ArticleJournal of molecular biology2011
Structural constraints in collaborative competition of transcription factors against the nucleosome.
Article in Journal of molecular biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed, 63 citations in OpenAlex.
- Circadian regulation of stereotypic chromatin conformations at enhancers.bioRxiv : the preprint server for biology · 2024Article
- Physical interaction between MSL2 and CLAMP assures direct cooperativity and prevents competition at composite binding sites.Nucleic acids research · 2023Article
- A spatio-temporally constrained gene regulatory network directed by PBX1/2 acquires limb patterning specificity via HAND2.Nature communications · 2023Article
- Article
- HAND2 Assists MYCN Enhancer Invasion to Regulate a Noradrenergic Neuroblastoma Phenotype.Cancer research · 2023Article
- Profiling Accessible Chromatin and Nucleosomes in the Mammalian Genome.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Characterization of sequence determinants of enhancer function using natural genetic variation.eLife · 2022Article
- Managing the Steady State Chromatin Landscape by Nucleosome Dynamics.Annual review of biochemistry · 2022Review
- Mapping cis-regulatory elements in human neurons links psychiatric disease heritability and activity-regulated transcriptional programs.Cell reports · 2022Article
- Cooperative binding between distant transcription factors is a hallmark of active enhancers.Molecular cell · 2021Article
- HOX paralogs selectively convert binding of ubiquitous transcription factors into tissue-specific patterns of enhancer activation.PLoS genetics · 2020Article
- Ensembles of Breathing Nucleosomes: A Computational Study.Biophysical journal · 2020Article
- Super-enhancers in transcriptional regulation and genome organization.Nucleic acids research · 2019Article
- Quantitative Modeling of Nucleosome Unwrapping from Both Ends.Biophysical journal · 2019Article
- DNA sequence influences hexasome orientation to regulate DNA accessibility.Nucleic acids research · 2019Article
- Natural Genetic Variation Reveals Key Features of Epigenetic and Transcriptional Memory in Virus-Specific CD8 T Cells.Immunity · 2019Article
- Pou5f3, SoxB1, and Nanog remodel chromatin on high nucleosome affinity regions at zygotic genome activation.Genome research · 2019Article
- Regulation of circadian clock transcriptional output by CLOCK:BMAL1.PLoS genetics · 2018Article
- Multifaceted Targeting of the Chromatin Mediates Gonadotropin-Releasing Hormone Effects on Gene Expression in the Gonadotrope.Frontiers in endocrinology · 2018Review
- AP-1 Transcription Factors and the BAF Complex Mediate Signal-Dependent Enhancer Selection.Molecular cell · 2017Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
Cooperativity in transcription factor (TF) binding is essential in eukaryotic gene regulation and arises through diverse mechanisms. Here, we focus on one mechanism, collaborative competition, which is of interest because it arises both automatically (with no requirement for TF coevolution) and spontaneously (with no requirement for ATP-dependent nucleosome remodeling factors). Previous experimental studies of collaborative competition analyzed cases in which target sites for pairs of cooperating TFs were contained within the same side of the nucleosome. Here, we utilize new assays to measure cooperativity in protein binding to pairs of nucleosomal DNA target sites. We focus on the cases that are of greatest in vivo relevance, in which one binding site is located close to the end of a nucleosome and the other binding site is located at diverse positions throughout the nucleosome. Our results reveal energetically significant positive (favorable) cooperativity for pairs of sites on the same side of the nucleosome but, for the cases examined, energetically insignificant cooperativity between sites on opposite sides of the nucleosome. These findings imply a special significance for TF binding sites that are spaced within one-half nucleosome length (74 bp) or less along the genome and may prove useful for prediction of cooperatively acting TFs genome wide.
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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.