ArticlePloS one2025
Positional distribution of transcription factor binding sites in the human genome.
Article in PloS one, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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Who cites it
2 citing papers in PubMed.
- Robust cis-by-trans epistasis in the human plasma proteome highlights an ABO-centered interaction network.American journal of human genetics · 2026Article
- Manganese availability determines insulin sensitivity by enhancing Akt activity.bioRxiv : the preprint server for biology · 2026Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
As transcription factors (TFs) play a major role in gene regulation, we studied their binding motifs (positional weight matrices, PWMs) and binding sites (TFBSs) in the human genome, and how TFs bind DNA motifs, including the involvement of binding co-factors. Using the chromatin immunoprecipitation sequencing data recently released by ENCODE (Encyclopedia of DNA Elements), we obtained new PWMs for 196 TFs and revised PWMs for 119 TFs. From these and the PWMs previously obtained for 235 TFs, we inferred the canonical PWMs for 500 TFs, including 243 new PWMs. Analysis revealed that most TFBSs are in introns (42.6%) and intergenic regions (31.6%), with only 11.3% in promoters. However, the TFBS density is considerably higher in promoters, showing a bell-shaped distribution of TFBSs with a peak at the transcription start site. Many TFBSs lie close to CTCF (CCCTC-binding factor) binding sites. Tethered binding is far more frequent than co-binding, with the latter often requiring co-factors.
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Registered trials
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