ArticleNucleic acids research2020
Pervasive and CpG-dependent promoter-like characteristics of transcribed enhancers.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 32 citations in OpenAlex.
- Investigating the role of CpG islands and DNA methylation at 3'UTRs in cancer.Life science alliance · 2026Article
- Alternative splicing is coupled to gene expression in a subset of variably expressed genes.NPJ genomic medicine · 2024Article
- Integration of multi-omics data revealed the orphan CpG islands and enhancer-dominatediScience · 2024Article
- CpG island turnover events predict evolutionary changes in enhancer activity.Genome biology · 2024Article
- Article
- Alternative splicing is coupled to gene expression in a subset of variably expressed genes.bioRxiv : the preprint server for biology · 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
- Decoding regulatory associations of G-quadruplex with epigenetic and transcriptomic functional components.Frontiers in genetics · 2022Article
- Intragenic CpG Islands and Their Impact on Gene Regulation.Frontiers in cell and developmental biology · 2022Review
- Cap analysis of gene expression (CAGE) and noncoding regulatory elements.Seminars in immunopathology · 2022Review
- 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
- Enhancing Gonadotrope Gene Expression Through Regulatory lncRNAs.Endocrinology · 2021Review
- K-mer Content Changes with Node Degree in Promoter-Enhancer Network of Mouse ES Cells.International journal of molecular sciences · 2021Article
- Orphan CpG islands amplify poised enhancer regulatory activity and determine target gene responsiveness.Nature genetics · 2021Article
- HBA-DEALS: accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis.Genome biology · 2020Article
- Article
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The temporal and spatial expression of genes is controlled by promoters and enhancers. Findings obtained over the last decade that not only promoters but also enhancers are characterized by bidirectional, divergent transcription have challenged the traditional notion that promoters and enhancers represent distinct classes of regulatory elements. Over half of human promoters are associated with CpG islands (CGIs), relatively CpG-rich stretches of generally several hundred nucleotides that are often associated with housekeeping genes. Only about 6% of transcribed enhancers defined by CAGE-tag analysis are associated with CGIs. Here, we present an analysis of enhancer and promoter characteristics and relate them to the presence or absence of CGIs. We show that transcribed enhancers share a number of CGI-dependent characteristics with promoters, including statistically significant local overrepresentation of core promoter elements. CGI-associated enhancers are longer, display higher directionality of transcription, greater expression, a lesser degree of tissue specificity, and a higher frequency of transcription-factor binding events than non-CGI-associated enhancers. Genes putatively regulated by CGI-associated enhancers are enriched for transcription regulator activity. Our findings show that CGI-associated transcribed enhancers display a series of characteristics related to sequence, expression and function that distinguish them from enhancers not associated with CGIs.
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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.