ArticleScientific reports2017
Modelling the evolution of transcription factor binding preferences in complex eukaryotes.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 32 citations in OpenAlex.
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- Evolutionary Transitions in Social Behavior are Associated With Convergent and Partially Reversible Expansions of Transcription Factor Binding Sites.Genome biology and evolution · 2026Article
- Co-Var, a Measure to Determine Intra-protein, Inter-protein, Protein-DNA, or Protein-RNA Coevolution.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Conservation of cis-regulatory codes over half a billion years of evolution.Science advances · 2025Article
- Ohno-miRNAs: miRNA pairs derived from whole-genome duplication.PLoS computational biology · 2025Article
- The transcriptional coordination of functional gene clusters is dependent on multiple chromatin remodelers in a haploid strain of the budding yeast,Frontiers in fungal biology · 2025Article
- Conservation ofCells · 2024Article
- MSALigMap-A Tool for Mapping Active-Site Amino Acids in PDB Structures onto Known and Novel Unannotated Homologous Sequences with Similar Function.Life (Basel, Switzerland) · 2022Article
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- The impact of whole genome duplications on the human gene regulatory networks.PLoS computational biology · 2021Article
- A Bit Stickier, a Bit Slower, a Lot Stiffer: Specific vs. Nonspecific Binding of Gal4 to DNA.International journal of molecular sciences · 2021Article
- Epigenetics and transcription regulation during eukaryotic diversification: the saga of TFIID.Genes & development · 2019Article
- The forkhead-box family of transcription factors: key molecular players in colorectal cancer pathogenesis.Molecular cancer · 2019Review
- The Network of Cancer Genes (NCG): a comprehensive catalogue of known and candidate cancer genes from cancer sequencing screens.Genome biology · 2019Article
- Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transcription factors (TFs) exert their regulatory action by binding to DNA with specific sequence preferences. However, different TFs can partially share their binding sequences due to their common evolutionary origin. This "redundancy" of binding defines a way of organizing TFs in "motif families" by grouping TFs with similar binding preferences. Since these ultimately define the TF target genes, the motif family organization entails information about the structure of transcriptional regulation as it has been shaped by evolution. Focusing on the human TF repertoire, we show that a one-parameter evolutionary model of the Birth-Death-Innovation type can explain the TF empirical repartition in motif families, and allows to highlight the relevant evolutionary forces at the origin of this organization. Moreover, the model allows to pinpoint few deviations from the neutral scenario it assumes: three over-expanded families (including HOX and FOX genes), a set of "singleton" TFs for which duplication seems to be selected against, and a higher-than-average rate of diversification of the binding preferences of TFs with a Zinc Finger DNA binding domain. Finally, a comparison of the TF motif family organization in different eukaryotic species suggests an increase of redundancy of binding with organism complexity.
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