ArticleEpigenetics2012
Human-specific CpG "beacons" identify loci associated with human-specific traits and disease.
Article in Epigenetics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 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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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
21 citing papers in PubMed.
- Interrogating the Regulatory Function of HAQERs during Human Cortical Development.bioRxiv : the preprint server for biology · 2025Article
- Epigenomic insights into common human disease pathology.Cellular and molecular life sciences : CMLS · 2024Review
- Review
- Genome-Wide Study of Colocalization between Genomic Stretches: A Method and Applications to the Regulation of Gene Expression.Biology · 2022Article
- Evolution and dysfunction of human cognitive and social traits: A transcriptional regulation perspective.Evolutionary human sciences · 2022Review
- The genomic loci of specific human tRNA genes exhibit ageing-related DNA hypermethylation.Nature communications · 2021Article
- Intraspecific and interspecific investigations of skeletal DNA methylation and femur morphology in primates.American journal of physical anthropology · 2020Article
- DNA methylation in canine brains is related to domestication and dog-breed formation.PloS one · 2020Article
- Analyzing whole genome bisulfite sequencing data from highly divergent genotypes.Nucleic acids research · 2019Article
- Article
- Constitutional Epi/Genetic Conditions: Genetic, Epigenetic, and Environmental Factors.Journal of pediatric genetics · 2017Review
- Exaggerated CpH methylation in the autism-affected brain.Molecular autism · 2017Article
- Nicotinic receptors in non-human primates: Analysis of genetic and functional conservation with humans.Neuropharmacology · 2015Review
- Retrotransposition creates sloping shores: a graded influence of hypomethylated CpG islands on flanking CpG sites.Genome research · 2015Article
- Genome-wide study of correlations between genomic features and their relationship with the regulation of gene expression.DNA research : an international journal for rapid publication of reports on genes and genomes · 2015Article
- Infinium monkeys: Infinium 450K array for the Cynomolgus macaque (Macaca fascicularis).G3 (Bethesda, Md.) · 2014Article
- Mitochondrial permeability transition pore regulates Parkinson's disease development in mutant α-synuclein transgenic mice.Neurobiology of aging · 2014Article
- Human-specific epigenetic variation in the immunological Leukotriene B4 Receptor (LTB4R/BLT1) implicated in common inflammatory diseases.Genome medicine · 2014Article
- Article
- Comparative analysis using K-mer and K-flank patterns provides evidence for CpG island sequence evolution in mammalian genomes.Nucleic acids research · 2013Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Regulatory change has long been hypothesized to drive the delineation of the human phenotype from other closely related primates. Here we provide evidence that CpG dinucleotides play a special role in this process. CpGs enable epigenome variability via DNA methylation, and this epigenetic mark functions as a regulatory mechanism. Therefore, species-specific CpGs may influence species-specific regulation. We report non-polymorphic species-specific CpG dinucleotides (termed "CpG beacons") as a distinct genomic feature associated with CpG island (CGI) evolution, human traits and disease. Using an inter-primate comparison, we identified 21 extreme CpG beacon clusters (≥ 20/kb peaks, empirical p < 1.0 × 10(-3)) in humans, which include associations with four monogenic developmental and neurological disease related genes (Benjamini-Hochberg corrected p = 6.03 × 10(-3)). We also demonstrate that beacon-mediated CpG density gain in CGIs correlates with reduced methylation in these species in orthologous CGIs over time, via human, chimpanzee and macaque MeDIP-seq. Therefore mapping into both the genomic and epigenomic space the identified CpG beacon clusters define points of intersection where a substantial two-way interaction between genetic sequence and epigenetic state has occurred. Taken together, our data support a model for CpG beacons to contribute to CGI evolution from genesis to tissue-specific to constitutively active CGIs.
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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.