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pCRISPRia-v2 Citations (51)

Originally described in: Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation.
Horlbeck MA, Gilbert LA, Villalta JE, Adamson B, Pak RA, Chen Y, Fields AP, Park CY, Corn JE, Kampmann M, Weissman JS Elife. 2016 Sep 23;5. pii: e19760. doi: 10.7554/eLife.19760. PubMed Journal

Articles Citing pCRISPRia-v2

Articles
Discovery of stimulation-responsive immune enhancers with CRISPR activation. Simeonov DR, Gowen BG, Boontanrart M, Roth TL, Gagnon JD, Mumbach MR, Satpathy AT, Lee Y, Bray NL, Chan AY, Lituiev DS, Nguyen ML, Gate RE, Subramaniam M, Li Z, Woo JM, Mitros T, Ray GJ, Curie GL, Naddaf N, Chu JS, Ma H, Boyer E, Van Gool F, Huang H, Liu R, Tobin VR, Schumann K, Daly MJ, Farh KK, Ansel KM, Ye CJ, Greenleaf WJ, Anderson MS, Bluestone JA, Chang HY, Corn JE, Marson A. Nature. 2017 Sep 7;549(7670):111-115. doi: 10.1038/nature23875. Epub 2017 Aug 30. PubMed

Associated Plasmids
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
Atlastins remodel the endoplasmic reticulum for selective autophagy. Liang JR, Lingeman E, Ahmed S, Corn JE. J Cell Biol. 2018 Aug 24. pii: jcb.201804185. doi: 10.1083/jcb.201804185. PubMed

Associated Plasmids
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

Associated Plasmids
Titrating gene expression using libraries of systematically attenuated CRISPR guide RNAs. Jost M, Santos DA, Saunders RA, Horlbeck MA, Hawkins JS, Scaria SM, Norman TM, Hussmann JA, Liem CR, Gross CA, Weissman JS. Nat Biotechnol. 2020 Jan 13. pii: 10.1038/s41587-019-0387-5. doi: 10.1038/s41587-019-0387-5. PubMed

Associated Plasmids
A Genome-wide ER-phagy Screen Highlights Key Roles of Mitochondrial Metabolism and ER-Resident UFMylation. Liang JR, Lingeman E, Luong T, Ahmed S, Muhar M, Nguyen T, Olzmann JA, Corn JE. Cell. 2020 Mar 19;180(6):1160-1177.e20. doi: 10.1016/j.cell.2020.02.017. Epub 2020 Mar 10. PubMed

Associated Plasmids
The Histone Chaperone FACT Induces Cas9 Multi-turnover Behavior and Modifies Genome Manipulation in Human Cells. Wang AS, Chen LC, Wu RA, Hao Y, McSwiggen DT, Heckert AB, Richardson CD, Gowen BG, Kazane KR, Vu JT, Wyman SK, Shin JJ, Darzacq X, Walter JC, Corn JE. Mol Cell. 2020 Jul 16;79(2):221-233.e5. doi: 10.1016/j.molcel.2020.06.014. Epub 2020 Jun 29. PubMed

Associated Plasmids
Meningioma cells express primary cilia but do not transduce ciliary Hedgehog signals. Findakly S, Choudhury A, Daggubati V, Pekmezci M, Lang UE, Raleigh DR. Acta Neuropathol Commun. 2020 Jul 20;8(1):114. doi: 10.1186/s40478-020-00994-7. PubMed
GIGYF2 and 4EHP Inhibit Translation Initiation of Defective Messenger RNAs to Assist Ribosome-Associated Quality Control. Hickey KL, Dickson K, Cogan JZ, Replogle JM, Schoof M, D'Orazio KN, Sinha NK, Hussmann JA, Jost M, Frost A, Green R, Weissman JS, Kostova KK. Mol Cell. 2020 Sep 17;79(6):950-962.e6. doi: 10.1016/j.molcel.2020.07.007. Epub 2020 Jul 28. PubMed
Discovering functional sequences with RELICS, an analysis method for CRISPR screens. Fiaux PC, Chen HV, Chen PB, Chen AR, McVicker G. PLoS Comput Biol. 2020 Sep 16;16(9):e1008194. doi: 10.1371/journal.pcbi.1008194. eCollection 2020 Sep. PubMed
Multiplatform genomic profiling and magnetic resonance imaging identify mechanisms underlying intratumor heterogeneity in meningioma. Magill ST, Vasudevan HN, Seo K, Villanueva-Meyer JE, Choudhury A, John Liu S, Pekmezci M, Findakly S, Hilz S, Lastella S, Demaree B, Braunstein SE, Bush NAO, Aghi MK, Theodosopoulos PV, Sneed PK, Abate AR, Berger MS, McDermott MW, Lim DA, Ullian EM, Costello JF, Raleigh DR. Nat Commun. 2020 Sep 23;11(1):4803. doi: 10.1038/s41467-020-18582-7. PubMed
CRISPRi-mediated depletion of Spt4 and Spt5 reveals a role for DSIF in the control of HIV latency. Krasnopolsky S, Novikov A, Kuzmina A, Taube R. Biochim Biophys Acta Gene Regul Mech. 2021 Jan;1864(1):194656. doi: 10.1016/j.bbagrm.2020.194656. Epub 2020 Dec 15. PubMed
High-content imaging-based pooled CRISPR screens in mammalian cells. Yan X, Stuurman N, Ribeiro SA, Tanenbaum ME, Horlbeck MA, Liem CR, Jost M, Weissman JS, Vale RD. J Cell Biol. 2021 Feb 1;220(2). pii: 211696. doi: 10.1083/jcb.202008158. PubMed

Associated Plasmids
Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing. Nuñez JK, Chen J, Pommier GC, Cogan JZ, Replogle JM, Adriaens C, Ramadoss GN, Shi Q, Hung KL, Samelson AJ, Pogson AN, Kim JYS, Chung A, Leonetti MD, Chang HY, Kampmann M, Bernstein BE, Hovestadt V, Gilbert LA, Weissman JS. Cell. 2021 Apr 7. pii: S0092-8674(21)00353-6. doi: 10.1016/j.cell.2021.03.025. PubMed

Associated Plasmids
Targeting Conserved Sequences Circumvents the Evolution of Resistance in a Viral Gene Drive against Human Cytomegalovirus. Walter M, Perrone R, Verdin E. J Virol. 2021 Jul 12;95(15):e0080221. doi: 10.1128/JVI.00802-21. Epub 2021 Jul 12. PubMed
Genome-wide CRISPRi screening identifies OCIAD1 as a prohibitin client and regulatory determinant of mitochondrial Complex III assembly in human cells. Le Vasseur M, Friedman J, Jost M, Xu J, Yamada J, Kampmann M, Horlbeck MA, Salemi MR, Phinney BS, Weissman JS, Nunnari J. Elife. 2021 May 26;10. pii: 67624. doi: 10.7554/eLife.67624. 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
Paralogous synthetic lethality underlies genetic dependencies of the cancer-mutated gene STAG2. Bailey ML, Tieu D, Habsid A, Tong AHY, Chan K, Moffat J, Hieter P. Life Sci Alliance. 2021 Aug 30;4(11). pii: 4/11/e202101083. doi: 10.26508/lsa.202101083. Print 2021 Nov. PubMed
Mitotic Centromere-Associated Kinesin (MCAK/KIF2C) Regulates Cell Migration and Invasion by Modulating Microtubule Dynamics and Focal Adhesion Turnover. Moon HH, Kreis NN, Friemel A, Roth S, Schulte D, Solbach C, Louwen F, Yuan J, Ritter A. Cancers (Basel). 2021 Nov 12;13(22). pii: cancers13225673. doi: 10.3390/cancers13225673. PubMed
SIRT5 is a proviral factor that interacts with SARS-CoV-2 Nsp14 protein. Walter M, Chen IP, Vallejo-Gracia A, Kim IJ, Bielska O, Lam VL, Hayashi JM, Cruz A, Shah S, Gross JD, Krogan NJ, Schilling B, Ott M, Verdin E. bioRxiv. 2022 Jan 5. doi: 10.1101/2022.01.04.474979. PubMed
Time-resolved single-cell sequencing identifies multiple waves of mRNA decay during the mitosis-to-G1 phase transition. Krenning L, Sonneveld S, Tanenbaum M. Elife. 2022 Feb 1;11. pii: 71356. doi: 10.7554/eLife.71356. PubMed
Meningioma DNA methylation groups identify biological drivers and therapeutic vulnerabilities. Choudhury A, Magill ST, Eaton CD, Prager BC, Chen WC, Cady MA, Seo K, Lucas CG, Casey-Clyde TJ, Vasudevan HN, Liu SJ, Villanueva-Meyer JE, Lam TC, Pu JK, Li LF, Leung GK, Swaney DL, Zhang MY, Chan JW, Qiu Z, Martin MV, Susko MS, Braunstein SE, Bush NAO, Schulte JD, Butowski N, Sneed PK, Berger MS, Krogan NJ, Perry A, Phillips JJ, Solomon DA, Costello JF, McDermott MW, Rich JN, Raleigh DR. Nat Genet. 2022 May;54(5):649-659. doi: 10.1038/s41588-022-01061-8. Epub 2022 May 9. PubMed
Inhibition of a Chromatin and Transcription Modulator, SLTM, Increases HIV-1 Reactivation Identified by a CRISPR Inhibition Screen. Pedersen SF, Collora JA, Kim RN, Yang K, Razmi A, Catalano AA, Yeh YJ, Mounzer K, Tebas P, Montaner LJ, Ho YC. J Virol. 2022 Jul 13;96(13):e0057722. doi: 10.1128/jvi.00577-22. Epub 2022 Jun 22. PubMed
Ras-mutant cancers are sensitive to small molecule inhibition of V-type ATPases in mice. Tolani B, Celli A, Yao Y, Tan YZ, Fetter R, Liem CR, de Smith AJ, Vasanthakumar T, Bisignano P, Cotton AD, Seiple IB, Rubinstein JL, Jost M, Weissman JS. Nat Biotechnol. 2022 Dec;40(12):1834-1844. doi: 10.1038/s41587-022-01386-z. Epub 2022 Jul 25. PubMed
Brain-restricted mTOR inhibition with binary pharmacology. Zhang Z, Fan Q, Luo X, Lou K, Weiss WA, Shokat KM. Nature. 2022 Sep;609(7928):822-828. doi: 10.1038/s41586-022-05213-y. Epub 2022 Sep 14. 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
A dual MTOR/NAD+ acting gerotherapy. Li J, Kumar S, Miachin K, Bean NL, Halawi O, Lee S, Park J, Pierre TH, Hor JH, Ng SY, Wallace KJ, Rindtorff N, Miller TM, Niehoff ML, Farr SA, Kletzien RF, Colca J, Tanis SP, Chen Y, Griffett K, McCommis KS, Finck BN, Peterson TR. bioRxiv. 2023 Jan 19:2023.01.16.523975. doi: 10.1101/2023.01.16.523975. Preprint. PubMed
Ribosome rescue factor PELOTA modulates translation start site choice and protein isoform levels of transcription factor C/EBPalpha. Fernandez SG, Ferguson L, Ingolia NT. bioRxiv. 2023 Jan 17:2023.01.16.524343. doi: 10.1101/2023.01.16.524343. Preprint. PubMed
LRRC15 mediates an accessory interaction with the SARS-CoV-2 spike protein. Shilts J, Crozier TWM, Teixeira-Silva A, Gabaev I, Gerber PP, Greenwood EJD, Watson SJ, Ortmann BM, Gawden-Bone CM, Pauzaite T, Hoffmann M, Nathan JA, Pohlmann S, Matheson NJ, Lehner PJ, Wright GJ. PLoS Biol. 2023 Feb 3;21(2):e3001959. doi: 10.1371/journal.pbio.3001959. eCollection 2023 Feb. PubMed
Combinatory EHMT and PARP inhibition induces an interferon response and a CD8 T cell-dependent tumor regression in PARP inhibitor-resistant models. Nguyen LL, Watson ZL, Ortega R, Woodruff ER, Jordan KR, Iwanaga R, Yamamoto TM, Bailey CA, Jeong AD, Guntupalli SR, Behbakht K, Gbaja V, Arnoult N, Chuong EB, Bitler BG. bioRxiv. 2023 Feb 23:2023.02.23.529773. doi: 10.1101/2023.02.23.529773. Preprint. PubMed
Generation of Schwann cell derived melanocytes from hPSCs identifies pro-metastatic factors in melanoma. Samuel RM, Navickas A, Maynard A, Gaylord EA, Garcia K, Bhat S, Majd H, Richter MN, Elder N, Le D, Nguyen P, Shibata B, Llabata ML, Selleri L, Laird DJ, Darmanis S, Goodarzi H, Fattahi F. bioRxiv. 2023 Mar 7:2023.03.06.531220. doi: 10.1101/2023.03.06.531220. Preprint. PubMed
Long noncoding RNA Malat1 inhibits Tead3-Nfatc1-mediated osteoclastogenesis to suppress osteoporosis and bone metastasis. Zhao Y, Teng H, Deng Y, Sheldon M, Martinez C, Zhang J, Tian A, Sun Y, Nakagawa S, Yao F, Wang H, Ma L. Res Sq. 2023 Mar 20:rs.3.rs-2405644. doi: 10.21203/rs.3.rs-2405644/v1. Preprint. PubMed
p73 activates transcriptional signatures of basal lineage identity and ciliogenesis in pancreatic ductal adenocarcinoma. Hur SK, Somerville TDD, Wu XS, Maia-Silva D, Demerdash OE, Tuveson DA, Notta F, Vakoc CR. bioRxiv. 2023 Apr 21:2023.04.20.537667. doi: 10.1101/2023.04.20.537667. Preprint. PubMed
Translational fidelity screens in mammalian cells reveal eIF3 and eIF4G2 as regulators of start codon selectivity. She R, Luo J, Weissman JS. Nucleic Acids Res. 2023 Jul 7;51(12):6355-6369. doi: 10.1093/nar/gkad329. PubMed

Associated Plasmids
An mRNA processing pathway suppresses metastasis by governing translational control from the nucleus. Navickas A, Asgharian H, Winkler J, Fish L, Garcia K, Markett D, Dodel M, Culbertson B, Miglani S, Joshi T, Yin K, Nguyen P, Zhang S, Stevers N, Hwang HW, Mardakheh F, Goga A, Goodarzi H. Nat Cell Biol. 2023 Jun;25(6):892-903. doi: 10.1038/s41556-023-01141-9. Epub 2023 May 8. PubMed
Coupled protein quality control during nonsense-mediated mRNA decay. Inglis AJ, Guna A, Galvez-Merchan A, Pal A, Esantsi TK, Keys HR, Frenkel EM, Oania R, Weissman JS, Voorhees RM. J Cell Sci. 2023 May 15;136(10):jcs261216. doi: 10.1242/jcs.261216. Epub 2023 May 23. PubMed

Associated Plasmids
Spatial genomic, biochemical, and cellular mechanisms drive meningioma heterogeneity and evolution. Lucas CH, Mirchia K, Seo K, Najem H, Chen W, Zakimi N, Choudhury A, Liu SJ, Phillips J, Magill S, Horbinski C, Solomon D, Perry A, Vasudevan H, Heimberger A, Raleigh D. Res Sq [Preprint]. 2023 May 15:rs.3.rs-2921804. doi: 10.21203/rs.3.rs-2921804/v1. PubMed
Integration site-dependent HIV-1 promoter activity shapes host chromatin conformation. Collora JA, Ho YC. Genome Res. 2023 Jun;33(6):891-906. doi: 10.1101/gr.277698.123. Epub 2023 Jun 9. PubMed
Hedgehog target genes regulate lipid metabolism to drive basal cell carcinoma and medulloblastoma. Daggubati V, Vykunta A, Choudhury A, Qadeer Z, Mirchia K, Saulnier O, Zakimi N, Hines K, Paul M, Wang L, Jura N, Xu L, Reiter J, Taylor M, Weiss W, Raleigh D. Res Sq [Preprint]. 2023 Aug 3:rs.3.rs-3058335. doi: 10.21203/rs.3.rs-3058335/v1. PubMed
Spastin locally amplifies microtubule dynamics to pattern the axon for presynaptic cargo delivery. Aiken J, Holzbaur ELF. bioRxiv [Preprint]. 2023 Aug 9:2023.08.08.552320. doi: 10.1101/2023.08.08.552320. PubMed
Loss of the Novel Myelin Protein CMTM5 in Multiple Sclerosis Lesions and Its Involvement in Oligodendroglial Stress Responses. Zhan J, Gao Y, Heinig L, Beecken M, Huo Y, Zhang W, Wang P, Wei T, Tian R, Han W, Yu ACH, Kipp M, Kaddatz H. Cells. 2023 Aug 17;12(16):2085. doi: 10.3390/cells12162085. PubMed
The Parkinson's disease risk gene cathepsin B promotes fibrillar alpha-synuclein clearance, lysosomal function and glucocerebrosidase activity in dopaminergic neurons. Jones-Tabah J, He K, Senkevich K, Karpilovsky N, Deyab G, Cousineau Y, Nikanorova D, Goldsmith T, Del Cid Pellitero E, Chen CX, Luo W, You Z, Abdian N, Pietrantonio I, Goiran T, Ahmad J, Ruskey JA, Asayesh F, Spiegelman D, Waters C, Monchi O, Dauvilliers Y, Dupre N, Miliukhina I, Timofeeva A, Emelyanov A, Pchelina S, Greenbaum L, Hassin-Baer S, Alcalay RN, Milnerwood A, Durcan TM, Gan-Or Z, Fon EA. bioRxiv [Preprint]. 2023 Nov 15:2023.11.11.566693. doi: 10.1101/2023.11.11.566693. PubMed
Genome-wide CRISPRi Screen in Human iNeurons to Identify Novel Focal Cortical Dysplasia Genes. Tidball AM, Luo J, Walker JC, Takla TN, Carvill GL, Parent JM. bioRxiv [Preprint]. 2023 Dec 13:2023.12.13.571474. doi: 10.1101/2023.12.13.571474. PubMed
Functional interactions between neurofibromatosis tumor suppressors underlie Schwann cell tumor de-differentiation and treatment resistance. Vasudevan HN, Payne E, Delley CL, John Liu S, Mirchia K, Sale MJ, Lastella S, Nunez MS, Lucas CG, Eaton CD, Casey-Clyde T, Magill ST, Chen WC, Braunstein SE, Perry A, Jacques L, Reddy AT, Pekmezci M, Abate AR, McCormick F, Raleigh DR. Nat Commun. 2024 Jan 12;15(1):477. doi: 10.1038/s41467-024-44755-9. PubMed
Large tandem duplications in cancer result from transcription and DNA replication collisions. Yang Y, Badura ML, O'Leary PC, Delavan HM, Robinson TM, Egusa EA, Zhong X, Swinderman JT, Li H, Zhang M, Kim M, Ashworth A, Feng FY, Chou J, Yang L. medRxiv [Preprint]. 2024 Jan 10:2023.05.17.23290140. doi: 10.1101/2023.05.17.23290140. PubMed
Revealing the grammar of small RNA secretion using interpretable machine learning. Zirak B, Naghipourfar M, Saberi A, Pouyabahar D, Zarezadeh A, Luo L, Fish L, Huh D, Navickas A, Sharifi-Zarchi A, Goodarzi H. Cell Genom. 2024 Apr 10;4(4):100522. doi: 10.1016/j.xgen.2024.100522. Epub 2024 Mar 8. PubMed
The activation of the adaptor protein STING depends on its interactions with the phospholipid PI4P. Luteijn RD, van Terwisga SR, Ver Eecke JE, Onia L, Zaver SA, Woodward JJ, Wubbolts RW, Raulet DH, van Kuppeveld FJM. Sci Signal. 2024 Mar 12;17(827):eade3643. doi: 10.1126/scisignal.ade3643. Epub 2024 Mar 12. PubMed
Long noncoding RNA Malat1 protects against osteoporosis and bone metastasis. Zhao Y, Ning J, Teng H, Deng Y, Sheldon M, Shi L, Martinez C, Zhang J, Tian A, Sun Y, Nakagawa S, Yao F, Wang H, Ma L. Nat Commun. 2024 Mar 16;15(1):2384. doi: 10.1038/s41467-024-46602-3. PubMed
Spastin locally amplifies microtubule dynamics to pattern the axon for presynaptic cargo delivery. Aiken J, Holzbaur ELF. Curr Biol. 2024 Apr 22;34(8):1687-1704.e8. doi: 10.1016/j.cub.2024.03.010. Epub 2024 Mar 29. PubMed
The Parkinson's disease risk gene cathepsin B promotes fibrillar alpha-synuclein clearance, lysosomal function and glucocerebrosidase activity in dopaminergic neurons. Jones-Tabah J, He K, Senkevich K, Karpilovsky N, Deyab G, Cousineau Y, Nikanorova D, Goldsmith T, Del-Cid Pellitero E, Chen CX, Luo W, You Z, Abdian N, Pietrantonio I, Goiran T, Ahmad J, Ruskey JA, Asayesh F, Spiegelman D, Waters C, Monchi O, Dauvilliers Y, Dupre N, Miliukhina I, Timofeeva A, Emelyanov A, Pchelina S, Greenbaum L, HassinBaer S, Alcalay RN, Milnerwood A, Durcan TM, Gan-Or Z, Fon EA. Res Sq [Preprint]. 2024 Mar 19:rs.3.rs-3979098. doi: 10.21203/rs.3.rs-3979098/v1. PubMed
KCNJ2 inhibition mitigates mechanical injury in a human brain organoid model of traumatic brain injury. Lai JD, Berlind JE, Fricklas G, Lie C, Urenda JP, Lam K, Sta Maria N, Jacobs R, Yu V, Zhao Z, Ichida JK. Cell Stem Cell. 2024 Apr 4;31(4):519-536.e8. doi: 10.1016/j.stem.2024.03.004. PubMed

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