Categories: NATURE

Single-molecule states link transcription factor binding to gene expression


  • Spitz, F. & Furlong, E. E. M. Transcription factors: from enhancer binding to developmental control. Nat. Rev. Genet. 13, 613–626 (2012).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kelly, T. K. et al. Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules. Genome Res. 22, 2497–2506 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Krebs, A. R. et al. Genome-wide single-molecule footprinting reveals high RNA polymerase II turnover at paused promoters. Mol. Cell 67, 411–422 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Vierstra, J. et al. Global reference mapping of human transcription factor footprints. Nature 583, 729–736 (2020).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wunderlich, Z. & Mirny, L. A. Different gene regulation strategies revealed by analysis of binding motifs. Trends Genet. 25, 434–440 (2009).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Giniger, E. & Ptashne, M. Cooperative DNA binding of the yeast transcriptional activator GAL4. Proc. Natl Acad. Sci. USA 85, 382–386 (1988).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Pettersson, M. & Schaffner, W. Synergistic activation of transcription by multiple binding sites for NF-kappa B even in absence of co-operative factor binding to DNA. J. Mol. Biol. 214, 373–380 (1990).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Thanos, D. & Maniatis, T. Virus induction of human IFN beta gene expression requires the assembly of an enhanceosome. Cell 83, 1091–1100 (1995).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Mirny, L. A. Nucleosome-mediated cooperativity between transcription factors. Proc. Natl Acad. Sci. USA 107, 22534–22539 (2010).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Biddie, S. C. et al. Transcription factor AP1 potentiates chromatin accessibility and glucocorticoid receptor binding. Mol. Cell 43, 145–155 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Fryer, C. J. & Archer, T. K. Chromatin remodelling by the glucocorticoid receptor requires the BRG1 complex. Nature 393, 88–91 (1998).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Herschlag, D. & Johnson, F. B. Synergism in transcriptional activation: a kinetic view. Genes Dev. 7, 173–179 (1993).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Martinez-Corral, R. et al. Transcriptional kinetic synergy: a complex landscape revealed by integrating modeling and synthetic biology. Cell Syst. 14, 324–339 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Shipony, Z. et al. Long-range single-molecule mapping of chromatin accessibility in eukaryotes. Nat. Methods 17, 319–327 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Stergachis, A. B., Debo, B. M., Haugen, E., Churchman, L. S. & Stamatoyannopoulos, J. A. Single-molecule regulatory architectures captured by chromatin fiber sequencing. Science 368, 1449–1454 (2020).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Sönmezer, C. et al. Molecular co-occupancy identifies transcription factor binding cooperativity in vivo. Mol. Cell 81, 255–267 (2021).

    Article 
    PubMed 

    Google Scholar
     

  • Levo, M. et al. Systematic investigation of transcription factor activity in the context of chromatin using massively parallel binding and expression assays. Mol. Cell 65, 604–617 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Bintu, L. et al. Transcriptional regulation by the numbers: models. Curr. Opin. Genet. Dev. 15, 116–124 (2005).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gossen, M. et al. Transcriptional activation by tetracyclines in mammalian cells. Science 268, 1766–1769 (1995).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Vaisvila, R. et al. Enzymatic methyl sequencing detects DNA methylation at single-base resolution from picograms of DNA. Genome Res. 31, 1280–1289 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ackers, G. K., Johnson, A. D. & Shea, M. A. Quantitative model for gene regulation by lambda phage repressor. Proc. Natl Acad. Sci. USA 79, 1129–1133 (1982).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kim, H. D. & O’Shea, E. K. A quantitative model of transcription factor-activated gene expression. Nat. Struct. Mol. Biol. 15, 1192–1198 (2008).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Neely, K. E. et al. Activation domain-mediated targeting of the SWI/SNF complex to promoters stimulates transcription from nucleosome arrays. Mol. Cell 4, 649–655 (1999).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Yudkovsky, N., Logie, C., Hahn, S. & Peterson, C. L. Recruitment of the SWI/SNF chromatin remodeling complex by transcriptional activators. Genes Dev. 13, 2369–2374 (1999).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Neely, K. E., Hassan, A. H., Brown, C. E., Howe, L. & Workman, J. L. Transcription activator interactions with multiple SWI/SNF subunits. Mol. Cell. Biol. 22, 1615–1625 (2002).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Papillon, J. P. N. et al. Discovery of orally active inhibitors of Brahma homolog (BRM)/SMARCA2 ATPase activity for the treatment of Brahma related gene 1 (BRG1)/SMARCA4-mutant cancers. J. Med. Chem. 61, 10155–10172 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Martin, B. J. E. et al. Global identification of SWI/SNF targets reveals compensation by EP400. Cell https://doi.org/10.1016/j.cell.2023.10.006 (2023).

  • Kundu, T. K. et al. Activator-dependent transcription from chromatin in vitro involving targeted histone acetylation by p300. Mol. Cell 6, 551–561 (2000).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Alerasool, N., Leng, H., Lin, Z.-Y., Gingras, A.-C. & Taipale, M. Identification and functional characterization of transcriptional activators in human cells. Mol. Cell 82, 677–695 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Rada-Iglesias, A. et al. A unique chromatin signature uncovers early developmental enhancers in humans. Nature 470, 279–283 (2011).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Brower-Toland, B. et al. Specific contributions of histone tails and their acetylation to the mechanical stability of nucleosomes. J. Mol. Biol. 346, 135–146 (2005).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Lasko, L. M. et al. Discovery of a selective catalytic p300/CBP inhibitor that targets lineage-specific tumours. Nature 550, 128–132 (2017).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Raj, A., Peskin, C. S., Tranchina, D., Vargas, D. Y. & Tyagi, S. Stochastic mRNA synthesis in mammalian cells. PLoS Biol. 4, e309 (2006).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Suter, D. M. et al. Mammalian genes are transcribed with widely different bursting kinetics. Science 332, 472–474 (2011).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Chong, S., Chen, C., Ge, H. & Xie, X. S. Mechanism of transcriptional bursting in bacteria. Cell 158, 314–326 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Xiao, J. Y., Hafner, A. & Boettiger, A. N. How subtle changes in 3D structure can create large changes in transcription. Elife 10, e64320 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zuin, J. et al. Nonlinear control of transcription through enhancer–promoter interactions. Nature 604, 571–577 (2022).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gossen, M. & Bujard, H. Tight control of gene expression in mammalian cells by tetracycline-responsive promoters. Proc. Natl Acad. Sci. USA 89, 5547–5551 (1992).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kessler, D. S., Veals, S. A., Fu, X. Y. & Levy, D. E. Interferon-alpha regulates nuclear translocation and DNA-binding affinity of ISGF3, a multimeric transcriptional activator. Genes Dev. 4, 1753–1765 (1990).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Lazear, H. M., Schoggins, J. W. & Diamond, M. S. Shared and distinct functions of type I and type III interferons. Immunity 50, 907–923 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Platanitis, E. et al. A molecular switch from STAT2-IRF9 to ISGF3 underlies interferon-induced gene transcription. Nat. Commun. 10, 2921 (2019).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Rengachari, S. et al. Structural basis of STAT2 recognition by IRF9 reveals molecular insights into ISGF3 function. Proc. Natl Acad. Sci. USA 115, E601–E609 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bluyssen, H. A. & Levy, D. E. Stat2 is a transcriptional activator that requires sequence-specific contacts provided by stat1 and p48 for stable interaction with DNA. J. Biol. Chem. 272, 4600–4605 (1997).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Patel, M. C. et al. BRD4 coordinates recruitment of pause release factor P-TEFb and the pausing complex NELF/DSIF to regulate transcription elongation of interferon-stimulated genes. Mol. Cell. Biol. 33, 2497–2507 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Cui, K. et al. The chromatin-remodeling BAF complex mediates cellular antiviral activities by promoter priming. Mol. Cell. Biol. 24, 4476–4486 (2004).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Manry, J. et al. Evolutionary genetic dissection of human interferons. J. Exp. Med. 208, 2747–2759 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Krause, C. D. & Pestka, S. Cut, copy, move, delete: the study of human interferon genes reveal multiple mechanisms underlying their evolution in amniotes. Cytokine 76, 480–495 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Arimoto, K.-I., Miyauchi, S., Stoner, S. A., Fan, J.-B. & Zhang, D.-E. Negative regulation of type I IFN signaling. J. Leukoc. Biol. https://doi.org/10.1002/JLB.2MIR0817-342R (2018).

  • Mostafavi, S. et al. Parsing the interferon transcriptional network and its disease associations. Cell 164, 564–578 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Dogan, N. et al. Occupancy by key transcription factors is a more accurate predictor of enhancer activity than histone modifications or chromatin accessibility. Epigenetics Chromatin 8, 16 (2015).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Corces, M. R. et al. Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution. Nat. Genet. 48, 1193–1203 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Weirauch, M. T. et al. Evaluation of methods for modeling transcription factor sequence specificity. Nat. Biotechnol. 31, 126–134 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lee, D. Y., Hayes, J. J., Pruss, D. & Wolffe, A. P. A positive role for histone acetylation in transcription factor access to nucleosomal DNA. Cell 72, 73–84 (1993).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Struhl, K. Histone acetylation and transcriptional regulatory mechanisms. Genes Dev. 12, 599–606 (1998).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Narita, T. et al. Enhancers are activated by p300/CBP activity-dependent PIC assembly, RNAPII recruitment, and pause release. Mol. Cell 81, 2166–2182 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ferrie, J. J. et al. p300 is an obligate integrator of combinatorial transcription factor inputs. Mol. Cell 84, 234–243.e4 (2024).

  • Kornberg, R. D. & Lorch, Y. Irresistible force meets immovable object: transcription and the nucleosome. Cell 67, 833–836 (1991).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Boeger, H. Kinetic proofreading. Annu. Rev. Biochem. 91, 423–447 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Wong, F. & Gunawardena, J. Gene regulation in and out of equilibrium. Annu. Rev. Biophys. 49, 199–226 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Shelansky, R. & Boeger, H. Nucleosomal proofreading of activator-promoter interactions. Proc. Natl Acad. Sci. USA 117, 2456–2461 (2020).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Mahdavi, S., Salmon, G. L., Daghlian, P., Garcia, H. G. & Phillips, R. Flexibility and sensitivity in gene regulation out of equilibrium. Preprint at bioRxiv https://doi.org/10.1101/2023.04.11.536490 (2023).

  • Guharajan, S., Parisutham, V. & Brewster, R. C. Probing the dependence of transcription factor regulatory modes on promoter features. Preprint at bioRxiv https://doi.org/10.1101/2024.05.30.596689 (2024).

  • Vaisvila, R. et al. Discovery of cytosine deaminases enables base-resolution methylome mapping using a single enzyme. Mol. Cell 84, 854–866 (2024).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • He, R. et al. Human transcription factor combinations mapped by footprinting with deaminase. Preprint at bioRxiv https://doi.org/10.1101/2024.06.14.599019 (2024).

  • Policarpi, C., Munafò, M., Tsagkris, S., Carlini, V. & Hackett, J. A. Systematic epigenome editing captures the context-dependent instructive function of chromatin modifications. Nat. Genet. https://doi.org/10.1038/s41588-024-01706-w (2024).

  • DelRosso, N. et al. Large-scale mapping and mutagenesis of human transcriptional effector domains. Nature 616, 365–372 (2023).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Durrant, M. G. et al. Systematic discovery of recombinases for efficient integration of large DNA sequences into the human genome. Nat. Biotechnol. 41, 488–499 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Tycko, J. et al. High-throughput discovery and characterization of human transcriptional effectors. Cell 183, 2020–2035 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Iurlaro, M. et al. Mammalian SWI/SNF continuously restores local accessibility to chromatin. Nat. Genet. 53, 279–287 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Weinert, B. T. et al. Time-resolved analysis reveals rapid dynamics and broad scope of the CBP/p300 acetylome. Cell 174, 231–244 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Teague, B. Cytoflow: a Python toolbox for flow cytometry. Preprint at bioRxiv https://doi.org/10.1101/2022.07.22.501078 (2022).

  • Pedersen, B. S., Eyring, K., De, S., Yang, I. V. & Schwartz, D. A. Fast and accurate alignment of long bisulfite-seq reads. Preprint at https://arxiv.org/abs/1401.1129 (2014).

  • Virtanen, P. et al. SciPy 1.0: fundamental algorithms for scientific computing in Python. Nat. Methods 17, 261–272 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Corces, M. R. et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat. Methods 14, 959–962 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Robinson, J. T. et al. Integrative genomics viewer. Nat. Biotechnol. 29, 24–26 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Schep, A. N., Wu, B., Buenrostro, J. D. & Greenleaf, W. J. chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data. Nat. Methods 14, 975–978 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Marinov, G. K. ChIP-seq for the identification of functional elements in the human genome. Methods Mol. Biol. 1543, 3–18 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • 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).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Feng, J., Liu, T., Qin, B., Zhang, Y. & Liu, X. S. Identifying ChIP-seq enrichment using MACS. Nat. Protoc. 7, 1728–1740 (2012).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Marinov, G. K. Identification of candidate functional elements in the genome from ChIP-seq data. Methods Mol. Biol. 1543, 19–43 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Doughty, B. GreenleafLab/synthetic_enhancer_footprinting_additional_materials: SMF Paper Files. Zenodo https://doi.org/10.5281/zenodo.13841007 (2024).

  • Doughty, B. GreenleafLab/amplicon-smf: amplicon-smf v1.0.0. Zenodo https://doi.org/10.5281/zenodo.13840888 (2024).



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