9. Compe E, Egly JM (2016) Nucleotide excision
repair and transcriptional regulation: TFIIH
and beyond. Annu Rev Biochem 85:265–290
10. Kolesnikova O, Radu L, Poterszman A (2019)
TFIIH: a multi-subunit complex at the crossroads of transcription and DNA repair. Adv
Protein Chem Struct Biol 115:21–67
11. Sandoz J, Nagy Z, Catez P, Caliskan G, Geny S,
Renaud JB, Concordet JP, Poterszman A,
Tora L, Egly JM, Le May N, Coin F (2019)
Functional interplay between TFIIH and
KAT2A regulates higher-order chromatin
structure and class II gene expression. Nat
Commun 10(1):1288
12. Yeh CD, Richardson CD, Corn JE (2019)
Advances in genome editing through control
of DNA repair pathways. Nat Cell Biol 21
(12):1468–1478
13. Chu VT, Weber T, Wefers B, Wurst W,
Sander S, Rajewsky K, Kuhn R (2015) Increasing the efficiency of homology-directed repair
for CRISPR-Cas9-induced precise gene editing in mammalian cells. Nat Biotechnol 33
(5):543–548
14. Sluch VM, Chamling X, Wenger C, Duan Y,
Rice DS, Zack DJ (2018) Highly efficient scarless knock-in of reporter genes into human and
mouse pluripotent stem cells via transient antibiotic selection. PLoS One 13(11):e0201683
15. Sentmanat MF, Peters ST, Florian CP, Connelly JP, Pruett-Miller SM (2018) A survey of
validation strategies for CRISPR-Cas9 editing.
Sci Rep 8(1):888
16. Vouillot L, Thelie A, Pollet N (2015) Comparison of T7E1 and surveyor mismatch cleavage
assays to detect mutations triggered by engineered
nucleases.
G3
(Bethesda)
5
(3):407–415
17. Renaud JB, Boix C, Charpentier M, De Cian A,
Cochennec
J,
Duvernois-Berthet
E,
Perrouault L, Tesson L, Edouard J,
Thinard R, Cherifi Y, Menoret S,
Fontaniere S, de Croze N, Fraichard A,
Sohm F, Anegon I, Concordet JP, Giovannangeli C (2016) Improved genome editing efficiency and flexibility using modified
oligonucleotides with TALEN and CRISPRCas9 nucleases. Cell Rep 14(9):2263–2272
18. Shan Q, Wang Y, Li J, Gao C (2014) Genome
editing in rice and wheat using the CRISPR/
Cas system. Nat Protoc 9(10):2395–2410
19. Kim HJ, Lee HJ, Kim H, Cho SW, Kim JS
(2009) Targeted genome editing in human
cells with zinc finger nucleases constructed via
modular assembly. Genome Res 19
(7):1279–1288
20. Guschin DY, Waite AJ, Katibah GE, Miller JC,
Holmes MC, Rebar EJ (2010) A rapid and
general assay for monitoring endogenous
gene modification. Methods Mol Biol
649:247–256
21. Brinkman EK, Chen T, Amendola M, van
Steensel B (2014) Easy quantitative assessment
of genome editing by sequence trace decomposition. Nucleic Acids Res 42(22):e168
22. Paix A, Rasoloson D, Folkmann A, Seydoux G
(2019) Rapid tagging of human proteins with
fluorescent reporters by genome engineering
using double-stranded DNA donors. Curr Protoc Mol Biol 129(1):e102
23. Paix A, Schmidt H, Seydoux G (2016) Cas9assisted recombineering in C. elegans: genome
editing using in vivo assembly of linear DNAs.
Nucleic Acids Res 44(15):e128
24. Auer TO, Del Bene F (2014) CRISPR/Cas9
and TALEN-mediated knock-in approaches in
zebrafish. Methods 69(2):142–150
25. Liu Z, Chen O, Wall JBJ, Zheng M, Zhou Y,
Wang L, Ruth Vaseghi H, Qian L, Liu J (2017)
Systematic comparison of 2A peptides for cloning multi-genes in a polycistronic vector. Sci
Rep 7(1):2193
26. Chen X, Zaro JL, Shen WC (2013) Fusion
protein linkers: property, design and functionality. Adv Drug Deliv Rev 65(10):1357–1369
27. Koch B, Nijmeijer B, Kueblbeck M, Cai Y,
Walther N, Ellenberg J (2018) Generation
and validation of homozygous fluorescent
knock-in cells using CRISPR-Cas9 genome
editing. Nat Protoc 13(6):1465–1487
28. Kimple ME, Brill AL, Pasker RL (2013) Overview of affinity tags for protein purification.
Curr Protoc Protein Sci 73:19–23
29. Rossolillo P, Kolesnikova O, Essabri K, Ramon
Zamorano G, Poterszman A (in press) Production of multiprotein complexes using the Baculovirus expression system: homology based and
Restriction Free cloning strategies for construct design. Methods Mol Biol
30. Anders C, Niewoehner O, Duerst A, Jinek M
(2014) Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease. Nature 513(7519):569–573
Tagging Proteins with Fluorescent Reporters Using the CRISPR/Cas9 System. . .
57
repair and transcriptional regulation: TFIIH
and beyond. Annu Rev Biochem 85:265–290
10. Kolesnikova O, Radu L, Poterszman A (2019)
TFIIH: a multi-subunit complex at the crossroads of transcription and DNA repair. Adv
Protein Chem Struct Biol 115:21–67
11. Sandoz J, Nagy Z, Catez P, Caliskan G, Geny S,
Renaud JB, Concordet JP, Poterszman A,
Tora L, Egly JM, Le May N, Coin F (2019)
Functional interplay between TFIIH and
KAT2A regulates higher-order chromatin
structure and class II gene expression. Nat
Commun 10(1):1288
12. Yeh CD, Richardson CD, Corn JE (2019)
Advances in genome editing through control
of DNA repair pathways. Nat Cell Biol 21
(12):1468–1478
13. Chu VT, Weber T, Wefers B, Wurst W,
Sander S, Rajewsky K, Kuhn R (2015) Increasing the efficiency of homology-directed repair
for CRISPR-Cas9-induced precise gene editing in mammalian cells. Nat Biotechnol 33
(5):543–548
14. Sluch VM, Chamling X, Wenger C, Duan Y,
Rice DS, Zack DJ (2018) Highly efficient scarless knock-in of reporter genes into human and
mouse pluripotent stem cells via transient antibiotic selection. PLoS One 13(11):e0201683
15. Sentmanat MF, Peters ST, Florian CP, Connelly JP, Pruett-Miller SM (2018) A survey of
validation strategies for CRISPR-Cas9 editing.
Sci Rep 8(1):888
16. Vouillot L, Thelie A, Pollet N (2015) Comparison of T7E1 and surveyor mismatch cleavage
assays to detect mutations triggered by engineered
nucleases.
G3
(Bethesda)
5
(3):407–415
17. Renaud JB, Boix C, Charpentier M, De Cian A,
Cochennec
J,
Duvernois-Berthet
E,
Perrouault L, Tesson L, Edouard J,
Thinard R, Cherifi Y, Menoret S,
Fontaniere S, de Croze N, Fraichard A,
Sohm F, Anegon I, Concordet JP, Giovannangeli C (2016) Improved genome editing efficiency and flexibility using modified
oligonucleotides with TALEN and CRISPRCas9 nucleases. Cell Rep 14(9):2263–2272
18. Shan Q, Wang Y, Li J, Gao C (2014) Genome
editing in rice and wheat using the CRISPR/
Cas system. Nat Protoc 9(10):2395–2410
19. Kim HJ, Lee HJ, Kim H, Cho SW, Kim JS
(2009) Targeted genome editing in human
cells with zinc finger nucleases constructed via
modular assembly. Genome Res 19
(7):1279–1288
20. Guschin DY, Waite AJ, Katibah GE, Miller JC,
Holmes MC, Rebar EJ (2010) A rapid and
general assay for monitoring endogenous
gene modification. Methods Mol Biol
649:247–256
21. Brinkman EK, Chen T, Amendola M, van
Steensel B (2014) Easy quantitative assessment
of genome editing by sequence trace decomposition. Nucleic Acids Res 42(22):e168
22. Paix A, Rasoloson D, Folkmann A, Seydoux G
(2019) Rapid tagging of human proteins with
fluorescent reporters by genome engineering
using double-stranded DNA donors. Curr Protoc Mol Biol 129(1):e102
23. Paix A, Schmidt H, Seydoux G (2016) Cas9assisted recombineering in C. elegans: genome
editing using in vivo assembly of linear DNAs.
Nucleic Acids Res 44(15):e128
24. Auer TO, Del Bene F (2014) CRISPR/Cas9
and TALEN-mediated knock-in approaches in
zebrafish. Methods 69(2):142–150
25. Liu Z, Chen O, Wall JBJ, Zheng M, Zhou Y,
Wang L, Ruth Vaseghi H, Qian L, Liu J (2017)
Systematic comparison of 2A peptides for cloning multi-genes in a polycistronic vector. Sci
Rep 7(1):2193
26. Chen X, Zaro JL, Shen WC (2013) Fusion
protein linkers: property, design and functionality. Adv Drug Deliv Rev 65(10):1357–1369
27. Koch B, Nijmeijer B, Kueblbeck M, Cai Y,
Walther N, Ellenberg J (2018) Generation
and validation of homozygous fluorescent
knock-in cells using CRISPR-Cas9 genome
editing. Nat Protoc 13(6):1465–1487
28. Kimple ME, Brill AL, Pasker RL (2013) Overview of affinity tags for protein purification.
Curr Protoc Protein Sci 73:19–23
29. Rossolillo P, Kolesnikova O, Essabri K, Ramon
Zamorano G, Poterszman A (in press) Production of multiprotein complexes using the Baculovirus expression system: homology based and
Restriction Free cloning strategies for construct design. Methods Mol Biol
30. Anders C, Niewoehner O, Duerst A, Jinek M
(2014) Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease. Nature 513(7519):569–573
Tagging Proteins with Fluorescent Reporters Using the CRISPR/Cas9 System. . .
57