The DOI matches its Crossref record; 11 of the 11 references it cites were found in a registry or an index.
Identifying and Visualizing Functional PAM Diversity across CRISPR-Cas Systems
Open accessAbstract
SUMMARY CRISPR-Cas adaptive immune systems in prokaryotes boast a diversity of protein families and mechanisms of action, where most systems rely on protospacer-adjacent motifs (PAMs) for DNA target recognition. Here, we developed an in vivo, positive, and tunable screen termed PAM-SCANR (PAM screen achieved by NOT-gate repression) to elucidate functional PAMs as well as an interactive visualization scheme termed the PAM wheel to convey individual PAM sequences and their activities. PAM-SCANR and the PAM wheel identified known functional PAMs while revealing complex sequence-activity landscapes for the Bacillus halodurans I-C (Cascade), Escherichia coli I-E (Cascade), Streptococcus thermophilus II-A CRISPR1 (Cas9), and Francisella novicida V-A (Cpf1) systems. The PAM wheel was also readily applicable to existing high-throughput screens and garnered insights into SpyCas9 and SauCas9 PAM diversity. These tools offer powerful means of elucidating and visualizing functional PAMs toward accelerating our ability to understand and exploit the multitude of CRISPR-Cas systems in nature.
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Cites
A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity
Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. A., & Charpentier, E. (2012) · Science · doi:10.1126/science.1225829 · Cited by 17,116
Multiplex Genome Engineering Using CRISPR/Cas Systems
Cong, L., Ran, F. A., Cox, D., Lin, S., Barretto, R., Habib, N., Hsu, P. D., Wu, X., Jiang, W., Marraffini, L. A., et al. (2013) · Science · doi:10.1126/science.1231143 · Cited by 15,339
RNA-Guided Human Genome Engineering via Cas9
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The new frontier of genome engineering with CRISPR-Cas9
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Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression
Qi, L. S., Larson, M. H., Gilbert, L. A., Doudna, J. A., Weissman, J. S., Arkin, A. P., & Lim, W. A. (2013) · Cell · doi:10.1016/j.cell.2013.02.022 · Cited by 5,016 · cited 5×
“We used the catalytically dead Cas9 (dCas9) containing point mutations to the RuvC and HNH endonuclease domains (D10A, H840A), which was shown to bind target DNA and block transcription in E. coli (Bikard et al., 2013; Jinek et al., 2012; Qi et al., 2013).”
BackgroundMethodInfluentialIn vivo genome editing using Staphylococcus aureus Cas9
Ran, F. A., Cong, L., Yan, W. X., Scott, D. A., Gootenberg, J. S., Kriz, A. J., Zetsche, B., Shalem, O., Wu, X., Makarova, K. S., et al. (2015) · Nature · doi:10.1038/nature14299 · Cited by 2,687
CRISPR RNA Maturation by Trans-Encoded Small RNA and Host Factor RNase III
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RNA-guided editing of bacterial genomes using CRISPR-Cas systems
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Engineered CRISPR-Cas9 nucleases with altered PAM specificities
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“Furthermore, in vitro screens that rely on adaptor ligation are incompatible with type I systems that cleave and degrade DNA (Pattanayak et al., 2013; Zetsche et al., 2015).”
Background
Cited by
CRISPR–Cas9 Structures and Mechanisms
Jiang, F., & Doudna, J. A. (2017) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-062215-010822 · Cited by 2,029
Applications of CRISPR technologies in research and beyond
Barrangou, R., & Doudna, J. A. (2016) · Nature Biotechnology · doi:10.1038/nbt.3659 · Cited by 1,005
Self-citationCRISPR-P 2.0: An Improved CRISPR-Cas9 Tool for Genome Editing in Plants
Liu, H., Ding, Y., Zhou, Y., Jin, W., Xie, K., & Chen, L.-L. (2017) · Molecular Plant · doi:10.1016/j.molp.2017.01.003 · Cited by 837
Rock, J. M., Hopkins, F. F., Chavez, A., Diallo, M., Chase, M. R., Gerrick, E. R., Pritchard, J. R., Church, G. M., Rubin, E. J., Sassetti, C. M., et al. (2017) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.274 · Cited by 538
CRISPR-Cpf1 assisted genome editing of Corynebacterium glutamicum
Jiang, Y., Qian, F., Yang, J., Liu, Y., Dong, F., Xu, C., Sun, B., Chen, B., Xu, X., Li, Y., et al. (2017) · Nature Communications · doi:10.1038/ncomms15179 · Cited by 389
Metadata
- Authors
- Leenay, R. T., Maksimchuk, K. R., Slotkowski, R. A., Agrawal, R. N., Gomaa, A. A., Briner, A. E., Barrangou, R., & Beisel, C. L.
- Venue
- Molecular Cell
- Publisher
- Elsevier BV
- Published
- 2016-04
- Volume
- 62
- Issue
- 1
- Pages
- 137-147
- ISSN
- 1097-2765 (ISSN-L)
- OpenAlex
- W2327182906
- Cited by
- 336
- References
- 11
- FWCI
- 18.96
- Type
- journal article
- Language
- en
- Open access
- bronze
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- Leenay, R. T., Maksimchuk, K. R., Slotkowski, R. A., Agrawal, R. N., Gomaa, A. A., Briner, A. E., Barrangou, R., & Beisel, C. L. (2016). Identifying and Visualizing Functional PAM Diversity across CRISPR-Cas Systems. Molecular Cell. https://doi.org/10.1016/j.molcel.2016.02.031
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