proximity labeling review

<> MYC protein interactome profiling reveals functionally distinct regions that cooperate to drive tumorigenesis. application/pdf <> Increased expression of the isoform P2-HNF4α has recently been implicated in colorectal cancer. H�|Tَ�8|��GiQ, Proximity Labeling-assisted Identification of Endogenous Kinase Substrates. Function of a conserved sequence motif in biotin holoenzyme synthetases. Genet., 12 May 2020 endobj We would like to thank all the scientists whose results we discussed in this review and apologize to all scientists whose work we could not cite due to space limitations. Overview of available proximity labeling enzymes and their characteristics. p62-Dependent phase separation of patient-derived KEAP1 mutations and NRF2. doi: 10.7554/eLife.20882, Veal, E. A., Day, A. M., and Morgan, B. Directed evolution of split APEX2 peroxidase. (2019). Comparative interactome analysis of emerin, MAN1 and LEM2 reveals a unique role for LEM2 in nucleotide excision repair. Elzi, D. J., Song, M., Hakala, K., Weintraub, S. T., and Shiio, Y. 404 0 obj Sci. endobj 234, 1611–1614. Nat. doi: 10.1038/s41593-017-0047-43, Chu, Q., Rathore, A., Diedrich, J. K., Donaldson, C. J., Yates, J. R., and Saghatelian, A. The authors fused BirA to RAD18 and BAP to histones H3.1 and H2A. endobj Furthermore, experimental design also entails whether to use a qualitative or one of the many quantitative mass spectrometry approaches. J. doi: 10.1016/j.cell.2017.03.022, López-Soop, G., Rønningen, T., Rogala, A., Richartz, N., Blomhoff, H. K., Thiede, B., et al. Biol. Angew. endobj 391 0 obj doi: 10.1038/nprot.2016.018, Hwang, J., and Espenshade, P. J. 408 0 obj <> These methods take advantage of engineered enzymes that are fused to a chromatin factor of interest and can directly label all factors in proximity. Protoc. In an attempt to identify a more complete interaction map, Dubois et al. To identify proximal factors of ALT cell telomeres, BioID proximity labeling with TRF1-BirA∗ was used (Garcia-Exposito et al., 2016). A multi-layered structure of the interphase chromocenter revealed by proximity-based biotinylation. 423 0 obj Natl. endobj endobj Eisenberg, M. A., Prakash, O., and Hsiung, S. C. (1982). 17:182. doi: 10.1186/s13059-016-1043-1048, van Tienen, L. M., Mieszczanek, J., Fiedler, M., Rutherford, T. J., and Bienz, M. (2017). 381 0 obj Chem. The protein of interest (bait) is fused to the reporter enzyme and expressed in cells. Here, BirA∗ was fused to normal Lamin A or the truncated form characteristic to this disease, called progerin (Chojnowski et al., 2015). All methods described until now give insight into chromatin interactions that can occur genome-wide without any spatial information. In fact, biotinylation relies on the number and accessibility of the targeted amino acid residues, mostly lysine or tyrosine. endobj endobj 9:1188. doi: 10.1038/s41467-018-03523-3522, Lobingier, B. T., Hüttenhain, R., Eichel, K., Miller, K. B., Ting, A. Y., von Zastrow, M., et al. Furthermore, splitting the reporter enzyme results in smaller tags for the POI and therefore potentially less functional impact. The overlap between the qualitative and quantitative approaches provided 16 potential high-confidence interactors. Nat. (2013). <> Consequently, a time course biotin “painting” approach could even give insight into differences of secondary or tertiary protein structures. J. Histochem. Direct detection of biotinylated proteins by mass spectrometry. endobj 357 0 obj Rep. 7:12039. doi: 10.1038/s41598-017-12365-12369, Youn, J.-Y., Dunham, W. H., Hong, S. J., Knight, J. D. R., Bashkurov, M., Chen, G. I., et al. endobj [1209 0 R 669 0 R 1210 0 R 1211 0 R 1212 0 R 1213 0 R 1214 0 R 1215 0 R 1216 0 R 1217 0 R 1218 0 R 1219 0 R 1220 0 R 1221 0 R 668 0 R] Other factors influencing chromatin structure are DNA methylation, long non-coding RNAs and chromatin remodelers. Cell Rep. 17:2724. doi: 10.1016/j.celrep.2016.11.014, Schatz, P. J. eLife 6:e20882. <>/MediaBox[0 0 595.32 841.92]/Parent 2 0 R/Resources<>/Font<>/ProcSet[/PDF/Text/ImageC]/XObject<>>>/StructParents 266/Tabs/S/Type/Page>> To study GFI1B’s proxisome, a GFI1B-BioID2 fusion protein was used (McClellan et al., 2019). 42:e2. doi: 10.1093/bfgp/elu037, Graham, R. C., and Karnovsky, M. J. However, if the cell type or the enrichment strategy of the control differs significantly, it is always recommended to include an internal experimental control, rather than solely relying on the CRAPome database.