ArticleGenome biology2021
Evolution of mouse circadian enhancers from transposable elements.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 43 citations in OpenAlex.
- Gene regulatory innovations from transposable elements in primate cerebellum development.Nature communications · 2026Article
- Sleep and circadian regulation of DNA repair and retrotransposons in neuronal genome stability and neurodegenerative disease mechanisms.Frontiers in neuroscience · 2026Review
- PervasivebioRxiv : the preprint server for biology · 2025Article
- Liver-specific enhancers evolved from independent episodes of MITE domestication in Xenopus tropicalis.Mobile DNA · 2025Article
- Transcriptional and post-transcriptional regulation of transposable elements and their roles in development and disease.Nature reviews. Molecular cell biology · 2025Review
- Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-kB binding.Genome research · 2025Article
- Article
- Zygotic activation of transposable elements during zebrafish early embryogenesis.Nature communications · 2025Article
- A nuclear tRNA-derived fragment triggers immunity in Arabidopsis.Communications biology · 2025Article
- Multi-omics analysis reveals criticaliScience · 2025Article
- Widespread impact of transposable elements on the evolution of post-transcriptional regulation in the cotton genus Gossypium.Genome biology · 2025Article
- Regulatory transposable elements in the encyclopedia of DNA elements.Nature communications · 2024Article
- Pig H3K4me3, H3K27ac, and gene expression profiles reveal reproductive tissue-specific activity of transposable elements.Zoological research · 2024Article
- Transposable elements in mammalian chromatin organization.Nature reviews. Genetics · 2023Review
- Resolution of structural variation in diverse mouse genomes reveals chromatin remodeling due to transposable elements.Cell genomics · 2023Article
- Chiropterans Are a Hotspot for Horizontal Transfer of DNA Transposons in Mammalia.Molecular biology and evolution · 2023Article
- Widespread contribution of transposable elements to the rewiring of mammalian 3D genomes.Nature communications · 2023Article
- Transposable Elements Co-Option in Genome Evolution and Gene Regulation.International journal of molecular sciences · 2023Review
- Transposable elements orchestrate subgenome-convergent and -divergent transcription in common wheat.Nature communications · 2022Article
- Young transposable elements rewired gene regulatory networks in human and chimpanzee hippocampal intermediate progenitors.Development (Cambridge, England) · 2022Article
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundTransposable elements are increasingly recognized as a source of cis-regulatory variation. Previous studies have revealed that transposons are often bound by transcription factors and some have been co-opted into functional enhancers regulating host gene expression. However, the process by which transposons mature into complex regulatory elements, like enhancers, remains poorly understood. To investigate this process, we examined the contribution of transposons to the cis-regulatory network controlling circadian gene expression in the mouse liver, a well-characterized network serving an important physiological function.
resultsChIP-seq analyses reveal that transposons and other repeats contribute ~ 14% of the binding sites for core circadian regulators (CRs) including BMAL1, CLOCK, PER1/2, and CRY1/2, in the mouse liver. RSINE1, an abundant murine-specific SINE, is the only transposon family enriched for CR binding sites across all datasets. Sequence analyses and reporter assays reveal that the circadian regulatory activity of RSINE1 stems from the presence of imperfect CR binding motifs in the ancestral RSINE1 sequence. These motifs matured into canonical motifs through point mutations after transposition. Furthermore, maturation occurred preferentially within elements inserted in the proximity of ancestral CR binding sites. RSINE1 also acquired motifs that recruit nuclear receptors known to cooperate with CRs to regulate circadian gene expression specifically in the liver.
conclusionsOur results suggest that the birth of enhancers from transposons is predicated both by the sequence of the transposon and by the cis-regulatory landscape surrounding their genomic integration site.
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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.