Cell Biol. endobj
endobj (2019). 356 0 obj
Protoc. 343 0 obj [531 0 R 532 0 R 533 0 R 745 0 R 746 0 R 747 0 R 535 0 R 536 0 R 748 0 R 749 0 R 750 0 R 751 0 R 752 0 R 753 0 R] doi: 10.1002/anie.201905949, Zhu, C., Li, L., Zhang, Z., Bi, M., Wang, H., Su, W., et al. Multiple disordered loops function in corepressor-induced dimerization of the biotin repressor. doi: 10.15252/embr.201948150, Martino, J., Brunette, G. J., Barroso-González, J., Moiseeva, T. N., Smith, C. M., Bakkenist, C. J., et al. endobj Curr. 443 0 obj doi: 10.1074/jbc.M113.529578, Li, Y., Luo, H., Liu, T., Zacksenhaus, E., and Ben-David, Y. doi: 10.1128/MCB.23.24.9275-9282.2003. endobj (2013). 375 0 obj Mol. Chromatin remodelers play a key role in reshaping the chromatin landscape to grant access to transcription, replication or DNA-repair factors.
Genome Biol. doi: 10.1038/onc.2014.162, Liu, C.-H., Chien, M.-J., Chang, Y.-C., Cheng, Y.-H., Li, F.-A., and Mou, K. Y. Figure 1. 384 0 obj Proc. 234, 1611–1614. 339 0 obj 422 0 obj doi: 10.1016/j.devcel.2018.09.003, Zhang, P., Sun, Y., and Ma, L. (2015). 26, 804–817. Proc. Gross, A. J., and Sizer, I. W. (1959). J. Mol. <> Another example of coupling proximity and affinity purification with mass spectrometry is a study investigating the interactome of the DNA repair factor Ku70 (Abbasi and Schild-Poulter, 2019). Another drawback is that the strong biotin-streptavidin bond does not allow for efficient elution of biotinylated proteins from the beads. 22, 8088–8099. endobj MCM proteins: DNA damage, mutagenesis and repair. 23, 9275–9282. endobj Using antibodies does not lead to complex undetectable peptides. They can either influence the DNA-binding properties of histones through N-terminal modifications or directly move, evict or restructure nucleosomes in an ATP-dependent manner. 21, 228–239.
Here, BirA∗ was fused to normal Lamin A or the truncated form characteristic to this disease, called progerin (Chojnowski et al., 2015). J. Histochem. 686 0 obj <> 374 0 obj To circumvent this restriction, a method with the rapamycin inducible dimerization between FK506 binding protein (FKBP) and FKBP-rapamycin binding (FRB) combined with BioID was developed (Chojnowski et al., 2018). Acad.
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endobj doi: 10.1177/002215549704501101, Mazina, M. Y., Ziganshin, R. H., Magnitov, M. D., Golovnin, A. K., and Vorobyeva, N. E. (2020). <> Nat. Interactome rewiring following pharmacological targeting of BET bromodomains. 45, 1449–1454. endobj Consequently, proximity labeling was able to identify LSD1 dependence of the BHC complex. (B) Comparison of two studies with Lamin A as bait. <> doi: 10.1038/nmeth.3179, Lambert, J.-P., Picaud, S., Fujisawa, T., Hou, H., Savitsky, P., Uusküla-Reimand, L., et al. J. Proteomics 118, 81–94. J. Biol. endobj
endobj 9:3502. doi: 10.1038/s41467-018-05660-5660, Dubois, M.-L., Bastin, C., Lévesque, D., and Boisvert, F.-M. (2016). endobj After enrichment, proteins are analyzed by mass spectrometry to identify proteins interacting with the prey. doi: 10.1038/nbt1093-1138, Schiapparelli, L. M., McClatchy, D. B., Liu, H.-H., Sharma, P., Yates, J. R., and Cline, H. T. (2014). <>/MediaBox[0 0 595.32 841.92]/Parent 2 0 R/Resources<>/Font<>/ProcSet[/PDF/Text/ImageC]/XObject<>>>/StructParents 266/Tabs/S/Type/Page>> endobj endobj endobj
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<> Cell 44, 609–620. 337 0 obj (2017). Cytochem. <>
endobj <> doi: 10.1016/j.molcel.2019.06.010, Keywords: protein-protein interactions, proxisome, BioID, APEX2, dCas9, ChIP, affinity purification, mass spectrometry, Citation: Ummethum H and Hamperl S (2020) Proximity Labeling Techniques to Study Chromatin. endobj
This modification is associated with gene activation and overexpression of NSD2 has been linked to some forms of cancer (Kuo et al., 2011). (2018). 421 0 obj endobj Cell Cycle 16, 947–956.
146, 469–492. Nucleic Acids Res. However, the exact interaction dynamics between the two split fragments remain unknown, e.g., if the reconstitution is reversible. Therefore, proximity labeling enables the study of proxisomes even in insoluble cell compartments like the nuclear matrix, nucleoli and other nuclear structures – difficult to study with conventional methods. Because these radicals are very short lived (<1 ms), they can only react with amino acid residues in close proximity of the peroxidase (Mortensen and Skibsted, 1997). endobj 433 0 obj Recent developments in proximity labeling techniques have provided a valuable platform to study chromatin in new ways. Nucleic Acids Res. A. Determination of local chromatin interactions using a combined CRISPR and peroxidase APEX2 system. (2018). 365 0 obj Copy number gains of SOX2 arise in almost all squamous cell carcinomas (SQCC) of the lung, suggesting a functional role in disease progression (Weina and Utikal, 2014). With APEX-seq, it is possible to probe the vicinity not only for proteins, but also for various forms of RNAs. Biochem. 342 0 obj 392 0 obj
Proximity-labeling using engineered biotin ligases TurboID and miniTurbo enables detection of cell-type-specific and low abundance protein complexes and subcellular proteomes in Arabidopsis and other plants.
endobj The protein of interest (bait) is fused to the reporter enzyme and expressed in cells. Uncovering the in vivo proxisome using proximity-tagging methods. 366 0 obj 414 0 obj
9, 1530–1539.
In a similar approach, the nuclear vicinity of vesicle-associated membrane protein-associated protein B (VABP) was explored with rapamycin directed APEX2 (James et al., 2019). Chem.