ArticleNature2015
DNA-dependent formation of transcription factor pairs alters their binding specificity.
Article in Nature, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 344 papers.
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Who cites it
344 citing papers in PubMed, 585 citations in OpenAlex.
- Integrative analysis reveals extensive interactions among C2H2 zinc finger proteins at chromatin loop anchors.Nucleic acids research · 2026Article
- A transcription factor regulates development of a bacteria-housing eukaryotic cell through DNA damage mitigation.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- An atlas of transcription factor cooperation reveals how motif readers shape regulatory output.bioRxiv : the preprint server for biology · 2026Article
- GHT-SELEX demonstrates unexpectedly high intrinsic sequence specificity and complex DNA binding of many human transcription factors.Nature methods · 2026Article
- A group of TCP transcription factors is a missing link in strigolactone signaling.Journal of integrative plant biology · 2026Article
- Noncircadian BMAL1-YAP activity amplifies persistent inflammation in aged epidermis.Nature aging · 2026Article
- Readout of intrinsic and induced DNA shape by homeodomain transcription factor complexes.Biophysical journal · 2026Article
- BaGGLS: a Bayesian shrinkage framework for interpretable modeling of interactions in high-dimensional biological data.Bioinformatics (Oxford, England) · 2026Article
- Molecular basis of UV lesion binding and repair inhibition by ETS-family transcription factors.Nucleic acids research · 2026Article
- FABIAN-variant 2026: improved prediction of the effects of DNA variants on transcription factor binding.Nucleic acids research · 2026Article
- Data-intensive immune network modelling for One Health.Briefings in bioinformatics · 2026Review
- BPabZIP, a new bZIP protein motif that promotes binding near, and displacement of, nucleosomes.bioRxiv : the preprint server for biology · 2026Article
- Combinatorial pioneer transcription factor binding reinforces bivalent epigenetic states to preserve lineage fidelity.bioRxiv : the preprint server for biology · 2026Article
- Combinatorial transcription factor interactions drive modular gene regulatory networks.bioRxiv : the preprint server for biology · 2026Article
- Bipartite DNA binding domain of transcription factor BCL11B binds clustered short DNA sequence motifs.bioRxiv : the preprint server for biology · 2026Article
- Article
- Sequence-based modeling of low-affinity transcription factor-DNA binding through deep learning.NAR genomics and bioinformatics · 2026Article
- Interplay between circadian and other transcription factors-Implications for cycling transcriptome reprogramming.FEBS letters · 2026Review
- Mechanisms of enhanced or impaired DNA target selectivity driven by protein dimerization.PNAS nexus · 2026Article
- High-resolution map of chromatin accessibility - insights into the focused binding of a large number of transcription factors.Epigenetics & chromatin · 2026Article
284 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gene expression is regulated by transcription factors (TFs), proteins that recognize short DNA sequence motifs. Such sequences are very common in the human genome, and an important determinant of the specificity of gene expression is the cooperative binding of multiple TFs to closely located motifs. However, interactions between DNA-bound TFs have not been systematically characterized. To identify TF pairs that bind cooperatively to DNA, and to characterize their spacing and orientation preferences, we have performed consecutive affinity-purification systematic evolution of ligands by exponential enrichment (CAP-SELEX) analysis of 9,400 TF-TF-DNA interactions. This analysis revealed 315 TF-TF interactions recognizing 618 heterodimeric motifs, most of which have not been previously described. The observed cooperativity occurred promiscuously between TFs from diverse structural families. Structural analysis of the TF pairs, including a novel crystal structure of MEIS1 and DLX3 bound to their identified recognition site, revealed that the interactions between the TFs were predominantly mediated by DNA. Most TF pair sites identified involved a large overlap between individual TF recognition motifs, and resulted in recognition of composite sites that were markedly different from the individual TF's motifs. Together, our results indicate that the DNA molecule commonly plays an active role in cooperative interactions that define the gene regulatory lexicon.
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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.