ArticleGenome research2008
Evolution of the mammalian transcription factor binding repertoire via transposable elements.
Article in Genome research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 361 papers.
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Who cites it
361 citing papers in PubMed, 626 citations in OpenAlex.
- Review
- Transposable elements and homotypic niches drive immune dynamics and resistance in melanoma epigenetic-based immunotherapy.Science advances · 2026Article
- Transposable Element Activation: A Hallmark of Cancer.Cancer discovery · 2026Review
- Promoter-associated RNA polymerase III shapes RNA polymerase II-dependent inflammatory gene expression during viral infection.bioRxiv : the preprint server for biology · 2026Article
- Transposable element-mediated evolutionary expansion of Sox2- and Brn2-binding regulatory modules for mammalian neural-cell differentiation.Genome biology · 2026Article
- Cleavage region organizes the structural architecture of the SINE-derived B2 repressive ribozyme.Communications biology · 2026Article
- Remodeling ofScience advances · 2026Article
- TEITbase: a database for transposable element (TE)-initiated transcripts in human cancers.Database : the journal of biological databases and curation · 2026Article
- Investigating the Physiological Regulation of Transposable Elements In Vivo: Nuclei Preparation from Primary Mouse Tissues for Epigenomic Analyses and Computational Approaches to Interrogate the Repeat Genome.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Hominoid-specific transposable elements reshaped neural crest migration in craniofacial development.Molecular systems biology · 2025Article
- Transposable elements drive species-specific and tissue-specific transcriptomes in human development.Genome biology · 2025Article
- RNA polymerase III transcription-associated polyadenylation promotes the accumulation of noncoding retrotransposons during infection.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- The impact of environmental exposures on the epigenomic and transcriptomic landscape of transposable elements.bioRxiv : the preprint server for biology · 2025Article
- A phylogenetic approach uncovers cryptic endogenous retrovirus subfamilies in the primate lineage.Science advances · 2025Article
- Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-kB binding.Genome research · 2025Article
- Charting the regulatory landscape of TP53 on transposable elements in cancer.Genome research · 2025Article
- Deciphering the role of histone modifications in memory and exhausted CD8 T cells.Scientific reports · 2025Article
- Binding of NF-Y to transposable elements in mouse and human cells.Mobile DNA · 2025Article
- Transposable elements as genome regulators in normal and malignant haematopoiesis.Blood cancer journal · 2025Review
- Regulatory changes in the fatty acid elongase eloF underlie the evolution of sex-specific pheromone profiles in Drosophila prolongata.BMC biology · 2025Article
301 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
11 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Identification of lineage-specific innovations in genomic control elements is critical for understanding transcriptional regulatory networks and phenotypic heterogeneity. We analyzed, from an evolutionary perspective, the binding regions of seven mammalian transcription factors (ESR1, TP53, MYC, RELA, POU5F1, SOX2, and CTCF) identified on a genome-wide scale by different chromatin immunoprecipitation approaches and found that only a minority of sites appear to be conserved at the sequence level. Instead, we uncovered a pervasive association with genomic repeats by showing that a large fraction of the bona fide binding sites for five of the seven transcription factors (ESR1, TP53, POU5F1, SOX2, and CTCF) are embedded in distinctive families of transposable elements. Using the age of the repeats, we established that these repeat-associated binding sites (RABS) have been associated with significant regulatory expansions throughout the mammalian phylogeny. We validated the functional significance of these RABS by showing that they are over-represented in proximity of regulated genes and that the binding motifs within these repeats have undergone evolutionary selection. Our results demonstrate that transcriptional regulatory networks are highly dynamic in eukaryotic genomes and that transposable elements play an important role in expanding the repertoire of binding sites.
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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.