ArticleNucleic acids research2018
Shared nucleotide flanks confer transcriptional competency to bZip core motifs.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 27 citations in OpenAlex.
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- DNA-Protein Binding is Dominated by Short Anchoring Elements.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- ZBTB46 coordinates angiogenesis and immunity to control tumor outcome.Nature immunology · 2024Article
- Lineage-determining transcription factor-driven promoters regulate cell type-specific macrophage gene expression.Nucleic acids research · 2024Article
- GermlineeLife · 2024Article
- GermlinebioRxiv : the preprint server for biology · 2024Article
- MAE-seq refines regulatory elements across the genome.Nucleic acids research · 2024Article
- Genome-wide census of ATF4 binding sites and functional profiling of trait-associated genetic variants overlapping ATF4 binding motifs.PLoS genetics · 2023Article
- Structural basis for cell type specific DNA binding of C/EBPβ: The case of cell cycle inhibitor p15INK4b promoter.Journal of structural biology · 2022Article
- Flexibility of flanking DNA is a key determinant of transcription factor affinity for the core motif.Biophysical journal · 2022Article
- Sequence-specific dynamics of DNA response elements and their flanking sites regulate the recognition by AP-1 transcription factors.Nucleic acids research · 2021Article
- TFregulomeR reveals transcription factors' context-specific features and functions.Nucleic acids research · 2020Article
- Motif grammar: The basis of the language of gene expression.Computational and structural biotechnology journal · 2020Review
- A novel upstream transcription factor 1 target geneBiochemistry and biophysics reports · 2019Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
Sequence-specific DNA binding recruits transcription factors (TFs) to the genome to regulate gene expression. Here, we perform high resolution mapping of CEBP proteins to determine how sequence dictates genomic occupancy. We demonstrate a fundamental difference between the sequence repertoire utilized by CEBPs in vivo versus the palindromic sequence preference reported by classical in vitro models, by identifying a palindromic motif at <1% of the genomic binding sites. On the native genome, CEBPs bind a diversity of related 10 bp sequences resulting from the fusion of degenerate and canonical half-sites. Altered DNA specificity of CEBPs in cells occurs through heterodimerization with other bZip TFs, and approximately 40% of CEBP-binding sites in primary human cells harbor motifs characteristic of CEBP heterodimers. In addition, we uncover an important role for sequence bias at core-motif-flanking bases for CEBPs and demonstrate that flanking bases regulate motif function across mammalian bZip TFs. Favorable flanking bases confer efficient TF occupancy and transcriptional activity, and DNA shape may explain how the flanks alter TF binding. Importantly, motif optimization within the 10-mer is strongly correlated with cell-type-independent recruitment of CEBPβ, providing key insight into how sequence sub-optimization affects genomic occupancy of widely expressed CEBPs across cell types.
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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 Socratic graph.