CORALINA. A universal method for the generation of gRNA libraries for CRISPR-based screening

Köferle A, Worf K, Breunig C, Baumann V, Herrero J, Wiesbeck M, Hutter LH, Götz M, Fuchs C, Beck S, Stricker SH (2016)
BMC Genomics 17(1): 917.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
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Köferle, Anna; Worf, Karolina; Breunig, Christopher; Baumann, Valentin; Herrero, Javier; Wiesbeck, Maximilian; Hutter, Lukas H.; Götz, Magdalena; Fuchs, ChristianeUniBi ; Beck, Stephan; Stricker, Stefan H.
Abstract / Bemerkung
Background The bacterial CRISPR system is fast becoming the most popular genetic and epigenetic engineering tool due to its universal applicability and adaptability. The desire to deploy CRISPR-based methods in a large variety of species and contexts has created an urgent need for the development of easy, time- and cost-effective methods enabling large-scale screening approaches. Results Here we describe CORALINA (comprehensive gRNA library generation through controlled nuclease activity), a method for the generation of comprehensive gRNA libraries for CRISPR-based screens. CORALINA gRNA libraries can be derived from any source of DNA without the need of complex oligonucleotide synthesis. We show the utility of CORALINA for human and mouse genomic DNA, its reproducibility in covering the most relevant genomic features including regulatory, coding and non-coding sequences and confirm the functionality of CORALINA generated gRNAs. Conclusions The simplicity and cost-effectiveness make CORALINA suitable for any experimental system. The unprecedented sequence complexities obtainable with CORALINA libraries are a necessary pre-requisite for less biased large scale genomic and epigenomic screens.
BMC Genomics
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Köferle A, Worf K, Breunig C, et al. CORALINA. A universal method for the generation of gRNA libraries for CRISPR-based screening. BMC Genomics. 2016;17(1): 917.
Köferle, A., Worf, K., Breunig, C., Baumann, V., Herrero, J., Wiesbeck, M., Hutter, L. H., et al. (2016). CORALINA. A universal method for the generation of gRNA libraries for CRISPR-based screening. BMC Genomics, 17(1), 917. doi:10.1186/s12864-016-3268-z
Köferle, A., Worf, K., Breunig, C., Baumann, V., Herrero, J., Wiesbeck, M., Hutter, L. H., Götz, M., Fuchs, C., Beck, S., et al. (2016). CORALINA. A universal method for the generation of gRNA libraries for CRISPR-based screening. BMC Genomics 17:917.
Köferle, A., et al., 2016. CORALINA. A universal method for the generation of gRNA libraries for CRISPR-based screening. BMC Genomics, 17(1): 917.
A. Köferle, et al., “CORALINA. A universal method for the generation of gRNA libraries for CRISPR-based screening”, BMC Genomics, vol. 17, 2016, : 917.
Köferle, A., Worf, K., Breunig, C., Baumann, V., Herrero, J., Wiesbeck, M., Hutter, L.H., Götz, M., Fuchs, C., Beck, S., Stricker, S.H.: CORALINA. A universal method for the generation of gRNA libraries for CRISPR-based screening. BMC Genomics. 17, : 917 (2016).
Köferle, Anna, Worf, Karolina, Breunig, Christopher, Baumann, Valentin, Herrero, Javier, Wiesbeck, Maximilian, Hutter, Lukas H., Götz, Magdalena, Fuchs, Christiane, Beck, Stephan, and Stricker, Stefan H. “CORALINA. A universal method for the generation of gRNA libraries for CRISPR-based screening”. BMC Genomics 17.1 (2016): 917.

5 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Targeted removal of epigenetic barriers during transcriptional reprogramming.
Baumann V, Wiesbeck M, Breunig CT, Braun JM, Köferle A, Ninkovic J, Götz M, Stricker SH., Nat Commun 10(1), 2019
PMID: 31073172
Rapid and Sensitive Assessment of Globin Chains for Gene and Cell Therapy of Hemoglobinopathies.
Loucari CC, Patsali P, van Dijk TB, Stephanou C, Papasavva P, Zanti M, Kurita R, Nakamura Y, Christou S, Sitarou M, Philipsen S, Lederer CW, Kleanthous M., Hum Gene Ther Methods 29(1), 2018
PMID: 29325430
One step generation of customizable gRNA vectors for multiplex CRISPR approaches through string assembly gRNA cloning (STAgR).
Breunig CT, Durovic T, Neuner AM, Baumann V, Wiesbeck MF, Köferle A, Götz M, Ninkovic J, Stricker SH., PLoS One 13(4), 2018
PMID: 29702666
The epigenomic basis of common diseases.
Rodger EJ, Chatterjee A., Clin Epigenetics 9(), 2017
PMID: 28149333

49 References

Daten bereitgestellt von Europe PubMed Central.

CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III.
Deltcheva E, Chylinski K, Sharma CM, Gonzales K, Chao Y, Pirzada ZA, Eckert MR, Vogel J, Charpentier E., Nature 471(7340), 2011
PMID: 21455174
Multiplex genome engineering using CRISPR/Cas systems.
Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA, Zhang F., Science 339(6121), 2013
PMID: 23287718
Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells.
Wu X, Scott DA, Kriz AJ, Chiu AC, Hsu PD, Dadon DB, Cheng AW, Trevino AE, Konermann S, Chen S, Jaenisch R, Zhang F, Sharp PA., Nat. Biotechnol. 32(7), 2014
PMID: 24752079
A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity.
Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E., Science 337(6096), 2012
PMID: 22745249
Functional annotation of native enhancers with a Cas9-histone demethylase fusion.
Kearns NA, Pham H, Tabak B, Genga RM, Silverstein NJ, Garber M, Maehr R., Nat. Methods 12(5), 2015
PMID: 25775043
Efficient in vivo deletion of a large imprinted lncRNA by CRISPR/Cas9.
Han J, Zhang J, Chen L, Shen B, Zhou J, Hu B, Du Y, Tate PH, Huang X, Zhang W., RNA Biol 11(7), 2014
PMID: 25137067
Understanding functional miRNA-target interactions in vivo by site-specific genome engineering.
Bassett AR, Azzam G, Wheatley L, Tibbit C, Rajakumar T, McGowan S, Stanger N, Ewels PA, Taylor S, Ponting CP, Liu JL, Sauka-Spengler T, Fulga TA., Nat Commun 5(), 2014
PMID: 25135198
Use of the CRISPR/Cas9 system as an intracellular defense against HIV-1 infection in human cells.
Liao HK, Gu Y, Diaz A, Marlett J, Takahashi Y, Li M, Suzuki K, Xu R, Hishida T, Chang CJ, Esteban CR, Young J, Izpisua Belmonte JC., Nat Commun 6(), 2015
PMID: 25752527
Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system.
Chen B, Gilbert LA, Cimini BA, Schnitzbauer J, Zhang W, Li GW, Park J, Blackburn EH, Weissman JS, Qi LS, Huang B., Cell 155(7), 2013
PMID: 24360272
One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering.
Wang H, Yang H, Shivalila CS, Dawlaty MM, Cheng AW, Zhang F, Jaenisch R., Cell 153(4), 2013
PMID: 23643243
Efficient CRISPR-Cas9-mediated genome editing in Plasmodium falciparum.
Wagner JC, Platt RJ, Goldfless SJ, Zhang F, Niles JC., Nat. Methods 11(9), 2014
PMID: 25108687
Genetic modification of the diarrhoeal pathogen Cryptosporidium parvum.
Vinayak S, Pawlowic MC, Sateriale A, Brooks CF, Studstill CJ, Bar-Peled Y, Cipriano MJ, Striepen B., Nature 523(7561), 2015
PMID: 26176919
CRISPR/Cas9-mediated gene knockout in the ascidian Ciona intestinalis.
Sasaki H, Yoshida K, Hozumi A, Sasakura Y., Dev. Growth Differ. 56(7), 2014
PMID: 25212715
Simultaneous editing of three homoeoalleles in hexaploid bread wheat confers heritable resistance to powdery mildew.
Wang Y, Cheng X, Shan Q, Zhang Y, Liu J, Gao C, Qiu JL., Nat. Biotechnol. 32(9), 2014
PMID: 25038773
Large chromosomal deletions and heritable small genetic changes induced by CRISPR/Cas9 in rice.
Zhou H, Liu B, Weeks DP, Spalding MH, Yang B., Nucleic Acids Res. 42(17), 2014
PMID: 25200087
Heritable genome editing with CRISPR/Cas9 in the silkworm, Bombyx mori.
Wei W, Xin H, Roy B, Dai J, Miao Y, Gao G., PLoS ONE 9(7), 2014
PMID: 25013902
CRISPR/Cas9-mediated mutagenesis in the sea lamprey Petromyzon marinus: a powerful tool for understanding ancestral gene functions in vertebrates.
Square T, Romasek M, Jandzik D, Cattell MV, Klymkowsky M, Medeiros DM., Development 142(23), 2015
PMID: 26511928
Efficient gene targeting in zebrafish mediated by a zebrafish-codon-optimized cas9 and evaluation of off-targeting effect.
Liu D, Wang Z, Xiao A, Zhang Y, Li W, Zu Y, Yao S, Lin S, Zhang B., J Genet Genomics 41(1), 2013
PMID: 24480746
Use of the CRISPR/Cas9 system to produce genetically engineered pigs from in vitro-derived oocytes and embryos.
Whitworth KM, Lee K, Benne JA, Beaton BP, Spate LD, Murphy SL, Samuel MS, Mao J, O'Gorman C, Walters EM, Murphy CN, Driver J, Mileham A, McLaren D, Wells KD, Prather RS., Biol. Reprod. 91(3), 2014
PMID: 25100712
CRISPR/Cas-mediated genome editing in the rat via direct injection of one-cell embryos.
Shao Y, Guan Y, Wang L, Qiu Z, Liu M, Chen Y, Wu L, Li Y, Ma X, Liu M, Li D., Nat Protoc 9(10), 2014
PMID: 25255092
Efficient gene knockout in goats using CRISPR/Cas9 system.
Ni W, Qiao J, Hu S, Zhao X, Regouski M, Yang M, Polejaeva IA, Chen C., PLoS ONE 9(9), 2014
PMID: 25188313
Single-step generation of rabbits carrying a targeted allele of the tyrosinase gene using CRISPR/Cas9.
Honda A, Hirose M, Sankai T, Yasmin L, Yuzawa K, Honsho K, Izu H, Iguchi A, Ikawa M, Ogura A., Exp. Anim. 64(1), 2014
PMID: 25195632
High-throughput screens in mammalian cells using the CRISPR-Cas9 system.
Peng J, Zhou Y, Zhu S, Wei W., FEBS J. 282(11), 2015
PMID: 25731961
Enzymatically Generated CRISPR Libraries for Genome Labeling and Screening.
Lane AB, Strzelecka M, Ettinger A, Grenfell AW, Wittmann T, Heald R., Dev. Cell 34(3), 2015
PMID: 26212133
Synthesis of an arrayed sgRNA library targeting the human genome.
Schmidt T, Schmid-Burgk JL, Hornung V., Sci Rep 5(), 2015
PMID: 26446710
BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis.
Canver MC, Smith EC, Sher F, Pinello L, Sanjana NE, Shalem O, Chen DD, Schupp PG, Vinjamur DS, Garcia SP, Luc S, Kurita R, Nakamura Y, Fujiwara Y, Maeda T, Yuan GC, Zhang F, Orkin SH, Bauer DE., Nature 527(7577), 2015
PMID: 26375006
Brave new epigenomes: the dawn of epigenetic engineering.
Koeferle A, Stricker SH, Beck S., Genome Med 7(1), 2015
PMID: 26089986
Inverse PCR.
Sambrook J, Russell DW., CSH Protoc 2006(1), 2006
PMID: 22485271
Enzymatic assembly of DNA molecules up to several hundred kilobases.
Gibson DG, Young L, Chuang RY, Venter JC, Hutchison CA 3rd, Smith HO., Nat. Methods 6(5), 2009
PMID: 19363495
Cutadapt removes adapter sequences from high-throughput sequencing reads
Martin M., 2011
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead B, Trapnell C, Pop M, Salzberg SL., Genome Biol. 10(3), 2009
PMID: 19261174

Gilks WR, Richardson S, Spiegelhalter DJ., 1998
Engineered CRISPR-Cas9 nucleases with altered PAM specificities.
Kleinstiver BP, Prew MS, Tsai SQ, Topkar VV, Nguyen NT, Zheng Z, Gonzales AP, Li Z, Peterson RT, Yeh JR, Aryee MJ, Joung JK., Nature 523(7561), 2015
PMID: 26098369
Orthogonal Cas9 proteins for RNA-guided gene regulation and editing.
Esvelt KM, Mali P, Braff JL, Moosburner M, Yaung SJ, Church GM., Nat. Methods 10(11), 2013
PMID: 24076762
In vivo genome editing using Staphylococcus aureus Cas9.
Ran FA, Cong L, Yan WX, Scott DA, Gootenberg JS, Kriz AJ, Zetsche B, Shalem O, Wu X, Makarova KS, Koonin EV, Sharp PA, Zhang F., Nature 520(7546), 2015
PMID: 25830891
Catalytic properties and specificity of the extracellular nuclease of Staphylococcus aureus.
Cuatrecasas P, Fuchs S, Anfinsen CB., J. Biol. Chem. 242(7), 1967
PMID: 4290246
Initial sequencing and analysis of the human genome.
Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann Y, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blocker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowki J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S, Chen YJ, Szustakowki J; International Human Genome Sequencing Consortium., Nature 409(6822), 2001
PMID: 11237011
Initial sequencing and comparative analysis of the mouse genome.
Mouse Genome Sequencing Consortium, Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, Barlow K, Beck S, Berry E, Birren B, Bloom T, Bork P, Botcherby M, Bray N, Brent MR, Brown DG, Brown SD, Bult C, Burton J, Butler J, Campbell RD, Carninci P, Cawley S, Chiaromonte F, Chinwalla AT, Church DM, Clamp M, Clee C, Collins FS, Cook LL, Copley RR, Coulson A, Couronne O, Cuff J, Curwen V, Cutts T, Daly M, David R, Davies J, Delehaunty KD, Deri J, Dermitzakis ET, Dewey C, Dickens NJ, Diekhans M, Dodge S, Dubchak I, Dunn DM, Eddy SR, Elnitski L, Emes RD, Eswara P, Eyras E, Felsenfeld A, Fewell GA, Flicek P, Foley K, Frankel WN, Fulton LA, Fulton RS, Furey TS, Gage D, Gibbs RA, Glusman G, Gnerre S, Goldman N, Goodstadt L, Grafham D, Graves TA, Green ED, Gregory S, Guigo R, Guyer M, Hardison RC, Haussler D, Hayashizaki Y, Hillier LW, Hinrichs A, Hlavina W, Holzer T, Hsu F, Hua A, Hubbard T, Hunt A, Jackson I, Jaffe DB, Johnson LS, Jones M, Jones TA, Joy A, Kamal M, Karlsson EK, Karolchik D, Kasprzyk A, Kawai J, Keibler E, Kells C, Kent WJ, Kirby A, Kolbe DL, Korf I, Kucherlapati RS, Kulbokas EJ, Kulp D, Landers T, Leger JP, Leonard S, Letunic I, Levine R, Li J, Li M, Lloyd C, Lucas S, Ma B, Maglott DR, Mardis ER, Matthews L, Mauceli E, Mayer JH, McCarthy M, McCombie WR, McLaren S, McLay K, McPherson JD, Meldrim J, Meredith B, Mesirov JP, Miller W, Miner TL, Mongin E, Montgomery KT, Morgan M, Mott R, Mullikin JC, Muzny DM, Nash WE, Nelson JO, Nhan MN, Nicol R, Ning Z, Nusbaum C, O'Connor MJ, Okazaki Y, Oliver K, Overton-Larty E, Pachter L, Parra G, Pepin KH, Peterson J, Pevzner P, Plumb R, Pohl CS, Poliakov A, Ponce TC, Ponting CP, Potter S, Quail M, Reymond A, Roe BA, Roskin KM, Rubin EM, Rust AG, Santos R, Sapojnikov V, Schultz B, Schultz J, Schwartz MS, Schwartz S, Scott C, Seaman S, Searle S, Sharpe T, Sheridan A, Shownkeen R, Sims S, Singer JB, Slater G, Smit A, Smith DR, Spencer B, Stabenau A, Stange-Thomann N, Sugnet C, Suyama M, Tesler G, Thompson J, Torrents D, Trevaskis E, Tromp J, Ucla C, Ureta-Vidal A, Vinson JP, Von Niederhausern AC, Wade CM, Wall M, Weber RJ, Weiss RB, Wendl MC, West AP, Wetterstrand K, Wheeler R, Whelan S, Wierzbowski J, Willey D, Williams S, Wilson RK, Winter E, Worley KC, Wyman D, Yang S, Yang SP, Zdobnov EM, Zody MC, Lander ES., Nature 420(6915), 2002
PMID: 12466850
DNA targeting specificity of RNA-guided Cas9 nucleases.
Hsu PD, Scott DA, Weinstein JA, Ran FA, Konermann S, Agarwala V, Li Y, Fine EJ, Wu X, Shalem O, Cradick TJ, Marraffini LA, Bao G, Zhang F., Nat. Biotechnol. 31(9), 2013
PMID: 23873081
Genome-wide inactivation of porcine endogenous retroviruses (PERVs)
Yang L, Guell M, Niu D, George H, Lesha E, Grishin D, Aach J, Shrock E, Xu W, Poci J., 2015
Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system.
Zetsche B, Gootenberg JS, Abudayyeh OO, Slaymaker IM, Makarova KS, Essletzbichler P, Volz SE, Joung J, van der Oost J, Regev A, Koonin EV, Zhang F., Cell 163(3), 2015
PMID: 26422227
Genetic screens in human cells using the CRISPR-Cas9 system.
Wang T, Wei JJ, Sabatini DM, Lander ES., Science 343(6166), 2013
PMID: 24336569


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