The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
CRISPRTarget: Bioinformatic prediction and analysis of crRNA targets
Open accessAbstract
The bacterial and archaeal CRISPR/Cas adaptive immune system targets specific protospacer nucleotide sequences in invading organisms. This requires base pairing between processed CRISPR RNA and the target protospacer. For type I and II CRISPR/Cas systems, protospacer adjacent motifs (PAM) are essential for target recognition, and for type III, mismatches in the flanking sequences are important in the antiviral response. In this study, we examine the properties of each class of CRISPR. We use this information to provide a tool (CRISPRTarget) that predicts the most likely targets of CRISPR RNAs (http://bioanalysis.otago.ac.nz/CRISPRTarget). This can be used to discover targets in newly sequenced genomic or metagenomic data. To test its utility, we discover features and targets of well-characterized Streptococcus thermophilus and Sulfolobus solfataricus type II and III CRISPR/Cas systems. Finally, in Pectobacterium species, we identify new CRISPR targets and propose a model of temperate phage exposure and subsequent inhibition by the type I CRISPR/Cas systems.
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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
CRISPR RNA Maturation by Trans-Encoded Small RNA and Host Factor RNase III
Deltcheva, E., Chylinski, K., Sharma, C. M., Gonzales, K., Chao, Y., Pirzada, Z. A., Eckert, M. R., Vogel, J., & Charpentier, E. (2011) · Nature · doi:10.1038/nature09886 · Cited by 2,563
RNA-guided genetic silencing systems in bacteria and archaea
Wiedenheft, B., Sternberg, S. H., & Doudna, J. A. (2012) · Nature · doi:10.1038/nature10886 · Cited by 1,851
Cited by
Smargon, A. A., Cox, D. B. T., Pyzocha, N. K., Zheng, K., Slaymaker, I. M., Gootenberg, J. S., Abudayyeh, O. A., Essletzbichler, P., Shmakov, S., Makarova, K. S., et al. (2017) · Molecular Cell · doi:10.1016/j.molcel.2016.12.023 · Cited by 575
Programmable RNA editing with compact CRISPR–Cas13 systems from uncultivated microbes
Xu, C., Zhou, Y., Xiao, Q., He, B., Geng, G., Wang, Z., Cao, B., Dong, X., Bai, W., Wang, Y., et al. (2021) · Nature Methods · doi:10.1038/s41592-021-01124-4 · Cited by 351
Marine viruses discovered via metagenomics shed light on viral strategies throughout the oceans
Coutinho, F. H., Silveira, C. B., Gregoracci, G. B., Thompson, C. C., Edwards, R. A., Brussaard, C. P. D., Dutilh, B. E., & Thompson, F. L. (2017) · Nature Communications · doi:10.1038/ncomms15955 · Cited by 346
A Thermostable Cas9 with Increased Lifetime in Human Plasma
Harrington, L. B., Paez-Espino, D., Staahl, B. T., Chen, J. S., Ma, E., Kyrpides, N. C., & Doudna, J. A. (2017) · Nature Communications · doi:10.1038/s41467-017-01408-4 · Cited by 205
Characterization and Repurposing of Type I and Type II CRISPR–Cas Systems in Bacteria
Hidalgo-Cantabrana, C., Goh, Y. J., & Barrangou, R. (2019) · Journal of Molecular Biology · doi:10.1016/j.jmb.2018.09.013 · Cited by 63
Metadata
- Authors
- Biswas, A., Gagnon, J. N., Brouns, S. J. J., Fineran, P. C., & Brown, C. M.
- Venue
- RNA Biology
- Publisher
- Informa UK Limited
- Published
- 2013-03-14
- Volume
- 10
- Issue
- 5
- Pages
- 817-827
- ISSN
- 1547-6286 (ISSN-L)
- 1555-8584
- OpenAlex
- W2148245360
- Cited by
- 318
- References
- 3
- FWCI
- 6.72
- Type
- journal article
- Language
- en
- Open access
- hybrid
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- Biswas, A., Gagnon, J. N., Brouns, S. J. J., Fineran, P. C., & Brown, C. M. (2013). CRISPRTarget: Bioinformatic prediction and analysis of crRNA targets. RNA Biology. https://doi.org/10.4161/rna.24046
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