CHOPCHOP V3: Expanding the CRISPR Web Toolbox Beyond Genome Editing

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2019 May 21

PMID 31106371

Citations 735

Authors

Kornel Labun

Tessa G Montague

Maximilian Krause

Yamila N Torres Cleuren

Hakon Tjeldnes

Eivind Valen

Affiliations

Soon will be listed here.

Abstract

The CRISPR-Cas system is a powerful genome editing tool that functions in a diverse array of organisms and cell types. The technology was initially developed to induce targeted mutations in DNA, but CRISPR-Cas has now been adapted to target nucleic acids for a range of purposes. CHOPCHOP is a web tool for identifying CRISPR-Cas single guide RNA (sgRNA) targets. In this major update of CHOPCHOP, we expand our toolbox beyond knockouts. We introduce functionality for targeting RNA with Cas13, which includes support for alternative transcript isoforms and RNA accessibility predictions. We incorporate new DNA targeting modes, including CRISPR activation/repression, targeted enrichment of loci for long-read sequencing, and prediction of Cas9 repair outcomes. Finally, we expand our results page visualization to reveal alternative isoforms and downstream ATG sites, which will aid users in avoiding the expression of truncated proteins. The CHOPCHOP web tool now supports over 200 genomes and we have released a command-line script for running larger jobs and handling unsupported genomes. CHOPCHOP v3 can be found at https://chopchop.cbu.uib.no.

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References

Lorenz R, Bernhart S, Honer Zu Siederdissen C, Tafer H, Flamm C, Stadler P . ViennaRNA Package 2.0. Algorithms Mol Biol. 2011; 6:26. PMC: 3319429. DOI: 10.1186/1748-7188-6-26. View

Cong L, Ran F, Cox D, Lin S, Barretto R, Habib N . Multiplex genome engineering using CRISPR/Cas systems. Science. 2013; 339(6121):819-23. PMC: 3795411. DOI: 10.1126/science.1231143. View

Qi L, Larson M, Gilbert L, Doudna J, Weissman J, Arkin A . Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell. 2013; 152(5):1173-83. PMC: 3664290. DOI: 10.1016/j.cell.2013.02.022. View

Gilbert L, Larson M, Morsut L, Liu Z, Brar G, Torres S . CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell. 2013; 154(2):442-51. PMC: 3770145. DOI: 10.1016/j.cell.2013.06.044. View

Hsu P, Scott D, Weinstein J, Ran F, Konermann S, Agarwala V . DNA targeting specificity of RNA-guided Cas9 nucleases. Nat Biotechnol. 2013; 31(9):827-32. PMC: 3969858. DOI: 10.1038/nbt.2647. View

Perez-Pinera P, Kocak D, Vockley C, Adler A, Kabadi A, Polstein L . RNA-guided gene activation by CRISPR-Cas9-based transcription factors. Nat Methods. 2013; 10(10):973-6. PMC: 3911785. DOI: 10.1038/nmeth.2600. View

Maeder M, Linder S, Cascio V, Fu Y, Ho Q, Joung J . CRISPR RNA-guided activation of endogenous human genes. Nat Methods. 2013; 10(10):977-9. PMC: 3794058. DOI: 10.1038/nmeth.2598. View

Cheng A, Wang H, Yang H, Shi L, Katz Y, Theunissen T . Multiplexed activation of endogenous genes by CRISPR-on, an RNA-guided transcriptional activator system. Cell Res. 2013; 23(10):1163-71. PMC: 3790238. DOI: 10.1038/cr.2013.122. View

Gagnon J, Valen E, Thyme S, Huang P, Akhmetova L, Ahkmetova L . Efficient mutagenesis by Cas9 protein-mediated oligonucleotide insertion and large-scale assessment of single-guide RNAs. PLoS One. 2014; 9(5):e98186. PMC: 4038517. DOI: 10.1371/journal.pone.0098186. View

10.

Xu H, Xiao T, Chen C, Li W, Meyer C, Wu Q . Sequence determinants of improved CRISPR sgRNA design. Genome Res. 2015; 25(8):1147-57. PMC: 4509999. DOI: 10.1101/gr.191452.115. View

11.

Chari R, Mali P, Moosburner M, Church G . Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach. Nat Methods. 2015; 12(9):823-6. PMC: 5292764. DOI: 10.1038/nmeth.3473. View

12.

Moreno-Mateos M, Vejnar C, Beaudoin J, Fernandez J, Mis E, Khokha M . CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo. Nat Methods. 2015; 12(10):982-8. PMC: 4589495. DOI: 10.1038/nmeth.3543. View

13.

La Russa M, Qi L . The New State of the Art: Cas9 for Gene Activation and Repression. Mol Cell Biol. 2015; 35(22):3800-9. PMC: 4609748. DOI: 10.1128/MCB.00512-15. View

14.

Sakuma T, Nakade S, Sakane Y, Suzuki K, Yamamoto T . MMEJ-assisted gene knock-in using TALENs and CRISPR-Cas9 with the PITCh systems. Nat Protoc. 2015; 11(1):118-33. DOI: 10.1038/nprot.2015.140. View

15.

Doench J, Fusi N, Sullender M, Hegde M, Vaimberg E, Donovan K . Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nat Biotechnol. 2016; 34(2):184-191. PMC: 4744125. DOI: 10.1038/nbt.3437. View

16.

McKenna A, Findlay G, Gagnon J, Horwitz M, Schier A, Shendure J . Whole-organism lineage tracing by combinatorial and cumulative genome editing. Science. 2016; 353(6298):aaf7907. PMC: 4967023. DOI: 10.1126/science.aaf7907. View

17.

Abudayyeh O, Gootenberg J, Konermann S, Joung J, Slaymaker I, Cox D . C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Science. 2016; 353(6299):aaf5573. PMC: 5127784. DOI: 10.1126/science.aaf5573. View

18.

Thyme S, Akhmetova L, Montague T, Valen E, Schier A . Internal guide RNA interactions interfere with Cas9-mediated cleavage. Nat Commun. 2016; 7:11750. PMC: 4906408. DOI: 10.1038/ncomms11750. View

19.

Suzuki K, Tsunekawa Y, Hernandez-Benitez R, Wu J, Zhu J, Kim E . In vivo genome editing via CRISPR/Cas9 mediated homology-independent targeted integration. Nature. 2016; 540(7631):144-149. PMC: 5331785. DOI: 10.1038/nature20565. View

20.

Smargon A, Cox D, Pyzocha N, Zheng K, Slaymaker I, Gootenberg J . Cas13b Is a Type VI-B CRISPR-Associated RNA-Guided RNase Differentially Regulated by Accessory Proteins Csx27 and Csx28. Mol Cell. 2017; 65(4):618-630.e7. PMC: 5432119. DOI: 10.1016/j.molcel.2016.12.023. View