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For: Horlbeck MA, Gilbert LA, Villalta JE, Adamson B, Pak RA, Chen Y, Fields AP, Park CY, Corn JE, Kampmann M, Weissman JS. Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation. eLife 2016;5:e19760. [PMID: 27661255 PMCID: PMC5094855 DOI: 10.7554/elife.19760] [Citation(s) in RCA: 570] [Impact Index Per Article: 63.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 09/22/2016] [Indexed: 12/16/2022]  Open
Number Cited by Other Article(s)
1
Sharma P, Kim CY, Keys HR, Imada S, Joseph AB, Ferro L, Kunchok T, Anderson R, Sun Y, Yilmaz ÖH, Weng JK, Jain A. Genetically encoded fluorescent reporter for polyamines. Nat Commun 2025;16:4921. [PMID: 40425580 PMCID: PMC12117157 DOI: 10.1038/s41467-025-60147-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2024] [Accepted: 05/16/2025] [Indexed: 05/29/2025]  Open
2
Wang Z, Yu H, Gu Z, Shi X, Ma J, Shao Q, Yao Y, Yao S, Xu Y, Gu Y, Dai J, Liu Q, Shi J, Qi R, Jin Y, Liu Y, Shen X, Huang W, Liu HJ, Jin M, Liu W, Brook M, Chen D. RNA-binding proteins DND1 and NANOS3 cooperatively suppress the entry of germ cell lineage. Nat Commun 2025;16:4792. [PMID: 40410171 PMCID: PMC12102168 DOI: 10.1038/s41467-025-57490-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2024] [Accepted: 02/24/2025] [Indexed: 05/25/2025]  Open
3
Teng H, Hang Q, Zheng C, Yan Y, Liu S, Zhao Y, Deng Y, Nie L, Wu W, Sheldon M, Yu Z, Shi W, Gao J, Meng C, Martinez C, Zhang J, Yao F, Sun Y, Zhao D, Gan B, Meng T, Ma L. In vivo CRISPR activation screen identifies acyl-CoA-binding protein as a driver of bone metastasis. Sci Transl Med 2025;17:eado7225. [PMID: 40397713 DOI: 10.1126/scitranslmed.ado7225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 12/03/2024] [Accepted: 04/29/2025] [Indexed: 05/23/2025]
4
Zolboot N, Xiao Y, Du JX, Ghanem MM, Choi SY, Junn MJ, Zampa F, Huang Z, MacRae IJ, Lippi G. MicroRNA mechanisms instructing Purkinje cell specification. Neuron 2025;113:1629-1646.e15. [PMID: 40179877 DOI: 10.1016/j.neuron.2025.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2024] [Revised: 01/22/2025] [Accepted: 03/04/2025] [Indexed: 04/05/2025]
5
Naara S, Cui Z, Izgutdina A, VanLandingham NK, Nazarenko A, Woerner LC, Hua Fu BX, Gilbert LA, Johnson DE, Grandis JR. Neddylation as a target in PIK3CA-mutated head and neck cancer. Biochem Biophys Res Commun 2025;759:151703. [PMID: 40154000 PMCID: PMC12036330 DOI: 10.1016/j.bbrc.2025.151703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2025] [Revised: 03/22/2025] [Accepted: 03/24/2025] [Indexed: 04/01/2025]
6
Gu S, Bodai Z, Anderson RA, So HYA, Cowan QT, Komor AC. Elucidating the genetic mechanisms governing cytosine base editing outcomes through CRISPRi screens. Nat Commun 2025;16:4685. [PMID: 40394064 DOI: 10.1038/s41467-025-59948-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 05/09/2025] [Indexed: 05/22/2025]  Open
7
Akers JF, LaScola M, Bothe A, Suh H, Jung C, Stolp ZD, Ghosh T, Yan LL, Wang Y, Macurak M, Devan A, McKinney MC, Grismer TS, Reyes AV, Ross EJ, Hu T, Xu SL, Ban N, Kostova KK. ZNF574 is a quality control factor for defective ribosome biogenesis intermediates. Mol Cell 2025;85:2048-2060.e9. [PMID: 40328246 PMCID: PMC12101526 DOI: 10.1016/j.molcel.2025.04.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2024] [Revised: 03/08/2025] [Accepted: 04/15/2025] [Indexed: 05/08/2025]
8
Fu H, Itoh Y, Sawaguchi T, Otake S, Omata C, Saitoh M, Miyazawa K. Identification of a Distal Enhancer That Regulates TGF-β-Induced SNAI1 Expression. Cancer Sci 2025. [PMID: 40364580 DOI: 10.1111/cas.70091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2024] [Revised: 04/14/2025] [Accepted: 04/23/2025] [Indexed: 05/15/2025]  Open
9
Zhang T, Zhang Y, Wang X, Hu H, Lin CG, Xu Y, Zheng H. Genome-wide CRISPR activation screen identifies ARL11 as a sensitivity determinant of PARP inhibitor therapy. Cancer Gene Ther 2025;32:521-537. [PMID: 40123001 DOI: 10.1038/s41417-025-00893-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2024] [Revised: 02/16/2025] [Accepted: 03/13/2025] [Indexed: 03/25/2025]
10
Kim Y, Oh J, Kim JR, Lee D, Kim JY. CRISPRi screening identifies PIKfyve as a co-therapeutic target for obinutuzumab. Clin Transl Med 2025;15:e70333. [PMID: 40342289 PMCID: PMC12059204 DOI: 10.1002/ctm2.70333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2025] [Revised: 04/22/2025] [Accepted: 04/28/2025] [Indexed: 05/11/2025]  Open
11
Zorab JM, Li H, Awasthi R, Schinasi A, Cho Y, O'Loughlin T, Wu X. Serotonin and neurotensin inputs in the vCA1 dictate opposing social valence. Nature 2025:10.1038/s41586-025-08809-2. [PMID: 40307550 DOI: 10.1038/s41586-025-08809-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 02/19/2025] [Indexed: 05/02/2025]
12
Lee JS, Dan T, Zhang H, Cheng Y, Rehfeld F, Brugarolas J, Mendell JT. An ultraconserved snoRNA-like element in long noncoding RNA CRNDE promotes ribosome biogenesis and cell proliferation. Mol Cell 2025;85:1543-1560.e10. [PMID: 40185099 PMCID: PMC12009208 DOI: 10.1016/j.molcel.2025.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Revised: 01/02/2025] [Accepted: 03/05/2025] [Indexed: 04/07/2025]
13
Chen B, Lyssiotis CA, Shah YM. Mitochondria-organelle crosstalk in establishing compartmentalized metabolic homeostasis. Mol Cell 2025;85:1487-1508. [PMID: 40250411 DOI: 10.1016/j.molcel.2025.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2024] [Revised: 02/21/2025] [Accepted: 03/04/2025] [Indexed: 04/20/2025]
14
Berlind JE, Lai JD, Lie C, Vicente J, Lam K, Guo S, Chang J, Yu V, Ichida JK. KCTD20 suppression mitigates excitotoxicity in tauopathy patient organoids. Neuron 2025;113:1169-1189.e7. [PMID: 40049159 PMCID: PMC12005969 DOI: 10.1016/j.neuron.2025.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 12/13/2024] [Accepted: 02/04/2025] [Indexed: 04/19/2025]
15
Zhang Z, Fu X, Wright N, Wang W, Ye Y, Asbury J, Li Y, Zhu C, Wu R, Wang S, Sun S. PTPσ-mediated PI3P regulation modulates neurodegeneration in C9ORF72-ALS/FTD. Neuron 2025;113:1190-1205.e9. [PMID: 40073860 PMCID: PMC12005967 DOI: 10.1016/j.neuron.2025.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Revised: 12/09/2024] [Accepted: 02/06/2025] [Indexed: 03/14/2025]
16
Okubo C, Nakamura M, Sato M, Shichino Y, Mito M, Takashima Y, Iwasaki S, Takahashi K. EIF3D safeguards the homeostasis of key signaling pathways in human primed pluripotency. SCIENCE ADVANCES 2025;11:eadq5484. [PMID: 40203091 PMCID: PMC11980838 DOI: 10.1126/sciadv.adq5484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2024] [Accepted: 03/04/2025] [Indexed: 04/11/2025]
17
Minakaki G, Safren N, Bustos BI, Lubbe SJ, Mencacci NE, Krainc D. Commander complex regulates lysosomal function and is implicated in Parkinson's disease risk. Science 2025;388:204-211. [PMID: 40209002 DOI: 10.1126/science.adq6650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 12/02/2024] [Accepted: 02/12/2025] [Indexed: 04/12/2025]
18
Saini A, Hopkins LS, Serna VA, McCullen MVD, Selner NG, Bhattarai B, Fachi JL, Glynn R, Hayer KE, Bassing CH, Colonna M, Oltz EM. Cell type-specific enhancers regulate IL-22 expression in innate and adaptive lymphoid cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.04.02.646834. [PMID: 40291691 PMCID: PMC12026504 DOI: 10.1101/2025.04.02.646834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/30/2025]
19
Teter OM, McQuade A, Hagan V, Liang W, Dräger NM, Sattler SM, Holmes BB, Castillo VC, Papakis V, Leng K, Boggess S, Nowakowski TJ, Wells J, Kampmann M. CRISPRi-based screen of autism spectrum disorder risk genes in microglia uncovers roles of ADNP in microglia endocytosis and synaptic pruning. Mol Psychiatry 2025:10.1038/s41380-025-02997-z. [PMID: 40188316 DOI: 10.1038/s41380-025-02997-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 03/06/2025] [Accepted: 03/26/2025] [Indexed: 04/07/2025]
20
Liu M, Yue Y, Chen X, Xian K, Dong C, Shi M, Xiong H, Tian K, Li Y, Zhang QC, He A. Genome-coverage single-cell histone modifications for embryo lineage tracing. Nature 2025;640:828-839. [PMID: 40011786 PMCID: PMC12003199 DOI: 10.1038/s41586-025-08656-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 01/16/2025] [Indexed: 02/28/2025]
21
Cui X, Yang H, Cai C, Beaman C, Yang X, Liu H, Ren X, Amador Z, Jones IR, Keough KC, Zhang M, Fair T, Abnousi A, Mishra S, Ye Z, Hu M, Pollen AA, Pollard KS, Shen Y. Comparative characterization of human accelerated regions in neurons. Nature 2025;640:991-999. [PMID: 40011774 DOI: 10.1038/s41586-025-08622-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 01/10/2025] [Indexed: 02/28/2025]
22
Fielden J, Siegner SM, Gallagher DN, Schröder MS, Dello Stritto MR, Lam S, Kobel L, Schlapansky MF, Jackson SP, Cejka P, Jost M, Corn JE. Comprehensive interrogation of synthetic lethality in the DNA damage response. Nature 2025;640:1093-1102. [PMID: 40205037 PMCID: PMC12018271 DOI: 10.1038/s41586-025-08815-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 02/19/2025] [Indexed: 04/11/2025]
23
Carter AC, Koreman GT, Petrocelli JE, Robb JE, Bushinsky EM, Trowbridge SK, Kingsley DM, Walsh CA, Song JHT, Greenberg ME. FOS binding sites are a hub for the evolution of activity-dependent gene regulatory programs in human neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.31.646366. [PMID: 40236085 PMCID: PMC11996375 DOI: 10.1101/2025.03.31.646366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/17/2025]
24
Rahimian E, Koochak M, Traikov S, Schroeder M, Brilloff S, Schäfer S, Kufrin V, Küchler S, Krüger A, Mirtschink P, Baretton G, Schröck E, Schewe DM, Ball CR, Bornhäuser M, Glimm H, Bill M, Wurm AA. A quiescence-like/TGF-β1-specific CRISPRi screen reveals drug uptake transporters as secondary targets of kinase inhibitors in AML. Drug Resist Updat 2025;81:101242. [PMID: 40184725 DOI: 10.1016/j.drup.2025.101242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2024] [Revised: 02/26/2025] [Accepted: 03/23/2025] [Indexed: 04/07/2025]
25
Kufrin V, Seiler A, Brilloff S, Rothfuß H, Küchler S, Schäfer S, Rahimian E, Baumgarten J, Ding L, Buchholz F, Ball CR, Bornhäuser M, Glimm H, Bill M, Wurm AA. The histone modifier KAT2A presents a selective target in a subset of well-differentiated microsatellite-stable colorectal cancers. Cell Death Differ 2025:10.1038/s41418-025-01479-7. [PMID: 40140561 DOI: 10.1038/s41418-025-01479-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 01/27/2025] [Accepted: 03/14/2025] [Indexed: 03/28/2025]  Open
26
Kim YM, Akana RV, Sun C, Laveroni O, Jerby L. Redirecting cytotoxic lymphocytes to breast cancer tumors via metabolite-sensing receptors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.21.644686. [PMID: 40196673 PMCID: PMC11974742 DOI: 10.1101/2025.03.21.644686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 04/09/2025]
27
Villegas NK, Gaudreault YR, Keller A, Kearns P, Stapleton JA, Plesa C. Optimizing in vitro Transcribed CRISPR-Cas9 Single-Guide RNA Libraries for Improved Uniformity and Affordability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.24.644170. [PMID: 40196484 PMCID: PMC11974757 DOI: 10.1101/2025.03.24.644170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 04/09/2025]
28
Chia BS, Seah YFS, Wang B, Shen K, Srivastava D, Chew WL. Engineering a New Generation of Gene Editors: Integrating Synthetic Biology and AI Innovations. ACS Synth Biol 2025;14:636-647. [PMID: 39999982 PMCID: PMC11934138 DOI: 10.1021/acssynbio.4c00686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2024] [Revised: 01/06/2025] [Accepted: 01/16/2025] [Indexed: 02/27/2025]
29
Saxena T, Quan A, Chan E, Kozlova N, Matai L, Lee JD, Rupaimoole R, Beca F, Muranen T, Slack FJ. EGFR-induced lncRNA TRIDENT promotes drug resistance in non-small cell lung cancer via phospho-TRIM28-mediated DNA damage repair. Proc Natl Acad Sci U S A 2025;122:e2415389122. [PMID: 40030013 PMCID: PMC11912419 DOI: 10.1073/pnas.2415389122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2024] [Accepted: 01/06/2025] [Indexed: 03/19/2025]  Open
30
Li X, Zhang W, Fang Y, Sun T, Chen J, Tian R. Large-scale CRISPRi screens link metabolic stress to glioblastoma chemoresistance. J Transl Med 2025;23:289. [PMID: 40050992 PMCID: PMC11887098 DOI: 10.1186/s12967-025-06261-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2024] [Accepted: 02/14/2025] [Indexed: 03/09/2025]  Open
31
Pattali RK, Ornelas IJ, Nguyen CD, Xu D, Divekar NS, Nuñez NK. CRISPRoff epigenome editing for programmable gene silencing in human cell lines and primary T cells. Methods Enzymol 2025;712:517-551. [PMID: 40121086 PMCID: PMC12052198 DOI: 10.1016/bs.mie.2025.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2025]
32
Li E, Benitez C, Boggess SC, Koontz M, Rose IVL, Martinez D, Dräger N, Teter OM, Samelson AJ, Pierce N, Ullian EM, Kampmann M. CRISPRi-based screens in iAssembloids to elucidate neuron-glia interactions. Neuron 2025;113:701-718.e8. [PMID: 39814010 PMCID: PMC11886924 DOI: 10.1016/j.neuron.2024.12.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 11/25/2024] [Accepted: 12/17/2024] [Indexed: 01/18/2025]
33
Edington AR, Connor OM, Love AC, Marlar-Pavey M, Friedman JR. Functionally conserved inner mitochondrial membrane proteins CCDC51 and Mdm33 demarcate a subset of fission events. J Cell Biol 2025;224:e202403140. [PMID: 39718510 PMCID: PMC11668171 DOI: 10.1083/jcb.202403140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 10/11/2024] [Accepted: 11/20/2024] [Indexed: 12/25/2024]  Open
34
Chesner LN, Polesso F, Graff JN, Hawley JE, Smith AK, Lundberg A, Das R, Shenoy T, Sjöström M, Zhao F, Hu YM, Linder S, Chen WS, Hawkins RM, Shrestha R, Zhu X, Foye A, Li H, Kim LM, Bhalla M, O’loughlin T, Kuzuoglu-Ozturk D, Hua JT, Badura ML, Wilkinson S, Trostel SY, Bergman AM, Ruggero D, Drake CG, Sowalsky AG, Fong L, Cooperberg MR, Zwart W, Guan X, Ashworth A, Xia Z, Quigley DA, Gilbert LA, Feng FY, Moran AE. Androgen Receptor Inhibition Increases MHC Class I Expression and Improves Immune Response in Prostate Cancer. Cancer Discov 2025;15:481-494. [PMID: 39652470 PMCID: PMC11873725 DOI: 10.1158/2159-8290.cd-24-0559] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 09/10/2024] [Accepted: 12/03/2024] [Indexed: 03/04/2025]
35
Kovalski JR, Sarioglu G, Subramanyam V, Hernandez G, Rademaker G, Oses-Prieto JA, Slota M, Mohan N, Yiakis K, Liu I, Wen KW, Kim GE, Miglani S, Burlingame AL, Goodarzi H, Perera RM, Ruggero D. Functional screen identifies RBM42 as a mediator of oncogenic mRNA translation specificity. Nat Cell Biol 2025;27:518-529. [PMID: 39905246 DOI: 10.1038/s41556-024-01604-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 12/20/2024] [Indexed: 02/06/2025]
36
Pacalin NM, Steinhart Z, Shi Q, Belk JA, Dorovskyi D, Kraft K, Parker KR, Shy BR, Marson A, Chang HY. Bidirectional epigenetic editing reveals hierarchies in gene regulation. Nat Biotechnol 2025;43:355-368. [PMID: 38760566 PMCID: PMC11569274 DOI: 10.1038/s41587-024-02213-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 03/19/2024] [Indexed: 05/19/2024]
37
Novy B, Dagunts A, Weishaar T, Holland EE, Adoff H, Hutchinson E, De Maria M, Kampmann M, Tsvetanova NG, Lobingier BT. An engineered trafficking biosensor reveals a role for DNAJC13 in DOR downregulation. Nat Chem Biol 2025;21:360-370. [PMID: 39223388 PMCID: PMC11867885 DOI: 10.1038/s41589-024-01705-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 07/17/2024] [Indexed: 09/04/2024]
38
Hsiung CCS, Wilson CM, Sambold NA, Dai R, Chen Q, Teyssier N, Misiukiewicz S, Arab A, O'Loughlin T, Cofsky JC, Shi J, Gilbert LA. Engineered CRISPR-Cas12a for higher-order combinatorial chromatin perturbations. Nat Biotechnol 2025;43:369-383. [PMID: 38760567 PMCID: PMC11919711 DOI: 10.1038/s41587-024-02224-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 03/28/2024] [Indexed: 05/19/2024]
39
Schmidt H, Zhang M, Chakarov D, Bansal V, Mourelatos H, Sánchez-Rivera FJ, Lowe SW, Ventura A, Leslie CS, Pritykin Y. Genome-wide CRISPR guide RNA design and specificity analysis with GuideScan2. Genome Biol 2025;26:41. [PMID: 40011959 PMCID: PMC11863968 DOI: 10.1186/s13059-025-03488-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 01/28/2025] [Indexed: 02/28/2025]  Open
40
Kirk RW, Sun L, Xiao R, Clark EA, Nelson S. Multiplexed CRISPRi Reveals a Transcriptional Switch Between KLF Activators and Repressors in the Maturing Neocortex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.07.636951. [PMID: 39975013 PMCID: PMC11839100 DOI: 10.1101/2025.02.07.636951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/21/2025]
41
Zheng X, Thompson PC, White CM, Jin X. Massively parallel in vivo Perturb-seq screening. Nat Protoc 2025:10.1038/s41596-024-01119-3. [PMID: 39939709 DOI: 10.1038/s41596-024-01119-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2024] [Accepted: 11/25/2024] [Indexed: 02/14/2025]
42
Rohm D, Black JB, McCutcheon SR, Barrera A, Berry SS, Morone DJ, Nuttle X, de Esch CE, Tai DJC, Talkowski ME, Iglesias N, Gersbach CA. Activation of the imprinted Prader-Willi syndrome locus by CRISPR-based epigenome editing. CELL GENOMICS 2025;5:100770. [PMID: 39947136 PMCID: PMC11872474 DOI: 10.1016/j.xgen.2025.100770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 10/01/2024] [Accepted: 01/17/2025] [Indexed: 02/19/2025]
43
Boggess SC, Gandhi V, Tsai MC, Marzette E, Teyssier N, Chou JYY, Hu X, Cramer A, Yadanar L, Shroff K, Jeong CG, Eidenschenk C, Hanson JE, Tian R, Kampmann M. A Massively Parallel CRISPR-Based Screening Platform for Modifiers of Neuronal Activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.02.28.582546. [PMID: 39990495 PMCID: PMC11844385 DOI: 10.1101/2024.02.28.582546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2025]
44
Abbasi AF, Asim MN, Dengel A. Transitioning from wet lab to artificial intelligence: a systematic review of AI predictors in CRISPR. J Transl Med 2025;23:153. [PMID: 39905452 PMCID: PMC11796103 DOI: 10.1186/s12967-024-06013-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2024] [Accepted: 12/18/2024] [Indexed: 02/06/2025]  Open
45
Muhar MF, Farnung J, Cernakova M, Hofmann R, Henneberg LT, Pfleiderer MM, Denoth-Lippuner A, Kalčic F, Nievergelt AS, Peters Al-Bayati M, Sidiropoulos ND, Beier V, Mann M, Jessberger S, Jinek M, Schulman BA, Bode JW, Corn JE. C-terminal amides mark proteins for degradation via SCF-FBXO31. Nature 2025;638:519-527. [PMID: 39880951 PMCID: PMC11821526 DOI: 10.1038/s41586-024-08475-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 12/02/2024] [Indexed: 01/31/2025]
46
Pena IA, Shi JS, Chang SM, Yang J, Block S, Adelmann CH, Keys HR, Ge P, Bathla S, Witham IH, Sienski G, Nairn AC, Sabatini DM, Lewis CA, Kory N, Vander Heiden MG, Heiman M. SLC25A38 is required for mitochondrial pyridoxal 5'-phosphate (PLP) accumulation. Nat Commun 2025;16:978. [PMID: 39856062 PMCID: PMC11760969 DOI: 10.1038/s41467-025-56130-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2024] [Accepted: 01/08/2025] [Indexed: 01/30/2025]  Open
47
Fu BXH, Xu A, Li H, Johnson DE, Grandis JR, Gilbert LA. Loss of Fanconi anemia proteins causes a reliance on lysosomal exocytosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.23.634631. [PMID: 39896609 PMCID: PMC11785144 DOI: 10.1101/2025.01.23.634631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2025]
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Sivakumar S, Wang Y, Goetsch SC, Pandit V, Wang L, Zhao H, Sundarrajan A, Armendariz D, Takeuchi C, Nzima M, Chen WC, Dederich AE, El Hayek L, Gao T, Ghazawi R, Gogate A, Kaur K, Kim HB, McCoy MK, Niederstrasser H, Oura S, Pinzon-Arteaga CA, Sanghvi M, Schmitz DA, Yu L, Zhang Y, Zhou Q, Kraus WL, Xu L, Wu J, Posner BA, Chahrour MH, Hon GC, Munshi NV. Benchmarking and optimizing Perturb-seq in differentiating human pluripotent stem cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.21.633969. [PMID: 39896670 PMCID: PMC11785042 DOI: 10.1101/2025.01.21.633969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/04/2025]
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Arvidsson E, Lobo DD, Sabarese E, Duarte F, Nobre RJ, Quintino L, Lundberg C. A systematic screening assay identifies efficient small guide RNAs for CRISPR activation. Front Bioeng Biotechnol 2025;13:1336313. [PMID: 39917018 PMCID: PMC11799263 DOI: 10.3389/fbioe.2025.1336313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 01/06/2025] [Indexed: 02/09/2025]  Open
50
Rengarajan S, Derks J, Bellott DW, Slavov N, Page DC. Post-transcriptional cross- and auto-regulation buffer expression of the human RNA helicases DDX3X and DDX3Y. Genome Res 2025;35:20-30. [PMID: 39794123 PMCID: PMC11789639 DOI: 10.1101/gr.279707.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Accepted: 11/26/2024] [Indexed: 01/13/2025]
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