ArticleNature communications2020
Eukaryotic transcription factors can track and control their target genes using DNA antennas.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed, 68 citations in OpenAlex.
- Compaction of chromatin domains regulates target search times of proteins.PLoS computational biology · 2026Article
- Uncovering the Mechanistic Landscape of Regulatory DNA with Deep Learning.bioRxiv : the preprint server for biology · 2025Article
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- Theory on the Design Principles of Protein Molecular Oscillatory Machines.The journal of physical chemistry. B · 2025Article
- DNA-Protein Binding is Dominated by Short Anchoring Elements.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Mechanisms for DNA Interplay in Eukaryotic Transcription Factors.Annual review of biophysics · 2025Review
- Modeling and designing enhancers by introducing and harnessing transcription factor binding units.Nature communications · 2025Article
- Asymmetry of Motif Conservation Within Their Homotypic Pairs Distinguishes DNA-Binding Domains of Target Transcription Factors in ChIP-Seq Data.International journal of molecular sciences · 2025Article
- Comprehensive analysis of computational approaches in plant transcription factors binding regions discovery.Heliyon · 2024Article
- How to scan naked DNA using promiscuous recognition and no clamping: a model for pioneer transcription factors.Nucleic acids research · 2024Article
- PeculiarGenes · 2024Article
- Article
- TFscope: systematic analysis of the sequence features involved in the binding preferences of transcription factors.Genome biology · 2024Article
- Skipping events impose repeated binding attempts: profound kinetic implications of protein-DNA conformational changes.Nucleic acids research · 2024Article
- PTFSpot: deep co-learning on transcription factors and their binding regions attains impeccable universality in plants.Briefings in bioinformatics · 2024Article
- Analyzing paramagnetic NMR data on target DNA search by proteins using a discrete-state kinetic model for translocation.Biopolymers · 2024Article
- scGRN: a comprehensive single-cell gene regulatory network platform of human and mouse.Nucleic acids research · 2024Article
- A scale-free universal relational information matrix (N-space) reconciles the information problem: N-space as the fabric of reality.Communicative & integrative biology · 2023Article
- Conformational Change of Transcription Factors from Search to Specific Binding: AThe journal of physical chemistry. B · 2022Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Eukaryotic transcription factors (TF) function by binding to short 6-10 bp DNA recognition sites located near their target genes, which are scattered through vast genomes. Such process surmounts enormous specificity, efficiency and celerity challenges using a molecular mechanism that remains poorly understood. Combining biophysical experiments, theory and bioinformatics, we dissect the interplay between the DNA-binding domain of Engrailed, a Drosophila TF, and the regulatory regions of its target genes. We find that Engrailed binding affinity is strongly amplified by the DNA regions flanking the recognition site, which contain long tracts of degenerate recognition-site repeats. Such DNA organization operates as an antenna that attracts TF molecules in a promiscuous exchange among myriads of intermediate affinity binding sites. The antenna ensures a local TF supply, enables gene tracking and fine control of the target site's basal occupancy. This mechanism illuminates puzzling gene expression data and suggests novel engineering strategies to control gene expression.
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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.