ArticleGenome biology2011
Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights.
Article in Genome biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 76 papers.
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Who cites it
76 citing papers in PubMed, 125 citations in OpenAlex.
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- Missense variants in human forkhead transcription factors reveal determinants of forkhead DNA bispecificity.bioRxiv : the preprint server for biology · 2025Article
- Activity of the pleiotropic drug resistance transcription factors Pdr1p and Pdr3p is modulated by binding site flanking sequences.FEBS letters · 2024Article
- Overexpression of the Transcription Factor Azf1 Reveals Novel Regulatory Functions and Impacts β-Glucosidase Production inJournal of fungi (Basel, Switzerland) · 2023Article
- Amoeba predation of Cryptococcus: A quantitative and population genomic evaluation of the accidental pathogen hypothesis.PLoS pathogens · 2023Article
- Yeast transcription factor Msn2 binds to G4 DNA.Nucleic acids research · 2023Article
- Molecular background of HAC1-driven improvement in the secretion of recombinant protein inBiotechnology reports (Amsterdam, Netherlands) · 2023Article
- Double DAP-seq uncovered synergistic DNA binding of interacting bZIP transcription factors.Nature communications · 2023Article
- Identifying strengths and weaknesses of methods for computational network inference from single-cell RNA-seq data.G3 (Bethesda, Md.) · 2023Article
- Comprehensive transcriptome analysis of different potato cultivars provides insight into early blight disease caused by Alternaria solani.BMC plant biology · 2023Article
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- Context-dependent CpG methylation directs cell-specific binding of transcription factor ZBTB38.Epigenetics · 2022Article
- NetREX-CF integrates incomplete transcription factor data with gene expression to reconstruct gene regulatory networks.Communications biology · 2022Article
- Transcriptional regulation of ergosterol biosynthesis genes in response to iron deficiency.Environmental microbiology · 2022Article
- Regulation of heme utilization and homeostasis in Candida albicans.PLoS genetics · 2022Article
- Prediction and Experimental Validation of a New Salinity-Responsive Cis-Regulatory Element (CRE) in a Tilapia Cell Line.Life (Basel, Switzerland) · 2022Article
- Transcriptional Profiling of Resistant and Susceptible Cultivars of Grapevine (Frontiers in microbiology · 2022Article
- Machine learning predicts nucleosome binding modes of transcription factors.BMC bioinformatics · 2021Article
16 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundTranscription factors (TFs) play a central role in regulating gene expression by interacting with cis-regulatory DNA elements associated with their target genes. Recent surveys have examined the DNA binding specificities of most Saccharomyces cerevisiae TFs, but a comprehensive evaluation of their data has been lacking.
resultsWe analyzed in vitro and in vivo TF-DNA binding data reported in previous large-scale studies to generate a comprehensive, curated resource of DNA binding specificity data for all characterized S. cerevisiae TFs. Our collection comprises DNA binding site motifs and comprehensive in vitro DNA binding specificity data for all possible 8-bp sequences. Investigation of the DNA binding specificities within the basic leucine zipper (bZIP) and VHT1 regulator (VHR) TF families revealed unexpected plasticity in TF-DNA recognition: intriguingly, the VHR TFs, newly characterized by protein binding microarrays in this study, recognize bZIP-like DNA motifs, while the bZIP TF Hac1 recognizes a motif highly similar to the canonical E-box motif of basic helix-loop-helix (bHLH) TFs. We identified several TFs with distinct primary and secondary motifs, which might be associated with different regulatory functions. Finally, integrated analysis of in vivo TF binding data with protein binding microarray data lends further support for indirect DNA binding in vivo by sequence-specific TFs.
conclusionsThe comprehensive data in this curated collection allow for more accurate analyses of regulatory TF-DNA interactions, in-depth structural studies of TF-DNA specificity determinants, and future experimental investigations of the TFs' predicted target genes and regulatory roles.
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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.