ArticleMolecular cell2012
DNA sequence preferences of transcriptional activators correlate more strongly than repressors with nucleosomes.
Article in Molecular cell, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 1 citations in OpenAlex.
- Human TMIGD1 Promoter Exhibits Robust Activity in Prokaryotic Cells.Biochemistry · 2026Article
- Assessing sufficiency and necessity of enhancer activities for gene expression and the mechanisms of transcription activation.Genes & development · 2018Review
- Transcriptional Regulation of the Ambient Temperature Response by H2A.Z Nucleosomes and HSF1 Transcription Factors in Arabidopsis.Molecular plant · 2017Article
- How motif environment influences transcription factor search dynamics: Finding a needle in a haystack.BioEssays : news and reviews in molecular, cellular and developmental biology · 2016Review
- Negative selection maintains transcription factor binding motifs in human cancer.BMC genomics · 2016Article
- Differential Nucleosome Occupancies across Oct4-Sox2 Binding Sites in Murine Embryonic Stem Cells.PloS one · 2015Article
- Promoter-proximal transcription factor binding is transcriptionally active when coupled with nucleosome repositioning in immediate vicinity.Nucleic acids research · 2014Article
- Nucleosome organization in the vicinity of transcription factor binding sites in the human genome.BMC genomics · 2014Article
- Coregulation of transcription factor binding and nucleosome occupancy through DNA features of mammalian enhancers.Molecular cell · 2014Article
- Clustered regulatory elements at nucleosome-depleted regions punctuate a constant nucleosomal landscape in Schizosaccharomyces pombe.BMC genomics · 2013Article
- Positive and negative design for nonconsensus protein-DNA binding affinity in the vicinity of functional binding sites.Biophysical journal · 2013Article
- Reprogramming cells for brain repair.Brain sciences · 2013Article
- Contribution of nucleosome binding preferences and co-occurring DNA sequences to transcription factor binding.BMC genomics · 2013Article
- Nucleosome assembly factors CAF-1 and HIR modulate epigenetic switching frequencies in an H3K56 acetylation-associated manner in Candida albicans.Eukaryotic cell · 2013Article
- Uncovering the interplay between DNA sequence preferences of transcription factors and nucleosomes.Cell cycle (Georgetown, Tex.) · 2012Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 3 countries.
Funding
Abstract
Transcription factors (TFs) and histone octamers are two abundant classes of DNA binding proteins that coordinate the transcriptional program in cells. Detailed studies of individual TFs have shown that TFs bind to nucleosome-occluded DNA sequences and induce nucleosome disruption/repositioning, while recent global studies suggest this is not the only mechanism used by all TFs. We have analyzed to what extent the intrinsic DNA binding preferences of TFs and histones play a role in determining nucleosome occupancy, in addition to nonintrinsic factors such as the enzymatic activity of chromatin remodelers. The majority of TFs in budding yeast have an intrinsic sequence preference overlapping with nucleosomal histones. TFs with intrinsic DNA binding properties highly correlated with those of histones tend to be associated with gene activation and might compete with histones to bind to genomic DNA. Consistent with this, we show that activators induce more nucleosome disruption upon transcriptional activation than repressors.
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