ArticleProceedings of the National Academy of Sciences of the United States of America2018
Positional specificity of different transcription factor classes within enhancers.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers, 1 of them a synthesis that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
54 citing papers in PubMed, 1 synthesis or guideline pooled it, 98 citations in OpenAlex.
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- A generic reference defined by consensus peaks for single-cell ATAC-seq data analysis.Nature communications · 2026Article
- Chromatin state dynamics during the Plasmodium falciparum intraerythrocytic development cycle.BMC genomics · 2026Article
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- Revisiting models of enhancer-promoter communication in gene regulation.Genome research · 2025Review
- Ultrastable and versatile multimeric ensembles of FoxP3 on microsatellites.Molecular cell · 2025Article
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- Genome access is transcription factor-specific and defined by nucleosome position.Molecular cell · 2024Article
- Functional dissection of complex and molecular trait variants at single nucleotide resolution.bioRxiv : the preprint server for biology · 2024Article
- Evolutionary Dynamics of Chromatin Structure and Duplicate Gene Expression in Diploid and Allopolyploid Cotton.Molecular biology and evolution · 2024Article
- Context-specific functions of chromatin remodellers in development and disease.Nature reviews. Genetics · 2024Review
- Distinct regulatory networks control toxin gene expression in elapid and viperid snakes.BMC genomics · 2024Article
- Review
- Molecular Mechanism of Nucleosome Recognition by the Pioneer Transcription Factor Sox.Journal of chemical information and modeling · 2023Article
- Integration of ATAC-Seq and RNA-Seq reveals FOSL2 drives human liver progenitor-like cell aging by regulating inflammatory factors.BMC genomics · 2023Article
- Pharmacological disruption of mSWI/SNF complex activity restricts SARS-CoV-2 infection.Nature genetics · 2023Article
- Regulatory networks driving expression of genes critical for glioblastoma are controlled by the transcription factor c-Jun and the pre-existing epigenetic modifications.Clinical epigenetics · 2023Article
- Deciphering the multi-scale, quantitative cis-regulatory code.Molecular cell · 2023Review
- TFSyntax: a database of transcription factors binding syntax in mammalian genomes.Nucleic acids research · 2023Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
Gene expression is controlled by sequence-specific transcription factors (TFs), which bind to regulatory sequences in DNA. TF binding occurs in nucleosome-depleted regions of DNA (NDRs), which generally encompass regions with lengths similar to those protected by nucleosomes. However, less is known about where within these regions specific TFs tend to be found. Here, we characterize the positional bias of inferred binding sites for 103 TFs within ∼500,000 NDRs across 47 cell types. We find that distinct classes of TFs display different binding preferences: Some tend to have binding sites toward the edges, some toward the center, and some at other positions within the NDR. These patterns are highly consistent across cell types, suggesting that they may reflect TF-specific intrinsic structural or functional characteristics. In particular, TF classes with binding sites at NDR edges are enriched for those known to interact with histones and chromatin remodelers, whereas TFs with central enrichment interact with other TFs and cofactors such as p300. Our results suggest distinct regiospecific binding patterns and functions of TF classes within enhancers.
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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.