Dhanasekaran, R. et al. The MYC oncogene—the grand orchestrator of cancer growth and immune evasion. Nat. Rev. Clin. Oncol. 19, 23–36 (2022).
Lourenco, C. et al. MYC protein interactors in gene transcription and cancer. Nat. Rev. Cancer 21, 579–591 (2021).
Baluapuri, A., Wolf, E. & Eilers, M. Target gene-independent functions of MYC oncoproteins. Nat. Rev. Mol. Cell Biol. 21, 255–267 (2020).
Herold, S. et al. Recruitment of BRCA1 limits MYCN-driven accumulation of stalled RNA polymerase. Nature 567, 545–549 (2019).
Roeschert, I. et al. Combined inhibition of Aurora-A and ATR kinase results in regression of MYCN-amplified neuroblastoma. Nat. Cancer 2, 312–326 (2021).
Endres, T. et al. Ubiquitylation of MYC couples transcription elongation with double-strand break repair at active promoters. Mol. Cell. 81, 830–844.e813 (2021).
Saldivar, J. C., Cortez, D. & Cimprich, K. A. The essential kinase ATR: ensuring faithful duplication of a challenging genome. Nat. Rev. Mol. Cell Biol. 18, 622–636 (2017).
Tarsounas, M. & Sung, P. The antitumorigenic roles of BRCA1-BARD1 in DNA repair and replication. Nat. Rev. Mol. Cell. Biol. 21, 284–299 (2020).
Boija, A. et al. Transcription factors activate genes through the phase-separation capacity of their activation domains. Cell 175, 1842–1855.e1816 (2018).
Lorenzin, F. et al. Different promoter affinities account for specificity in MYC-dependent gene regulation. eLife 5, e15161 (2016).
Walz, S. et al. Activation and repression by oncogenic MYC shape tumour-specific gene expression profiles. Nature 511, 483–487 (2014).
Lin, C. Y. et al. Transcriptional amplification in tumor cells with elevated c-Myc. Cell 151, 56–67 (2012).
Rosales, T. et al. Partition of Myc into immobile vs. mobile complexes within nuclei. Sci. Rep. 3, 1953 (2013).
Trader, D. J., Simanski, S. & Kodadek, T. A reversible and highly selective inhibitor of the proteasomal ubiquitin receptor rpn13 is toxic to multiple myeloma cells. J. Am. Chem. Soc. 137, 6312–6319 (2015).
Lamberto, I. et al. Structure-guided development of a potent and selective non-covalent active-site inhibitor of USP7. Cell Chem. Biol. 24, 1490–1500.e1411 (2017).
Gregory, M. A., Qi, Y. & Hann, S. R. Phosphorylation by glycogen synthase kinase-3 controls c-Myc proteolysis and subnuclear localization. J. Biol. Chem. 278, 51606–51612 (2003).
Kaida, D. et al. Spliceostatin A targets SF3b and inhibits both splicing and nuclear retention of pre-mRNA. Nat. Chem. Biol. 3, 576–583 (2007).
Carter, D. R. et al. Therapeutic targeting of the MYC signal by inhibition of histone chaperone FACT in neuroblastoma. Sci. Transl. Med. 7, 312ra176 (2015).
Cugusi, S. et al. Heat shock induces premature transcript termination and reconfigures the human transcriptome. Mol. Cell 82, 1573–1588.e10 (2022).
Wang, H. et al. Improved low molecular weight Myc–Max inhibitors. Mol. Cancer Ther. 6, 2399–2408 (2007).
Li, Y., Ma, X., Wu, W., Chen, Z. & Meng, G. PML nuclear body biogenesis, carcinogenesis, and targeted therapy. Trends Cancer 6, 889–906 (2020).
Arabi, A., Rustum, C., Hallberg, E. & Wright, A. P. Accumulation of c-Myc and proteasomes at the nucleoli of cells containing elevated c-Myc protein levels. J. Cell Sci. 116, 1707–1717 (2003).
Drygin, D. et al. Targeting RNA polymerase I with an oral small molecule CX-5461 inhibits ribosomal RNA synthesis and solid tumor growth. Cancer Res. 71, 1418–1430 (2011).
Nie, Z. et al. c-Myc is a universal amplifier of expressed genes in lymphocytes and embryonic stem cells. Cell 151, 68–79 (2012).
Lam, S. S. et al. Directed evolution of APEX2 for electron microscopy and proximity labeling. Nat. Methods 12, 51–54 (2015).
van Riggelen, J. et al. The interaction between Myc and Miz1 is required to antagonize TGFβ-dependent autocrine signaling during lymphoma formation and maintenance. Genes Dev. 24, 1281–1294 (2010).
Baluapuri, A. et al. MYC recruits SPT5 to RNA polymerase ii to promote processive transcription elongation. Mol. Cell 74, 674–687.e611 (2019).
Papadopoulos, D. et al. MYCN recruits the nuclear exosome complex to RNA polymerase II to prevent transcription-replication conflicts. Mol. Cell 82, 159–176.e112 (2022).
Das, S. K. et al. MYC assembles and stimulates topoisomerases 1 and 2 in a “topoisome”. Mol. Cell 82, 140–158.e112 (2022).
Nikiforov, M. A. et al. TRRAP-dependent and TRRAP-independent transcriptional activation by Myc family oncoproteins. Mol. Cell. Biol. 22, 5054–5063 (2002).
Fuchs, M. et al. The p400 complex is an essential E1A transformation target. Cell 106, 297–307 (2001).
Hingorani, S. R. et al. Trp53R172H and KrasG12D cooperate to promote chromosomal instability and widely metastatic pancreatic ductal adenocarcinoma in mice. Cancer Cell 7, 469–483 (2005).
Krenz, B. et al. MYC- and MIZ1-dependent vesicular transport of double-strand RNA controls immune evasion in pancreatic ductal adenocarcinoma. Cancer Res. 81, 4242–4256 (2021).
Chaudhury, I., Stroik, D. R. & Sobeck, A. FANCD2-controlled chromatin access of the Fanconi-associated nuclease FAN1 is crucial for the recovery of stalled replication forks. Mol. Cell. Biol. 34, 3939–3954 (2014).
Dupre, A. et al. A forward chemical genetic screen reveals an inhibitor of the Mre11–Rad50–Nbs1 complex. Nat. Chem. Biol. 4, 119–125 (2008).
Qiao, X. et al. UBR5 is coamplified with MYC in breast tumors and encodes an ubiquitin ligase that limits MYC-dependent apoptosis. Cancer Res. 80, 1414–1427 (2020).
Welcker, M. et al. The Fbw7 tumor suppressor regulates glycogen synthase kinase 3 phosphorylation-dependent c-Myc protein degradation. Proc. Natl Acad. Sci. USA 101, 9085–9090 (2004).
Diefenbacher, M. E. et al. The deubiquitinase USP28 controls intestinal homeostasis and promotes colorectal cancer. J. Clin. Invest. 124, 3407–3418 (2014).
Sun, X. X. et al. The nucleolar ubiquitin-specific protease USP36 deubiquitinates and stabilizes c-Myc. Proc. Natl Acad. Sci. USA 112, 3734–3739 (2015).
Michel, M. A., Swatek, K. N., Hospenthal, M. K. & Komander, D. Ubiquitin linkage-specific affimers reveal insights into K6-linked ubiquitin signaling. Mol. Cell 68, 233–246.e235 (2017).
Heidelberger, J. B. et al. Proteomic profiling of VCP substrates links VCP to K6-linked ubiquitylation and c-Myc function. EMBO Rep. 19, e44754 (2018).
He, X. et al. Probing the roles of SUMOylation in cancer cell biology by using a selective SAE inhibitor. Nat. Chem. Biol. 13, 1164–1171 (2017).
Hamperl, S. & Cimprich, K. A. Conflict resolution in the genome: how transcription and replication make it work. Cell 167, 1455–1467 (2016).
Yan, W. X. et al. BLISS is a versatile and quantitative method for genome-wide profiling of DNA double-strand breaks. Nat. Commun. 8, 15058 (2017).
Thomas, L. R. et al. Interaction with WDR5 promotes target gene recognition and tumorigenesis by MYC. Mol. Cell 58, 440–452 (2015).
Choe, K. N. et al. HUWE1 interacts with PCNA to alleviate replication stress. EMBO Rep. 17, 874–886 (2016).
Zhang, D., Zaugg, K., Mak, T. W. & Elledge, S. J. A role for the deubiquitinating enzyme USP28 in control of the DNA-damage response. Cell 126, 529–542 (2006).
de Vivo, A. et al. The OTUD5–UBR5 complex regulates FACT-mediated transcription at damaged chromatin. Nucleic Acids Res. 47, 729–746 (2019).
Kress, T. R., Sabo, A. & Amati, B. MYC: connecting selective transcriptional control to global RNA production. Nat. Rev. Cancer 15, 593–607 (2015).
Gaillard, H., Garcia-Muse, T. & Aguilera, A. Replication stress and cancer. Nat. Rev. Cancer 15, 276–289 (2015).
Meers, M. P., Bryson, T. D., Henikoff, J. G. & Henikoff, S. Improved CUT&RUN chromatin profiling tools. eLife 8, e46314 (2019).
Koulouras, G. et al. EasyFRAP-web: a web-based tool for the analysis of fluorescence recovery after photobleaching data. Nucleic Acids Res. 46, W467–W472 (2018).
Wolter, S. et al. rapidSTORM: accurate, fast open-source software for localization microscopy. Nat. Methods 9, 1040–1041 (2012).
Kock, B. et al. Confinement and deformation of single cells and their nuclei inside size-adapted microtubes. Adv. Healthcare Materials 3, 1753–1758 (2014).
Kiskowski, M. A., Hancock, J. F. & Kenworthy, A. K. On the use of Ripley’s K-function and its derivatives to analyze domain size. Biophys. J. 97, 1095–1103 (2009).
Cho, K. F. et al. Proximity labeling in mammalian cells with TurboID and split-TurboID. Nat. Protoc. 15, 3971–3999 (2020).
Rappsilber, J., Mann, M. & Ishihama, Y. Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. Nat. Protoc. 2, 1896–1906 (2007).
Li, J. et al. TMTpro reagents: a set of isobaric labeling mass tags enables simultaneous proteome-wide measurements across 16 samples. Nat. Methods 17, 399–404 (2020).
Zhang, L. & Elias, J. E. Relative protein quantification using tandem mass tag mass spectrometry. Methods Mol. Biol. 1550, 185–198 (2017).
Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
Amemiya, H. M., Kundaje, A. & Boyle, A. P. The ENCODE blacklist: identification of problematic regions of the genome. Sci. Rep. 9, 9354 (2019).
Quinlan, A. R. BEDTools: the Swiss-army tool for genome feature analysis. Curr. Protoc. Bioinformatics https://doi.org/10.1002/0471250953.bi1112s47 (2014).
Smith, T., Heger, A. & Sudbery, I. UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy. Genome Res. 27, 491–499 (2017).
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).
Cox, J. et al. Andromeda: a peptide search engine integrated into the MaxQuant environment. J. Proteome Res. 10, 1794–1805 (2011).
Petelski, A. A. et al. Multiplexed single-cell proteomics using SCoPE2. Nat. Protoc. 16, 5398–5425 (2021).
Elias, J. E. & Gygi, S. P. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat. Methods 4, 207–214 (2007).
Ritchie, M. E. et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 43, e47 (2015).
Perez-Riverol, Y. et al. The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences. Nucleic Acids Res. 50, D543–D552 (2022).
More News
Author Correction: Stepwise activation of a metabotropic glutamate receptor – Nature
Changing rainforest to plantations shifts tropical food webs
Streamlined skull helps foxes take a nosedive