May 3, 2024
Tracking chromatin state changes using nanoscale photo-proximity labelling – Nature

Tracking chromatin state changes using nanoscale photo-proximity labelling – Nature

  • Scott, D. E., Bayly, A. R., Abell, C. & Skidmore, J. Small molecules, big targets: drug discovery faces the protein–protein interaction challenge. Nat. Rev. Drug Discov. 15, 533–550 (2016).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Veltman, J. A. & Brunner, H. G. De novo mutations in human genetic disease. Nat. Rev. Genet. 13, 565–575 (2012).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Campbell, R. M. & Tummino, P. J. Cancer epigenetics drug discovery and development: the challenge of hitting the mark. J. Clin. Invest. 124, 64–69 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Geri, J. B. et al. Microenvironment mapping via Dexter energy transfer on immune cells. Science 367, 1091–1097 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 
    ADS 

    Google Scholar
     

  • Ruffner, H., Bauer, A. & Bouwmeester, T. Human protein–protein interaction networks and the value for drug discovery. Drug Discov. Today 12, 709–716 (2007).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kouzarides, T. Chromatin modifications and their function. Cell 128, 693–705 (2007).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ganesan, A., Arimondo, P. B., Rots, M. G., Jeronimo, C. & Berdasco, M. The timeline of epigenetic drug discovery: from reality to dreams. Clin. Epigenet. 11, 174 (2019).

    Article 
    CAS 

    Google Scholar
     

  • Schick, S. et al. Systematic characterization of BAF mutations provides insights into intracomplex synthetic lethalities in human cancers. Nat. Genet. 51, 1399–1410 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Cheng, F. et al. Comprehensive characterization of protein–protein interactions perturbed by disease mutations. Nat. Genet. 53, 342–353 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Cheng, Y. et al. Targeting epigenetic regulators for cancer therapy: mechanisms and advances in clinical trials. Signal Transduct. Target. Ther. 4, 62 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Weinberg, D. N., Allis, C. D. & Lu, C. Oncogenic mechanisms of histone H3 mutations. Cold Spring Harb. Perspect. Med. 7, a026443 (2017).

  • Bagert, J. D. et al. Oncohistone mutations enhance chromatin remodeling and alter cell fates. Nat. Chem. Biol. 17, 403–411 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Nacev, B. A. et al. The expanding landscape of ‘oncohistone’ mutations in human cancers. Nature 567, 473–478 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 
    ADS 

    Google Scholar
     

  • Müller, M. M. & Muir, T. W. Histones: at the crossroads of peptide and protein chemistry. Chem. Rev. 115, 2296–2349 (2015).

    Article 
    PubMed 

    Google Scholar
     

  • Vermeulen, M. & Déjardin, J. Locus-specific chromatin isolation. Nat. Rev. Mol. Cell Biol. 21, 249–250 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Van Mierlo, G. & Vermeulen, M. Chromatin proteomics to study epigenetics—challenges and opportunities. Mol. Cell. Proteomics 20, 100056 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ciferri, C. et al. Molecular architecture of human polycomb repressive complex 2. eLife 1, e00005 (2012).

  • Ruthenburg, A. J. et al. Recognition of a mononucleosomal histone modification pattern by BPTF via multivalent interactions. Cell 145, 692–706 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhao, S., Yue, Y., Li, Y. & Li, H. Identification and characterization of ‘readers’ for novel histone modifications. Curr. Opin. Chem. Biol. 51, 57–65 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Burton, A. J. et al. In situ chromatin interactomics using a chemical bait and trap approach. Nat. Chem. 12, 520–527 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kleiner, R. E., Hang, L. E., Molloy, K. R., Chait, B. T. & Kapoor, T. M. A chemical proteomics approach to reveal direct protein–protein interactions in living cells. Cell Chem. Biol. 25, 110–120 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Seath, C. P., Trowbridge, A. D., Muir, T. W. & MacMillan, D. W. C. Reactive intermediates for interactome mapping. Chem. Soc. Rev. 50, 2911–2926 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Villaseñor, R. et al. ChromID identifies the protein interactome at chromatin marks. Nat. Biotechnol. 38, 728–736 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ummethum, H. & Hamperl, S. Proximity labeling techniques to study chromatin. Front. Genet. 11, 450 (2020).

  • Baldi, S., Korber, P. & Becker, P. B. Beads on a string—nucleosome array arrangements and folding of the chromatin fiber. Nat. Struct. Mol. Biol. 27, 109–118 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Stevens, A. J. et al. A promiscuous split intein with expanded protein engineering applications. Proc. Natl Acad. Sci. USA 114, 8538–8543 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 
    ADS 

    Google Scholar
     

  • Stevens, A. J. et al. Design of a split intein with exceptional protein splicing activity. J. Am. Chem. Soc. 138, 2162–2165 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Scott, W. A. & Campos, E. I. Interactions with histone H3 & tools to study them. Front. Cell Dev. Biol. 8, 701 (2020).

  • Pan, D. et al. Mechanism of centromere recruitment of the CENP-A chaperone HJURP and its implications for centromere licensing. Nat. Commun. 10, 4046 (2019).

  • Chen, C. C. et al. Establishment of centromeric chromatin by the CENP-A assembly factor CAL1 requires FACT-mediated transcription. Dev. Cell 34, 73–84 (2015).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bennett, R. L. et al. A mutation in histone H2B represents a new class of oncogenic driver. Cancer Discov. 9, 1438–1451 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • McGinty, R. K. & Tan, S. Nucleosome structure and function. Chem. Rev. 115, 2255–2273 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • McBride, M. J. et al. The nucleosome acidic patch and H2A ubiquitination underlie mSWI/SNF recruitment in synovial sarcoma. Nat. Struct. Mol. Biol. 27, 836–845 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Dao, H. T., Dul, B. E., Dann, G. P., Liszczak, G. P. & Muir, T. W. A basic motif anchoring ISWI to nucleosome acidic patch regulates nucleosome spacing. Nat. Chem. Biol. 16, 134–142 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Skrajna, A. et al. Comprehensive nucleosome interactome screen establishes fundamental principles of nucleosome binding. Nucleic Acids Res. 48, 9415–9432 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Anink-Groenen, L. C. M., Maarleveld, T. R., Verschure, P. J. & Bruggeman, F. J. Mechanistic stochastic model of histone modification pattern formation. Epigenetics Chromatin 7, 30 (2014).

  • Tachiwana, H. et al. Chromatin structure-dependent histone incorporation revealed by a genome-wide deposition assay. eLife 10, e66290 (2021).

  • Grandi, F. C., Modi, H., Kampman, L. & Corces, M. R. Chromatin accessibility profiling by ATAC-seq. Nat. Protoc. 17, 1518–1552 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Xu, T. et al. Structure of nucleosome-bound DNA methyltransferases DNMT3A and DNMT3B. Nature 586, 151–155 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 
    ADS 

    Google Scholar
     

  • Bolton, M. A. et al. Aurora B kinase exists in a complex with survivin and INCENP and its kinase activity is stimulated by survivin binding and phosphorylation. Mol. Biol. Cell 13, 3064–3077 (2002).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hodges, C., Kirkland, J. G. & Crabtree, G. R. The many roles of BAF (mSWI/SNF) and PBAF complexes in cancer. Cold Spring Harb. Perspect. Med. 6, a026930 (2016).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Filippakopoulos, P. et al. Selective inhibition of BET bromodomains. Nature 468, 1067–1073 (2010).

    Article 
    CAS 
    PubMed 
    PubMed Central 
    ADS 

    Google Scholar
     

  • Shi, J. & Vakoc, C. R. The mechanisms behind the therapeutic activity of BET bromodomain inhibition. Mol. Cell 54, 728–736 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Savitski, M. M. et al. Multiplexed proteome dynamics profiling reveals mechanisms controlling protein homeostasis. Cell 173, 260–274 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Stein, E. M. et al. The DOT1L inhibitor pinometostat reduces H3K79 methylation and has modest clinical activity in adult acute leukemia. Blood 131, 2662–2669 (2018).

    Article 

    Google Scholar
     

  • Gilan, O. et al. Functional interdependence of BRD4 and DOT1L in MLL leukemia. Nat. Struct. Mol. Biol. 23, 673–681 (2016).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Osman, S. & Cramer, P. Structural biology of RNA polymerase II transcription: 20 years on. Annu. Rev. Cell Dev. Biol. 36, 1–34 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Cramer, P. Organization and regulation of gene transcription. Nature 573, 45–54 (2019).

    Article 
    CAS 
    PubMed 
    ADS 

    Google Scholar
     

  • Young, R. A. RNA polymerase II. Annu. Rev. Biochem. 60, 689–715 (1991).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Santo, L. et al. AT7519, a novel small molecule multi-cyclin-dependent kinase inhibitor, induces apoptosis in multiple myeloma via GSK-3Β activation and RNA polymerase II inhibition. Oncogene 29, 2325–2336 (2010).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Harlen, K. M. & Churchman, L. S. The code and beyond: transcription regulation by the RNA polymerase II carboxy-terminal domain. Nat. Rev. Mol. Cell Biol. 18, 263–273 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Trowbridge, A. D. et al. Small molecule photocatalysis enables drug target identification via energy transfer. Proc. Natl Acad. Sci. USA 119, e2208077119 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Cox, J. & Mann, M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 26, 1367–1372 (2008).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Tyanova, S. et al. The Perseus computational platform for comprehensive analysis of (prote)omics data. Nat. Methods 13, 731–740 (2016).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Traube, F. R. et al. Isotope-dilution mass spectrometry for exact quantification of noncanonical DNA nucleosides. Nat. Protoc. 14, 283–312 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Zhou, Y. et al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat. Commun. 10, 1523 (2019).

    Article 
    PubMed 
    PubMed Central 
    ADS 

    Google Scholar
     

  • Babicki, S. et al. Heatmapper: web-enabled heat mapping for all. Nucleic Acids Res. 44, 147–153 (2016).

    Article 

    Google Scholar
     

  • Source link