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Low overlap of transcription factor DNA binding and regulatory targets

  • Lee, T. I. & Young, R. A. Transcriptional regulation and its misregulation in disease. Cell 152, 1237–1251 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lambert, S. A. et al. The human transcription factors. Cell 172, 650–665 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Hahn, S. & Young, E. T. Transcriptional regulation in Saccharomyces cerevisiae: transcription factor regulation and function, mechanisms of initiation, and roles of activators and coactivators. Genetics 189, 705–736 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Takahashi, K. & Yamanaka, S. A decade of transcription factor-mediated reprogramming to pluripotency. Nat. Rev. Mol. Cell Bio. 17, 183–193 (2016).

    Article 
    CAS 

    Google Scholar
     

  • Soto, L. F. et al. Compendium of human transcription factor effector domains. Mol. Cell 82, 514–526 (2022).

    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.e7 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Sahu, B. et al. Sequence determinants of human gene regulatory elements. Nat. Genet. 54, 283–294 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Panne, D. The enhanceosome. Curr. Opin. Struc. Biol. 18, 236–242 (2008).

    Article 
    CAS 

    Google Scholar
     

  • Arnosti, D. N. & Kulkarni, M. M. Transcriptional enhancers: Intelligent enhanceosomes or flexible billboards? J. Cell. Biochem. 94, 890–898 (2005).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • de Boer, C. G. et al. Deciphering eukaryotic gene-regulatory logic with 100 million random promoters. Nat. Biotechnol. 38, 56–65 (2020).

    Article 
    PubMed 

    Google Scholar
     

  • King, D. M. et al. Synthetic and genomic regulatory elements reveal aspects of cis-regulatory grammar in mouse embryonic stem cells. eLife 9, e41279 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Cusanovich, D. A., Pavlovic, B., Pritchard, J. K. & Gilad, Y. The functional consequences of variation in transcription factor binding. PLoS Genet. 10, e1004226 (2014).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gitter, A. et al. Backup in gene regulatory networks explains differences between binding and knockout results. Mol. Syst. Biol. 5, 276–276 (2009).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hu, Z., Killion, P. J. & Iyer, V. R. Genetic reconstruction of a functional transcriptional regulatory network. Nat. Genet. 39, 683–687 (2007).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Lenstra, T. L. & Holstege, F. C. P. The discrepancy between chromatin factor location and effect. Nucleus 3, 213–219 (2012).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kang, Y. et al. Dual threshold optimization and network inference reveal convergent evidence from TF binding locations and TF perturbation responses. Genome Res. 30, 459–471 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Chua, G. et al. Identifying transcription factor functions and targets by phenotypic activation. Proc. Natl Acad. Sci. USA 103, 12045–12050 (2006).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Rossi, M. J. et al. A high-resolution protein architecture of the budding yeast genome. Nature 592, 309–314 (2021).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sopko, R. et al. Mapping pathways and phenotypes by systematic gene overexpression. Mol. Cell 21, 319–330 (2006).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Hackett, S. R. et al. Learning causal networks using inducible transcription factors and transcriptome‐wide time series. Mol. Syst. Biol. 16, e9174 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Donczew, R. & Hahn, S. BET family members Bdf1/2 modulate global transcription initiation and elongation in Saccharomyces cerevisiae. eLife 10, e69619 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Warfield, L., Donczew, R., Mahendrawada, L. & Hahn, S. Yeast Mediator facilitates transcription initiation at most promoters via a Tail-independent mechanism. Mol. Cell 82, 4033–4048.e7 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Donczew, R., Warfield, L., Pacheco, D., Erijman, A. & Hahn, S. Two roles for the yeast transcription coactivator SAGA and a set of genes redundantly regulated by TFIID and SAGA. eLife 9, e50109 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Huisinga, K. L. & Pugh, B. F. A genome-wide housekeeping role for TFIID and a highly regulated stress-related role for SAGA in Saccharomyces cerevisiae. Mol. Cell 13, 573–585 (2004).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Erijman, A. et al. A high-throughput screen for transcription activation domains reveals their sequence features and permits prediction by deep learning. Mol. Cell 78, 890–902.e6 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sanborn, A. L. et al. Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator. eLife 10, e68068 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zentner, G. E., Kasinathan, S., Xin, B., Rohs, R. & Henikoff, S. ChEC–seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo. Nat. Commun. 6, 8733 (2015).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Schofield, J. A. & Hahn, S. Broad compatibility between yeast UAS elements and core promoters and identification of promoter elements that determine cofactor specificity. Cell Rep. 42, 112387 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Grant, C. E., Bailey, T. L. & Noble, W. S. FIMO: scanning for occurrences of a given motif. Bioinformatics 27, 1017–1018 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Brodsky, S. et al. Intrinsically disordered regions direct transcription factor in vivo binding specificity. Mol. Cell 79, 459–471.e4 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kumar, D. K. et al. Complementary strategies for directing in vivo transcription factor binding through DNA binding domains and intrinsically disordered regions. Mol. Cell 83, 1462–1473.e5 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Mehta, G. D. et al. Single-molecule analysis reveals linked cycles of RSC chromatin remodeling and Ace1p transcription factor binding in yeast. Mol. Cell 72, 875–887.e9 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Nguyen, V. Q. et al. Spatiotemporal coordination of transcription preinitiation complex assembly in live cells. Mol. Cell 81, 3560–3575.e6 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kim, J. M. et al. Single-molecule imaging of chromatin remodelers reveals role of ATPase in promoting fast kinetics of target search and dissociation from chromatin. eLife 10, e69387 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Staller, M. V. Transcription factors perform a 2-step search of the nucleus. Genetics 222, iyac111 (2022).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Swygert, S. G. et al. Condensin-dependent chromatin compaction represses transcription globally during quiescence. Mol. Cell 73, 533–546.e4 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Seong, K. M. et al. A new method for the construction of a mutant library with a predictable occurrence rate using Poisson distribution. J. Microbiol. Methods 69, 442–450 (2007).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Kim, J. & Struhl, K. Determinants of half-site spacing preferences that distinguish AP-1 and ATF/CREB bZIP domains. Nucleic Acids Res. 23, 2531–2537 (1995).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Brzovic, P. S. et al. The acidic transcription activator Gcn4 binds the mediator subunit Gal11/Med15 using a simple protein interface forming a fuzzy complex. Mol. Cell 44, 942–953 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Drysdale, C. M. et al. The transcriptional activator GCN4 contains multiple activation domains that are critically dependent on hydrophobic amino acids. Mol. Cell. Biol. 15, 1220–1233 (1995).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Nishimura, K., Fukagawa, T., Takisawa, H., Kakimoto, T. & Kanemaki, M. An auxin-based degron system for the rapid depletion of proteins in nonplant cells. Nat. Methods 6, 917–922 (2009).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Sudarsanam, P., Cao, Y., Wu, L., Laurent, B. C. & Winston, F. The nucleosome remodeling complex, Snf/Swi, is required for the maintenance of transcription in vivo and is partially redundant with the histone acetyltransferase, Gcn5. EMBO J. 18, 3101–3106 (1999).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • McIsaac, R. S., Petti, A. A., Bussemaker, H. J. & Botstein, D. Perturbation-based analysis and modeling of combinatorial regulation in the yeast sulfur assimilation pathway. Mol. Biol. Cell 23, 2993–3007 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Rubin-Bejerano, I., Mandel, S., Robzyk, K. & Kassir, Y. Induction of meiosis in Saccharomyces cerevisiae depends on conversion of the transcriptional repressor Ume6 to a positive regulator by its regulated association with the transcriptional activator Ime1. Mol. Cell. Biol. 16, 2518–2526 (1996).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lee, B. et al. Systematic analysis of tup1 and cyc8 mutants reveals distinct roles for TUP1 and CYC8 and offers new insight into the regulation of gene transcription by the yeast Tup1–Cyc8 complex. PLoS Genet. 19, e1010876 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Weikum, E. R., Knuesel, M. T., Ortlund, E. A. & Yamamoto, K. R. Glucocorticoid receptor control of transcription: precision and plasticity via allostery. Nat. Rev. Mol. Cell Biol. 18, 159–174 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 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
     

  • Wong, E. D. et al. Saccharomyces genome database update: server architecture, pan-genome nomenclature, and external resources. Genetics 224, iyac191 (2023).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Weirauch, M. T. et al. Determination and Inference of eukaryotic transcription factor sequence specificity. Cell 158, 1431–1443 (2014).

    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
     

  • Brachmann, C. B. et al. Designer deletion strains derived from Saccharomyces cerevisiae S288C: A useful set of strains and plasmids for PCR‐mediated gene disruption and other applications. Yeast 14, 115–132 (1998).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Grünberg, S., Henikoff, S., Hahn, S. & Zentner, G. E. Mediator binding to UASs is broadly uncoupled from transcription and cooperative with TFIID recruitment to promoters. EMBO J. 35, 2435–2446 (2016).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Donczew, R., Lalou, A., Devys, D., Tora, L. & Hahn, S. An improved ChEC–seq method accurately maps the genome-wide binding of transcription coactivators and sequence-specific transcription factors. Preprint at bioRxiv https://doi.org/10.1101/2021.02.12.430999 (2021).

  • Warfield, L. et al. Transcription of nearly all yeast RNA polymerase ii-transcribed genes is dependent on transcription factor TFIID. Mol. Cell 68, 118–129.e5 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bonnet, J. et al. The SAGA coactivator complex acts on the whole transcribed genome and is required for RNA polymerase II transcription. Genes Dev. 28, 1999–2012 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Duffy, E. E. et al. Tracking distinct RNA populations using efficient and reversible covalent chemistry. Mol. Cell 59, 858–866 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Duffy, E. E. & Simon, M. D. Enriching s(4) U-RNA using methane thiosulfonate (MTS) chemistry. Curr. Protoc. Chem. Biol. 8, 234–250 (2016).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576–589 (2010).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Park, D., Morris, A. R., Battenhouse, A. & Iyer, V. R. Simultaneous mapping of transcript ends at single-nucleotide resolution and identification of widespread promoter-associated non-coding RNA governed by TATA elements. Nucleic Acids Res. 42, 3736–3749 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Anders, S., Pyl, P. T. & Huber, W. HTSeq-a Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166–169 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Navarrete-Perea, J., Yu, Q., Gygi, S. P. & Paulo, J. A. Streamlined tandem mass tag (SL-TMT) protocol: an efficient strategy for quantitative (phospho)proteome profiling using tandem mass tag-synchronous precursor selection-MS3. J. Proteome Res. 17, 2226–2236 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Herbig, E. et al. Mechanism of Mediator recruitment by tandem Gcn4 activation domains and three Gal11 activator-binding domains. Mol. Cell. Biol. 30, 2376–2390 (2010).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Castro-Mondragon, J. A. et al. JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles. Nucleic Acids Res. 50, D165–D173 (2021).

    Article 
    PubMed Central 

    Google Scholar
     

  • Rawal, Y. et al. Gcn4 binding in coding regions can activate internal and canonical 5′ promoters in yeast. Mol. Cell 70, 297–311.e4 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Chereji, R. V., Ramachandran, S., Bryson, T. D. & Henikoff, S. Precise genome-wide mapping of single nucleosomes and linkers in vivo. Genome Biol. 19, 19 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Johnston, M. A model fungal gene regulatory mechanism: the GAL genes of Saccharomyces cerevisiae. Microbiol. Rev. 51, 458–476 (1987).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Takagi, Y. & Kornberg, R. D. Mediator as a general transcription factor. J. Biol. Chem. 281, 80–89 (2006).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Hahn, S. & Guarente, L. Yeast HAP2 and HAP3: transcriptional activators in a heteromeric complex. Science 240, 317–321 (1988).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Prochasson, P., Florens, L., Swanson, S. K., Washburn, M. P. & Workman, J. L. The HIR corepressor complex binds to nucleosomes generating a distinct protein/DNA complex resistant to remodeling by SWI/SNF. Genes Dev. 19, 2534–2539 (2005).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Chittuluru, J. R. et al. Structure and nucleosome interaction of the yeast NuA4 and Piccolo–NuA4 histone acetyltransferase complexes. Nat. Struct. Mol. Biol. 18, 1196–1203 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Smith, C. L., Horowitz-Scherer, R., Flanagan, J. F., Woodcock, C. L. & Peterson, C. L. Structural analysis of the yeast SWI/SNF chromatin remodeling complex. Nat. Struct. Biol. 10, 141–145 (2003).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Keleher, C. A., Redd, M. J., Schultz, J., Carlson, M. & Johnson, A. D. Ssn6–Tup1 is a general repressor of transcription in yeast. Cell 68, 709–719 (1992).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Chou, S., Lane, S. & Liu, H. Regulation of mating and filamentation genes by two distinct Ste12 complexes in Saccharomyces cerevisiae. Mol. Cell. Biol. 26, 4794–4805 (2006).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kurihara, L. J., Stewart, B. G., Gammie, A. E. & Rose, M. D. Kar4p, a karyogamy-specific component of the yeast pheromone response pathway. Mol. Cell. Biol. 16, 3990–4002 (1996).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Nielsen, P. et al. Transcriptional regulation of the Saccharomyces cerevisiae amino acid permease gene BAP2. Mol. Gen. Genet. 264, 613–622 (2001).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Jia, Y., Rothermel, B., Thornton, J. & Butow, R. A. A basic helix-loop-helix–leucine zipper transcription complex in yeast functions in a signaling pathway from mitochondria to the nucleus. Mol. Cell. Biol. 17, 1110–1117 (1997).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • van Werven, F. J. et al. Cooperative action of NC2 and Mot1p to regulate TATA-binding protein function across the genome. Genes Dev. 22, 2359–2369 (2008).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Eriksson, P. R., Ganguli, D., Nagarajavel, V. & Clark, D. J. Regulation of histone gene expression in budding yeast. Genetics 191, 7–20 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Martin, D. E., Soulard, A. & Hall, M. N. TOR regulates ribosomal protein gene expression via PKA and the forkhead transcription factor FHL1. Cell 119, 969–979 (2004).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Iraqui, I., Vissers, S., André, B. & Urrestarazu, A. Transcriptional Induction by aromatic amino acids in Saccharomyces cerevisiae. Mol. Cell. Biol. 19, 3360–3371 (1999).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Holmberg, S. & Schjerling, P. Cha4p of Saccharomyces cerevisiae activates transcription via serine/threonine response elements. Genetics 144, 467–478 (1996).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gasmi, N. et al. The switch from fermentation to respiration in Saccharomyces cerevisiae is regulated by the Ert1 transcriptional activator/repressor. Genetics 198, 547–560 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Soontorngun, N., Larochelle, M., Drouin, S., Robert, F. & Turcotte, B. Regulation of gluconeogenesis in Saccharomyces cerevisiae is mediated by activator and repressor functions of Rds2. Mol. Cell. Biol. 27, 7895–7905 (2007).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Raitt, D. C. et al. The Skn7 response regulator of Saccharomyces cerevisiae interacts with Hsf1 in vivo and is required for the induction of heat shock genes by oxidative stress. Mol. Biol. Cell 11, 2335–2347 (2000).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lorenz, M. C. & Heitman, J. Regulators of pseudohyphal differentiation in Saccharomyces cerevisiae identified through multicopy suppressor analysis in ammonium permease mutant strains. Genetics 150, 1443–1457 (1998).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Thomas, P. D. et al. PANTHER: making genome‐scale phylogenetics accessible to all. Protein Sci. 31, 8–22 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

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