ArticleEpigenetics2017
Orphan CpG islands define a novel class of highly active enhancers.
Article in Epigenetics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 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
31 citing papers in PubMed, 65 citations in OpenAlex.
- Review
- Interplay Between 3D Chromatin Architecture and Gene Regulation at theInternational journal of molecular sciences · 2025Article
- Multiple human enhancer RNAs contain long translated open reading frames.Genes & development · 2025Article
- Prediction of Enhancer RNAs in Chicken Genome.International journal of molecular sciences · 2025Article
- Roles of transposable elements and DNA methylation in the formation of CpG islands and CpG-depleted regulatory elements.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Epigenetic signatures of intergenerational exposure to violence in three generations of Syrian refugees.Scientific reports · 2025Article
- Article
- Role of the histone variant H2A.Z.1 in memory, transcription, and alternative splicing is mediated by lysine modification.Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology · 2024Article
- CpG island turnover events predict evolutionary changes in enhancer activity.Genome biology · 2024Article
- Spatial chromatin accessibility sequencing resolves high-order spatial interactions of epigenomic markers.eLife · 2024Article
- Article
- Transcription factor expression repertoire basis for epigenetic and transcriptional subtypes of colorectal cancers.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Profiling the immune epigenome across global cattle breeds.Genome biology · 2023Article
- Connectome and regulatory hubs of CAGE highly active enhancers.Scientific reports · 2023Article
- Gene body methylation in cancer: molecular mechanisms and clinical applications.Clinical epigenetics · 2022Review
- MIR retrotransposons link the epigenome and the transcriptome of coding genes in acute myeloid leukemia.Nature communications · 2022Article
- Intragenic CpG Islands and Their Impact on Gene Regulation.Frontiers in cell and developmental biology · 2022Review
- A bipartite element with allele-specific functions safeguards DNA methylation imprints at the Dlk1-Dio3 locus.Developmental cell · 2021Article
- Developmental programming of DNA methylation and gene expression patterns is associated with extreme cardiovascular tolerance to anoxia in the common snapping turtle.Epigenetics & chromatin · 2021Article
- Epigenetic Regulation of microRNAs in Cancer: Shortening the Distance from Bench to Bedside.International journal of molecular sciences · 2021Review
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
CpG islands (CGI) are critical genomic regulatory elements that support transcriptional initiation and are associated with the promoters of most human genes. CGI are distinguished from the bulk genome by their high CpG density, lack of DNA methylation, and euchromatic features. While CGI are canonically known as strong promoters, thousands of 'orphan' CGI lie far from any known transcript, leaving their function an open question. We undertook a comprehensive analysis of the epigenetic state of orphan CGI across over 100 cell types. Here we show that most orphan CGI display the chromatin features of active enhancers (H3K4me1, H3K27Ac) in at least one cell type. Relative to classical enhancers, these enhancer CGI (ECGI) are stronger, as gauged by chromatin state and in functional assays, are more broadly expressed, and are more highly conserved. Likewise, ECGI engage in more genomic contacts and are enriched for transcription factor binding relative to classical enhancers. In human cancers, these epigenetic differences between ECGI vs. classical enhancers manifest in distinct alterations in DNA methylation. Thus, ECGI define a class of highly active enhancers, strengthened by the broad transcriptional activity, CpG density, hypomethylation, and chromatin features they share with promoter CGI. In addition to indicating a role for thousands of orphan CGI, these findings suggests that enhancer activity may be an intrinsic function of CGI in general and provides new insights into the evolution of enhancers and their epigenetic regulation during development and tumorigenesis.
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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.