.Löchner, Hendrik Cooper, Chase L.Beisel, Barbara Di Ventura
Published in: Biotechnology Notes, Issue 3, 2022, Page(s) 8-14, ISSN 2665-9069
Publisher: KeAi Communications
DOI: 10.1016/j.biotno.2021.12.001

TracrRNA reprogramming enables direct PAM-independent detection of RNA with diverse DNA-targeting Cas12 nucleases

Author(s): Chunlei Jiao, Natalia L. Peeck, Jiaqi Yu, Mohammad Ghaem Maghami, Sarah Kono, Daphne Collias, Sandra L. Martinez Diaz, Rachael Larose, Chase L. Beisel
Published in: Nature Communications, Issue 15, 2024, Page(s) 5909, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-024-50243-x

Spacer prioritization in CRISPR–Cas9 immunity is enabled by the leader RNA

Author(s): Chunyu Liao, Sahil Sharma, Sarah L. Svensson, Anuja Kibe, Zasha Weinberg, Omer S. Alkhnbashi, Thorsten Bischler, Rolf Backofen, Neva Caliskan, Cynthia M. Sharma, Chase L. Beisel
Published in: Nature Microbiology, Issue 7(4), 2022, Page(s) 530-541, ISSN 2058-5276
Publisher: Nature Publishing Group
DOI: 10.1038/s41564-022-01074-3

MprF-mediated immune evasion is necessary for Lactiplantibacillus plantarum resilience in the Drosophila gut during inflammation

Author(s): Aranzazu Arias-Rojas, Adini Q. Arifah, Georgia Angelidou, Belal Alshaar, Ursula Schombel, Emma Forest, Dagmar Frahm, Volker Brinkmann, Nicole Paczia, Chase L. Beisel, Nicolas Gisch, Igor Iatsenko
Published in: PLOS Pathogens, Issue 20, 2024, Page(s) e1012462, ISSN 1553-7374
Publisher: PLOS
DOI: 10.1371/journal.ppat.1012462

Rapid cell-free characterization of multi-subunit CRISPR effectors and transposons

Author(s): Franziska Wimmer, Ioannis Mougiakos, Frank Englert, Chase L. Beisel
Published in: Molecular Cell, Issue 82(6), 2022, Page(s) 1210-1224.e6, ISSN 1097-2765
Publisher: Cell Press
DOI: 10.1016/j.molcel.2022.01.026

CRISPR-based screening of small RNA modulators of bile susceptibility in <i>Bacteroides thetaiotaomicron</i>

Author(s): Gianluca Prezza, Chunyu Liao, Sarah Reichardt, Chase L. Beisel, Alexander J. Westermann
Published in: Proceedings of the National Academy of Sciences, Issue 121, 2024, Page(s) e2311323121, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.2311323121

Shortened CRISPR-Cas9 arrays enable multiplexed gene targeting in bacteria from a smaller DNA footprint

Author(s): Sandra Gawlitt, Chunyu Liao, Tatjana Achmedov, Chase L. Beisel
Published in: RNA Biology, Issue 20, 2025, Page(s) 666-680, ISSN 1547-6286
Publisher: Landes Bioscience
DOI: 10.1080/15476286.2023.2247247

The miniature CRISPR-Cas12m effector binds DNA to block transcription

Author(s): Wen Y. Wu; Prarthana Mohanraju; Chunyu Liao; Belén Adiego-Pérez; Sjoerd C.A. Creutzburg; Kira S. Makarova; Karlijn Keessen; Timon A. Lindeboom; Tahseen S. Khan; Stijn Prinsen; Rob Joosten; Winston X. Yan; Anzhela Migur; Charlie Laffeber; David A. Scott; Joyce H.G. Lebbink; Eugene V. Koonin; Chase L. Beisel; John van der Oost
Published in: Molecular Cell, Issue 82(23), 2022, Page(s) 4487-4502, ISSN 1097-2765
Publisher: Cell Press
DOI: 10.1016/j.molcel.2022.11.003

A resurrected ancestor of Cas12a expands target access and substrate recognition for nucleic acid editing and detection

Author(s): Ylenia Jabalera, Igor Tascón, Sara Samperio, Jorge P. López-Alonso, Monika Gonzalez-Lopez, Ana M. Aransay, Guillermo Abascal-Palacios, Chase L. Beisel, Iban Ubarretxena-Belandia, Raul Perez-Jimenez
Published in: Nature Biotechnology, Issue (in press), 2024, ISSN 1087-0156
Publisher: Nature Publishing Group
DOI: 10.1038/s41587-024-02461-3

RNA targeting unleashes indiscriminate nuclease activity of CRISPR–Cas12a2

Author(s): Jack PK Bravo, Thomson Hallmark, Bronson Naegle, Chase L Beisel, Ryan N Jackson, David W Taylor
Published in: Nature, Issue (in press), 2023, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-022-05560-w

A Hitchhiker’s guide to CRISPR editing tools in bacteria

Author(s): Nicolas Krink, Pablo Iván Nikel, Chase L Beisel
Published in: EMBO Reports, Issue 25, 2024, Page(s) 1694-1699, ISSN 1469-3178
Publisher: EMBO Press
DOI: 10.1038/s44319-024-00086-w

Optimized metrics for orthogonal combinatorial CRISPR screens

Author(s): Ronay Cetin, Martin Wegner, Leah Luwisch, Sarada Saud, Tatjana Achmedov, Sebastian Süsser, Antonella Vera-Guapi, Konstantin Müller, Yves Matthess, Eva Quandt, Simone Schaubeck, Chase L. Beisel, Manuel Kaulich
Published in: Scientific Reports, Issue 13, 2023, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-023-34597-8

RNA recording in single bacterial cells using reprogrammed tracrRNAs

Author(s): Chunlei Jiao, Claas Reckstadt, Fabian König, Christina Homberger, Jiaqi Yu, Jörg Vogel, Alexander J. Westermann, Cynthia M. Sharma & Chase L. Beisel
Published in: Nature Biotechnology, Issue (in press), 2023, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41587-022-01604-8

Cas12a2 elicits abortive infection through RNA-triggered destruction of dsDNA

Author(s): Oleg Dmytrenko, Gina C. Neumann, Thomson Hallmark, Dylan J. Keiser, Valerie M. Crowley, Elena Vialetto, Ioannis Mougiakos, Katharina G. Wandera, Hannah Domgaard, Johannes Weber, Thomas Gaudin, Josie Metcalf, Benjamin N. Gray, Matthew B. Begemann, Ryan N. Jackson, Chase L. Beisel
Published in: Nature, Issue 613, 2023, Page(s) 588-594, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-022-05559-3

Phage anti-CRISPR control by an RNA- and DNA-binding helix–turn–helix protein

Author(s): Nils Birkholz, Kotaro Kamata, Maximilian Feussner, Max E. Wilkinson, Christian Cuba Samaniego, Angela Migur, Dari Kimanius, Marijn Ceelen, Sam C. Went, Ben Usher, Tim R. Blower, Chris M. Brown, Chase L. Beisel, Zasha Weinberg, Robert D. Fagerlund, Simon A. Jackson, Peter C. Fineran
Published in: Nature, Issue 631, 2024, Page(s) 670-677, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-024-07644-1

Cas12a2 elicits abortive infection through RNA-triggered destruction of dsDNA

Author(s): Oleg Dmytrenko, Gina C Neumann, Thomson Hallmark, Dylan J Keiser, Valerie M Crowley, Elena Vialetto, Ioannis Mougiakos, Katharina G Wandera, Hannah Domgaard, Johannes Weber, Thomas Gaudin, Josie Metcalf, Benjamin N Gray, Matthew B Begemann, Ryan N Jackson, Chase L Beisel
Published in: Nature, Issue (in press), 2023, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1101/2022.06.13.495973

Expanding the flexibility of base editing for high-throughput genetic screens in bacteria

Author(s): Sandra Gawlitt, Scott P Collins, Yanying Yu, Samuel A Blackman, Lars Barquist, Chase L Beisel
Published in: Nucleic Acids Research, Issue 52, 2024, Page(s) 4079-4097, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkae174

Non-peer reviewed articles (4)

Phages to the rescue: in situ editing of the gut microbiota

Author(s): Charlotte Kamm, Chase L. Beisel
Published in: Trends in Microbiology, Issue 32, 2024, Page(s) 934-935, ISSN 0966-842X
Publisher: Elsevier BV
DOI: 10.1016/j.tim.2024.09.001

For the CRISPR Fan(zor)atics: RNA-guided DNA endonucleases discovered in eukaryotes

Author(s): Constantinos Patinios, Chase L. Beisel
Published in: Molecular Cell, Issue 83, 2024, Page(s) 3046-3048, ISSN 1097-2765
Publisher: Cell Press
DOI: 10.1016/j.molcel.2023.08.019

Improved prediction of bacterial CRISPRi guide efficiency through data integration and automated machine learning

Author(s): Yanying Yu, Sandra Gawlitt, Lisa Barros de Andrade e Sousa, Erinc Merdivan, Marie Piraud, Chase Beisel, Lars Barquist
Published in: BioRxiv, Issue Posted May 28, 2022, 2022, ISSN 2692-8205
Publisher: CSHL press
DOI: 10.1101/2022.05.27.493707

The tracrRNA in CRISPR Biology and Technologies

Author(s): Chunyu Liao, Chase L. Beisel
Published in: Annual Review of Genetics, Issue 55, 2021, Page(s) 161-181, ISSN 1545-2948
Publisher: Annual Reviews
DOI: 10.1146/annurev-genet-071719-022559

Other (1)

Targeted DNA ADP-ribosylation triggers templated repair in bacteria and base mutagenesis in eukaryotes

Author(s): Constantinos Patinios, Darshana Gupta, Harris V. Bassett, Scott P. Collins, Charlotte Kamm, Anuja Kibe, Yanyan Wang, Chengsong Zhao, Katie Vollen, Christophe Toussaint, Kathryn M. Polkoff, Thuan Nguyen, Irene Calvin, Angela Migur, Ibrahim S. Al’Abri, Tatjana Achmedov, Alessandro Del Re, Antoine-Emmanuel Saliba, Nathan Crook, Anna N. Stepanova, Jose M. Alonso, Chase L. Beisel
Published in: BioRxiv, 2024
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.11.17.623984