Considerations and practical implications of performing a phenotypic CRISPR/Cas survival screen, PLoS ONE | DeepDyve (2024)

(DasS, ChadwickBP. Influence of repressive histone and DNA methylation upon D4Z4 transcription in non-myogenic cells.PLoS ONE.2016;11: 1–26. doi: 10.1371/journal.pone.016002227467759)

DasS, ChadwickBP. Influence of repressive histone and DNA methylation upon D4Z4 transcription in non-myogenic cells.PLoS ONE.2016;11: 1–26. doi: 10.1371/journal.pone.016002227467759, DasS, ChadwickBP. Influence of repressive histone and DNA methylation upon D4Z4 transcription in non-myogenic cells.PLoS ONE.2016;11: 1–26. doi: 10.1371/journal.pone.016002227467759

R. Lemmers, Patrick Vliet, R. Klooster, S. Sacconi, P. Camaño, J. Dauwerse, L. Snider, K. Straasheijm, Gert Ommen, G. Padberg, Daniel Miller, S. Tapscott, R. Tawil, R. Frants, S. Maarel (2010)

Science, 329

Akihiro Urasaki, Ghislaine Morvan, K. Kawakami (2006)

Genetics, 174

Qing Feng, L. Snider, S. Jagannathan, R. Tawil, S. Maarel, S. Tapscott, R. Bradley (2015)

eLife, 4

(AnsseauE, VanderplanckC, WautersA, HarperSQ, CoppéeF, BelayewA. Antisense oligonucleotides used to target the DUX4 mRNA as therapeutic approaches in faciosscapulohumeral muscular dystrophy (FSHD). Genes. 2017;8. doi: 10.3390/genes803009328273791)

AnsseauE, VanderplanckC, WautersA, HarperSQ, CoppéeF, BelayewA. Antisense oligonucleotides used to target the DUX4 mRNA as therapeutic approaches in faciosscapulohumeral muscular dystrophy (FSHD). Genes. 2017;8. doi: 10.3390/genes803009328273791, AnsseauE, VanderplanckC, WautersA, HarperSQ, CoppéeF, BelayewA. Antisense oligonucleotides used to target the DUX4 mRNA as therapeutic approaches in faciosscapulohumeral muscular dystrophy (FSHD). Genes. 2017;8. doi: 10.3390/genes803009328273791

(BanerjiCRS, ZammitPS, PanamarovaM. Lymphocytes contribute to DUX4 target genes in 1 FSHD muscle biopsies.Biorxiv. 2019. 10.1101/717652)

BanerjiCRS, ZammitPS, PanamarovaM. Lymphocytes contribute to DUX4 target genes in 1 FSHD muscle biopsies.Biorxiv. 2019. 10.1101/717652, BanerjiCRS, ZammitPS, PanamarovaM. Lymphocytes contribute to DUX4 target genes in 1 FSHD muscle biopsies.Biorxiv. 2019. 10.1101/717652

Le Cong, F. Ran, David Cox, Shuailiang Lin, Robert Barretto, Naomi Habib, P. Hsu, Xuebing Wu, Wenyan Jiang, L. Marraffini, Feng Zhang (2013)

Science, 339

(LuteijnRD, van DiemenF, BlomenVA, BoerIGJ, Manikam SadasivamS, van KuppeveltTH, et al. A Genome-Wide Haploid Genetic Screen Identifies Heparan Sulfate-Associated Genes and the Macropinocytosis Modulator TMED10 as Factors Supporting Vaccinia Virus Infection. Journal of Virology. 2019;93. doi: 10.1128/JVI.02160-1830996093)

LuteijnRD, van DiemenF, BlomenVA, BoerIGJ, Manikam SadasivamS, van KuppeveltTH, et al. A Genome-Wide Haploid Genetic Screen Identifies Heparan Sulfate-Associated Genes and the Macropinocytosis Modulator TMED10 as Factors Supporting Vaccinia Virus Infection. Journal of Virology. 2019;93. doi: 10.1128/JVI.02160-1830996093, LuteijnRD, van DiemenF, BlomenVA, BoerIGJ, Manikam SadasivamS, van KuppeveltTH, et al. A Genome-Wide Haploid Genetic Screen Identifies Heparan Sulfate-Associated Genes and the Macropinocytosis Modulator TMED10 as Factors Supporting Vaccinia Virus Infection. Journal of Virology. 2019;93. doi: 10.1128/JVI.02160-1830996093

Anita Heuvel, A. Mahfouz, S. Kloet, J. Balog, B. Engelen, R. Tawil, S. Tapscott, S. Maarel (2018)

Human Molecular Genetics, 28

Sunny Das, B. Chadwick (2016)

PLoS ONE, 11

EY Chen (2013)

BMC Bioinformatics

(BanerjiCRS, KnoppP, MoyleLA, SeveriniS, OrrellRW, TeschendorffAE, et al. β-catenin is central to DUX4-driven network rewiring in facioscapulohumeral muscular dystrophy. Journal of the Royal Society Interface. 2015;12. doi: 10.1098/rsif.2014.079725551153)

BanerjiCRS, KnoppP, MoyleLA, SeveriniS, OrrellRW, TeschendorffAE, et al. β-catenin is central to DUX4-driven network rewiring in facioscapulohumeral muscular dystrophy. Journal of the Royal Society Interface. 2015;12. doi: 10.1098/rsif.2014.079725551153, BanerjiCRS, KnoppP, MoyleLA, SeveriniS, OrrellRW, TeschendorffAE, et al. β-catenin is central to DUX4-driven network rewiring in facioscapulohumeral muscular dystrophy. Journal of the Royal Society Interface. 2015;12. doi: 10.1098/rsif.2014.079725551153

(ShadleSC, ZhongJW, CampbellAE, ConerlyML, JagannathanS, WongCJ, et al. DUX4-induced dsRNA and MYC mRNA stabilization activate apoptotic pathways in human cell models of facioscapulohumeral dystrophy. PLoS Genetics. 2017;13: 1–25. doi: 10.1371/journal.pgen.100665828273136)

ShadleSC, ZhongJW, CampbellAE, ConerlyML, JagannathanS, WongCJ, et al. DUX4-induced dsRNA and MYC mRNA stabilization activate apoptotic pathways in human cell models of facioscapulohumeral dystrophy. PLoS Genetics. 2017;13: 1–25. doi: 10.1371/journal.pgen.100665828273136, ShadleSC, ZhongJW, CampbellAE, ConerlyML, JagannathanS, WongCJ, et al. DUX4-induced dsRNA and MYC mRNA stabilization activate apoptotic pathways in human cell models of facioscapulohumeral dystrophy. PLoS Genetics. 2017;13: 1–25. doi: 10.1371/journal.pgen.100665828273136

(VuoristoS, Hydén-GranskogC, YoshiharaM, GawriyskiL, DamdimopoulosA, BhagatS, et al. DUX4 regulates oocyte to embryo transition in human.Biorxiv. 2019. 10.1101/732289)

VuoristoS, Hydén-GranskogC, YoshiharaM, GawriyskiL, DamdimopoulosA, BhagatS, et al. DUX4 regulates oocyte to embryo transition in human.Biorxiv. 2019. 10.1101/732289, VuoristoS, Hydén-GranskogC, YoshiharaM, GawriyskiL, DamdimopoulosA, BhagatS, et al. DUX4 regulates oocyte to embryo transition in human.Biorxiv. 2019. 10.1101/732289

(BosnakovskiD, ChoiSH, StrasserJM, TosoEA, WaltersMA, KybaM. High-throughput screening identifies inhibitors of DUX4-induced myoblast toxicity.Skeletal Muscle. 2014;4: 1–11. doi: 10.1186/2044-5040-4-124383888)

BosnakovskiD, ChoiSH, StrasserJM, TosoEA, WaltersMA, KybaM. High-throughput screening identifies inhibitors of DUX4-induced myoblast toxicity.Skeletal Muscle. 2014;4: 1–11. doi: 10.1186/2044-5040-4-124383888, BosnakovskiD, ChoiSH, StrasserJM, TosoEA, WaltersMA, KybaM. High-throughput screening identifies inhibitors of DUX4-induced myoblast toxicity.Skeletal Muscle. 2014;4: 1–11. doi: 10.1186/2044-5040-4-124383888

(MulherkarN, KuehneAI, KranzuschPJ, AprilM, CaretteJE, RaabenM, et al. Ebola Virus entry requires the cholesterol transporter Niemann-Pick C1. Nature. 2012;477: 340–343. doi: 10.1038/nature10348.Ebola)

MulherkarN, KuehneAI, KranzuschPJ, AprilM, CaretteJE, RaabenM, et al. Ebola Virus entry requires the cholesterol transporter Niemann-Pick C1. Nature. 2012;477: 340–343. doi: 10.1038/nature10348.Ebola, MulherkarN, KuehneAI, KranzuschPJ, AprilM, CaretteJE, RaabenM, et al. Ebola Virus entry requires the cholesterol transporter Niemann-Pick C1. Nature. 2012;477: 340–343. doi: 10.1038/nature10348.Ebola

CRS Banerji (2017)

Nature Communications

Linda Geng, Zizhen Yao, L. Snider, Abraham Fong, J. Cech, Janet Young, S. Maarel, W. Ruzzo, R. Gentleman, R. Tawil, S. Tapscott (2012)

Developmental cell, 22 1

(CaretteJE, PruszakJ, VaradarajanM, BlomenVA, GokhaleS, CamargoFD, et al. Generation of iPSCs from cultured human malignant cells. Blood. 2010;115: 4039–4042. doi: 10.1182/blood-2009-07-23184520233975)

CaretteJE, PruszakJ, VaradarajanM, BlomenVA, GokhaleS, CamargoFD, et al. Generation of iPSCs from cultured human malignant cells. Blood. 2010;115: 4039–4042. doi: 10.1182/blood-2009-07-23184520233975, CaretteJE, PruszakJ, VaradarajanM, BlomenVA, GokhaleS, CamargoFD, et al. Generation of iPSCs from cultured human malignant cells. Blood. 2010;115: 4039–4042. doi: 10.1182/blood-2009-07-23184520233975

S. Agha‐Mohammadi, M. O’Malley, A. Etemad, Zhong Wang, Xiao Xiao, M. Lotze (2004)

The Journal of Gene Medicine, 6

S. Winokur, Yi-Wen Chen, P. Masny, Jorge Martin, J. Ehmsen, S. Tapscott, S. Maarel, Y. Hayashi, K. Flanigan (2003)

Human molecular genetics, 12 22

(BlomenVA, MájekP, JaeLT, BigenzahnJW, NieuwenhuisJ, StaringJ, et al. Gene essentiality and synthetic lethality in haploid human cells. Science. 2015;350: 1092–6. doi: 10.1126/science.aac755726472760)

BlomenVA, MájekP, JaeLT, BigenzahnJW, NieuwenhuisJ, StaringJ, et al. Gene essentiality and synthetic lethality in haploid human cells. Science. 2015;350: 1092–6. doi: 10.1126/science.aac755726472760, BlomenVA, MájekP, JaeLT, BigenzahnJW, NieuwenhuisJ, StaringJ, et al. Gene essentiality and synthetic lethality in haploid human cells. Science. 2015;350: 1092–6. doi: 10.1126/science.aac755726472760

(van AttekumM, TerpstraS, ReinenE, KaterA, ElderingE. Macrophage-mediated chronic lymphocytic leukemia cell survival is independent of APRIL signaling. Cell Death Discovery. 2016;2. doi: 10.1038/cddiscovery.2016.2027551513)

van AttekumM, TerpstraS, ReinenE, KaterA, ElderingE. Macrophage-mediated chronic lymphocytic leukemia cell survival is independent of APRIL signaling. Cell Death Discovery. 2016;2. doi: 10.1038/cddiscovery.2016.2027551513, van AttekumM, TerpstraS, ReinenE, KaterA, ElderingE. Macrophage-mediated chronic lymphocytic leukemia cell survival is independent of APRIL signaling. Cell Death Discovery. 2016;2. doi: 10.1038/cddiscovery.2016.2027551513

(BosnakovskiD, ChanSSK, RechtOO, HartweckLM, GustafsonCJ, AthmanLL, et al. Muscle pathology from stochastic low level DUX4 expression in an FSHD mouse model. Nature Communications. 2017;8: 1–9. doi: 10.1038/s41467-016-0009-628232747)

BosnakovskiD, ChanSSK, RechtOO, HartweckLM, GustafsonCJ, AthmanLL, et al. Muscle pathology from stochastic low level DUX4 expression in an FSHD mouse model. Nature Communications. 2017;8: 1–9. doi: 10.1038/s41467-016-0009-628232747, BosnakovskiD, ChanSSK, RechtOO, HartweckLM, GustafsonCJ, AthmanLL, et al. Muscle pathology from stochastic low level DUX4 expression in an FSHD mouse model. Nature Communications. 2017;8: 1–9. doi: 10.1038/s41467-016-0009-628232747

C. Banerji, M. Panamarova, H. Hebaishi, Robert White, F. Relaix, S. Severini, P. Zammit (2017)

Nature Communications, 8

Max Shen, Mandana Arbab, Jonathan Hsu, D. Worstell, Sannie Culbertson, Olga Krabbe, C. Cassa, David Liu, D. Gifford, R. Sherwood (2018)

Nature, 563

(OlbrichT, Vega-SendinoM, MurgaM, de CarcerG, MalumbresM, OrtegaS, et al. A Chemical Screen Identifies Compounds Capable of Selecting for Haploidy in Mammalian Cells. Cell Reports. 2019;28: 597–604.e4. doi: 10.1016/j.celrep.2019.06.06031315040)

OlbrichT, Vega-SendinoM, MurgaM, de CarcerG, MalumbresM, OrtegaS, et al. A Chemical Screen Identifies Compounds Capable of Selecting for Haploidy in Mammalian Cells. Cell Reports. 2019;28: 597–604.e4. doi: 10.1016/j.celrep.2019.06.06031315040, OlbrichT, Vega-SendinoM, MurgaM, de CarcerG, MalumbresM, OrtegaS, et al. A Chemical Screen Identifies Compounds Capable of Selecting for Haploidy in Mammalian Cells. Cell Reports. 2019;28: 597–604.e4. doi: 10.1016/j.celrep.2019.06.06031315040

(CullotG, BoutinJ, ToutainJ, PratF, PennamenP, RooryckC, et al. CRISPR-Cas9 genome editing induces megabase-scale chromosomal truncations. Nature Communications. 2019;10: 1–14. doi: 10.1038/s41467-018-07882-830602773)

CullotG, BoutinJ, ToutainJ, PratF, PennamenP, RooryckC, et al. CRISPR-Cas9 genome editing induces megabase-scale chromosomal truncations. Nature Communications. 2019;10: 1–14. doi: 10.1038/s41467-018-07882-830602773, CullotG, BoutinJ, ToutainJ, PratF, PennamenP, RooryckC, et al. CRISPR-Cas9 genome editing induces megabase-scale chromosomal truncations. Nature Communications. 2019;10: 1–14. doi: 10.1038/s41467-018-07882-830602773

A. Lek, Yuanfan Zhang, K. Woodman, Shushu Huang, A. DeSimone, Justin Cohen, Vincent Ho, J. Conner, L. Mead, Andrew Kodani, A. Pakuła, Neville Sanjana, O. King, Peter Jones, K. Wagner, M. Lek, L. Kunkel (2020)

Science Translational Medicine, 12

(JaeLT, RaabenM, RiemersmaM, BeusekomE Van, BlomenVA, VeldsA, et al. Deciphering the Glycosylome of Dystroglycanopathies Using Haploid Screens for Lassa Virus Entry.2014;340: 479–483. doi: 10.1126/science.1233675.Deciphering)

JaeLT, RaabenM, RiemersmaM, BeusekomE Van, BlomenVA, VeldsA, et al. Deciphering the Glycosylome of Dystroglycanopathies Using Haploid Screens for Lassa Virus Entry.2014;340: 479–483. doi: 10.1126/science.1233675.Deciphering, JaeLT, RaabenM, RiemersmaM, BeusekomE Van, BlomenVA, VeldsA, et al. Deciphering the Glycosylome of Dystroglycanopathies Using Haploid Screens for Lassa Virus Entry.2014;340: 479–483. doi: 10.1126/science.1233675.Deciphering

(KnoppP, KromYD, BanerjiCRS, PanamarovaM, MoyleLA, den HamerB, et al. DUX4 induces a transcriptome more characteristic of a less-differentiated cell state and inhibits myogenesis. Journal of Cell Science. 2016;129: 3816–3831. doi: 10.1242/jcs.18037227744317)

KnoppP, KromYD, BanerjiCRS, PanamarovaM, MoyleLA, den HamerB, et al. DUX4 induces a transcriptome more characteristic of a less-differentiated cell state and inhibits myogenesis. Journal of Cell Science. 2016;129: 3816–3831. doi: 10.1242/jcs.18037227744317, KnoppP, KromYD, BanerjiCRS, PanamarovaM, MoyleLA, den HamerB, et al. DUX4 induces a transcriptome more characteristic of a less-differentiated cell state and inhibits myogenesis. Journal of Cell Science. 2016;129: 3816–3831. doi: 10.1242/jcs.18037227744317

(LemmersRJ, Van Der VlietPJ, BalogJ, GoemanJJ, ArindrartoW, KromYD, et al. Deep characterization of a common D4Z4 variant identifies biallelic DUX4 expression as a modifier for disease penetrance in FSHD2. European Journal of Human Genetics. 2018;26: 94–106. doi: 10.1038/s41431-017-0015-029162933)

LemmersRJ, Van Der VlietPJ, BalogJ, GoemanJJ, ArindrartoW, KromYD, et al. Deep characterization of a common D4Z4 variant identifies biallelic DUX4 expression as a modifier for disease penetrance in FSHD2. European Journal of Human Genetics. 2018;26: 94–106. doi: 10.1038/s41431-017-0015-029162933, LemmersRJ, Van Der VlietPJ, BalogJ, GoemanJJ, ArindrartoW, KromYD, et al. Deep characterization of a common D4Z4 variant identifies biallelic DUX4 expression as a modifier for disease penetrance in FSHD2. European Journal of Human Genetics. 2018;26: 94–106. doi: 10.1038/s41431-017-0015-029162933

(CongL, RanFA, CoxD, LinS, BarrettoR, HsuPD, et al. Multiplex Genome Engineering Using CRISPR/Cas Systems. Science. 2013;339: 819–823. doi: 10.1126/science.123114323287718)

CongL, RanFA, CoxD, LinS, BarrettoR, HsuPD, et al. Multiplex Genome Engineering Using CRISPR/Cas Systems. Science. 2013;339: 819–823. doi: 10.1126/science.123114323287718, CongL, RanFA, CoxD, LinS, BarrettoR, HsuPD, et al. Multiplex Genome Engineering Using CRISPR/Cas Systems. Science. 2013;339: 819–823. doi: 10.1126/science.123114323287718

(TawilR, Van Der MaarelSM. Facioscapulohumeral muscular dystrophy. Muscle and Nerve. 2006;34: 1–15. doi: 10.1002/mus.2052216508966)

TawilR, Van Der MaarelSM. Facioscapulohumeral muscular dystrophy. Muscle and Nerve. 2006;34: 1–15. doi: 10.1002/mus.2052216508966, TawilR, Van Der MaarelSM. Facioscapulohumeral muscular dystrophy. Muscle and Nerve. 2006;34: 1–15. doi: 10.1002/mus.2052216508966

CRS Banerji (2015)

Journal of the Royal Society Interface

M. Love, W. Huber, S. Anders (2014)

Genome Biology, 15

D. Bosnakovski, Sarah Lamb, T. Şimşek, Zhaohui Xu, A. Belayew, R. Perlingeiro, M. Kyba (2008)

Experimental Neurology, 214

(HashimshonyT, SenderovichN, AvitalG, KlochendlerA, de LeeuwY, AnavyL, et al. CEL-Seq2: Sensitive highly-multiplexed single-cell RNA-Seq. Genome Biology. 2016;17: 1–7. doi: 10.1186/s13059-015-0866-z26753840)

HashimshonyT, SenderovichN, AvitalG, KlochendlerA, de LeeuwY, AnavyL, et al. CEL-Seq2: Sensitive highly-multiplexed single-cell RNA-Seq. Genome Biology. 2016;17: 1–7. doi: 10.1186/s13059-015-0866-z26753840, HashimshonyT, SenderovichN, AvitalG, KlochendlerA, de LeeuwY, AnavyL, et al. CEL-Seq2: Sensitive highly-multiplexed single-cell RNA-Seq. Genome Biology. 2016;17: 1–7. doi: 10.1186/s13059-015-0866-z26753840

(BarrangouR, FremauxR, DeveauH, RichardsM, BoyavalP, MoineauS, et al. CRISPR provides acquired resistance against viruses in prokaryotes.Sciencee. 2007;315: 1709–1712. doi: 10.1126/science.113814017379808)

BarrangouR, FremauxR, DeveauH, RichardsM, BoyavalP, MoineauS, et al. CRISPR provides acquired resistance against viruses in prokaryotes.Sciencee. 2007;315: 1709–1712. doi: 10.1126/science.113814017379808, BarrangouR, FremauxR, DeveauH, RichardsM, BoyavalP, MoineauS, et al. CRISPR provides acquired resistance against viruses in prokaryotes.Sciencee. 2007;315: 1709–1712. doi: 10.1126/science.113814017379808

N Mulherkar (2012)

Nature, 477

D Bosnakovski (2017)

Journal of Cell Science, 130

T. Hashimshony, F. Wagner, Noa Sher, I. Yanai (2012)

Cell reports, 2 3

M Bibikova (2002)

Genetics, 161

(EssletzbichlerP, KonopkaT, SantoroF, ChenD, GappB V., KralovicsR, et al. Megabase-scale deletion using CRISPR/Cas9 to generate a fully haploid human cell line. Genome Research. 2014;24: 2059–2065. doi: 10.1101/gr.177220.11425373145)

EssletzbichlerP, KonopkaT, SantoroF, ChenD, GappB V., KralovicsR, et al. Megabase-scale deletion using CRISPR/Cas9 to generate a fully haploid human cell line. Genome Research. 2014;24: 2059–2065. doi: 10.1101/gr.177220.11425373145, EssletzbichlerP, KonopkaT, SantoroF, ChenD, GappB V., KralovicsR, et al. Megabase-scale deletion using CRISPR/Cas9 to generate a fully haploid human cell line. Genome Research. 2014;24: 2059–2065. doi: 10.1101/gr.177220.11425373145

Maxim Kuleshov, Matthew Jones, A. Rouillard, Nicolas Fernandez, Qiaonan Duan, Zichen Wang, Simon Koplev, S. Jenkins, Kathleen Jagodnik, Alexander Lachmann, Michael McDermott, Caroline Monteiro, Gregory Gundersen, Avi Ma’ayan (2016)

Nucleic Acids Research, 44

Dominic Grün, A. Lyubimova, L. Kester, K. Wiebrands, O. Basak, Nobuo Sasaki, H. Clevers, A. Oudenaarden (2015)

Nature, 525

E. Pastorello, Michelangelo Cao, C. Trevisan (2012)

Clinical Neurology and Neurosurgery, 114

(DmitrievP, Bou SaadaY, DibC, AnsseauE, BaratA, HamadeA, et al. DUX4-induced constitutive DNA damage and oxidative stress contribute to aberrant differentiation of myoblasts from FSHD patients. Free Radical Biology and Medicine. 2016;99: 244–258. doi: 10.1016/j.freeradbiomed.2016.08.00727519269)

DmitrievP, Bou SaadaY, DibC, AnsseauE, BaratA, HamadeA, et al. DUX4-induced constitutive DNA damage and oxidative stress contribute to aberrant differentiation of myoblasts from FSHD patients. Free Radical Biology and Medicine. 2016;99: 244–258. doi: 10.1016/j.freeradbiomed.2016.08.00727519269, DmitrievP, Bou SaadaY, DibC, AnsseauE, BaratA, HamadeA, et al. DUX4-induced constitutive DNA damage and oxidative stress contribute to aberrant differentiation of myoblasts from FSHD patients. Free Radical Biology and Medicine. 2016;99: 244–258. doi: 10.1016/j.freeradbiomed.2016.08.00727519269

(BrounsSJ, JoreMM, LundgrenM, WestraER, SlijkhuisR, SnijdersA, et al. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science. 2008;321: 960–964. doi: 10.1126/science.115968918703739)

BrounsSJ, JoreMM, LundgrenM, WestraER, SlijkhuisR, SnijdersA, et al. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science. 2008;321: 960–964. doi: 10.1126/science.115968918703739, BrounsSJ, JoreMM, LundgrenM, WestraER, SlijkhuisR, SnijdersA, et al. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science. 2008;321: 960–964. doi: 10.1126/science.115968918703739

(HimedaCL, JonesTI, JonesPL. CRISPR/dCas9-mediated transcriptional inhibition ameliorates the epigenetic dysregulation at D4Z4 and represses DUX4-fl in FSH muscular dystrophy. Molecular Therapy. 2016;24: 527–535. doi: 10.1038/mt.2015.20026527377)

HimedaCL, JonesTI, JonesPL. CRISPR/dCas9-mediated transcriptional inhibition ameliorates the epigenetic dysregulation at D4Z4 and represses DUX4-fl in FSH muscular dystrophy. Molecular Therapy. 2016;24: 527–535. doi: 10.1038/mt.2015.20026527377, HimedaCL, JonesTI, JonesPL. CRISPR/dCas9-mediated transcriptional inhibition ameliorates the epigenetic dysregulation at D4Z4 and represses DUX4-fl in FSH muscular dystrophy. Molecular Therapy. 2016;24: 527–535. doi: 10.1038/mt.2015.20026527377

(WangT, BirsoyK, HughesNW, KrupczakKM, PostY, WeiJJ, et al. Identification and characterization of essential genes in the human genome. Science. 2015;350: 1096–1101. doi: 10.1126/science.aac704126472758)

WangT, BirsoyK, HughesNW, KrupczakKM, PostY, WeiJJ, et al. Identification and characterization of essential genes in the human genome. Science. 2015;350: 1096–1101. doi: 10.1126/science.aac704126472758, WangT, BirsoyK, HughesNW, KrupczakKM, PostY, WeiJJ, et al. Identification and characterization of essential genes in the human genome. Science. 2015;350: 1096–1101. doi: 10.1126/science.aac704126472758

M. Attekum, S. Terpstra, E. Reinen, A. Kater, E. Eldering (2016)

Cell Death Discovery, 2

L. Snider, Linda Geng, R. Lemmers, M. Kyba, C. Ware, Angelique Nelson, R. Tawil, G. Filippova, S. Maarel, S. Tapscott, Daniel Miller (2010)

PLoS Genetics, 6

Teresa Olbrich, Maria Vega-Sendino, M. Murga, G. Cárcer, Marcos Malumbres, S. Ortega, Sergio Ruiz, O. Fernandez-Capetillo (2019)

Cell Reports, 28

(BosnakovskiD, LambS, SimsekT, XuZ, BelayewA, PerlingeiroR, et al. DUX4c, an FSHD candidate gene, interferes with myogenic regulators and abolishes myoblast differentiation. Experimental Neurology. 2008;214: 87–96. doi: 10.1016/j.expneurol.2008.07.02218723017)

BosnakovskiD, LambS, SimsekT, XuZ, BelayewA, PerlingeiroR, et al. DUX4c, an FSHD candidate gene, interferes with myogenic regulators and abolishes myoblast differentiation. Experimental Neurology. 2008;214: 87–96. doi: 10.1016/j.expneurol.2008.07.02218723017, BosnakovskiD, LambS, SimsekT, XuZ, BelayewA, PerlingeiroR, et al. DUX4c, an FSHD candidate gene, interferes with myogenic regulators and abolishes myoblast differentiation. Experimental Neurology. 2008;214: 87–96. doi: 10.1016/j.expneurol.2008.07.02218723017

J. Carette, M. Raaben, A. Wong, A. Herbert, G. Obernosterer, N. Mulherkar, A. Kuehne, P. Kranzusch, A. Griffin, G. Ruthel, P. Cin, J. Dye, S. Whelan, K. Chandran, T. Brummelkamp (2011)

Nature, 477

T. Hashimshony, N. Senderovich, Gal Avital, A. Klochendler, Yaron Leeuw, Leon Anavy, David Gennert, Shuqiang Li, K. Livak, O. Rozenblatt-Rosen, Y. Dor, A. Regev, I. Yanai (2016)

Genome Biology, 17

(JagannathanS, ShadleSC, ResnickR, SniderL, TawilRN, van der MaarelSM, et al. Model systems of DUX4 expression recapitulate the transcriptional profile of FSHD cells. Human Molecular Genetics. 2016;25: ddw271. doi: 10.1093/hmg/ddw27128171552)

JagannathanS, ShadleSC, ResnickR, SniderL, TawilRN, van der MaarelSM, et al. Model systems of DUX4 expression recapitulate the transcriptional profile of FSHD cells. Human Molecular Genetics. 2016;25: ddw271. doi: 10.1093/hmg/ddw27128171552, JagannathanS, ShadleSC, ResnickR, SniderL, TawilRN, van der MaarelSM, et al. Model systems of DUX4 expression recapitulate the transcriptional profile of FSHD cells. Human Molecular Genetics. 2016;25: ddw271. doi: 10.1093/hmg/ddw27128171552

T Wang (2015)

Science, 350

L. Jae, M. Raaben, M. Riemersma, E. Beusekom, V. Blomen, A. Velds, R. Kerkhoven, J. Carette, H. Topaloğlu, P. Meinecke, M. Wessels, D. Lefeber, S. Whelan, H. Bokhoven, T. Brummelkamp (2013)

Science, 340

(ChristianM, CermakT, DoyleEL, SchmidtC, ZhangF, HummelA, et al. Targeting DNA double-strand breaks with TAL effector nucleases. Genetics. 2010;186: 756–761. doi: 10.1534/genetics.110.12071720660643)

ChristianM, CermakT, DoyleEL, SchmidtC, ZhangF, HummelA, et al. Targeting DNA double-strand breaks with TAL effector nucleases. Genetics. 2010;186: 756–761. doi: 10.1534/genetics.110.12071720660643, ChristianM, CermakT, DoyleEL, SchmidtC, ZhangF, HummelA, et al. Targeting DNA double-strand breaks with TAL effector nucleases. Genetics. 2010;186: 756–761. doi: 10.1534/genetics.110.12071720660643

Stan Brouns, M. Jore, Magnus Lundgren, E. Westra, R. Slijkhuis, A. Snijders, M. Dickman, K. Makarova, E. Koonin, J. Oost (2008)

Science, 321

(BosnakovskiD, XuZ, Ji GangE, GalindoCL, LiuM, SimsekT, et al. An isogenetic myoblast expression screen identifies DUX4-mediated FSHD-associated molecular pathologies. EMBO Journal. 2008;27: 2766–2779. doi: 10.1038/emboj.2008.20118833193)

BosnakovskiD, XuZ, Ji GangE, GalindoCL, LiuM, SimsekT, et al. An isogenetic myoblast expression screen identifies DUX4-mediated FSHD-associated molecular pathologies. EMBO Journal. 2008;27: 2766–2779. doi: 10.1038/emboj.2008.20118833193, BosnakovskiD, XuZ, Ji GangE, GalindoCL, LiuM, SimsekT, et al. An isogenetic myoblast expression screen identifies DUX4-mediated FSHD-associated molecular pathologies. EMBO Journal. 2008;27: 2766–2779. doi: 10.1038/emboj.2008.20118833193

(HashimshonyT, WagnerF, SherN, YanaiI. CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification. Cell Reports. 2012;2: 666–673. doi: 10.1016/j.celrep.2012.08.00322939981)

HashimshonyT, WagnerF, SherN, YanaiI. CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification. Cell Reports. 2012;2: 666–673. doi: 10.1016/j.celrep.2012.08.00322939981, HashimshonyT, WagnerF, SherN, YanaiI. CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification. Cell Reports. 2012;2: 666–673. doi: 10.1016/j.celrep.2012.08.00322939981

B. Andersson, M. Beran, S. Pathak, A. Goodacre, B. Barlogie, K. McCredie (1987)

Cancer genetics and cytogenetics, 24 2

(JinekM, EastA, ChengA, LinS, MaE, DoudnaJ. RNA-programmed genome editing in human cells. eLife. 2013;2013: 1–9. doi: 10.7554/eLife.0047123386978)

JinekM, EastA, ChengA, LinS, MaE, DoudnaJ. RNA-programmed genome editing in human cells. eLife. 2013;2013: 1–9. doi: 10.7554/eLife.0047123386978, JinekM, EastA, ChengA, LinS, MaE, DoudnaJ. RNA-programmed genome editing in human cells. eLife. 2013;2013: 1–9. doi: 10.7554/eLife.0047123386978

(MezzadraR, De BruijnM, JaeLT, Gomez-EerlandR, DuursmaA, ScheerenFA, et al. SLFN11 can sensitize tumor cells towards IFN-γ-mediated T cell killing. PLoS ONE. 2019;14: 1–16. doi: 10.1371/journal.pone.021205330753225)

MezzadraR, De BruijnM, JaeLT, Gomez-EerlandR, DuursmaA, ScheerenFA, et al. SLFN11 can sensitize tumor cells towards IFN-γ-mediated T cell killing. PLoS ONE. 2019;14: 1–16. doi: 10.1371/journal.pone.021205330753225, MezzadraR, De BruijnM, JaeLT, Gomez-EerlandR, DuursmaA, ScheerenFA, et al. SLFN11 can sensitize tumor cells towards IFN-γ-mediated T cell killing. PLoS ONE. 2019;14: 1–16. doi: 10.1371/journal.pone.021205330753225

Kendall Sanson, Ruth Hanna, Mudra Hegde, Katherine Donovan, Christine Strand, Meagan Sullender, Emma Vaimberg, A. Goodale, D. Root, F. Piccioni, John Doench (2018)

Nature Communications, 9

Yang-Gyun Kim, Pearl Kim, Alan Herbert, Alexander Rich (1997)

Proceedings of the National Academy of Sciences of the United States of America, 94 24

P. Knopp, Y. Krom, C. Banerji, M. Panamarova, L. Moyle, B. Hamer, S. Maarel, P. Zammit (2016)

Journal of Cell Science, 129

(MillerJC, TanS, QiaoG, BarlowKA, WangJ, XiaDF, et al. A TALE nuclease architecture for efficient genome editing. Nature Biotechnology. 2011;29: 143–150. doi: 10.1038/nbt.175521179091)

MillerJC, TanS, QiaoG, BarlowKA, WangJ, XiaDF, et al. A TALE nuclease architecture for efficient genome editing. Nature Biotechnology. 2011;29: 143–150. doi: 10.1038/nbt.175521179091, MillerJC, TanS, QiaoG, BarlowKA, WangJ, XiaDF, et al. A TALE nuclease architecture for efficient genome editing. Nature Biotechnology. 2011;29: 143–150. doi: 10.1038/nbt.175521179091

(PapatheodorouaP, CaretteJE, BellGW, SchwanC, GuttenbergG, BrummelkampTR, et al. Lipolysis-stimulated lipoprotein receptor (LSR) is the host receptor for the binary toxin Clostridium difficile transferase (CDT).Proceedings of the National Academy of Sciences of the United States of America. 2011;108: 16422–16427. doi: 10.1073/pnas.110977210821930894)

PapatheodorouaP, CaretteJE, BellGW, SchwanC, GuttenbergG, BrummelkampTR, et al. Lipolysis-stimulated lipoprotein receptor (LSR) is the host receptor for the binary toxin Clostridium difficile transferase (CDT).Proceedings of the National Academy of Sciences of the United States of America. 2011;108: 16422–16427. doi: 10.1073/pnas.110977210821930894, PapatheodorouaP, CaretteJE, BellGW, SchwanC, GuttenbergG, BrummelkampTR, et al. Lipolysis-stimulated lipoprotein receptor (LSR) is the host receptor for the binary toxin Clostridium difficile transferase (CDT).Proceedings of the National Academy of Sciences of the United States of America. 2011;108: 16422–16427. doi: 10.1073/pnas.110977210821930894

(YuJSL, YusaK. Genome-wide CRISPR-Cas9 screening in mammalian cells. Methods. 2019;164–165: 29–35. doi: 10.1016/j.ymeth.2019.04.01531034882)

YuJSL, YusaK. Genome-wide CRISPR-Cas9 screening in mammalian cells. Methods. 2019;164–165: 29–35. doi: 10.1016/j.ymeth.2019.04.01531034882, YuJSL, YusaK. Genome-wide CRISPR-Cas9 screening in mammalian cells. Methods. 2019;164–165: 29–35. doi: 10.1016/j.ymeth.2019.04.01531034882

D. Bosnakovski, Zhaohui Xu, Eun Gang, C. Galindo, Mingju Liu, T. Şimşek, H. Garner, S. Agha‐Mohammadi, A. Tassin, F. Coppée, A. Belayew, R. Perlingeiro, M. Kyba (2008)

The EMBO Journal, 27

(LekA, ZhangY, WoodmanKG, HuangS, DeSimoneAM, CohenJ, et al. Applying genome-wide CRISPR-Cas9 screens for therapeutic discovery in facioscapulohumeral muscular dystrophy. Science Translational Medicine. 2020;12: 9–11. doi: 10.1126/scitranslmed.aay027132213627)

LekA, ZhangY, WoodmanKG, HuangS, DeSimoneAM, CohenJ, et al. Applying genome-wide CRISPR-Cas9 screens for therapeutic discovery in facioscapulohumeral muscular dystrophy. Science Translational Medicine. 2020;12: 9–11. doi: 10.1126/scitranslmed.aay027132213627, LekA, ZhangY, WoodmanKG, HuangS, DeSimoneAM, CohenJ, et al. Applying genome-wide CRISPR-Cas9 screens for therapeutic discovery in facioscapulohumeral muscular dystrophy. Science Translational Medicine. 2020;12: 9–11. doi: 10.1126/scitranslmed.aay027132213627

(JonesTI, HimedaCL, PerezDP, JonesPL. Large family cohorts of lymphoblastoid cells provide a new cellular model for investigating facioscapulohumeral muscular dystrophy. Neuromuscular Disorders. 2017;27: 221–238. doi: 10.1016/j.nmd.2016.12.00728161093)

JonesTI, HimedaCL, PerezDP, JonesPL. Large family cohorts of lymphoblastoid cells provide a new cellular model for investigating facioscapulohumeral muscular dystrophy. Neuromuscular Disorders. 2017;27: 221–238. doi: 10.1016/j.nmd.2016.12.00728161093, JonesTI, HimedaCL, PerezDP, JonesPL. Large family cohorts of lymphoblastoid cells provide a new cellular model for investigating facioscapulohumeral muscular dystrophy. Neuromuscular Disorders. 2017;27: 221–238. doi: 10.1016/j.nmd.2016.12.00728161093

(ChenEY, TanCM, KouY, DuanQ, WangZ, Meirelles GV., et al. Enrichr: Interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics. 2013;14. doi: 10.1186/1471-2105-14-1423323936)

ChenEY, TanCM, KouY, DuanQ, WangZ, Meirelles GV., et al. Enrichr: Interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics. 2013;14. doi: 10.1186/1471-2105-14-1423323936, ChenEY, TanCM, KouY, DuanQ, WangZ, Meirelles GV., et al. Enrichr: Interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics. 2013;14. doi: 10.1186/1471-2105-14-1423323936

Michelle Christian, T. Čermák, Erin Doyle, Clarice Schmidt, Feng Zhang, Aaron Hummel, A. Bogdanove, D. Voytas (2010)

Genetics, 186

(LoveMI, HuberW, AndersS. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology. 2014;15: 1–21. doi: 10.1186/s13059-014-0550-825516281)

LoveMI, HuberW, AndersS. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology. 2014;15: 1–21. doi: 10.1186/s13059-014-0550-825516281, LoveMI, HuberW, AndersS. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology. 2014;15: 1–21. doi: 10.1186/s13059-014-0550-825516281

(DixitM, AnsseauE, TassinA, WinokurS, ShiR, QianH, et al. DUX4, a candidate gene of facioscapulohumeral muscular dystrophy, encodes a transcriptional activator of PITX1. Proceedings of the National Academy of Sciences of the United States of America. 2007;104: 18157–18162. doi: 10.1073/pnas.070865910417984056)

DixitM, AnsseauE, TassinA, WinokurS, ShiR, QianH, et al. DUX4, a candidate gene of facioscapulohumeral muscular dystrophy, encodes a transcriptional activator of PITX1. Proceedings of the National Academy of Sciences of the United States of America. 2007;104: 18157–18162. doi: 10.1073/pnas.070865910417984056, DixitM, AnsseauE, TassinA, WinokurS, ShiR, QianH, et al. DUX4, a candidate gene of facioscapulohumeral muscular dystrophy, encodes a transcriptional activator of PITX1. Proceedings of the National Academy of Sciences of the United States of America. 2007;104: 18157–18162. doi: 10.1073/pnas.070865910417984056

D. Bosnakovski, Sunny Chan, Olivia Recht, L. Hartweck, Collin Gustafson, Laura Athman, D. Lowe, M. Kyba (2017)

Nature Communications, 8

(PastorelloE, CaoM, TrevisanCP. Atypical onset in a series of 122 cases with FacioScapuloHumeral Muscular Dystrophy. Clinical Neurology and Neurosurgery. 2012;114: 230–234. doi: 10.1016/j.clineuro.2011.10.02222079131)

PastorelloE, CaoM, TrevisanCP. Atypical onset in a series of 122 cases with FacioScapuloHumeral Muscular Dystrophy. Clinical Neurology and Neurosurgery. 2012;114: 230–234. doi: 10.1016/j.clineuro.2011.10.02222079131, PastorelloE, CaoM, TrevisanCP. Atypical onset in a series of 122 cases with FacioScapuloHumeral Muscular Dystrophy. Clinical Neurology and Neurosurgery. 2012;114: 230–234. doi: 10.1016/j.clineuro.2011.10.02222079131

C. Mussolino, Robert Morbitzer, Fabienne Lütge, N. Dannemann, T. Lahaye, T. Cathomen (2011)

Nucleic Acids Research, 39

(AnderssonBS, BeranM, PathakS, GoodacreA, BarlogieB, McCredieKB. Ph-positive chronic myeloid leukemia with near-haploid conversion in vivo and establishment of a continuously growing cell line with similar cytogenetic pattern. Cancer Genetics and Cytogenetics. 1987;24: 335–343. doi: 10.1016/0165-4608(87)90116-63466682)

AnderssonBS, BeranM, PathakS, GoodacreA, BarlogieB, McCredieKB. Ph-positive chronic myeloid leukemia with near-haploid conversion in vivo and establishment of a continuously growing cell line with similar cytogenetic pattern. Cancer Genetics and Cytogenetics. 1987;24: 335–343. doi: 10.1016/0165-4608(87)90116-63466682, AnderssonBS, BeranM, PathakS, GoodacreA, BarlogieB, McCredieKB. Ph-positive chronic myeloid leukemia with near-haploid conversion in vivo and establishment of a continuously growing cell line with similar cytogenetic pattern. Cancer Genetics and Cytogenetics. 1987;24: 335–343. doi: 10.1016/0165-4608(87)90116-63466682

Jennifer Whiddon, Ashlee Langford, Chao-Jen Wong, Jun Zhong, S. Tapscott (2017)

Nature genetics, 49

S. Jagannathan, Sean Shadle, R. Resnick, L. Snider, R. Tawil, S. Maarel, R. Bradley, S. Tapscott (2016)

Human molecular genetics, 25 20

(BibikovaM, GolicM, GolicKG, CarrollD. Targeted Chromosomal Cleavage and Mutagenesis in Drosophila Using Zinc-Finger Nucleases. Genetics. 2002;161: 1169–1175. doi: 10.1093/genetics/161.3.116912136019)

BibikovaM, GolicM, GolicKG, CarrollD. Targeted Chromosomal Cleavage and Mutagenesis in Drosophila Using Zinc-Finger Nucleases. Genetics. 2002;161: 1169–1175. doi: 10.1093/genetics/161.3.116912136019, BibikovaM, GolicM, GolicKG, CarrollD. Targeted Chromosomal Cleavage and Mutagenesis in Drosophila Using Zinc-Finger Nucleases. Genetics. 2002;161: 1169–1175. doi: 10.1093/genetics/161.3.116912136019

J. Carette, J. Pruszak, Malini Varadarajan, V. Blomen, S. Gokhale, F. Camargo, Marius Wernig, R. Jaenisch, T. Brummelkamp (2010)

Blood, 115 20

J. Soutourina (2017)

Nature Reviews Molecular Cell Biology, 19

(SniderL, GengLN, LemmersRJLF, KybaM, WareCB, NelsonAM, et al. Facioscapulohumeral dystrophy: Incomplete suppression of a retrotransposed gene. PLoS Genetics. 2010;6: 1–14. doi: 10.1371/journal.pgen.100118121060811)

SniderL, GengLN, LemmersRJLF, KybaM, WareCB, NelsonAM, et al. Facioscapulohumeral dystrophy: Incomplete suppression of a retrotransposed gene. PLoS Genetics. 2010;6: 1–14. doi: 10.1371/journal.pgen.100118121060811, SniderL, GengLN, LemmersRJLF, KybaM, WareCB, NelsonAM, et al. Facioscapulohumeral dystrophy: Incomplete suppression of a retrotransposed gene. PLoS Genetics. 2010;6: 1–14. doi: 10.1371/journal.pgen.100118121060811

(KuleshovMV., JonesMR, RouillardAD, FernandezNF, DuanQ, WangZ, et al. Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic acids research. 2016;44: W90–W97. doi: 10.1093/nar/gkw37727141961)

KuleshovMV., JonesMR, RouillardAD, FernandezNF, DuanQ, WangZ, et al. Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic acids research. 2016;44: W90–W97. doi: 10.1093/nar/gkw37727141961, KuleshovMV., JonesMR, RouillardAD, FernandezNF, DuanQ, WangZ, et al. Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic acids research. 2016;44: W90–W97. doi: 10.1093/nar/gkw37727141961

Sean Shadle, Jun Zhong, Amy Campbell, M. Conerly, S. Jagannathan, Chao-Jen Wong, Timothy Morello, S. Maarel, S. Tapscott (2017)

PLoS Genetics, 13

R. Barrangou, C. Fremaux, H. Deveau, Melissa Richards, P. Boyaval, S. Moineau, D. Romero, P. Horvath (2007)

Science, 315

M. Bibikova, D. Carroll, D. Segal, J. Trautman, Jeff Smith, Yang-Gyun Kim, S. Chandrasegaran (2001)

Molecular and Cellular Biology, 21

Petr Dmitriev, Y. Saada, Carla Dib, E. Ansseau, Ana Barat, Aline Hamade, P. Dessen, Thomas Robert, V. Lazar, R. Louzada, C. Dupuy, V. Zakharova, G. Carnac, M. Lipinski, Y. Vassetzky (2016)

Free radical biology & medicine, 99

(RashnonejadA, Amini-ChermahiniG, TaylorNK, WeinN, HarperSQ. Designed U7 snRNAs inhibit DUX4 expression and improve FSHD-associated outcomes in DUX4 overexpressing cells and FSHD patient myotubes. Molecular Therapy—Nucleic Acids. 2021;23: 476–486. doi: 10.1016/j.omtn.2020.12.00433510937)

RashnonejadA, Amini-ChermahiniG, TaylorNK, WeinN, HarperSQ. Designed U7 snRNAs inhibit DUX4 expression and improve FSHD-associated outcomes in DUX4 overexpressing cells and FSHD patient myotubes. Molecular Therapy—Nucleic Acids. 2021;23: 476–486. doi: 10.1016/j.omtn.2020.12.00433510937, RashnonejadA, Amini-ChermahiniG, TaylorNK, WeinN, HarperSQ. Designed U7 snRNAs inhibit DUX4 expression and improve FSHD-associated outcomes in DUX4 overexpressing cells and FSHD patient myotubes. Molecular Therapy—Nucleic Acids. 2021;23: 476–486. doi: 10.1016/j.omtn.2020.12.00433510937

V. Blomen, P. Májek, L. Jae, J. Bigenzahn, Joppe Nieuwenhuis, J. Staring, R. Sacco, Ferdy Diemen, N. Olk, Alexey Stukalov, C. Marceau, H. Janssen, J. Carette, K. Bennett, J. Colinge, G. Superti-Furga, T. Brummelkamp (2015)

Science, 350

A Lek (2020)

Science Translational Medicine, 12

S. Urlinger, U. Baron, Marion Thellmann, M. Hasan, H. Bujard, W. Hillen (2000)

Proceedings of the National Academy of Sciences of the United States of America, 97 14

M. Bibikova, Mary Golic, K. Golic, D. Carroll (2002)

Genetics, 161 3

L. Jae, M. Raaben, A. Herbert, A. Kuehne, A. Wirchnianski, Timothy Soh, S. Stubbs, H. Janssen, M. Damme, P. Saftig, S. Whelan, J. Dye, T. Brummelkamp (2014)

Science, 344

(RickardAM, PetekLM, MillerDG. Endogenous DUX4 expression in FSHD myotubes is sufficient to cause cell death and disrupts RNA splicing and cell migration pathways. Human Molecular Genetics. 2015;24: 5901–5914. doi: 10.1093/hmg/ddv31526246499)

RickardAM, PetekLM, MillerDG. Endogenous DUX4 expression in FSHD myotubes is sufficient to cause cell death and disrupts RNA splicing and cell migration pathways. Human Molecular Genetics. 2015;24: 5901–5914. doi: 10.1093/hmg/ddv31526246499, RickardAM, PetekLM, MillerDG. Endogenous DUX4 expression in FSHD myotubes is sufficient to cause cell death and disrupts RNA splicing and cell migration pathways. Human Molecular Genetics. 2015;24: 5901–5914. doi: 10.1093/hmg/ddv31526246499

MI Love (2014)

Genome Biology, 15

A. Rashnonejad, G. Amini-Chermahini, N. Taylor, N. Wein, S. Harper (2020)

Molecular Therapy. Nucleic Acids, 23

Y. Kim, Jooyeun Cha, S. Chandrasegaran (1996)

Proceedings of the National Academy of Sciences of the United States of America, 93 3

S. Choi, Micah Gearhart, Ziyou Cui, D. Bosnakovski, Minjee Kim, Natalie Schennum, M. Kyba (2016)

Nucleic Acids Research, 44

T. Dull, R. Zufferey, M. Kelly, R. Mandel, M. Nguyen, D. Trono, L. Naldini (1998)

Journal of Virology, 72

(TsumagariK, ChangSC, LaceyM, BaribaultC, ChitturS V., SowdenJ, et al. Gene expression during normal and FSHD myogenesis. BMC Medical Genomics. 2011;4. doi: 10.1186/1755-8794-4-421223598)

TsumagariK, ChangSC, LaceyM, BaribaultC, ChitturS V., SowdenJ, et al. Gene expression during normal and FSHD myogenesis. BMC Medical Genomics. 2011;4. doi: 10.1186/1755-8794-4-421223598, TsumagariK, ChangSC, LaceyM, BaribaultC, ChitturS V., SowdenJ, et al. Gene expression during normal and FSHD myogenesis. BMC Medical Genomics. 2011;4. doi: 10.1186/1755-8794-4-421223598

(LemmersRJLF, VlietPJ Van Der, KloosterR, CamañoP, DauwerseJG, SniderL, et al. A unifying genetic model for facioscapulohumeral muscular dystrophy. Science. 2010;329: 1650–1653. doi: 10.1126/science.118904420724583)

LemmersRJLF, VlietPJ Van Der, KloosterR, CamañoP, DauwerseJG, SniderL, et al. A unifying genetic model for facioscapulohumeral muscular dystrophy. Science. 2010;329: 1650–1653. doi: 10.1126/science.118904420724583, LemmersRJLF, VlietPJ Van Der, KloosterR, CamañoP, DauwerseJG, SniderL, et al. A unifying genetic model for facioscapulohumeral muscular dystrophy. Science. 2010;329: 1650–1653. doi: 10.1126/science.118904420724583

Maxime Ferreboeuf, V. Mariot, Bettina Bessières, Alexandre Vasiljevic, T. Attié-Bitach, Sophie Collardeau, J. Morere, S. Roche, F. Magdinier, Jérôme Robin-Ducellier, Philippe Rameau, Sandra Whalen, Claude Desnuelle, S. Sacconi, V. Mouly, G. Butler-Browne, J. Dumonceaux (2013)

Neuromuscular Disorders, 23

Rabi Tawil, S. Maarel (2006)

Muscle & Nerve, 34

LT Jae (2014)

, 340

(LiT, HuangS, JiangWZ, WrightD, SpaldingMH, WeeksDP, et al. TAL nucleases (TALNs): Hybrid proteins composed of TAL effectors and FokI DNA-cleavage domain.Nucleic Acids Research. 2011;39: 359–372. doi: 10.1093/nar/gkq70420699274)

LiT, HuangS, JiangWZ, WrightD, SpaldingMH, WeeksDP, et al. TAL nucleases (TALNs): Hybrid proteins composed of TAL effectors and FokI DNA-cleavage domain.Nucleic Acids Research. 2011;39: 359–372. doi: 10.1093/nar/gkq70420699274, LiT, HuangS, JiangWZ, WrightD, SpaldingMH, WeeksDP, et al. TAL nucleases (TALNs): Hybrid proteins composed of TAL effectors and FokI DNA-cleavage domain.Nucleic Acids Research. 2011;39: 359–372. doi: 10.1093/nar/gkq70420699274

(ShenMW, ArbabM, HsuJY, WorstellD, SannieJ, KrabbeO, et al. Predictable and precise template-free CRISPR editing of pathogenic variants. Nature. 2018;563: 646–651. doi: 10.1038/s41586-018-0686-x30405244)

ShenMW, ArbabM, HsuJY, WorstellD, SannieJ, KrabbeO, et al. Predictable and precise template-free CRISPR editing of pathogenic variants. Nature. 2018;563: 646–651. doi: 10.1038/s41586-018-0686-x30405244, ShenMW, ArbabM, HsuJY, WorstellD, SannieJ, KrabbeO, et al. Predictable and precise template-free CRISPR editing of pathogenic variants. Nature. 2018;563: 646–651. doi: 10.1038/s41586-018-0686-x30405244

(ChoiSH, GearhartMD, CuiZ, BosnakovskiD, KimM, SchennumN, et al. DUX4 recruits p300/CBP through its C-terminus and induces global H3K27 acetylation changes. Nucleic Acids Research. 2016;44: 5161–5173. doi: 10.1093/nar/gkw14126951377)

ChoiSH, GearhartMD, CuiZ, BosnakovskiD, KimM, SchennumN, et al. DUX4 recruits p300/CBP through its C-terminus and induces global H3K27 acetylation changes. Nucleic Acids Research. 2016;44: 5161–5173. doi: 10.1093/nar/gkw14126951377, ChoiSH, GearhartMD, CuiZ, BosnakovskiD, KimM, SchennumN, et al. DUX4 recruits p300/CBP through its C-terminus and induces global H3K27 acetylation changes. Nucleic Acids Research. 2016;44: 5161–5173. doi: 10.1093/nar/gkw14126951377

(FerreboeufM, MariotV, BessièresB, VasiljevicA, Attié-BitachT, CollardeauS, et al. DUX4 and DUX4 downstream target genes are expressed in fetal FSHD muscles. Human Molecular Genetics. 2014;23: 171–181. doi: 10.1093/hmg/ddt40923966205)

FerreboeufM, MariotV, BessièresB, VasiljevicA, Attié-BitachT, CollardeauS, et al. DUX4 and DUX4 downstream target genes are expressed in fetal FSHD muscles. Human Molecular Genetics. 2014;23: 171–181. doi: 10.1093/hmg/ddt40923966205, FerreboeufM, MariotV, BessièresB, VasiljevicA, Attié-BitachT, CollardeauS, et al. DUX4 and DUX4 downstream target genes are expressed in fetal FSHD muscles. Human Molecular Genetics. 2014;23: 171–181. doi: 10.1093/hmg/ddt40923966205

G. Cullot, J. Boutin, J. Toutain, F. Prat, P. Pennamen, C. Rooryck, Martin Teichmann, Emilie Rousseau, I. Lamrissi‐Garcia, V. Guyonnet-Duperat, Alice Bibeyran, Magalie Lalanne, V. Prouzet-Mauléon, B. Turcq, C. Ged, J. Blouin, E. Richard, S. Dabernat, F. Moreau-Gaudry, A. Bedel (2019)

Nature Communications, 10

(UrasakiA, MorvanG, KawakamiK. Functional dissection of the Tol2 transposable element identified the minimal cis-sequence and a highly repetitive sequence in the subterminal region essential for transposition. Genetics. 2006;174: 639–649. doi: 10.1534/genetics.106.06024416959904)

UrasakiA, MorvanG, KawakamiK. Functional dissection of the Tol2 transposable element identified the minimal cis-sequence and a highly repetitive sequence in the subterminal region essential for transposition. Genetics. 2006;174: 639–649. doi: 10.1534/genetics.106.06024416959904, UrasakiA, MorvanG, KawakamiK. Functional dissection of the Tol2 transposable element identified the minimal cis-sequence and a highly repetitive sequence in the subterminal region essential for transposition. Genetics. 2006;174: 639–649. doi: 10.1534/genetics.106.06024416959904

(WinokurST, ChenYW, MasnyPS, MartinJH, EhmsenJT, TapscottSJ, et al. Expression profiling of FSHD muscle supports a defect in specific stages of myogenic differentiation. Human Molecular Genetics. 2003;12: 2895–2907. doi: 10.1093/hmg/ddg32714519683)

WinokurST, ChenYW, MasnyPS, MartinJH, EhmsenJT, TapscottSJ, et al. Expression profiling of FSHD muscle supports a defect in specific stages of myogenic differentiation. Human Molecular Genetics. 2003;12: 2895–2907. doi: 10.1093/hmg/ddg32714519683, WinokurST, ChenYW, MasnyPS, MartinJH, EhmsenJT, TapscottSJ, et al. Expression profiling of FSHD muscle supports a defect in specific stages of myogenic differentiation. Human Molecular Genetics. 2003;12: 2895–2907. doi: 10.1093/hmg/ddg32714519683

Daniel Wolfe, S. Dudek, M. Ritchie, S. Pendergrass (2013)

BioData Mining, 6

(IacoA De, PlanetE, ColuccioA, VerpS, DucJ, TronoD. A family of double-homeodomain transcription factors regulates zygotic genome activation in placental mammals.Nature Genetics. 2017;49: 941–945. doi: 10.1038/ng.385828459456)

IacoA De, PlanetE, ColuccioA, VerpS, DucJ, TronoD. A family of double-homeodomain transcription factors regulates zygotic genome activation in placental mammals.Nature Genetics. 2017;49: 941–945. doi: 10.1038/ng.385828459456, IacoA De, PlanetE, ColuccioA, VerpS, DucJ, TronoD. A family of double-homeodomain transcription factors regulates zygotic genome activation in placental mammals.Nature Genetics. 2017;49: 941–945. doi: 10.1038/ng.385828459456

(UrlingerS, BaronU, ThellmannM, HasanMT, BujardH, HillenW. Exploring the sequence space for tetracycline-dependent transcriptional activators: Novel mutations yield expanded range and sensitivity. Proceedings of the National Academy of Sciences of the United States of America. 2000;97: 7963–7968. doi: 10.1073/pnas.13019219710859354)

UrlingerS, BaronU, ThellmannM, HasanMT, BujardH, HillenW. Exploring the sequence space for tetracycline-dependent transcriptional activators: Novel mutations yield expanded range and sensitivity. Proceedings of the National Academy of Sciences of the United States of America. 2000;97: 7963–7968. doi: 10.1073/pnas.13019219710859354, UrlingerS, BaronU, ThellmannM, HasanMT, BujardH, HillenW. Exploring the sequence space for tetracycline-dependent transcriptional activators: Novel mutations yield expanded range and sensitivity. Proceedings of the National Academy of Sciences of the United States of America. 2000;97: 7963–7968. doi: 10.1073/pnas.13019219710859354

Manjusha Dixit, E. Ansseau, A. Tassin, S. Winokur, R. Shi, H. Qian, S. Sauvage, C. Mattéotti, A. Acker, O. Leo, D. Figlewicz, M. Barro, D. Laoudj-Chenivesse, A. Belayew, F. Coppée, Yi-Wen Chen (2007)

Proceedings of the National Academy of Sciences, 104

C. Himeda, T. Jones, Peter Jones (2016)

Molecular therapy : the journal of the American Society of Gene Therapy, 24 3

J. Deenen, Hisse Arnts, S. Maarel, G. Padberg, J. Verschuuren, E. Bakker, S. Weinreich, A. Verbeek, B. Engelen (2014)

Neurology, 83

(RongY, NakamuraS, HirataT, MotookaD, LiuYS, HeZA, et al. Genome-wide screening of genes required for glycosylphosphatidylinositol biosynthesis.PLoS ONE. 2015;10: 1–18. doi: 10.1371/journal.pone.013855326383639)

RongY, NakamuraS, HirataT, MotookaD, LiuYS, HeZA, et al. Genome-wide screening of genes required for glycosylphosphatidylinositol biosynthesis.PLoS ONE. 2015;10: 1–18. doi: 10.1371/journal.pone.013855326383639, RongY, NakamuraS, HirataT, MotookaD, LiuYS, HeZA, et al. Genome-wide screening of genes required for glycosylphosphatidylinositol biosynthesis.PLoS ONE. 2015;10: 1–18. doi: 10.1371/journal.pone.013855326383639

R. Mezzadra, Marjolein Bruijn, L. Jae, R. Gomez-Eerland, Anja Duursma, F. Scheeren, T. Brummelkamp, T. Schumacher (2019)

PLoS ONE, 14

Jeffrey Smith, Marina Bibikova, Frank Whitby, Attipalli Reddy, Attipalli Reddy, S. Chandrasegaran, Dana Carroll (2000)

Nucleic acids research, 28 17

E Ansseau (2017)

Antisense oligonucleotides used to target the DUX4 mRNA as therapeutic approaches in faciosscapulohumeral muscular dystrophy

(BosnakovskiD, TosoEA, HartweckLM, MagliA, LeeHA, ThompsonER, et al. The DUX4 homeodomains mediate inhibition of myogenesis and are functionally exchangeable with the Pax7 homeodomain. Journal of Cell Science. 2017;130: 3685–3697. doi: 10.1242/jcs.20542728935672)

BosnakovskiD, TosoEA, HartweckLM, MagliA, LeeHA, ThompsonER, et al. The DUX4 homeodomains mediate inhibition of myogenesis and are functionally exchangeable with the Pax7 homeodomain. Journal of Cell Science. 2017;130: 3685–3697. doi: 10.1242/jcs.20542728935672, BosnakovskiD, TosoEA, HartweckLM, MagliA, LeeHA, ThompsonER, et al. The DUX4 homeodomains mediate inhibition of myogenesis and are functionally exchangeable with the Pax7 homeodomain. Journal of Cell Science. 2017;130: 3685–3697. doi: 10.1242/jcs.20542728935672

(MorgensDW, DeansRM, LiA, BassikMC. Systematic comparison of CRISPR/Cas9 and RNAi screens for essential genes. Nature Biotechnology. 2016;34: 634–636. doi: 10.1038/nbt.3567)

MorgensDW, DeansRM, LiA, BassikMC. Systematic comparison of CRISPR/Cas9 and RNAi screens for essential genes. Nature Biotechnology. 2016;34: 634–636. doi: 10.1038/nbt.3567, MorgensDW, DeansRM, LiA, BassikMC. Systematic comparison of CRISPR/Cas9 and RNAi screens for essential genes. Nature Biotechnology. 2016;34: 634–636. doi: 10.1038/nbt.3567

R. Luteijn, Ferdy Diemen, V. Blomen, I. Boer, Saravanan Sadasivam, T. Kuppevelt, I. Drexler, T. Brummelkamp, R. Lebbink, E. Wiertz (2019)

Journal of Virology, 93

P. Papatheodorou, J. Carette, G. Bell, Carsten Schwan, G. Guttenberg, T. Brummelkamp, K. Aktories (2011)

Proceedings of the National Academy of Sciences, 108

(DullT, ZuffereyR, KellyM, MandelRJ, NguyenM, TronoD, et al. A third-generation lentivirus vector with a conditional packaging system. Journal of virology. 1998;72: 8463–71. doi: 10.1128/JVI.72.11.8463-8471.19989765382)

DullT, ZuffereyR, KellyM, MandelRJ, NguyenM, TronoD, et al. A third-generation lentivirus vector with a conditional packaging system. Journal of virology. 1998;72: 8463–71. doi: 10.1128/JVI.72.11.8463-8471.19989765382, DullT, ZuffereyR, KellyM, MandelRJ, NguyenM, TronoD, et al. A third-generation lentivirus vector with a conditional packaging system. Journal of virology. 1998;72: 8463–71. doi: 10.1128/JVI.72.11.8463-8471.19989765382

A. Iaco, E. Planet, Andrea Coluccio, Sonia Verp, Julien Duc, D. Trono (2017)

Nature genetics, 49

Amanda Rickard, Lisa Petek, Daniel Miller (2015)

Human molecular genetics, 24 20

P. Hendrickson, J. Dorais, J. Dorais, Edward Grow, Jennifer Whiddon, Jong-won Lim, Candice Wike, Bradley Weaver, Christian Pflueger, B. Emery, A. Wilcox, D. Nix, C. Peterson, S. Tapscott, D. Carrell, B. Cairns (2017)

Nature genetics, 49

Tingyu Li, Sheng Huang, W. Jiang, D. Wright, M. Spalding, D. Weeks, Bing Yang (2010)

Nucleic Acids Research, 39

(DeenenJCW, ArntsH, Van Der MaarelSM, PadbergGW, VerschuurenJJGM, BakkerE, et al. Population-based incidence and prevalence of facioscapulohumeral dystrophy. Neurology. 2014;83: 1056–1059. doi: 10.1212/WNL.000000000000079725122204)

DeenenJCW, ArntsH, Van Der MaarelSM, PadbergGW, VerschuurenJJGM, BakkerE, et al. Population-based incidence and prevalence of facioscapulohumeral dystrophy. Neurology. 2014;83: 1056–1059. doi: 10.1212/WNL.000000000000079725122204, DeenenJCW, ArntsH, Van Der MaarelSM, PadbergGW, VerschuurenJJGM, BakkerE, et al. Population-based incidence and prevalence of facioscapulohumeral dystrophy. Neurology. 2014;83: 1056–1059. doi: 10.1212/WNL.000000000000079725122204

E. Chen, Christopher Tan, Y. Kou, Qiaonan Duan, Zichen Wang, G. Meirelles, N. Clark, Avi Ma’ayan (2013)

BMC Bioinformatics, 14

D. Bosnakovski, S. Choi, J. Strasser, E. Toso, M. Walters, M. Kyba (2014)

Skeletal Muscle, 4

(SansonKR, HannaRE, HegdeM, DonovanKF, StrandC, SullenderME, et al. Optimized libraries for CRISPR-Cas9 genetic screens with multiple modalities. Nature Communications. 2018;9: 1–15. doi: 10.1038/s41467-017-02088-w29317637)

SansonKR, HannaRE, HegdeM, DonovanKF, StrandC, SullenderME, et al. Optimized libraries for CRISPR-Cas9 genetic screens with multiple modalities. Nature Communications. 2018;9: 1–15. doi: 10.1038/s41467-017-02088-w29317637, SansonKR, HannaRE, HegdeM, DonovanKF, StrandC, SullenderME, et al. Optimized libraries for CRISPR-Cas9 genetic screens with multiple modalities. Nature Communications. 2018;9: 1–15. doi: 10.1038/s41467-017-02088-w29317637

N. Gerhards, V. Blomen, M. Mutlu, Joppe Nieuwenhuis, D. Howald, C. Guyader, J. Jonkers, T. Brummelkamp, S. Rottenberg (2018)

Molecular Oncology, 12

(MussolinoC, MorbitzerR, LütgeF, DannemannN, LahayeT, CathomenT. A novel TALE nuclease scaffold enables high genome editing activity in combination with low toxicity. Nucleic Acids Research. 2011;39: 9283–9293. doi: 10.1093/nar/gkr59721813459)

MussolinoC, MorbitzerR, LütgeF, DannemannN, LahayeT, CathomenT. A novel TALE nuclease scaffold enables high genome editing activity in combination with low toxicity. Nucleic Acids Research. 2011;39: 9283–9293. doi: 10.1093/nar/gkr59721813459, MussolinoC, MorbitzerR, LütgeF, DannemannN, LahayeT, CathomenT. A novel TALE nuclease scaffold enables high genome editing activity in combination with low toxicity. Nucleic Acids Research. 2011;39: 9283–9293. doi: 10.1093/nar/gkr59721813459

T. Jones, C. Himeda, D. Perez, Peter Jones (2017)

Neuromuscular Disorders, 27

(WolfeD, DudekS, RitchieMD, PendergrassSA. Visualizing genomic information across chromosomes with PhenoGram. BioData Mining. 2013;6: 1–12. doi: 10.1186/1756-0381-6-123294634)

WolfeD, DudekS, RitchieMD, PendergrassSA. Visualizing genomic information across chromosomes with PhenoGram. BioData Mining. 2013;6: 1–12. doi: 10.1186/1756-0381-6-123294634, WolfeD, DudekS, RitchieMD, PendergrassSA. Visualizing genomic information across chromosomes with PhenoGram. BioData Mining. 2013;6: 1–12. doi: 10.1186/1756-0381-6-123294634

John Doench, Nicoló Fusi, Meagan Sullender, Mudra Hegde, Emma Vaimberg, Katherine Donovan, Ian Smith, Z. Tothova, Craig Wilen, R. Orchard, H. Virgin, J. Listgarten, D. Root (2015)

Nature biotechnology, 34

Yao Rong, S. Nakamura, T. Hirata, D. Motooka, Yi-Shi Liu, Zeng’an He, Xiao-Dong Gao, Y. Maeda, T. Kinosh*ta, Morihisa Fujita (2015)

PLoS ONE, 10

(GengLN, YaoZ, SniderL, FongAP, CechJN, YoungJM, et al. DUX4 Activates Germline Genes, Retroelements, and Immune Mediators: Implications for Facioscapulohumeral Dystrophy. Developmental Cell. 2012;22: 38–51. doi: 10.1016/j.devcel.2011.11.01322209328)

GengLN, YaoZ, SniderL, FongAP, CechJN, YoungJM, et al. DUX4 Activates Germline Genes, Retroelements, and Immune Mediators: Implications for Facioscapulohumeral Dystrophy. Developmental Cell. 2012;22: 38–51. doi: 10.1016/j.devcel.2011.11.01322209328, GengLN, YaoZ, SniderL, FongAP, CechJN, YoungJM, et al. DUX4 Activates Germline Genes, Retroelements, and Immune Mediators: Implications for Facioscapulohumeral Dystrophy. Developmental Cell. 2012;22: 38–51. doi: 10.1016/j.devcel.2011.11.01322209328

C. Banerji, M. Panamarova, P. Zammit (2019)

bioRxiv

Christelle Robert, M. Watson (2015)

Genome Biology, 16

(BibikovaM, CarrollD, SegalDJ, TrautmanJK, SmithJ, KimY-G, et al. Stimulation of hom*ologous Recombination through Targeted Cleavage by Chimeric Nucleases. Molecular and Cellular Biology. 2001;21: 289–297. doi: 10.1128/MCB.21.1.289-297.200111113203)

BibikovaM, CarrollD, SegalDJ, TrautmanJK, SmithJ, KimY-G, et al. Stimulation of hom*ologous Recombination through Targeted Cleavage by Chimeric Nucleases. Molecular and Cellular Biology. 2001;21: 289–297. doi: 10.1128/MCB.21.1.289-297.200111113203, BibikovaM, CarrollD, SegalDJ, TrautmanJK, SmithJ, KimY-G, et al. Stimulation of hom*ologous Recombination through Targeted Cleavage by Chimeric Nucleases. Molecular and Cellular Biology. 2001;21: 289–297. doi: 10.1128/MCB.21.1.289-297.200111113203

(BosnakovskiD, GearhartMD, TosoEA, RechtOO, CucakA, JainAK, et al. p53-independent DUX4 pathology in cell and animal models of facioscapulohumeral muscular dystrophy. DMM Disease Models and Mechanisms. 2017;10: 1211–1216. doi: 10.1242/dmm.03006428754837)

BosnakovskiD, GearhartMD, TosoEA, RechtOO, CucakA, JainAK, et al. p53-independent DUX4 pathology in cell and animal models of facioscapulohumeral muscular dystrophy. DMM Disease Models and Mechanisms. 2017;10: 1211–1216. doi: 10.1242/dmm.03006428754837, BosnakovskiD, GearhartMD, TosoEA, RechtOO, CucakA, JainAK, et al. p53-independent DUX4 pathology in cell and animal models of facioscapulohumeral muscular dystrophy. DMM Disease Models and Mechanisms. 2017;10: 1211–1216. doi: 10.1242/dmm.03006428754837

(KimYG, KimPS, HerbertA, RichA. Construction of a Z-DNA-specific restriction endonuclease. Proceedings of the National Academy of Sciences of the United States of America. 1997;94: 12875–12879. doi: 10.1073/pnas.94.24.128759371768)

KimYG, KimPS, HerbertA, RichA. Construction of a Z-DNA-specific restriction endonuclease. Proceedings of the National Academy of Sciences of the United States of America. 1997;94: 12875–12879. doi: 10.1073/pnas.94.24.128759371768, KimYG, KimPS, HerbertA, RichA. Construction of a Z-DNA-specific restriction endonuclease. Proceedings of the National Academy of Sciences of the United States of America. 1997;94: 12875–12879. doi: 10.1073/pnas.94.24.128759371768

(SmithJ, BibikovaM, WhitbyF, ReddyA, ChandrasegaranS, CarrollD. Requirements for double-strand cleavage by chimeric restriction enzymes with zinc finger DNA-recognition domains. Nucleic Acids Research. 2000;28: 3361–3369. doi: 10.1093/nar/28.17.336110954606)

SmithJ, BibikovaM, WhitbyF, ReddyA, ChandrasegaranS, CarrollD. Requirements for double-strand cleavage by chimeric restriction enzymes with zinc finger DNA-recognition domains. Nucleic Acids Research. 2000;28: 3361–3369. doi: 10.1093/nar/28.17.336110954606, SmithJ, BibikovaM, WhitbyF, ReddyA, ChandrasegaranS, CarrollD. Requirements for double-strand cleavage by chimeric restriction enzymes with zinc finger DNA-recognition domains. Nucleic Acids Research. 2000;28: 3361–3369. doi: 10.1093/nar/28.17.336110954606

(Agha-Mohammadi S, O’MalleyM, EtemadA, WangZ, XiaoX, LotzeMT. Second-generation tetracycline-regulatable promoter: Repositioned tet operator elements optimize transactivator synergy while shorter minimal promoter offers tight basal leakiness. Journal of Gene Medicine. 2004;6: 817–828. doi: 10.1002/jgm.56615241789)

Agha-Mohammadi S, O’MalleyM, EtemadA, WangZ, XiaoX, LotzeMT. Second-generation tetracycline-regulatable promoter: Repositioned tet operator elements optimize transactivator synergy while shorter minimal promoter offers tight basal leakiness. Journal of Gene Medicine. 2004;6: 817–828. doi: 10.1002/jgm.56615241789, Agha-Mohammadi S, O’MalleyM, EtemadA, WangZ, XiaoX, LotzeMT. Second-generation tetracycline-regulatable promoter: Repositioned tet operator elements optimize transactivator synergy while shorter minimal promoter offers tight basal leakiness. Journal of Gene Medicine. 2004;6: 817–828. doi: 10.1002/jgm.56615241789

C. Banerji, P. Knopp, L. Moyle, S. Severini, R. Orrell, A. Teschendorff, P. Zammit (2015)

Journal of The Royal Society Interface, 12

M. Jinek, Alexandra East, Aaron Cheng, Steven Lin, E. Ma, J. Doudna (2013)

eLife, 2

D Bosnakovski (2017)

DMM Disease Models and Mechanisms, 10

(WhiddonJL, LangfordAT, WongCJ, ZhongJW, TapscottSJ. Conservation and innovation in the DUX4-family gene network. Nature Genetics. 2017;49: 935–940. doi: 10.1038/ng.384628459454)

WhiddonJL, LangfordAT, WongCJ, ZhongJW, TapscottSJ. Conservation and innovation in the DUX4-family gene network. Nature Genetics. 2017;49: 935–940. doi: 10.1038/ng.384628459454, WhiddonJL, LangfordAT, WongCJ, ZhongJW, TapscottSJ. Conservation and innovation in the DUX4-family gene network. Nature Genetics. 2017;49: 935–940. doi: 10.1038/ng.384628459454

K Tsumagari (2011)

BMC Medical Genomics

R. Lemmers, Patrick Vliet, J. Balog, J. Goeman, W. Arindrarto, Y. Krom, K. Straasheijm, Rashmie Debipersad, Gizem Özel, J. Sowden, L. Snider, K. Mul, S. Sacconi, B. Engelen, S. Tapscott, R. Tawil, S. Maarel (2017)

European Journal of Human Genetics, 26

JSL Yu (2019)

Genome-wide CRISPR-Cas9 screening in mammalian cells

Jeffrey Miller, Siyuan Tan, Guijuan Qiao, Kyle Barlow, Jianbin Wang, Danny Xia, Xiangdong Meng, David Paschon, Elo Leung, Sarah Hinkley, Gladys Dulay, Kevin Hua, Irina Ankoudinova, G. Cost, F. Urnov, Steve Zhang, M. Holmes, Lei Zhang, P. Gregory, E. Rebar (2011)

Nature Biotechnology, 29

(FengQ, SniderL, JagannathanS, TawilR, van der MaarelSM, TapscottSJ, et al. A feedback loop between nonsense-mediated decay and the retrogene DUX4 in facioscapulohumeral muscular dystrophy.eLife. 2015;2015: 1–13. doi: 10.7554/eLife.0499625564732)

FengQ, SniderL, JagannathanS, TawilR, van der MaarelSM, TapscottSJ, et al. A feedback loop between nonsense-mediated decay and the retrogene DUX4 in facioscapulohumeral muscular dystrophy.eLife. 2015;2015: 1–13. doi: 10.7554/eLife.0499625564732, FengQ, SniderL, JagannathanS, TawilR, van der MaarelSM, TapscottSJ, et al. A feedback loop between nonsense-mediated decay and the retrogene DUX4 in facioscapulohumeral muscular dystrophy.eLife. 2015;2015: 1–13. doi: 10.7554/eLife.0499625564732

RD Luteijn (2019)

Journal of Virology

Patrick Essletzbichler, T. Konopka, Federica Santoro, Doris Chen, Bianca Gapp, R. Kralovics, T. Brummelkamp, S. Nijman, T. Bürckstümmer (2014)

Genome Research, 24

Koji Tsumagari, Shao-Chi Chang, M. Lacey, Carl Baribault, S. Chittur, J. Sowden, R. Tawil, G. Crawford, M. Ehrlich (2011)

BMC Medical Genomics, 4

G. Gasiunas, R. Barrangou, P. Horvath, V. Šikšnys (2012)

Proceedings of the National Academy of Sciences, 109

(GerhardsNM, BlomenVA, MutluM, NieuwenhuisJ, HowaldD, GuyaderC, et al. Haploid genetic screens identify genetic vulnerabilities to microtubule-targeting agents. Molecular Oncology. 2018;12: 953–971. doi: 10.1002/1878-0261.1230729689640)

GerhardsNM, BlomenVA, MutluM, NieuwenhuisJ, HowaldD, GuyaderC, et al. Haploid genetic screens identify genetic vulnerabilities to microtubule-targeting agents. Molecular Oncology. 2018;12: 953–971. doi: 10.1002/1878-0261.1230729689640, GerhardsNM, BlomenVA, MutluM, NieuwenhuisJ, HowaldD, GuyaderC, et al. Haploid genetic screens identify genetic vulnerabilities to microtubule-targeting agents. Molecular Oncology. 2018;12: 953–971. doi: 10.1002/1878-0261.1230729689640

S. Vuoristo, C. Hydén-Granskog, M. Yoshihara, L. Gawriyski, A. Damdimopoulos, S. Bhagat, K. Hashimoto, K. Krjutškov, S. Ezer, P. Paluoja, K. Lundin, P. Paloviita, G. Recher, Vipin Ranga, T. Airenne, Mahlet Tamirat, Eeva-Mari Jouhilahti, T. Otonkoski, J. Tapanainen, H. Kawaji, Y. Murakawa, T. Bürglin, M. Varjosalo, Mark Johnson, T. Tuuri, S. Katayama, J. Kere (2019)

bioRxiv

(HendricksonPG, DoráisJA, GrowEJ, WhiddonJL, LimJW, WikeCL, et al. Conserved roles of mouse DUX and human DUX4 in activating cleavage-stage genes and MERVL/HERVL retrotransposons. Nature Genetics. 2017;49: 925–934. doi: 10.1038/ng.384428459457)

HendricksonPG, DoráisJA, GrowEJ, WhiddonJL, LimJW, WikeCL, et al. Conserved roles of mouse DUX and human DUX4 in activating cleavage-stage genes and MERVL/HERVL retrotransposons. Nature Genetics. 2017;49: 925–934. doi: 10.1038/ng.384428459457, HendricksonPG, DoráisJA, GrowEJ, WhiddonJL, LimJW, WikeCL, et al. Conserved roles of mouse DUX and human DUX4 in activating cleavage-stage genes and MERVL/HERVL retrotransposons. Nature Genetics. 2017;49: 925–934. doi: 10.1038/ng.384428459457

M van Attekum (2016)

Cell Death Discovery

DW Morgens (2016)

Nature Biotechnology, 34

(DoenchJG, FusiN, SullenderM, HegdeM, VaimbergEW, DonovanKF, et al. Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nature Biotechnology. 2016;34: 184–191. doi: 10.1038/nbt.343726780180)

DoenchJG, FusiN, SullenderM, HegdeM, VaimbergEW, DonovanKF, et al. Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nature Biotechnology. 2016;34: 184–191. doi: 10.1038/nbt.343726780180, DoenchJG, FusiN, SullenderM, HegdeM, VaimbergEW, DonovanKF, et al. Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nature Biotechnology. 2016;34: 184–191. doi: 10.1038/nbt.343726780180

(JaeLT, RaabenM, HerbertAS, KuehneAI, WirchnianskiAS, SohTK, et al. Lassa virus entry requires a trigger-induced receptor switch. Science. 2014;344: 1506–1510. doi: 10.1126/science.125248024970085)

JaeLT, RaabenM, HerbertAS, KuehneAI, WirchnianskiAS, SohTK, et al. Lassa virus entry requires a trigger-induced receptor switch. Science. 2014;344: 1506–1510. doi: 10.1126/science.125248024970085, JaeLT, RaabenM, HerbertAS, KuehneAI, WirchnianskiAS, SohTK, et al. Lassa virus entry requires a trigger-induced receptor switch. Science. 2014;344: 1506–1510. doi: 10.1126/science.125248024970085

D. Bosnakovski, E. Toso, L. Hartweck, A. Magli, Heather Lee, Eliza Thompson, A. Dandapat, R. Perlingeiro, M. Kyba (2017)

Journal of Cell Science, 130

(Van Den HeuvelA, MahfouzA, KloetSL, BalogJ, Van EngelenBGM, TawilR, et al. Single-cell RNA sequencing in facioscapulohumeral muscular dystrophy disease etiology and development. Human Molecular Genetics. 2019;28: 1064–1075. doi: 10.1093/hmg/ddy40030445587)

Van Den HeuvelA, MahfouzA, KloetSL, BalogJ, Van EngelenBGM, TawilR, et al. Single-cell RNA sequencing in facioscapulohumeral muscular dystrophy disease etiology and development. Human Molecular Genetics. 2019;28: 1064–1075. doi: 10.1093/hmg/ddy40030445587, Van Den HeuvelA, MahfouzA, KloetSL, BalogJ, Van EngelenBGM, TawilR, et al. Single-cell RNA sequencing in facioscapulohumeral muscular dystrophy disease etiology and development. Human Molecular Genetics. 2019;28: 1064–1075. doi: 10.1093/hmg/ddy40030445587

(GasiunasG, BarrangouR, HorvathP, SiksnysV. Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proceedings of the National Academy of Sciences of the United States of America. 2012;109: 2579–2586. doi: 10.1073/pnas.110939710922308331)

GasiunasG, BarrangouR, HorvathP, SiksnysV. Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proceedings of the National Academy of Sciences of the United States of America. 2012;109: 2579–2586. doi: 10.1073/pnas.110939710922308331, GasiunasG, BarrangouR, HorvathP, SiksnysV. Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proceedings of the National Academy of Sciences of the United States of America. 2012;109: 2579–2586. doi: 10.1073/pnas.110939710922308331

(SoutourinaJ.Transcription regulation by the Mediator complex. Nature Reviews Molecular Cell Biology. 2018;19: 262–274. doi: 10.1038/nrm.2017.11529209056)

SoutourinaJ.Transcription regulation by the Mediator complex. Nature Reviews Molecular Cell Biology. 2018;19: 262–274. doi: 10.1038/nrm.2017.11529209056, SoutourinaJ.Transcription regulation by the Mediator complex. Nature Reviews Molecular Cell Biology. 2018;19: 262–274. doi: 10.1038/nrm.2017.11529209056

(BanerjiCRS, PanamarovaM, HebaishiH, WhiteRB, RelaixF, SeveriniS, et al. PAX7 target genes are globally repressed in facioscapulohumeral muscular dystrophy skeletal muscle. Nature Communications. 2017;8. doi: 10.1038/s41467-017-00021-928364116)

BanerjiCRS, PanamarovaM, HebaishiH, WhiteRB, RelaixF, SeveriniS, et al. PAX7 target genes are globally repressed in facioscapulohumeral muscular dystrophy skeletal muscle. Nature Communications. 2017;8. doi: 10.1038/s41467-017-00021-928364116, BanerjiCRS, PanamarovaM, HebaishiH, WhiteRB, RelaixF, SeveriniS, et al. PAX7 target genes are globally repressed in facioscapulohumeral muscular dystrophy skeletal muscle. Nature Communications. 2017;8. doi: 10.1038/s41467-017-00021-928364116

D. Bosnakovski, Micah Gearhart, E. Toso, Olivia Recht, Anja Cucak, Abhinav Jain, M. Barton, M. Kyba (2017)

Disease Models & Mechanisms, 10

(RobertC, WatsonM. Errors in RNA-Seq quantification affect genes of relevance to human disease. Genome Biology. 2015;16: 1–16. doi: 10.1186/s13059-014-0572-225583448)

RobertC, WatsonM. Errors in RNA-Seq quantification affect genes of relevance to human disease. Genome Biology. 2015;16: 1–16. doi: 10.1186/s13059-014-0572-225583448, RobertC, WatsonM. Errors in RNA-Seq quantification affect genes of relevance to human disease. Genome Biology. 2015;16: 1–16. doi: 10.1186/s13059-014-0572-225583448

(GrünD, LyubimovaA, KesterL, WiebrandsK, BasakO, SasakiN, et al. Single-cell messenger RNA sequencing reveals rare intestinal cell types. Nature. 2015;525: 251–255. doi: 10.1038/nature1496626287467)

GrünD, LyubimovaA, KesterL, WiebrandsK, BasakO, SasakiN, et al. Single-cell messenger RNA sequencing reveals rare intestinal cell types. Nature. 2015;525: 251–255. doi: 10.1038/nature1496626287467, GrünD, LyubimovaA, KesterL, WiebrandsK, BasakO, SasakiN, et al. Single-cell messenger RNA sequencing reveals rare intestinal cell types. Nature. 2015;525: 251–255. doi: 10.1038/nature1496626287467

(KimYG, ChaJ, ChandrasegaranS. Hybrid restriction enzymes: Zinc finger fusions to Fok I cleavage domain. Proceedings of the National Academy of Sciences of the United States of America. 1996;93: 1156–1160. doi: 10.1073/pnas.93.3.11568577732)

KimYG, ChaJ, ChandrasegaranS. Hybrid restriction enzymes: Zinc finger fusions to Fok I cleavage domain. Proceedings of the National Academy of Sciences of the United States of America. 1996;93: 1156–1160. doi: 10.1073/pnas.93.3.11568577732, KimYG, ChaJ, ChandrasegaranS. Hybrid restriction enzymes: Zinc finger fusions to Fok I cleavage domain. Proceedings of the National Academy of Sciences of the United States of America. 1996;93: 1156–1160. doi: 10.1073/pnas.93.3.11568577732

(2015)