pcDNA3 APEX2-NES Citations (59)
Originally described in: Directed evolution of APEX2 for electron microscopy and proximity labeling.Lam SS, Martell JD, Kamer KJ, Deerinck TJ, Ellisman MH, Mootha VK, Ting AY Nat Methods. 2014 Nov 24. doi: 10.1038/nmeth.3179. PubMed Journal
Articles Citing pcDNA3 APEX2-NES
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| Phosphorylation of NS5A Serine-235 is essential to hepatitis C virus RNA replication and normal replication compartment formation. Eyre NS, Hampton-Smith RJ, Aloia AL, Eddes JS, Simpson KJ, Hoffmann P, Beard MR. Virology. 2016 Apr;491:27-44. doi: 10.1016/j.virol.2016.01.018. Epub 2016 Feb 10. PubMed |
Proximity-dependent biotin labeling in yeast using the engineered ascorbate peroxidase APEX2.
Hwang J, Espenshade PJ.
Biochem J. 2016 Jun 7. pii: BCJ20160106.
PubMed
Associated Plasmids |
| Genetic dissection of Flaviviridae host factors through genome-scale CRISPR screens. Marceau CD, Puschnik AS, Majzoub K, Ooi YS, Brewer SM, Fuchs G, Swaminathan K, Mata MA, Elias JE, Sarnow P, Carette JE. Nature. 2016 Jul 7;535(7610):159-63. doi: 10.1038/nature18631. Epub 2016 Jun 17. PubMed |
| Static Clathrin Assemblies at the Peripheral Vacuole-Plasma Membrane Interface of the Parasitic Protozoan Giardia lamblia. Zumthor JP, Cernikova L, Rout S, Kaech A, Faso C, Hehl AB. PLoS Pathog. 2016 Jul 20;12(7):e1005756. doi: 10.1371/journal.ppat.1005756. eCollection 2016 Jul. PubMed |
| A Chemically Programmed Proximal Ligand Enhances the Catalytic Properties of a Heme Enzyme. Green AP, Hayashi T, Mittl PR, Hilvert D. J Am Chem Soc. 2016 Sep 7;138(35):11344-52. doi: 10.1021/jacs.6b07029. Epub 2016 Aug 26. PubMed |
| Development of a Proximity Labeling System to Map the Chlamydia trachomatis Inclusion Membrane. Rucks EA, Olson MG, Jorgenson LM, Srinivasan RR, Ouellette SP. Front Cell Infect Microbiol. 2017 Feb 15;7:40. doi: 10.3389/fcimb.2017.00040. eCollection 2017. PubMed |
Multidimensional Tracking of GPCR Signaling via Peroxidase-Catalyzed Proximity Labeling.
Paek J, Kalocsay M, Staus DP, Wingler L, Pascolutti R, Paulo JA, Gygi SP, Kruse AC.
Cell. 2017 Apr 6;169(2):338-349.e11. doi: 10.1016/j.cell.2017.03.028.
PubMed
Associated Plasmids |
| An Approach to Spatiotemporally Resolve Protein Interaction Networks in Living Cells. Lobingier BT, Huttenhain R, Eichel K, Miller KB, Ting AY, von Zastrow M, Krogan NJ. Cell. 2017 Apr 6;169(2):350-360.e12. doi: 10.1016/j.cell.2017.03.022. PubMed |
| The ciliary membrane-associated proteome reveals actin-binding proteins as key components of cilia. Kohli P, Hohne M, Jungst C, Bertsch S, Ebert LK, Schauss AC, Benzing T, Rinschen MM, Schermer B. EMBO Rep. 2017 Sep;18(9):1521-1535. doi: 10.15252/embr.201643846. Epub 2017 Jul 14. PubMed |
| Electron microscopy using the genetically encoded APEX2 tag in cultured mammalian cells. Martell JD, Deerinck TJ, Lam SS, Ellisman MH, Ting AY. Nat Protoc. 2017 Sep;12(9):1792-1816. doi: 10.1038/nprot.2017.065. Epub 2017 Aug 10. PubMed |
| Production and evaluation of parathyroid hormone receptor1 ligands with intrinsic or assembled peroxidase domains. Charest-Morin X, Poubelle PE, Marceau F. Sci Rep. 2017 Oct 12;7(1):13099. doi: 10.1038/s41598-017-13548-0. PubMed |
| Bifunctional fusion proteins containing the sequence of the bradykinin homologue maximakinin: activities at the rat bradykinin B2 receptor. Charest-Morin X, Lodge R, Marceau F. Can J Physiol Pharmacol. 2018 May;96(5):459-470. doi: 10.1139/cjpp-2017-0692. Epub 2018 Feb 7. PubMed |
Galectins Control mTOR in Response to Endomembrane Damage.
Jia J, Abudu YP, Claude-Taupin A, Gu Y, Kumar S, Choi SW, Peters R, Mudd MH, Allers L, Salemi M, Phinney B, Johansen T, Deretic V.
Mol Cell. 2018 Apr 5;70(1):120-135.e8. doi: 10.1016/j.molcel.2018.03.009.
PubMed
Associated Plasmids |
| C-BERST: defining subnuclear proteomic landscapes at genomic elements with dCas9-APEX2. Gao XD, Tu LC, Mir A, Rodriguez T, Ding Y, Leszyk J, Dekker J, Shaffer SA, Zhu LJ, Wolfe SA, Sontheimer EJ. Nat Methods. 2018 Jun;15(6):433-436. doi: 10.1038/s41592-018-0006-2. Epub 2018 May 7. PubMed |
| High-quality ultrastructural preservation using cryofixation for 3D electron microscopy of genetically labeled tissues. Tsang TK, Bushong EA, Boassa D, Hu J, Romoli B, Phan S, Dulcis D, Su CY, Ellisman MH. Elife. 2018 May 11;7. pii: 35524. doi: 10.7554/eLife.35524. PubMed |
| Proximity Labeling by a Recombinant APEX2-FGF1 Fusion Protein Reveals Interaction of FGF1 with the Proteoglycans CD44 and CSPG4. Zhen Y, Haugsten EM, Singh SK, Wesche J. Biochemistry. 2018 Jul 3;57(26):3807-3816. doi: 10.1021/acs.biochem.8b00120. Epub 2018 Jun 13. PubMed |
| Meloidogyne incognita PASSE-MURAILLE (MiPM) Gene Encodes a Cell-Penetrating Protein That Interacts With the CSN5 Subunit of the COP9 Signalosome. Bournaud C, Gillet FX, Murad AM, Bresso E, Albuquerque EVS, Grossi-de-Sa MF. Front Plant Sci. 2018 Jun 26;9:904. doi: 10.3389/fpls.2018.00904. eCollection 2018. PubMed |
Correlated Light-Serial Scanning Electron Microscopy (CoLSSEM) for ultrastructural visualization of single neurons in vivo.
Hirabayashi Y, Tapia JC, Polleux F.
Sci Rep. 2018 Sep 27;8(1):14491. doi: 10.1038/s41598-018-32820-5.
PubMed
Associated Plasmids |
| High-resolution mapping of centromeric protein association using APEX-chromatin fibers. Kyriacou E, Heun P. Epigenetics Chromatin. 2018 Nov 16;11(1):68. doi: 10.1186/s13072-018-0237-6. PubMed |
Proximity-CLIP provides a snapshot of protein-occupied RNA elements in subcellular compartments.
Benhalevy D, Anastasakis DG, Hafner M.
Nat Methods. 2018 Dec;15(12):1074-1082. doi: 10.1038/s41592-018-0220-y. Epub 2018 Nov 26.
PubMed
Associated Plasmids |
| Mapping the Proteome of the Synaptic Cleft through Proximity Labeling Reveals New Cleft Proteins. Cijsouw T, Ramsey AM, Lam TT, Carbone BE, Blanpied TA, Biederer T. Proteomes. 2018 Nov 28;6(4). pii: proteomes6040048. doi: 10.3390/proteomes6040048. PubMed |
Creation of versatile cloning platforms for transgene expression and dCas9-based epigenome editing.
Haldeman JM, Conway AE, Arlotto ME, Slentz DH, Muoio DM, Becker TC, Newgard CB.
Nucleic Acids Res. 2018 Dec 27. pii: 5264291. doi: 10.1093/nar/gky1286.
PubMed
Associated Plasmids |
| Misfolded GPI-anchored proteins are escorted through the secretory pathway by ER-derived factors. Zavodszky E, Hegde RS. Elife. 2019 May 16;8. pii: 46740. doi: 10.7554/eLife.46740. PubMed |
| Proximity labeling reveals novel interactomes in live Drosophila tissue. Mannix KM, Starble RM, Kaufman RS, Cooley L. Development. 2019 Jul 18;146(14). pii: dev.176644. doi: 10.1242/dev.176644. PubMed |
| Parcas is the predominant Rab11-GEF for rhodopsin transport in Drosophila photoreceptors. Otsuka Y, Satoh T, Nakayama N, Inaba R, Yamashita H, Satoh AK. J Cell Sci. 2019 Aug 7;132(15). pii: jcs.231431. doi: 10.1242/jcs.231431. PubMed |
| The cysteine-free single mutant C32S of APEX2 is a highly expressed and active fusion tag for proximity labeling applications. Huang MS, Lin WC, Chang JH, Cheng CH, Wang HY, Mou KY. Protein Sci. 2019 Sep;28(9):1703-1712. doi: 10.1002/pro.3685. Epub 2019 Aug 6. PubMed |
| Proximity Labeling of the Chlamydia trachomatis Inclusion Membrane. Olson MG, Jorgenson LM, Widner RE, Rucks EA. Methods Mol Biol. 2019;2042:245-278. doi: 10.1007/978-1-4939-9694-0_17. PubMed |
| Proximity Labeling To Map Host-Pathogen Interactions at the Membrane of a Bacterium-Containing Vacuole in Chlamydia trachomatis-Infected Human Cells. Olson MG, Widner RE, Jorgenson LM, Lawrence A, Lagundzin D, Woods NT, Ouellette SP, Rucks EA. Infect Immun. 2019 Oct 18;87(11). pii: IAI.00537-19. doi: 10.1128/IAI.00537-19. Print 2019 Nov. PubMed |
| Plasticity of the Cullin-RING Ligase Repertoire Shapes Sensitivity to Ligand-Induced Protein Degradation. Mayor-Ruiz C, Jaeger MG, Bauer S, Brand M, Sin C, Hanzl A, Mueller AC, Menche J, Winter GE. Mol Cell. 2019 Aug 22;75(4):849-858.e8. doi: 10.1016/j.molcel.2019.07.013. PubMed |
| Combining Proximity Labeling and Cross-Linking Mass Spectrometry for Proteomic Dissection of Nuclear Envelope Interactome. Liu CH, Chien MJ, Chang YC, Cheng YH, Li FA, Mou KY. J Proteome Res. 2020 Mar 6;19(3):1109-1118. doi: 10.1021/acs.jproteome.9b00609. Epub 2020 Feb 7. PubMed |
| A post-invasion role for Chlamydia type III effector TarP in modulating the dynamics and organization of host cell focal adhesions. Pedrosa AT, Murphy KN, Nogueira AT, Brinkworth AJ, Thwaites TR, Aaron J, Chew TL, Carabeo RA. J Biol Chem. 2020 Oct 23;295(43):14763-14779. doi: 10.1074/jbc.RA120.015219. Epub 2020 Aug 25. PubMed |
| SLC38A2 Overexpression Induces a Cancer-like Metabolic Profile and Cooperates with SLC1A5 in Pan-cancer Prognosis. Huang MS, Chang JH, Lin WC, Cheng YH, Li FA, Suen CS, Hwang MJ, Chang CK, Mou KY. Chem Asian J. 2020 Nov 16;15(22):3861-3872. doi: 10.1002/asia.202001056. Epub 2020 Oct 14. PubMed |
| SDE2 integrates into the TIMELESS-TIPIN complex to protect stalled replication forks. Rageul J, Park JJ, Zeng PP, Lee EA, Yang J, Hwang S, Lo N, Weinheimer AS, Scharer OD, Yeo JE, Kim H. Nat Commun. 2020 Oct 30;11(1):5495. doi: 10.1038/s41467-020-19162-5. PubMed |
LRRK2 mediates tubulation and vesicle sorting from lysosomes.
Bonet-Ponce L, Beilina A, Williamson CD, Lindberg E, Kluss JH, Saez-Atienzar S, Landeck N, Kumaran R, Mamais A, Bleck CKE, Li Y, Cookson MR.
Sci Adv. 2020 Nov 11;6(46). pii: 6/46/eabb2454. doi: 10.1126/sciadv.abb2454. Print 2020 Nov.
PubMed
Associated Plasmids |
Wnt-inducible Lrp6-APEX2 interacting proteins identify ESCRT machinery and Trk-fused gene as components of the Wnt signaling pathway.
Colozza G, Jami-Alahmadi Y, Dsouza A, Tejeda-Munoz N, Albrecht LV, Sosa EA, Wohlschlegel JA, De Robertis EM.
Sci Rep. 2020 Dec 9;10(1):21555. doi: 10.1038/s41598-020-78019-5.
PubMed
Associated Plasmids |
| E3 ubiquitin ligase Mindbomb 1 facilitates nuclear delivery of adenovirus genomes. Sarbanes SL, Blomen VA, Lam E, Heissel S, Luna JM, Brummelkamp TR, Falck-Pedersen E, Hoffmann HH, Rice CM. Proc Natl Acad Sci U S A. 2021 Jan 5;118(1). pii: 2015794118. doi: 10.1073/pnas.2015794118. Epub 2020 Dec 21. PubMed |
| Comparative Analysis of Hepatitis C Virus NS5A Dynamics and Localization in Assembly-Deficient Mutants. Riva L, Spriet C, Barois N, Popescu CI, Dubuisson J, Rouille Y. Pathogens. 2021 Feb 4;10(2). pii: pathogens10020172. doi: 10.3390/pathogens10020172. PubMed |
| Identification of cellular proteins interacting with PEDV M protein through APEX2 labeling. Dong S, Wang R, Yu R, Chen B, Si F, Xie C, Li Z. J Proteomics. 2021 May 30;240:104191. doi: 10.1016/j.jprot.2021.104191. Epub 2021 Mar 20. PubMed |
| Spatially resolved cell polarity proteomics of a human epiblast model. Wang S, Lin CW, Carleton AE, Cortez CL, Johnson C, Taniguchi LE, Sekulovski N, Townshend RF, Basrur V, Nesvizhskii AI, Zou P, Fu J, Gumucio DL, Duncan MC, Taniguchi K. Sci Adv. 2021 Apr 23;7(17). pii: 7/17/eabd8407. doi: 10.1126/sciadv.abd8407. Print 2021 Apr. PubMed |
| In vivo discovery of RNA proximal proteins via proximity-dependent biotinylation. Lin X, Fonseca MAS, Breunig JJ, Corona RI, Lawrenson K. RNA Biol. 2021 May 19:1-15. doi: 10.1080/15476286.2021.1917215. PubMed |
| Extracellular vesicles from neurons promote neural induction of stem cells through cyclin D1. Song L, Tian X, Schekman R. J Cell Biol. 2021 Sep 6;220(9). pii: 212508. doi: 10.1083/jcb.202101075. Epub 2021 Jul 26. PubMed |
Cell-type and subcellular compartment-specific APEX2 proximity labeling reveals activity-dependent nuclear proteome dynamics in the striatum.
Dumrongprechachan V, Salisbury RB, Soto G, Kumar M, MacDonald ML, Kozorovitskiy Y.
Nat Commun. 2021 Aug 11;12(1):4855. doi: 10.1038/s41467-021-25144-y.
PubMed
Associated Plasmids |
| Neuronal activity regulates the nuclear proteome to promote activity-dependent transcription. Herbst WA, Deng W, Wohlschlegel JA, Achiro JM, Martin KC. J Cell Biol. 2021 Dec 6;220(12). pii: 212684. doi: 10.1083/jcb.202103087. Epub 2021 Oct 7. PubMed |
| MITOL regulates phosphatidic acid-binding activity of RMDN3/PTPIP51. Ito N, Takahashi T, Shiiba I, Nagashima S, Inatome R, Yanagi S. J Biochem. 2021 Dec 29. pii: 6488375. doi: 10.1093/jb/mvab153. PubMed |
The ubiquitin-dependent ATPase p97 removes cytotoxic trapped PARP1 from chromatin.
Krastev DB, Li S, Sun Y, Wicks AJ, Hoslett G, Weekes D, Badder LM, Knight EG, Marlow R, Pardo MC, Yu L, Talele TT, Bartek J, Choudhary JS, Pommier Y, Pettitt SJ, Tutt ANJ, Ramadan K, Lord CJ.
Nat Cell Biol. 2022 Jan;24(1):62-73. doi: 10.1038/s41556-021-00807-6. Epub 2022 Jan 10.
PubMed
Associated Plasmids |
| In Situ Peroxidase Labeling Followed by Mass-Spectrometry Reveals TIA1 Interactome. Gourdomichali O, Zonke K, Kattan FG, Makridakis M, Kontostathi G, Vlahou A, Doxakis E. Biology (Basel). 2022 Feb 11;11(2). pii: biology11020287. doi: 10.3390/biology11020287. PubMed |
| APEX2-Mediated Proximity Labeling Resolves the DDIT4-Interacting Proteome. Naki M, Gourdomichali O, Zonke K, Kattan FG, Makridakis M, Kontostathi G, Vlahou A, Doxakis E. Int J Mol Sci. 2022 May 6;23(9). pii: ijms23095189. doi: 10.3390/ijms23095189. PubMed |
MicroID2: A Novel Biotin Ligase Enables Rapid Proximity Dependent Proteomics.
Johnson BS, Chafin L, Farkas D, Adair J, Elhance A, Farkas L, Bednash JS, Londino JD.
Mol Cell Proteomics. 2022 Jun 7:100256. doi: 10.1016/j.mcpro.2022.100256.
PubMed
Associated Plasmids |
A specific role for importin-5 and NASP in the import and nuclear hand-off of monomeric H3.
Pardal AJ, Bowman AJ.
Elife. 2022 Sep 6;11:e81755. doi: 10.7554/eLife.81755.
PubMed
Associated Plasmids |
| Heat shock protein Hspa13 regulates endoplasmic reticulum and cytosolic proteostasis through modulation of protein translocation. Espinoza MF, Nguyen KK, Sycks MM, Lyu Z, Quanrud GM, Montoya MR, Genereux JC. J Biol Chem. 2022 Dec;298(12):102597. doi: 10.1016/j.jbc.2022.102597. Epub 2022 Oct 14. PubMed |
| NIMA-related kinase 9 regulates the phosphorylation of the essential myosin light chain in the heart. Muller M, Eghbalian R, Boeckel JN, Frese KS, Haas J, Kayvanpour E, Sedaghat-Hamedani F, Lackner MK, Tugrul OF, Ruppert T, Tappu R, Martins Bordalo D, Kneuer JM, Piekarek A, Herch S, Schudy S, Keller A, Grammes N, Bischof C, Klinke A, Cardoso-Moreira M, Kaessmann H, Katus HA, Frey N, Steinmetz LM, Meder B. Nat Commun. 2022 Oct 20;13(1):6209. doi: 10.1038/s41467-022-33658-2. PubMed |
| Spatially resolved phosphoproteomics reveals fibroblast growth factor receptor recycling-driven regulation of autophagy and survival. Watson J, Ferguson HR, Brady RM, Ferguson J, Fullwood P, Mo H, Bexley KH, Knight D, Howell G, Schwartz JM, Smith MP, Francavilla C. Nat Commun. 2022 Nov 3;13(1):6589. doi: 10.1038/s41467-022-34298-2. PubMed |
| Characterization of huntingtin interactomes and their dynamic responses in living cells by proximity proteomics. Xu H, Bensalel J, Raju S, Capobianco E, Lu ML, Wei J. J Neurochem. 2023 Feb;164(4):512-528. doi: 10.1111/jnc.15726. Epub 2022 Nov 27. PubMed |
| Desmoglein 2 Functions as a Receptor for Fatty Acid Binding Protein 4 in Breast Cancer Epithelial Cells. Chen D, Wirth KM, Kizy S, Muretta JM, Markowski TW, Yong P, Sheka A, Abdelwahab H, Hertzel AV, Ikramuddin S, Yamamoto M, Bernlohr DA. Mol Cancer Res. 2023 Aug 1;21(8):836-848. doi: 10.1158/1541-7786.MCR-22-0763. PubMed |
| Glial-dependent clustering of voltage-gated ion channels in Drosophila precedes myelin formation. Rey S, Ohm H, Moschref F, Zeuschner D, Praetz M, Klambt C. Elife. 2023 Jun 6;12:e85752. doi: 10.7554/eLife.85752. PubMed |
| Structure and Function of RhoBTB1 Required for Substrate Specificity and Cullin-3 Ubiquitination. Kumar G, Fang S, Golosova D, Lu KT, Brozoski DT, Vazirabad I, Sigmund CD. Function (Oxf). 2023 Jul 3;4(5):zqad034. doi: 10.1093/function/zqad034. eCollection 2023. PubMed |
| Proteomic Analyses of the G Protein-Coupled Estrogen Receptor GPER1 Reveal Constitutive Links to Endoplasmic Reticulum, Glycosylation, Trafficking, and Calcium Signaling. Ahmadian Elmi M, Motamed N, Picard D. Cells. 2023 Nov 3;12(21):2571. doi: 10.3390/cells12212571. PubMed |
| Quantitative Measurement of Transthyretin Mistargeting by Proximity Labeling and Parallel Reaction Monitoring. Lyu Z, Genereux JC. Front Chem Biol. 2023;2:1288188. doi: 10.3389/fchbi.2023.1288188. Epub 2023 Nov 9. PubMed |
| APEX2-based proximity proteomic analysis identifies candidate interactors for Plasmodium falciparum knob-associated histidine-rich protein in infected erythrocytes. Charneau S, de Oliveira LS, Zenonos Z, Hopp CS, Bastos IMD, Loew D, Lombard B, Pandolfo Silveira A, de Carvalho Nardeli Basilio Lobo G, Bao SN, Grellier P, Rayner JC. Sci Rep. 2024 May 16;14(1):11242. doi: 10.1038/s41598-024-61295-w. PubMed |
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