ArticleGenes & development2009
Dynamic and complex transcription factor binding during an inducible response in yeast.
Article in Genes & development, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
64 citing papers in PubMed, 108 citations in OpenAlex.
- The importance of regulated resource reallocation during dynamic environmental shifts in yeast.The EMBO journal · 2026Article
- Predicting dynamic expression patterns in budding yeast with a fungal DNA language model.Research square · 2025Article
- Predicting dynamic expression patterns in budding yeast with a fungal DNA language model.bioRxiv : the preprint server for biology · 2025Article
- ChIP-exo and CRISPRi/a illuminate the role of Pdr1 and Yap1 in acetic acid tolerance inApplied and environmental microbiology · 2025Article
- MONITTR allows real-time imaging of transcription and endogenous proteins in C. elegans.The Journal of cell biology · 2025Article
- Regulated resource reallocation is transcriptionally hard wired into the yeast stress response.bioRxiv : the preprint server for biology · 2024Article
- Spontaneous Attenuation of Alcoholic Fermentation via the Dysfunction of Cyc8p inInternational journal of molecular sciences · 2023Article
- SIR telomere silencing depends on nuclear envelope lipids and modulates sensitivity to a lysolipid.The Journal of cell biology · 2023Article
- Unraveling the Molecular Basis of Mycosporine Biosynthesis in Fungi.International journal of molecular sciences · 2023Article
- Role of ROX1, SKN7, and YAP6 Stress Transcription Factors in the Production of Secondary Metabolites inInternational journal of molecular sciences · 2022Article
- Transcription factor network analysis identifies REST/NRSF as an intrinsic regulator of CNS regeneration in mice.Nature communications · 2022Article
- Spt20, a Structural Subunit of the SAGA Complex, Regulates Aspergillus fumigatus Biofilm Formation, Asexual Development, and Virulence.Applied and environmental microbiology · 2022Article
- Transcriptional regulation of the caspofungin-induced cell wall damage response in Candida albicans.Current genetics · 2020Review
- ATAC-seq normalization method can significantly affect differential accessibility analysis and interpretation.Epigenetics & chromatin · 2020Article
- A genetic analysis reveals novel histone residues required for transcriptional reprogramming upon stress.Nucleic acids research · 2020Article
- Nut1/Hos1 and Sas2/Rpd3 control the H3 acetylation of two different sets of osmotic stress-induced genes.Epigenetics · 2020Article
- Pathogenesis and Clinical Relevance ofFrontiers in microbiology · 2020Review
- Yeast AP-1 like transcription factors (Yap) and stress response: a current overview.Microbial cell (Graz, Austria) · 2019Review
- Sumoylation of DNA-bound transcription factor Sko1 prevents its association with nontarget promoters.PLoS genetics · 2019Article
- A prior-based integrative framework for functional transcriptional regulatory network inference.Nucleic acids research · 2017Article
4 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
8 authors at 4 institutions in 2 countries.
Funding
Abstract
Complex biological processes are often regulated, at least in part, by the binding of transcription factors to their targets. Recently, considerable effort has been made to analyze the binding of relevant factors to the suite of targets they regulate, thereby generating a regulatory circuit map. However, for most studies the dynamics of binding have not been analyzed, and thus the temporal order of events and mechanisms by which this occurs are poorly understood. We globally analyzed in detail the temporal order of binding of several key factors involved in the salt response of yeast to their target genes. Analysis of Yap4 and Sko1 binding to their target genes revealed multiple temporal classes of binding patterns: (1) constant binding, (2) rapid induction, (3) slow induction, and (4) transient induction. These results demonstrate that individual transcription factors can have multiple binding patterns and help define the different types of temporal binding patterns used in eukaryotic gene regulation. To investigate these binding patterns further, we also analyzed the binding of seven other key transcription factors implicated in osmotic regulation, including Hot1, Msn1, Msn2, Msn4, Skn7, and Yap6, and found significant coassociation among the different factors at their gene targets. Moreover, the binding of several key factors was correlated with distinct classes of Yap4- and Sko1-binding patterns and with distinct types of genes. Gene expression studies revealed association of Yap4, Sko1, and other transcription factor-binding patterns with different gene expression patterns. The integration and analysis of binding and expression information reveals a complex dynamic and hierarchical circuit in which specific combinations of transcription factors target distinct sets of genes at discrete times to coordinate a rapid and important biological response.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.