ArticleMolecular cell2020
Context-Dependent Gene Regulation by Homeodomain Transcription Factor Complexes Revealed by Shape-Readout Deficient Proteins.
Article in Molecular cell, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 38 citations in OpenAlex.
- Readout of intrinsic and induced DNA shape by homeodomain transcription factor complexes.Biophysical journal · 2026Article
- Review
- Quantitative modulation of a spatial enhancer through the biophysical properties of a transcription factor binding site.Science advances · 2026Article
- JASPAR 2026: expansion of transcription factor binding profiles and integration of deep learning models.Nucleic acids research · 2026Article
- Experimental approaches to investigate biophysical interactions between homeodomain transcription factors and DNA.Biochimica et biophysica acta. Gene regulatory mechanisms · 2025Review
- Combinatorial transcription factor binding encodes cis-regulatory wiring of mouse forebrain GABAergic neurogenesis.Developmental cell · 2025Article
- Towards the genomic sequence code of DNA fragility for machine learning.Nucleic acids research · 2024Article
- Deep DNAshape webserver: prediction and real-time visualization of DNA shape considering extended k-mers.Nucleic acids research · 2024Article
- Gene expression networks regulated by human personality.Molecular psychiatry · 2024Review
- Predicting DNA structure using a deep learning method.Nature communications · 2024Article
- A bioinformatics screen reveals hox and chromatin remodeling factors at the Drosophila histone locus.BMC genomic data · 2023Article
- A bioinformatics screen reveals Hox and chromatin remodeling factors at thebioRxiv : the preprint server for biology · 2023Article
- Generating specificity in genome regulation through transcription factor sensitivity to chromatin.Nature reviews. Genetics · 2022Review
- A global high-density chromatin interaction network reveals functional long-range and trans-chromosomal relationships.Genome biology · 2022Article
- It is in the flanks: Conformational flexibility of transcription factor binding sites.Biophysical journal · 2022Article
- Flexibility of flanking DNA is a key determinant of transcription factor affinity for the core motif.Biophysical journal · 2022Article
- Fluorescent labeling of genomic loci inCell reports methods · 2022Article
- Hox dosage contributes to flight appendage morphology in Drosophila.Nature communications · 2021Article
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
Abstract
Eukaryotic transcription factors (TFs) form complexes with various partner proteins to recognize their genomic target sites. Yet, how the DNA sequence determines which TF complex forms at any given site is poorly understood. Here, we demonstrate that high-throughput in vitro DNA binding assays coupled with unbiased computational analysis provide unprecedented insight into how different DNA sequences select distinct compositions and configurations of homeodomain TF complexes. Using inferred knowledge about minor groove width readout, we design targeted protein mutations that destabilize homeodomain binding both in vitro and in vivo in a complex-specific manner. By performing parallel systematic evolution of ligands by exponential enrichment sequencing (SELEX-seq), chromatin immunoprecipitation sequencing (ChIP-seq), RNA sequencing (RNA-seq), and Hi-C assays, we not only classify the majority of in vivo binding events in terms of complex composition but also infer complex-specific functions by perturbing the gene regulatory network controlled by a single complex.
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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.