ReviewComputational and structural biotechnology journal2014
Homotypic clusters of transcription factor binding sites: A model system for understanding the physical mechanics of gene expression.
Review in Computational and structural biotechnology journal, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed, 74 citations in OpenAlex.
- Decoding cis-regulatory elements in the germline of the human malaria vector Anopheles gambiae.Communications biology · 2026Article
- Mechanisms of enhanced or impaired DNA target selectivity driven by protein dimerization.PNAS nexus · 2026Article
- Rescue of tomato yellow leaf curl virus mutants harboring heterologous iterons throughJournal of virology · 2025Article
- Evolution and Comparative Genomics of the Transforming Growth Factor-β-Related Proteins in Nile Tilapia.Molecular biotechnology · 2025Article
- Mechanisms of enhanced or impaired DNA target selectivity driven by protein dimerization.bioRxiv : the preprint server for biology · 2025Article
- Predicting gene expression changes from chromatin structure modification.NPJ systems biology and applications · 2025Article
- An evolutionarily conserved constellation of functional cis-elements programs the virus-responsive fate of the human (epi)genome.Nucleic acids research · 2025Article
- CREB Regulates Cisplatin Resistance by Targeting TNKS and KDM6A in NSCLC cell-Derived Tumor Spheroid.International journal of biological sciences · 2025Article
- From homogeneity to heterogeneity: Refining stochastic simulations of gene regulation.Computational and structural biotechnology journal · 2025Article
- Less-is-more: selecting transcription factor binding regions informative for motif inference.Nucleic acids research · 2024Article
- Identification of functional enhancer variants associated with type I diabetes in CD4+ T cells.Frontiers in immunology · 2024Article
- High-throughput data and modeling reveal insights into the mechanisms of cooperative DNA-binding by transcription factor proteins.Nucleic acids research · 2023Article
- MORA and EnsembleTFpredictor: An ensemble approach to reveal functional transcription factor regulatory networks.PloS one · 2023Article
- Identifying the Gene Regulatory Network of the Starvation-Induced Transcriptional Activator Nla28.Journal of bacteriology · 2022Article
- Systematic analysis of low-affinity transcription factor binding site clusters in vitro and in vivo establishes their functional relevance.Nature communications · 2022Article
- FOXL2 and FOXA1 cooperatively assemble on the TP53 promoter in alternative dimer configurations.Nucleic acids research · 2022Article
- Notch-dependent DNA cis-regulatory elements and their dose-dependent control of C. elegans stem cell self-renewal.Development (Cambridge, England) · 2022Article
- TFEB Regulates ATP7B Expression to Promote Platinum Chemoresistance in Human Ovarian Cancer Cells.Cells · 2022Article
- Transcription Factor Dynamics.Cold Spring Harbor perspectives in biology · 2021Review
- Mechanisms of Binding Specificity among bHLH Transcription Factors.International journal of molecular sciences · 2021Review
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
The organization of binding sites in cis-regulatory elements (CREs) can influence gene expression through a combination of physical mechanisms, ranging from direct interactions between TF molecules to DNA looping and transient chromatin interactions. The study of simple and common building blocks in promoters and other CREs allows us to dissect how all of these mechanisms work together. Many adjacent TF binding sites for the same TF species form homotypic clusters, and these CRE architecture building blocks serve as a prime candidate for understanding interacting transcriptional mechanisms. Homotypic clusters are prevalent in both bacterial and eukaryotic genomes, and are present in both promoters as well as more distal enhancer/silencer elements. Here, we review previous theoretical and experimental studies that show how the complexity (number of binding sites) and spatial organization (distance between sites and overall distance from transcription start sites) of homotypic clusters influence gene expression. In particular, we describe how homotypic clusters modulate the temporal dynamics of TF binding, a mechanism that can affect gene expression, but which has not yet been sufficiently characterized. We propose further experiments on homotypic clusters that would be useful in developing mechanistic models of gene expression.
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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.