pHR-SFFV-dCas9-BFP-KRAB Citations (88)
Originally described in: CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes.Gilbert LA, Larson MH, Morsut L, Liu Z, Brar GA, Torres SE, Stern-Ginossar N, Brandman O, Whitehead EH, Doudna JA, Lim WA, Weissman JS, Qi LS Cell. 2013 Jul 9. pii: S0092-8674(13)00826-X. doi: 10.1016/j.cell.2013.06.044. PubMed Journal
Articles Citing pHR-SFFV-dCas9-BFP-KRAB
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| Engineering synthetic TALE and CRISPR/Cas9 transcription factors for regulating gene expression. Kabadi AM, Gersbach CA. Methods. 2014 Sep;69(2):188-97. doi: 10.1016/j.ymeth.2014.06.014. Epub 2014 Jul 8. PubMed |
| Comparison of TALE designer transcription factors and the CRISPR/dCas9 in regulation of gene expression by targeting enhancers. Gao X, Tsang JC, Gaba F, Wu D, Lu L, Liu P. Nucleic Acids Res. 2014 Nov 10;42(20):e155. doi: 10.1093/nar/gku836. Epub 2014 Sep 15. PubMed |
| Contributions of unique intracellular domains to switchlike biosensing by Toll-like receptor 4. Daringer NM, Schwarz KA, Leonard JN. J Biol Chem. 2015 Apr 3;290(14):8764-77. doi: 10.1074/jbc.M114.610063. Epub 2015 Feb 18. PubMed |
| Mature T cell responses are controlled by microRNA-142. Sun Y, Oravecz-Wilson K, Mathewson N, Wang Y, McEachin R, Liu C, Toubai T, Wu J, Rossi C, Braun T, Saunders T, Reddy P. J Clin Invest. 2015 Jul 1;125(7):2825-40. doi: 10.1172/JCI78753. Epub 2015 Jun 22. PubMed |
| CRISPR Technology for Genome Activation and Repression in Mammalian Cells. Du D, Qi LS. Cold Spring Harb Protoc. 2016 Jan 4;2016(1):pdb.prot090175. doi: 10.1101/pdb.prot090175. PubMed |
| Engineering Synthetic Gene Circuits in Living Cells with CRISPR Technology. Jusiak B, Cleto S, Perez-Pinera P, Lu TK. Trends Biotechnol. 2016 Jan 22. pii: S0167-7799(15)00274-7. doi: 10.1016/j.tibtech.2015.12.014. PubMed |
Programmable RNA Tracking in Live Cells with CRISPR/Cas9.
Nelles DA, Fang MY, O'Connell MR, Xu JL, Markmiller SJ, Doudna JA, Yeo GW.
Cell. 2016 Mar 16. pii: S0092-8674(16)30204-5. doi: 10.1016/j.cell.2016.02.054.
PubMed
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| Novel Small-Molecule CX3CR1 Antagonist Impairs Metastatic Seeding and Colonization of Breast Cancer Cells. Shen F, Zhang Y, Jernigan DL, Feng X, Yan J, Garcia FU, Meucci O, Salvino JM, Fatatis A. Mol Cancer Res. 2016 Jun;14(6):518-27. doi: 10.1158/1541-7786.MCR-16-0013. Epub 2016 Mar 21. PubMed |
| CRISPR knockout screening outperforms shRNA and CRISPRi in identifying essential genes. Evers B, Jastrzebski K, Heijmans JP, Grernrum W, Beijersbergen RL, Bernards R. Nat Biotechnol. 2016 Jun;34(6):631-3. doi: 10.1038/nbt.3536. Epub 2016 Apr 25. PubMed |
| Benchmarking of TALE- and CRISPR/dCas9-Based Transcriptional Regulators in Mammalian Cells for the Construction of Synthetic Genetic Circuits. Lebar T, Jerala R. ACS Synth Biol. 2016 Oct 21;5(10):1050-1058. Epub 2016 Jun 28. PubMed |
| A Precision Medicine Approach to the Rescue of Function on Malignant Calmodulinopathic Long-QT Syndrome. Limpitikul WB, Dick IE, Tester DJ, Boczek NJ, Limphong P, Yang W, Choi MH, Babich J, DiSilvestre D, Kanter RJ, Tomaselli GF, Ackerman MJ, Yue DT. Circ Res. 2017 Jan 6;120(1):39-48. doi: 10.1161/CIRCRESAHA.116.309283. Epub 2016 Oct 20. PubMed |
A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response.
Adamson B, Norman TM, Jost M, Cho MY, Nunez JK, Chen Y, Villalta JE, Gilbert LA, Horlbeck MA, Hein MY, Pak RA, Gray AN, Gross CA, Dixit A, Parnas O, Regev A, Weissman JS.
Cell. 2016 Dec 15;167(7):1867-1882.e21. doi: 10.1016/j.cell.2016.11.048.
PubMed
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Live cell imaging of low- and non-repetitive chromosome loci using CRISPR-Cas9.
Qin P, Parlak M, Kuscu C, Bandaria J, Mir M, Szlachta K, Singh R, Darzacq X, Yildiz A, Adli M.
Nat Commun. 2017 Mar 14;8:14725. doi: 10.1038/ncomms14725.
PubMed
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| CRISPR/Cas9-mediated genome editing induces exon skipping by alternative splicing or exon deletion. Mou H, Smith JL, Peng L, Yin H, Moore J, Zhang XO, Song CQ, Sheel A, Wu Q, Ozata DM, Li Y, Anderson DG, Emerson CP, Sontheimer EJ, Moore MJ, Weng Z, Xue W. Genome Biol. 2017 Jun 14;18(1):108. doi: 10.1186/s13059-017-1237-8. PubMed |
Elimination of Toxic Microsatellite Repeat Expansion RNA by RNA-Targeting Cas9.
Batra R, Nelles DA, Pirie E, Blue SM, Marina RJ, Wang H, Chaim IA, Thomas JD, Zhang N, Nguyen V, Aigner S, Markmiller S, Xia G, Corbett KD, Swanson MS, Yeo GW.
Cell. 2017 Aug 24;170(5):899-912.e10. doi: 10.1016/j.cell.2017.07.010. Epub 2017 Aug 10.
PubMed
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| Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements. Mumbach MR, Satpathy AT, Boyle EA, Dai C, Gowen BG, Cho SW, Nguyen ML, Rubin AJ, Granja JM, Kazane KR, Wei Y, Nguyen T, Greenside PG, Corces MR, Tycko J, Simeonov DR, Suliman N, Li R, Xu J, Flynn RA, Kundaje A, Khavari PA, Marson A, Corn JE, Quertermous T, Greenleaf WJ, Chang HY. Nat Genet. 2017 Nov;49(11):1602-1612. doi: 10.1038/ng.3963. Epub 2017 Sep 25. PubMed |
TET proteins safeguard bivalent promoters from de novo methylation in human embryonic stem cells.
Verma N, Pan H, Dore LC, Shukla A, Li QV, Pelham-Webb B, Teijeiro V, Gonzalez F, Krivtsov A, Chang CJ, Papapetrou EP, He C, Elemento O, Huangfu D.
Nat Genet. 2018 Jan;50(1):83-95. doi: 10.1038/s41588-017-0002-y. Epub 2017 Dec 4.
PubMed
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On the design of CRISPR-based single-cell molecular screens.
Hill AJ, McFaline-Figueroa JL, Starita LM, Gasperini MJ, Matreyek KA, Packer J, Jackson D, Shendure J, Trapnell C.
Nat Methods. 2018 Feb 19. pii: nmeth.4604. doi: 10.1038/nmeth.4604.
PubMed
Associated Plasmids |
Genome-wide determination of on-target and off-target characteristics for RNA-guided DNA methylation by dCas9 methyltransferases.
Lin L, Liu Y, Xu F, Huang J, Daugaard TF, Petersen TS, Hansen B, Ye L, Zhou Q, Fang F, Yang L, Li S, Floe L, Jensen KT, Shrock E, Chen F, Yang H, Wang J, Liu X, Xu X, Bolund L, Nielsen AL, Luo Y.
Gigascience. 2018 Mar 1;7(3):1-19. doi: 10.1093/gigascience/giy011.
PubMed
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| Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element. Cho SW, Xu J, Sun R, Mumbach MR, Carter AC, Chen YG, Yost KE, Kim J, He J, Nevins SA, Chin SF, Caldas C, Liu SJ, Horlbeck MA, Lim DA, Weissman JS, Curtis C, Chang HY. Cell. 2018 May 31;173(6):1398-1412.e22. doi: 10.1016/j.cell.2018.03.068. Epub 2018 May 3. PubMed |
| The ER membrane protein complex interacts cotranslationally to enable biogenesis of multipass membrane proteins. Shurtleff MJ, Itzhak DN, Hussmann JA, Schirle Oakdale NT, Costa EA, Jonikas M, Weibezahn J, Popova KD, Jan CH, Sinitcyn P, Vembar SS, Hernandez H, Cox J, Burlingame AL, Brodsky JL, Frost A, Borner GH, Weissman JS. Elife. 2018 May 29;7. pii: 37018. doi: 10.7554/eLife.37018. PubMed |
| Specificity of RNAi, LNA and CRISPRi as loss-of-function methods in transcriptional analysis. Stojic L, Lun ATL, Mangei J, Mascalchi P, Quarantotti V, Barr AR, Bakal C, Marioni JC, Gergely F, Odom DT. Nucleic Acids Res. 2018 Jul 6;46(12):5950-5966. doi: 10.1093/nar/gky437. PubMed |
A Network of Noncoding Regulatory RNAs Acts in the Mammalian Brain.
Kleaveland B, Shi CY, Stefano J, Bartel DP.
Cell. 2018 Jul 12;174(2):350-362.e17. doi: 10.1016/j.cell.2018.05.022. Epub 2018 Jun 7.
PubMed
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| Endogenous HIF2A reporter systems for high-throughput functional screening. Zaini MN, Patel SA, Syafruddin SE, Rodrigues P, Vanharanta S. Sci Rep. 2018 Aug 13;8(1):12063. doi: 10.1038/s41598-018-30499-2. PubMed |
| Delivery of an Artificial Transcription Regulator dCas9-VPR by Extracellular Vesicles for Therapeutic Gene Activation. Lainscek D, Kadunc L, Keber MM, Bratkovic IH, Romih R, Jerala R. ACS Synth Biol. 2018 Dec 21;7(12):2715-2725. doi: 10.1021/acssynbio.8b00192. Epub 2018 Dec 7. PubMed |
| LncEGFL7OS regulates human angiogenesis by interacting with MAX at the EGFL7/miR-126 locus. Zhou Q, Yu B, Anderson C, Huang ZP, Hanus J, Zhang W, Han Y, Bhattacharjee PS, Srinivasan S, Zhang K, Wang DZ, Wang S. Elife. 2019 Feb 11;8. pii: 40470. doi: 10.7554/eLife.40470. PubMed |
| Ceapins block the unfolded protein response sensor ATF6alpha by inducing a neomorphic inter-organelle tether. Torres SE, Gallagher CM, Plate L, Gupta M, Liem CR, Guo X, Tian R, Stroud RM, Kampmann M, Weissman JS, Walter P. Elife. 2019 May 31;8. pii: 46595. doi: 10.7554/eLife.46595. PubMed |
| Rational targeting of a NuRD subcomplex guided by comprehensive in situ mutagenesis. Sher F, Hossain M, Seruggia D, Schoonenberg VAC, Yao Q, Cifani P, Dassama LMK, Cole MA, Ren C, Vinjamur DS, Macias-Trevino C, Luk K, McGuckin C, Schupp PG, Canver MC, Kurita R, Nakamura Y, Fujiwara Y, Wolfe SA, Pinello L, Maeda T, Kentsis A, Orkin SH, Bauer DE. Nat Genet. 2019 Jul;51(7):1149-1159. doi: 10.1038/s41588-019-0453-4. Epub 2019 Jun 28. PubMed |
| PUMILIO, but not RBMX, binding is required for regulation of genomic stability by noncoding RNA NORAD. Elguindy MM, Kopp F, Goodarzi M, Rehfeld F, Thomas A, Chang TC, Mendell JT. Elife. 2019 Jul 25;8. pii: 48625. doi: 10.7554/eLife.48625. PubMed |
CRISPR Interference-Based Platform for Multimodal Genetic Screens in Human iPSC-Derived Neurons.
Tian R, Gachechiladze MA, Ludwig CH, Laurie MT, Hong JY, Nathaniel D, Prabhu AV, Fernandopulle MS, Patel R, Abshari M, Ward ME, Kampmann M.
Neuron. 2019 Aug 5. pii: S0896-6273(19)30640-3. doi: 10.1016/j.neuron.2019.07.014.
PubMed
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| New factors for protein transport identified by a genome-wide CRISPRi screen in mammalian cells. Bassaganyas L, Popa SJ, Horlbeck M, Puri C, Stewart SE, Campelo F, Ashok A, Butnaru CM, Brouwers N, Heydari K, Ripoche J, Weissman J, Rubinsztein DC, Schekman R, Malhotra V, Moreau K, Villeneuve J. J Cell Biol. 2019 Nov 4;218(11):3861-3879. doi: 10.1083/jcb.201902028. Epub 2019 Sep 5. PubMed |
Compromised function of the ESCRT pathway promotes endolysosomal escape of tau seeds and propagation of tau aggregation.
Chen JJ, Nathaniel DL, Raghavan P, Nelson M, Tian R, Tse E, Hong JY, See SK, Mok SA, Hein MY, Southworth DR, Grinberg LT, Gestwicki JE, Leonetti MD, Kampmann M.
J Biol Chem. 2019 Oct 2. pii: RA119.009432. doi: 10.1074/jbc.RA119.009432.
PubMed
Associated Plasmids |
| Rab7 regulates primary cilia disassembly through cilia excision. Wang G, Hu HB, Chang Y, Huang Y, Song ZQ, Zhou SB, Chen L, Zhang YC, Wu M, Tu HQ, Yuan JF, Wang N, Pan X, Li AL, Zhou T, Zhang XM, He K, Li HY. J Cell Biol. 2019 Dec 2;218(12):4030-4041. doi: 10.1083/jcb.201811136. Epub 2019 Oct 16. PubMed |
| Off-target effects of CRISPRa on interleukin-6 expression. Soubeyrand S, Lau P, Peters V, McPherson R. PLoS One. 2019 Oct 28;14(10):e0224113. doi: 10.1371/journal.pone.0224113. eCollection 2019. PubMed |
| Myristoleic acid produced by enterococci reduces obesity through brown adipose tissue activation. Quan LH, Zhang C, Dong M, Jiang J, Xu H, Yan C, Liu X, Zhou H, Zhang H, Chen L, Zhong FL, Luo ZB, Lam SM, Shui G, Li D, Jin W. Gut. 2020 Jul;69(7):1239-1247. doi: 10.1136/gutjnl-2019-319114. Epub 2019 Nov 19. PubMed |
| CRISPRa-mediated FOXP3 gene upregulation in mammalian cells. Forstneric V, Oven I, Ogorevc J, Lainscek D, Praznik A, Lebar T, Jerala R, Horvat S. Cell Biosci. 2019 Nov 21;9:93. doi: 10.1186/s13578-019-0357-0. eCollection 2019. PubMed |
| The MITF-SOX10 regulated long non-coding RNA DIRC3 is a melanoma tumour suppressor. Coe EA, Tan JY, Shapiro M, Louphrasitthiphol P, Bassett AR, Marques AC, Goding CR, Vance KW. PLoS Genet. 2019 Dec 27;15(12):e1008501. doi: 10.1371/journal.pgen.1008501. eCollection 2019 Dec. PubMed |
| Systems Genetics in Human Endothelial Cells Identifies Non-coding Variants Modifying Enhancers, Expression, and Complex Disease Traits. Stolze LK, Conklin AC, Whalen MB, Lopez Rodriguez M, Ounap K, Selvarajan I, Toropainen A, Ord T, Li J, Eshghi A, Solomon AE, Fang Y, Kaikkonen MU, Romanoski CE. Am J Hum Genet. 2020 Jun 4;106(6):748-763. doi: 10.1016/j.ajhg.2020.04.008. Epub 2020 May 21. PubMed |
| Tuning the Expression of Long Noncoding RNA Loci with CRISPR Interference. Stojic L. Methods Mol Biol. 2020;2161:1-16. doi: 10.1007/978-1-0716-0680-3_1. PubMed |
| Histone methyltransferase activity programs nuclear peripheral genome positioning. See K, Kiseleva AA, Smith CL, Liu F, Li J, Poleshko A, Epstein JA. Dev Biol. 2020 Oct 1;466(1-2):90-98. doi: 10.1016/j.ydbio.2020.07.010. Epub 2020 Jul 24. PubMed |
| eQTL Colocalization Analyses Identify NTN4 as a Candidate Breast Cancer Risk Gene. Beesley J, Sivakumaran H, Moradi Marjaneh M, Shi W, Hillman KM, Kaufmann S, Hussein N, Kar S, Lima LG, Ham S, Moller A, Chenevix-Trench G, Edwards SL, French JD. Am J Hum Genet. 2020 Oct 1;107(4):778-787. doi: 10.1016/j.ajhg.2020.08.006. Epub 2020 Aug 31. PubMed |
| The sustained expression of Cas9 targeting toxic RNAs reverses disease phenotypes in mouse models of myotonic dystrophy type 1. Batra R, Nelles DA, Roth DM, Krach F, Nutter CA, Tadokoro T, Thomas JD, Sznajder LJ, Blue SM, Gutierrez HL, Liu P, Aigner S, Platoshyn O, Miyanohara A, Marsala M, Swanson MS, Yeo GW. Nat Biomed Eng. 2021 Feb;5(2):157-168. doi: 10.1038/s41551-020-00607-7. Epub 2020 Sep 14. PubMed |
Identification and characterization of the long noncoding RNA Dreg1 as a novel regulator of Gata3.
Chan WF, Coughlan HD, Iannarella N, Smyth GK, Johanson TM, Keenan CR, Allan RS.
Immunol Cell Biol. 2020 Sep 24. doi: 10.1111/imcb.12408.
PubMed
Associated Plasmids |
| TGFbeta promotes widespread enhancer chromatin opening and operates on genomic regulatory domains. Guerrero-Martinez JA, Ceballos-Chavez M, Koehler F, Peiro S, Reyes JC. Nat Commun. 2020 Dec 3;11(1):6196. doi: 10.1038/s41467-020-19877-5. PubMed |
| Genome-Scale Perturbation of Long Noncoding RNA Expression Using CRISPR Interference. Liu SJ, Horlbeck MA, Weissman JS, Lim DA. Methods Mol Biol. 2021;2254:323-338. doi: 10.1007/978-1-0716-1158-6_20. PubMed |
| A stress-induced tyrosine-tRNA depletion response mediates codon-based translational repression and growth suppression. Huh D, Passarelli MC, Gao J, Dusmatova SN, Goin C, Fish L, Pinzaru AM, Molina H, Ren Z, McMillan EA, Asgharian H, Goodarzi H, Tavazoie SF. EMBO J. 2021 Jan 15;40(2):e106696. doi: 10.15252/embj.2020106696. Epub 2020 Dec 21. PubMed |
| Transcription factor competition at the gamma-globin promoters controls hemoglobin switching. Liu N, Xu S, Yao Q, Zhu Q, Kai Y, Hsu JY, Sakon P, Pinello L, Yuan GC, Bauer DE, Orkin SH. Nat Genet. 2021 Apr;53(4):511-520. doi: 10.1038/s41588-021-00798-y. Epub 2021 Mar 1. PubMed |
| The incorporation loci of H3.3K36M determine its preferential prevalence in chondroblastomas. Zhang Y, Fang D. Cell Death Dis. 2021 Mar 24;12(4):311. doi: 10.1038/s41419-021-03597-9. PubMed |
| HOXBLINC long non-coding RNA activation promotes leukemogenesis in NPM1-mutant acute myeloid leukemia. Zhu G, Luo H, Feng Y, Guryanova OA, Xu J, Chen S, Lai Q, Sharma A, Xu B, Zhao Z, Feng R, Ni H, Claxton D, Guo Y, Mesa RA, Qiu Y, Yang FC, Li W, Nimer SD, Huang S, Xu M. Nat Commun. 2021 Mar 29;12(1):1956. doi: 10.1038/s41467-021-22095-2. PubMed |
| CRISPR Interference Efficiently Silences Latent and Lytic Viral Genes in Kaposi's Sarcoma-Associated Herpesvirus-Infected Cells. Brackett K, Mungale A, Lopez-Isidro M, Proctor DA, Najarro G, Arias C. Viruses. 2021 Apr 28;13(5). pii: v13050783. doi: 10.3390/v13050783. PubMed |
| Enhanced targeted DNA methylation of the CMV and endogenous promoters with dCas9-DNMT3A3L entails distinct subsequent histone modification changes in CHO cells. Marx N, Dhiman H, Schmieder V, Freire CM, Nguyen LN, Klanert G, Borth N. Metab Eng. 2021 Jul;66:268-282. doi: 10.1016/j.ymben.2021.04.014. Epub 2021 May 16. PubMed |
| In vivo CRISPR screening for novel noncoding RNA functional targets in glioblastoma models. Attenello FJ, Tsung K, Bishara I, Loh YE, Chen TC. J Neurosci Res. 2021 Sep;99(9):2029-2045. doi: 10.1002/jnr.24850. Epub 2021 May 10. PubMed |
| Silencing PEX26 as an unconventional mode to kill drug-resistant cancer cells and forestall drug resistance. Dahabieh MS, Huang F, Goncalves C, Flores Gonzalez RE, Prabhu S, Bolt A, Di Pietro E, Khoury E, Heath J, Xu ZY, Remy-Sarrazin J, Mann KK, Orthwein A, Boisvert FM, Braverman N, Miller WH, Del Rincon SV. Autophagy. 2021 Jun 21:1-19. doi: 10.1080/15548627.2021.1936932. PubMed |
| Heterogeneity in NECTIN4 Expression Across Molecular Subtypes of Urothelial Cancer Mediates Sensitivity to Enfortumab Vedotin. Chu CE, Sjostrom M, Egusa EA, Gibb EA, Badura ML, Zhu J, Koshkin VS, Stohr BA, Meng MV, Pruthi RS, Friedlander TW, Lotan Y, Black PC, Porten SP, Feng FY, Chou J. Clin Cancer Res. 2021 Sep 15;27(18):5123-5130. doi: 10.1158/1078-0432.CCR-20-4175. Epub 2021 Jun 9. PubMed |
| CRISPR mediated targeting of DUX4 distal regulatory element represses DUX4 target genes dysregulated in Facioscapulohumeral muscular dystrophy. Das S, Chadwick BP. Sci Rep. 2021 Jun 15;11(1):12598. doi: 10.1038/s41598-021-92096-0. PubMed |
| CRISPR Interference (CRISPRi) and CRISPR Activation (CRISPRa) to Explore the Oncogenic lncRNA Network. Morelli E, Gulla' A, Amodio N, Taiana E, Neri A, Fulciniti M, Munshi NC. Methods Mol Biol. 2021;2348:189-204. doi: 10.1007/978-1-0716-1581-2_13. PubMed |
| The AKT modulator A-443654 reduces alpha-synuclein expression and normalizes ER stress and autophagy. Gandelman M, Dansithong W, Kales SC, Paul S, Maag G, Aoyama E, Zakharov A, Rai G, Dexheimer T, Whitehill BM, Sun H, Jadhav A, Simeonov A, Henderson MJ, Huynh DP, Pulst SM, Scoles DR. J Biol Chem. 2021 Oct;297(4):101191. doi: 10.1016/j.jbc.2021.101191. Epub 2021 Sep 11. PubMed |
Enhanced prime editing systems by manipulating cellular determinants of editing outcomes.
Chen PJ, Hussmann JA, Yan J, Knipping F, Ravisankar P, Chen PF, Chen C, Nelson JW, Newby GA, Sahin M, Osborn MJ, Weissman JS, Adamson B, Liu DR.
Cell. 2021 Oct 28;184(22):5635-5652.e29. doi: 10.1016/j.cell.2021.09.018.
PubMed
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| A bipartite element with allele-specific functions safeguards DNA methylation imprints at the Dlk1-Dio3 locus. Aronson BE, Scourzic L, Shah V, Swanzey E, Kloetgen A, Polyzos A, Sinha A, Azziz A, Caspi I, Li J, Pelham-Webb B, Glenn RA, Vierbuchen T, Wichterle H, Tsirigos A, Dawlaty MM, Stadtfeld M, Apostolou E. Dev Cell. 2021 Nov 22;56(22):3052-3065.e5. doi: 10.1016/j.devcel.2021.10.004. Epub 2021 Oct 27. PubMed |
| ecDNA hubs drive cooperative intermolecular oncogene expression. Hung KL, Yost KE, Xie L, Shi Q, Helmsauer K, Luebeck J, Schopflin R, Lange JT, Chamorro Gonzalez R, Weiser NE, Chen C, Valieva ME, Wong IT, Wu S, Dehkordi SR, Duffy CV, Kraft K, Tang J, Belk JA, Rose JC, Corces MR, Granja JM, Li R, Rajkumar U, Friedlein J, Bagchi A, Satpathy AT, Tjian R, Mundlos S, Bafna V, Henssen AG, Mischel PS, Liu Z, Chang HY. Nature. 2021 Dec;600(7890):731-736. doi: 10.1038/s41586-021-04116-8. Epub 2021 Nov 24. PubMed |
CRISPR activation and interference screens decode stimulation responses in primary human T cells.
Schmidt R, Steinhart Z, Layeghi M, Freimer JW, Bueno R, Nguyen VQ, Blaeschke F, Ye CJ, Marson A.
Science. 2022 Feb 4;375(6580):eabj4008. doi: 10.1126/science.abj4008. Epub 2022 Feb 4.
PubMed
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| HOTTIP-dependent R-loop formation regulates CTCF boundary activity and TAD integrity in leukemia. Luo H, Zhu G, Eshelman MA, Fung TK, Lai Q, Wang F, Zeisig BB, Lesperance J, Ma X, Chen S, Cesari N, Cogle C, Chen B, Xu B, Yang FC, So CWE, Qiu Y, Xu M, Huang S. Mol Cell. 2022 Feb 17;82(4):833-851.e11. doi: 10.1016/j.molcel.2022.01.014. PubMed |
| Regulation of protein secretion through chemical regulation of endoplasmic reticulum retention signal cleavage. Praznik A, Fink T, Franko N, Lonzaric J, Bencina M, Jerala N, Plaper T, Roskar S, Jerala R. Nat Commun. 2022 Mar 14;13(1):1323. doi: 10.1038/s41467-022-28971-9. PubMed |
| Leucyl-tRNA synthetase is a tumour suppressor in breast cancer and regulates codon-dependent translation dynamics. Passarelli MC, Pinzaru AM, Asgharian H, Liberti MV, Heissel S, Molina H, Goodarzi H, Tavazoie SF. Nat Cell Biol. 2022 Mar;24(3):307-315. doi: 10.1038/s41556-022-00856-5. Epub 2022 Mar 14. PubMed |
| Avian influenza viruses suppress innate immunity by inducing trans-transcriptional readthrough via SSU72. Zhao Y, Huang F, Zou Z, Bi Y, Yang Y, Zhang C, Liu Q, Shang D, Yan Y, Ju X, Mei S, Xie P, Li X, Tian M, Tan S, Lu H, Han Z, Liu K, Zhang Y, Liang J, Liang Z, Zhang Q, Chang J, Liu WJ, Feng C, Li T, Zhang MQ, Wang X, Gao GF, Liu Y, Jin N, Jiang C. Cell Mol Immunol. 2022 Jun;19(6):702-714. doi: 10.1038/s41423-022-00843-8. Epub 2022 Mar 24. PubMed |
| Identification of novel Ebola virus inhibitors using biologically contained virus. Vanmechelen B, Stroobants J, Chiu W, Schepers J, Marchand A, Chaltin P, Vermeire K, Maes P. Antiviral Res. 2022 Apr;200:105294. doi: 10.1016/j.antiviral.2022.105294. Epub 2022 Mar 23. PubMed |
| CRISPR activation screen identifies BCL-2 proteins and B3GNT2 as drivers of cancer resistance to T cell-mediated cytotoxicity. Joung J, Kirchgatterer PC, Singh A, Cho JH, Nety SP, Larson RC, Macrae RK, Deasy R, Tseng YY, Maus MV, Zhang F. Nat Commun. 2022 Mar 25;13(1):1606. doi: 10.1038/s41467-022-29205-8. PubMed |
| Epigenetic Repression of STING by MYC Promotes Immune Evasion and Resistance to Immune Checkpoint Inhibitors in Triple-Negative Breast Cancer. Lee KM, Lin CC, Servetto A, Bae J, Kandagatla V, Ye D, Kim G, Sudhan DR, Mendiratta S, Gonzalez Ericsson PI, Balko JM, Lee J, Barnes S, Malladi VS, Tabrizi S, Reddy SM, Yum S, Chang CW, Hutchinson KE, Yost SE, Yuan Y, Chen ZJ, Fu YX, Hanker AB, Arteaga CL. Cancer Immunol Res. 2022 Jul 1;10(7):829-843. doi: 10.1158/2326-6066.CIR-21-0826. PubMed |
| Building regulatory landscapes reveals that an enhancer can recruit cohesin to create contact domains, engage CTCF sites and activate distant genes. Rinzema NJ, Sofiadis K, Tjalsma SJD, Verstegen MJAM, Oz Y, Valdes-Quezada C, Felder AK, Filipovska T, van der Elst S, de Andrade Dos Ramos Z, Han R, Krijger PHL, de Laat W. Nat Struct Mol Biol. 2022 Jun;29(6):563-574. doi: 10.1038/s41594-022-00787-7. Epub 2022 Jun 16. PubMed |
| Coiled-coil heterodimer-based recruitment of an exonuclease to CRISPR/Cas for enhanced gene editing. Lainscek D, Forstneric V, Mikolic V, Malensek S, Pecan P, Bencina M, Sever M, Podgornik H, Jerala R. Nat Commun. 2022 Jun 23;13(1):3604. doi: 10.1038/s41467-022-31386-1. PubMed |
Directed evolution of adeno-associated virus for efficient gene delivery to microglia.
Lin R, Zhou Y, Yan T, Wang R, Li H, Wu Z, Zhang X, Zhou X, Zhao F, Zhang L, Li Y, Luo M.
Nat Methods. 2022 Jul 25. pii: 10.1038/s41592-022-01547-7. doi: 10.1038/s41592-022-01547-7.
PubMed
Associated Plasmids |
| A Ctnnb1 enhancer regulates neocortical neurogenesis by controlling the abundance of intermediate progenitors. Wang J, Wang A, Tian K, Hua X, Zhang B, Zheng Y, Kong X, Li W, Xu L, Wang J, Li Z, Liu Y, Zhou Y. Cell Discov. 2022 Aug 2;8(1):74. doi: 10.1038/s41421-022-00421-2. PubMed |
| SOX9 maintains human foetal lung tip progenitor state by enhancing WNT and RTK signalling. Sun D, Llora Batlle O, van den Ameele J, Thomas JC, He P, Lim K, Tang W, Xu C, Meyer KB, Teichmann SA, Marioni JC, Jackson SP, Brand AH, Rawlins EL. EMBO J. 2022 Nov 2;41(21):e111338. doi: 10.15252/embj.2022111338. Epub 2022 Sep 19. PubMed |
| CRISPR Activation/Interference Screen to Identify Genetic Networks in HDAC-Inhibitor-Resistant Cells. Jung P, Schmalbrock L, Wirth M. Methods Mol Biol. 2023;2589:429-454. doi: 10.1007/978-1-0716-2788-4_28. PubMed |
Maximizing CRISPRi efficacy and accessibility with dual-sgRNA libraries and optimal effectors.
Replogle JM, Bonnar JL, Pogson AN, Liem CR, Maier NK, Ding Y, Russell BJ, Wang X, Leng K, Guna A, Norman TM, Pak RA, Ramos DM, Ward ME, Gilbert LA, Kampmann M, Weissman JS, Jost M.
Elife. 2022 Dec 28;11:e81856. doi: 10.7554/eLife.81856.
PubMed
Associated Plasmids |
| CRISPR interference for sequence-specific regulation of fibroblast growth factor receptor A in Schistosoma mansoni. Du X, McManus DP, French JD, Collinson N, Sivakumaran H, MacGregor SR, Fogarty CE, Jones MK, You H. Front Immunol. 2023 Jan 13;13:1105719. doi: 10.3389/fimmu.2022.1105719. eCollection 2022. PubMed |
| Inhibition of the MNK1/2-eIF4E Axis Augments Palbociclib-Mediated Antitumor Activity in Melanoma and Breast Cancer. Prabhu SA, Moussa O, Goncalves C, LaPierre JH, Chou H, Huang F, Richard VR, Ferruzo PYM, Guettler EM, Soria-Bretones I, Kirby L, Gagnon N, Su J, Silvester J, Krisna SS, Rose AAN, Sheppard KE, Cescon DW, Mallette FA, Zahedi RP, Borchers CH, Del Rincon SV, Miller WH. Mol Cancer Ther. 2023 Feb 1;22(2):192-204. doi: 10.1158/1535-7163.MCT-22-0092. PubMed |
| Multimodal CRISPR perturbations of GWAS loci associated with coronary artery disease in vascular endothelial cells. Wunnemann F, Fotsing Tadjo T, Beaudoin M, Lalonde S, Lo KS, Kleinstiver BP, Lettre G. PLoS Genet. 2023 Mar 16;19(3):e1010680. doi: 10.1371/journal.pgen.1010680. eCollection 2023 Mar. PubMed |
| Regulation of CD19 CAR-T cell activation based on an engineered downstream transcription factor. Lainscek D, Golob-Urbanc A, Mikolic V, Pantovic-Zalig J, Malensek S, Jerala R. Mol Ther Oncolytics. 2023 Apr 26;29:77-90. doi: 10.1016/j.omto.2023.04.005. eCollection 2023 Jun 15. PubMed |
| Multiplex single-cell chemical genomics reveals the kinase dependence of the response to targeted therapy. McFaline-Figueroa JL, Srivatsan S, Hill AJ, Gasperini M, Jackson DL, Saunders L, Domcke S, Regalado SG, Lazarchuck P, Alvarez S, Monnat RJ, Shendure J, Trapnell C. bioRxiv. 2023 Jun 14:2023.03.10.531983. doi: 10.1101/2023.03.10.531983. Preprint. PubMed |
| Multiomics analyses reveal DARS1-AS1/YBX1-controlled posttranscriptional circuits promoting glioblastoma tumorigenesis/radioresistance. Zheng C, Wei Y, Zhang Q, Sun M, Wang Y, Hou J, Zhang P, Lv X, Su D, Jiang Y, Gumin J, Sahni N, Hu B, Wang W, Chen X, McGrail DJ, Zhang C, Huang S, Xu H, Chen J, Lang FF, Hu J, Chen Y. Sci Adv. 2023 Aug 4;9(31):eadf3984. doi: 10.1126/sciadv.adf3984. Epub 2023 Aug 4. PubMed |
| Systematic mapping and modeling of 3D enhancer-promoter interactions in early mouse embryonic lineages reveal regulatory principles that determine the levels and cell-type specificity of gene expression. Murphy D, Salataj E, Di Giammartino DC, Rodriguez-Hernaez J, Kloetgen A, Garg V, Char E, Uyehara CM, Ee LS, Lee U, Stadtfeld M, Hadjantonakis AK, Tsirigos A, Polyzos A, Apostolou E. bioRxiv [Preprint]. 2023 Jul 19:2023.07.19.549714. doi: 10.1101/2023.07.19.549714. PubMed |
| CRISPR interference to evaluate modifiers of C9ORF72-mediated toxicity in FTD. Pickles S, Zanetti Alepuz D, Koike Y, Yue M, Tong J, Liu P, Zhou Y, Jansen-West K, Daughrity LM, Song Y, DeTure M, Oskarsson B, Graff-Radford NR, Boeve BF, Petersen RC, Josephs KA, Dickson DW, Ward ME, Dong L, Prudencio M, Cook CN, Petrucelli L. Front Cell Dev Biol. 2023 Aug 7;11:1251551. doi: 10.3389/fcell.2023.1251551. eCollection 2023. PubMed |
| Mapping the Genetic Interaction Network of PARP inhibitor Response. Simpson D, Ling J, Jing Y, Adamson B. bioRxiv [Preprint]. 2023 Aug 20:2023.08.19.553986. doi: 10.1101/2023.08.19.553986. PubMed |
| YY1 is regulated by ALKBH5-mediated m6A modification and promotes autophagy and cancer progression through targeting ATG4B. Wang S, Nie J, Xu K, Liu Y, Tong W, Li A, Zuo W, Liu Z, Yang F. Aging (Albany NY). 2023 Sep 18;15(18):9590-9613. doi: 10.18632/aging.205037. Epub 2023 Sep 18. PubMed |
| Determinants of DDX3X sensitivity uncovered using a helicase activity in translation reporter. Wilkins KC, Schroeder T, Gu S, Revalde JL, Floor SN. bioRxiv [Preprint]. 2023 Sep 14:2023.09.14.557805. doi: 10.1101/2023.09.14.557805. PubMed |
| Dissecting key regulators of transcriptome kinetics through scalable single-cell RNA profiling of pooled CRISPR screens. Xu Z, Sziraki A, Lee J, Zhou W, Cao J. Nat Biotechnol. 2023 Sep 25. doi: 10.1038/s41587-023-01948-9. PubMed |
| Mechanosensitive super-enhancers regulate genes linked to atherosclerosis in endothelial cells. Li J, Zhu J, Gray O, Sobreira DR, Wu D, Huang RT, Miao B, Sakabe NJ, Krause MD, Kaikkonen MU, Romanoski CE, Nobrega MA, Fang Y. J Cell Biol. 2024 Mar 4;223(3):e202211125. doi: 10.1083/jcb.202211125. Epub 2024 Jan 17. PubMed |
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