ArticleGenome research2006
Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection.
Article in Genome research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 88 papers.
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Who cites it
88 citing papers in PubMed, 128 citations in OpenAlex.
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- A systematic genome-wide account of binding sites for the model transcription factor Gcn4.Genome research · 2022Article
- Kinetic origin of nucleosome invasion by pioneer transcription factors.Biophysical journal · 2021Article
- Deciphering eukaryotic gene-regulatory logic with 100 million random promoters.Nature biotechnology · 2020Article
- Homotypic cooperativity and collective binding are determinants of bHLH specificity and function.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
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- Evolution and Diversification ofFrontiers in plant science · 2019Article
- The Zn2Cys6-type transcription factor LeuB cross-links regulation of leucine biosynthesis and iron acquisition in Aspergillus fumigatus.PLoS genetics · 2018Article
- Patterns of chromatin accessibility along the anterior-posterior axis in the early Drosophila embryo.PLoS genetics · 2018Article
- Gcn4 Binding in Coding Regions Can Activate Internal and Canonical 5' Promoters in Yeast.Molecular cell · 2018Article
- Assessing sufficiency and necessity of enhancer activities for gene expression and the mechanisms of transcription activation.Genes & development · 2018Review
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- Dry and wet approaches for genome-wide functional annotation of conventional and unconventional transcriptional activators.Computational and structural biotechnology journal · 2016Review
- Zelda is differentially required for chromatin accessibility, transcription factor binding, and gene expression in the early Drosophila embryo.Genome research · 2015Article
- Unraveling determinants of transcription factor binding outside the core binding site.Genome research · 2015Article
28 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
Abstract
Sequence motifs that are potentially recognized by DNA-binding proteins occur far more often in genomic DNA than do observed in vivo protein-DNA interactions. To determine how chromatin influences the utilization of particular DNA-binding sites, we compared the in vivo genome-wide binding location of the yeast transcription factor Leu3 to the binding location observed on the same genomic DNA in the absence of any protein cofactors. We found that the DNA-sequence motif recognized by Leu3 in vitro and in vivo was functionally indistinguishable, but Leu3 bound different genomic locations under the two conditions. Accounting for nucleosome occupancy in addition to DNA-sequence motifs significantly improved the prediction of protein-DNA interactions in vivo, but not the prediction of sites bound by purified Leu3 in vitro. Use of histone modification data does not further improve binding predictions, presumably because their effect is already manifest in the global histone distribution. Measurements of nucleosome occupancy in strains that differ in Leu3 genotype show that low nucleosome occupancy at loci bound by Leu3 is not a consequence of Leu3 binding. These results permit quantitation of the epigenetic influence that chromatin exerts on DNA binding-site selection, and provide evidence for an instructive, functionally important role for nucleosome occupancy in determining patterns of regulatory factor targeting genome-wide.
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