Russian version English version
Volume 18   Issue 2   Year 2023
Tetuev R.K., Nazipova N.N.

Statistical Model for Predicting TALEN-DNA Binding Sites Based On Moving Average

Mathematical Biology & Bioinformatics. 2023;18(2):621-645.

doi: 10.17537/2023.18.621.

References

  1. Bibikova M., Golic M., Golic K.G., Carroll D. Targeted Chromosomal Cleavage and Mutagenesis in Drosophila Using Zinc-Finger Nucleases. Genetics. 2002;161(3):1169–1175. doi: 10.1093/genetics/161.3.1169
  2. Qasim W., Zhan H., Samarasinghe S., Adams S., Amrolia P., Stafford S., Butler K., Rivat C., Wright G., Somana K. et al. Molecular remission of infant B-ALL after infusion of universal TALEN gene-edited CAR T cells. Science Translational Medicine. 2017;9. Article No. eaaj2013. doi: 10.1126/scitranslmed.aaj2013
  3. Menz J., Modrzejewski D., Hartung F., Wilhelm R., Sprink T. Genome edited crops touch the market: a view on the global development and regulatory environment. Front. Plant Sci. 2020;11. Article No. 586027. doi: 10.3389/fpls.2020.586027
  4. Pickar-Oliver A., Gersbach C.A. The next generation of CRISPR–Cas technologies and applications. Nat. Rev. Mol. Cell Biol. 2019;20:490–507. doi: 10.1038/s41580-019-0131-5
  5. Zhang B. CRISPR/Cas gene therapy. J. Cell Physiol. 2021;236:2459–2481. doi: 10.1002/jcp.30064
  6. Saifaldeen M., Al-Ansari D.E., Ramotar D., Aouida M. CRISPR FokI Dead Cas9 System: Principles and Applications in Genome Engineering. Cells. 2020;9(11). Article No. 2518. doi: 10.3390/cells9112518
  7. Gao H., Wu X., Chai J., Han Z. Crystal structure of a TALE protein reveals an extended N-terminal DNA binding region. Cell Res. 2012;22:1716–1720. doi: 10.1038/cr.2012.156
  8. Yuan M., Ke Y., Huang R., Ma L., Yang Z., Chu Z., Xiao J., Li X., Wang S. A host basal transcription factor is a key component for infection of rice by TALE-carrying bacteria. eLife. 2016;5. Article No. e19605. doi: 10.7554/eLife.19605
  9. Moscou M.J., Bogdanove A.J. A simple cipher governs DNA recognition by TAL effectors. Science. 2009;326:1501. doi: 10.1126/science.1178817
  10. Yang J., Zhang Y., Yuan P., Zhou Y., Cai C., Ren Q., Wen D., Chu C., Qi H., Wei W. Complete decoding of TAL effectors for DNA recognition. Cell Res. 2014;24:628–631. doi: 10.1038/cr.2014.19
  11. Miller J., Zhang L., Xia D.F., Campo J.J., Ankoudinova I.V., Guschin D.Y., Babiarz J.E., Meng X., Hinkley S.J., Lam S.C. Improved specificity of TALE-based genome editing using an expanded RVD repertoire. Nat. Methods. 2015;12:465–471. doi: 10.1038/nmeth.3330
  12. Mak A.N.S., Bradley P., Cernadas R.A., Bogdanove A.J., Stoddard B.L. The crystal structure of TAL effector PthXo1 bound to its DNA target. Science. 2012;335:716–719. doi: 10.1126/science.1216211
  13. Deng D., Yan C., Pan X., Mahfouz M., Wang J., Zhu J.-K., Shi Y., Yan N. Structural basis for sequence-specific recognition of DNA by TAL effectors. Science. 2012;335:720–723 doi: 10.1126/science.1215670
  14. Streubel J., Blücher C., Landgraf A. Boch J. TAL effector RVD specificities and efficiencies. Nat. Biotechnol. 2012;30:593–595 doi: 10.1038/nbt.2304
  15. Becker S., Boch J. TALE and TALEN genome editing technologies. Gene and Genome Editing. 2021;2. Article No. 100007. doi: 10.1016/j.ggedit.2021.100007
  16. Boch J., Scholze H., Schornack S., Landgraf A., Hahn S., Kay S., Lahaye T., Nickstadt A., Bonas U. Breaking the Code of DNA Binding Specificity of TAL-Type III Effectors. Science. 2009;326(5959):1509–1512. doi: 10.1126/science.1178811
  17. Hockemeyer D., Wang H., Kiani S., Lai C.S., Gao Q., Cassady J.P., Cost G.J., Zhang L., Santiago Y., Miller J.C., et al. Genetic engineering of human pluripotent cells using TALE nucleases. Nat. Biotechnol. 2011;29:731–734. doi: 10.1038/nbt.1927
  18. Guilinger J.P., Pattanayak V., Reyon D., Tsai S.Q., Sander J.D., Joung J.K., Liu D.R. Broad specificity profiling of TALENs results in engineered nucleases with improved DNA-cleavage specificity. Nat. Methods. 2014;11(4):429–435. doi: 10.1038/nmeth.2845
  19. Doyle E.L., Booher N.J., Standage D.S., Voytas D.F., Brendel V.P., VanDyk J.K., Bogdanove A.J. TAL Effector-Nucleotide Targeter (TALE-NT) 2.0: tools for TAL effector design and target prediction. Nucleic Acids Res. 2012;40. P. W117–W122. doi: 10.1093/nar/gks608
  20. Grau J., Boch J., Posch S. TALENoffer: genome-wide TALEN off-target prediction. Bioinformatics. 2013;29:2931–2932. doi: 10.1093/bioinformatics/btt501
  21. Cong L., Zhou R., Kuo Y.C., Cunniff M., Zhang F. Comprehensive interrogation of natural TALE DNA-binding modules and transcriptional repressor domains. Nat. Commun. 2012;3. Article No. 968. doi: 10.1038/ncomms1962
  22. Richter A., Streubel J., Blücher C., Szurek B., Reschke M., Grau J., Boch J. A TAL effector repeat architecture for frameshift binding. Nat. Commun. 2014;5. Article No. 3447. doi: 10.1038/ncomms4447
  23. Sakuma T., Ochiai H., Kaneko T., Mashimo T., Tokumasu D., Sakane Y., Suzuki K., Miyamoto T., Sakamoto N., Matsuura S., Yamamoto T. Repeating pattern of non-RVD variations in DNA-binding modules enhances TALEN activity. Sci. Rep. 2013;3. Article No. 3379. doi: 10.1038/srep03379
  24. Sakuma T., Yamamoto T. Engineering Customized TALENs Using the Platinum Gate TALEN Kit. Methods Mol. Biol. 2016. V.1338:61–70. doi: 10.1007/978-1-4939-2932-0_6
  25. Xue J., Lu Z., Liu W., Wang S., Lu D., Wang X., He X. The genetic arms race between plant and Xanthomonas: lessons learned from TALE biology. Sci. China Life Sci. 2021;64(1):51–65. doi: 10.1007/s11427-020-1699-4
  26. Streubel J., Blücher C., Landgraf A., Boch J. TAL effector RVD specificities and efficiencies. Nat. Biotechnol. 2012;30:593–595. doi: 10.1038/nbt.2304
  27. Čermák T., Doyle E.L., Christian M., Wang L., Zhang Y., Schmidt C., Baller J.A., Somia N.V., Bogdanove A.J., Voytas D.F. Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucleic Acids Res. 2011;39. Article No. e82. doi: 10.1093/nar/gkr218
  28. Balwierz P.J., Carninci P., Daub C.O., Kawai J., Hayashizaki Y., Van Belle W., Beisel C., van Nimwegen E. Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data. Genome Biol. 2009;10. Article No. R79. doi: 10.1186/gb-2009-10-7-r79
  29. Bradley D., Roth G. Adaptive Thresholding using the Integral Image. Journal of Graphics GPU and Game Tools. 2007;12:13–21. doi: 10.1080/2151237X.2007.10129236
  30. Umer M., Herceg Z. Deciphering the epigenetic code: an overview of DNA methylation analysis methods. Antioxid Redox Signal. 2013;18:1972–1986. doi: 10.1089/ars.2012.4923
  31. Jabbari K., Bernardi G. Cytosine methylation and CpG, TpG (CpA) and TpA frequencies. Gene. 2004;333:143–149. doi: 10.1016/j.gene.2004.02.043
  32. Herman J.G., Graff J.R., Myohanen S., Nelkin B.D., Baylin S.B. Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands. Proc. Natl. Acad. Sci. U.S.A. 1996;93(18):9821–9826. doi: 10.1073/pnas.93.18.9821
  33. Tetuev R.K., Olshevets M.M., Erman B., Atilgan C. A broken zipper model of the genome-wide TALEN off-target prediction using exponential moving average . In: Proceedings of the International Conference "Mathematical Biology and Bioinformatics". Ed. V.D. Lakhno. Vol. 6. Pushchino: IMPB RAS, 2016. P. 70–71.
  34. Li L., Piatek M.J., Atef A., Piatek A., Wibowo A., Fang X., Sabir J.S.M., Zhu J.-K., Mahfouz M.M. Rapid and highly efficient construction of TALE-based transcriptional regulators and nucleases for genome modification. Plant Mol. Biol. 2012;78:407–416. doi: 10.1007/s11103-012-9875-4
  35. Fine E.J., Cradick T.J., Zhao C.L., Lin Y., Bao G. An online bioinformatics tool predicts zinc finger and TALE nuclease off-target cleavage. Nucleic Acids Res. 2013;42. Article No. e42. doi: 10.1093/nar/gkt1326
  36. Heigwer F., Kerr G., Walther N., Glaeser K., Pelz O., Breinig M., Boutros M. E-TALEN: a web tool to design TALENs for genome engineering. Nucleic Acids Res. 2013;41. Article No. e190. doi: 10.1093/nar/gkt789
  37. Neff K.L., Argue D.P., Ma A.C., Lee H.B., Clark K.J., Ekker S.C. Mojo Hand, a TALEN design tool for genome editing applications. BMC Bioinform. 2013;14. Article No. 1. doi: 10.1186/1471-2105-14-1
  38. Montague T.G., Cruz J.M., Gagnon J.A., Church G.M., Valen E. CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing. Nucleic Acids Res. 2014;42. P. W401–W407. doi: 10.1093/nar/gku410
  39. Jensen T.L., Gøtzsche C.R., Woldbye D.P.D. Current and Future Prospects for Gene Therapy for Rare Genetic Diseases Affecting the Brain and Spinal Cord. Front. Mol. Neurosci. 2021;14. Article No. 695937. doi: 10.3389/fnmol.2021.695937
  40. Kaiser J. A gentler way to tweak genes: Epigenome editing. Science. 2022;376:1034–1035. doi: 10.1126/science.add2703
  41. Margueron R., Reinberg D. Chromatin structure and the inheritance of epigenetic information. Nat. Rev. Genet. 2010;11:285–296. doi: 10.1038/nrg2752
  42. Allis C.D., Jenuwein T. The molecular hallmarks of epigenetic control. Nat. Rev. Genet. 2016;17:487–500. doi: 10.1038/nrg.2016.59
  43. Nazipova N. Variety of Non-Coding RNAs in Eukaryotic Genomes. Mathematical Biology and Bioinformatics. 2021;16(2):256–298. doi: 10.17537/2021.16.256
  44. Cook P.R. A model for all genomes: The role of transcription factories. J. Mol. Biol. 2010;395:1–10. doi: 10.1016/j.jmb.2009.10.031
  45. Ueda J., Yamazaki T., Funakoshi H. Toward the Development of Epigenome Editing-Based Therapeutics: Potentials and Challenges. International Journal of Molecular Sciences. 2023;24(5). Article No. 4778. doi: 10.3390/ijms24054778
  46. Baker M.P., Reynolds H.M., Lumicisi B., Bryson C.J. Immunogenicity of protein therapeutics: The key causes, consequences and challenges. Self/Nonself. 2010;1:314–322. doi: 10.4161/self.1.4.13904
  47. de Groote M.L., Verschure P.J., Rots M.G. Epigenetic Editing: Targeted rewriting of epigenetic marks to modulate expression of selected target genes. Nucleic Acids Res. 2012;40:10596–10613. doi: 10.1093/nar/gks863
  48. Lei Y., Huang Y.H., Goodell M.A. DNA methylation and de-methylation using hybrid site-targeting proteins. Genome Biol. 2019;19. Article No. 187. doi: 10.1186/s13059-018-1566-2
  49. Mok B.Y., de Moraes M.H., Zeng J., Bosch D.E., Kotrys A.V., Raguram A., Hsu F., Radey M.C., Peterson S.B., Mootha V.K. et al. A bacterial cytidine deaminase toxin enables CRISPR-free mitochondrial base editing. Nature. 2020;583:631–637. doi: 10.1038/s41586-020-2477-4
  50. Mok B.Y., Kotrys A.V., Raguram A., Huang T.P., Mootha V.K., Liu D.R. CRISPR-free base editors with enhanced activity and expanded targeting scope in mitochondrial and nuclear DNA. Nat. Biotechnol. 2022;40:1378–1387. doi: 10.1038/s41587-022-01256-8
  51. Kang B.C., Bae S.J., Lee S., Lee J.S., Kim A., Lee H., Baek G., Seo H., Kim J., Kim J.-S. Chloroplast and mitochondrial DNA editing in plants. Nat. Plants. 2021;7:899–905. doi: 10.1038/s41477-021-00943-9
  52. Jain S., Shukla S., Yang C., Zhang M., Fatma Z., Lingamaneni M., Abesteh S., Lane S.T., Xiong X., Wang Y., et al. TALEN outperforms Cas9 in editing heterochromatin target sites. Nat. Commun. 2021;12:606–610. doi: 10.1038/s41467-020-20672-5
  53. Boyne A., Yang M., Pulicani S., Feola M., Tkach D., Hong R., Duclert A., Duchateau P., Juillerat A. Efficient multitool/multiplex gene engineering with TALE-BE. Front. Bioeng. Biotechnol. 2022;10. Article No. 1033669. doi: 10.3389/fbioe.2022.1033669
Table of Contents Original Article
Math. Biol. Bioinf.
2023;18(2):621-645
doi: 10.17537/2023.18.621
published in Russian

Abstract (rus.)
Abstract (eng.)
Full text (rus., pdf)
References

 

  Copyright IMPB RAS © 2005-2024