About

BE-FF (Base Editors Functional Finder) identifies base editors that can repair a given single-nucleotide variation.

Citation info: Roy Rabinowitz, Shiran Abadi, Shiri Almog, Daniel Offen, Prediction of synonymous corrections by the BE-FF computational tool expands the targeting scope of base editing, Nucleic Acids Research, gkaa215, https://doi.org/10.1093/nar/gkaa215

Base Editing

CRISPR base editing allows installation of point mutations at precise genomic loci. A base editor includes a dCas (deactivated-Cas) or nCas (nickase), fused to a deaminase enzyme. The base editor type is determined by the deaminase; cytidine deaminase forms a cytosine base editor (CBE) converting C to T, while adenosine deaminase forms an adenine base editor (ABE) converting A to G.

The activity window is defined as the positions within the target DNA that undergo base editing. Here we define the activity window positions as distance from the PAM sequence. The major activity window is the site were editing occurs at robust levels. The minor editing site is reported to have minimal levels of editing. BE-FF is defined to detect both major and minor base editing, however minor editing does not affect the result of the tool. In case of possible minor editing a notification will appear (coming soon!).

Currently BE-FF simulates base editing by 26 unique base editors (17 CBEs and 9 ABEs) for all queries:

BEFF

We defined 4 scenarios of mutation correction via base editing:

BEFF

The results output is divided to 2 sections; the upper results table shows only precise possible corrections (a), while the lower table shows the synonymous corrections (b-d).

Code
https://github.com/RoyRabinowitz/BE-FF

For additional questions and suggestions please contact royr2@mail.tau.ac.il
Related references:
For citing CRISPR:
• Jinek,M., Chylinski,K., Fonfara,I., Hauer,M., Doudna,J.A. and Charpentier,E. (2012) A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science. 337, 816–21.
• 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) Multiplex genome engineering using CRISPR/Cas systems. Science. 339, 819–23.

For citing Base Editing:
For all base editors:
Komor,A.C., Kim,Y.B., Packer,M.S., Zuris,J.A. and Liu,D.R. (2016) Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature, 533, 420–424.
For ABE:
Gaudelli,N.M., Komor,A.C., Rees,H.A., Packer,M.S., Badran,A.H., Bryson,D.I. and Liu,D.R. (2017) Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage. Nature, 551, 464–471.

References for specific base editors: (according to the BEs table)
1. Komor,A.C., Kim,Y.B., Packer,M.S., Zuris,J.A. and Liu,D.R. (2016) Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature, 533, 420–424.

2. Rees,H.A., Komor,A.C., Yeh,W.-H., Caetano-Lopes,J., Warman,M., Edge,A.S.B. and Liu,D.R. (2017) Improving the DNA specificity and applicability of base editing through protein engineering and protein delivery. Nat. Commun., 8, 15790.

3. Komor,A.C., Zhao,K.T., Packer,M.S., Gaudelli,N.M., Waterbury,A.L., Koblan,L.W., Kim,Y.B., Badran,A.H. and Liu,D.R. (2017) Improved base excision repair inhibition and bacteriophage Mu Gam protein yields C:G-to-T:A base editors with higher efficiency and product purity. Sci. Adv., 3, eaao4774.

4. Koblan,L.W., Doman,J.L., Wilson,C., Levy,J.M., Tay,T., Newby,G.A., Maianti,J.P., Raguram,A. and Liu,D.R. (2018) Improving cytidine and adenine base editors by expression optimization and ancestral reconstruction. Nat. Biotechnol., 36, 843–846.

5. Kim,Y.B., Komor,A.C., Levy,J.M., Packer,M.S., Zhao,K.T. and Liu,D.R. (2017) Increasing the genome-targeting scope and precision of base editing with engineered Cas9-cytidine deaminase fusions. Nat. Biotechnol., 35, 371–376.

6. Li,X., Wang,Y., Liu,Y., Yang,B., Wang,X., Wei,J., Lu,Z., Zhang,Y., Wu,J., Huang,X., et al. (2018) Base editing with a Cpf1-cytidine deaminase fusion. Nat. Biotechnol., 36, 324–327.

7. Nishida,K., Arazoe,T., Yachie,N., Banno,S., Kakimoto,M., Tabata,M., Mochizuki,M., Miyabe,A., Araki,M., Hara,K.Y., et al. (2016) Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems. Science, 353, aaf8729–aaf8729.

8. Nishimasu,H., Shi,X., Ishiguro,S., Gao,L., Hirano,S., Okazaki,S., Noda,T., Abudayyeh,O.O., Gootenberg,J.S., Mori,H., et al. (2018) Engineered CRISPR-Cas9 nuclease with expanded targeting space. Science, 361, 1259–1262.

9. Hu,J.H., Miller,S.M., Geurts,M.H., Tang,W., Chen,L., Sun,N., Zeina,C.M., Gao,X., Rees,H.A., Lin,Z., et al. (2018) Evolved Cas9 variants with broad PAM compatibility and high DNA specificity. Nature, 556, 57–63.

10. Gehrke,J.M., Cervantes,O., Clement,M.K., Wu,Y., Zeng,J., Bauer,D.E., Pinello,L. and Joung,J.K. (2018) An APOBEC3A-Cas9 base editor with minimized bystander and off-target activities. Nat. Biotechnol., 36, 977–982.

11. Jiang,W., Feng,S., Huang,S., Yu,W., Li,G., Yang,G., Liu,Y., Zhang,Y., Zhang,L., Hou,Y., et al. (2018) BE-PLUS: a new base editing tool with broadened editing window and enhanced fidelity. Cell Res., 28, 855–861.

12. Oakes,B.L., Fellmann,C., Rishi,H., Taylor,K.L., Ren,S.M., Nadler,D.C., Yokoo,R., Arkin,A.P., Doudna,J.A. and Savage,D.F. (2019) CRISPR-Cas9 Circular Permutants as Programmable Scaffolds for Genome Modification. Cell, 176, 254-267.e16.

13. Huang,T.P., Zhao,K.T., Miller,S.M., Gaudelli,N.M., Oakes,B.L., Fellmann,C., Savage,D.F. and Liu,D.R. (2019) Circularly permuted and PAM-modified Cas9 variants broaden the targeting scope of base editors. Nat. Biotechnol., 37, 626–631.

14. Thuronyi,B.W., Koblan,L.W., Levy,J.M., Yeh,W.-H., Zheng,C., Newby,G.A., Wilson,C., Bhaumik,M., Shubina-Oleinik,O., Holt,J.R., et al. (2019) Continuous evolution of base editors with expanded target compatibility and improved activity. Nat. Biotechnol., 37, 1070–1079.

15. Gaudelli,N.M., Komor,A.C., Rees,H.A., Packer,M.S., Badran,A.H., Bryson,D.I. and Liu,D.R. (2017) Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage. Nature, 551, 464–471.

16. Ryu,S.-M., Koo,T., Kim,K., Lim,K., Baek,G., Kim,S.-T., Kim,H.S., Kim,D.-E., Lee,H., Chung,E., et al. (2018) Adenine base editing in mouse embryos and an adult mouse model of Duchenne muscular dystrophy. Nat. Biotechnol., 36, 536–539.

17. Hua,K., Tao,X. and Zhu,J.-K. (2019) Expanding the base editing scope in rice by using Cas9 variants. Plant Biotechnol. J., 17, 499–504.

18. Yang,L., Zhang,X., Wang,L., Yin,S., Zhu,B., Xie,L., Duan,Q., Hu,H., Zheng,R., Wei,Y., et al. (2018) Increasing targeting scope of adenosine base editors in mouse and rat embryos through fusion of TadA deaminase with Cas9 variants. Protein Cell, 9, 814–819.