ArticleBMC genomics2007
Widespread Alu repeat-driven expansion of consensus DR2 retinoic acid response elements during primate evolution.
Article in BMC genomics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
46 citing papers in PubMed, 96 citations in OpenAlex.
- Flipons, Noncoding Transcripts and Retroelements: A Universal Host Defense.International journal of molecular sciences · 2026Review
- Transposable Elements Are Dynamically Regulated in Medium Spiny Neurons and May Contribute to the Molecular and Behavioral Adaptations to Cocaine.Biological psychiatry · 2026Article
- Zα and Zβ Localize ADAR1 to Flipons That Modulate Innate Immunity, Alternative Splicing, and Nonsynonymous RNA Editing.International journal of molecular sciences · 2025Review
- Flipons and small RNAs accentuate the asymmetries of pervasive transcription by the reset and sequence-specific microcoding of promoter conformation.The Journal of biological chemistry · 2023Review
- The Role of Transposable Elements of the Human Genome in Neuronal Function and Pathology.International journal of molecular sciences · 2022Review
- Viruses and Endogenous Retroviruses as Roots for Neuroinflammation and Neurodegenerative Diseases.Frontiers in neuroscience · 2021Review
- Alu element in the RNA binding motif protein, X-linked 2 (RBMX2) gene found to be linked to bipolar disorder.PloS one · 2021Article
- Retinoic Acids in the Treatment of Most Lethal Solid Cancers.Journal of clinical medicine · 2020Review
- Promoter methylation, transcription, and retrotransposition of LINE-1 in colorectal adenomas and adenocarcinomas.Cancer cell international · 2020Article
- Warning SINEs: Alu elements, evolution of the human brain, and the spectrum of neurological disease.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2018Review
- Liver X Receptor-Binding DNA Motif Associated With Atherosclerosis-Specific DNA Methylation Profiles ofJournal of the American Heart Association · 2018Article
- Molecular and functional genetics of the proopiomelanocortin gene, food intake regulation and obesity.FEBS letters · 2017Review
- Review
- Genome-wide mapping of infection-induced SINE RNAs reveals a role in selective mRNA export.Nucleic acids research · 2017Article
- Exploratory bioinformatics investigation reveals importance of "junk" DNA in early embryo development.BMC genomics · 2017Article
- Alu repeats as transcriptional regulatory platforms in macrophage responses to M. tuberculosis infection.Nucleic acids research · 2016Article
- Alu-miRNA interactions modulate transcript isoform diversity in stress response and reveal signatures of positive selection.Scientific reports · 2016Article
- Evidence for genetic regulation of mRNA expression of the dosage-sensitive gene retinoic acid induced-1 (RAI1) in human brain.Scientific reports · 2016Article
- Restricting retrotransposons: a review.Mobile DNA · 2016Review
- Expression in the human brain of retinoic acid induced 1, a protein associated with neurobehavioural disorders.Brain structure & function · 2015Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundNuclear receptors are hormone-regulated transcription factors whose signaling controls numerous aspects of development and physiology. Many receptors recognize DNA hormone response elements formed by direct repeats of RGKTCA motifs separated by 1 to 5 bp (DR1-DR5). Although many known such response elements are conserved in the mouse and human genomes, it is unclear to which extent transcriptional regulation by nuclear receptors has evolved specifically in primates.
resultsWe have mapped the positions of all consensus DR-type hormone response elements in the human genome, and found that DR2 motifs, recognized by retinoic acid receptors (RARs), are heavily overrepresented (108,582 elements). 90% of these are present in Alu repeats, which also contain lesser numbers of other consensus DRs, including 50% of consensus DR4 motifs. Few DR2s are in potentially mobile AluY elements and the vast majority are also present in chimp and macaque. 95.5% of Alu-DR2s are distributed throughout subclasses of AluS repeats, and arose largely through deamination of a methylated CpG dinucleotide in a non-consensus motif present in AluS sequences. We find that Alu-DR2 motifs are located adjacent to numerous known retinoic acid target genes, and show by chromatin immunoprecipitation assays in squamous carcinoma cells that several of these elements recruit RARs in vivo. These findings are supported by ChIP-on-chip data from retinoic acid-treated HL60 cells revealing RAR binding to several Alu-DR2 motifs.
conclusionThese data provide strong support for the notion that Alu-mediated expansion of DR elements contributed to the evolution of gene regulation by RARs and other nuclear receptors in primates and humans.
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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.