ArticleGenome research2014
Extreme HOT regions are CpG-dense promoters in C. elegans and humans.
Article in Genome research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed, 68 citations in OpenAlex.
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- Linking Benzene, in Utero Carcinogenicity and Fetal Hematopoietic Stem Cell Niches: A Mechanistic Review.International journal of molecular sciences · 2023Review
- CpG-binding protein CFP1 promotes ovarian cancer cell proliferation by regulating BST2 transcription.Cancer gene therapy · 2022Article
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- The Genome-Wide Binding Profile for Human RE1 Silencing Transcription Factor Unveils a Unique Genetic Circuitry in Hippocampus.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2021Article
- The dynamic broad epigenetic (H3K4me3, H3K27ac) domain as a mark of essential genes.Clinical epigenetics · 2021Review
- Sequence determinants, function, and evolution of CpG islands.Biochemical Society transactions · 2021Review
- AP-1 subunits converge promiscuously at enhancers to potentiate transcription.Genome research · 2021Article
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- Functional Transcription Factor Target Networks Illuminate Control of Epithelial Remodelling.Cancers · 2020Article
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
Most vertebrate promoters lie in unmethylated CpG-dense islands, whereas methylation of the more sparsely distributed CpGs in the remainder of the genome is thought to contribute to transcriptional repression. Nonmethylated CG dinucleotides are recognized by CXXC finger protein 1 (CXXC1, also known as CFP1), which recruits SETD1A (also known as Set1) methyltransferase for trimethylation of histone H3 lysine 4, an active promoter mark. Genomic regions enriched for CpGs are thought to be either absent or irrelevant in invertebrates that lack DNA methylation, such as C. elegans; however, a CXXC1 ortholog (CFP-1) is present. Here we demonstrate that C. elegans CFP-1 targets promoters with high CpG density, and these promoters are marked by high levels of H3K4me3. Furthermore, as for mammalian promoters, high CpG content is associated with nucleosome depletion irrespective of transcriptional activity. We further show that highly occupied target (HOT) regions identified by the binding of a large number of transcription factors are CpG-rich promoters in C. elegans and human genomes, suggesting that the unusually high factor association at HOT regions may be a consequence of CpG-linked chromatin accessibility. Our results indicate that nonmethylated CpG-dense sequence is a conserved genomic signal that promotes an open chromatin state, targeting by a CXXC1 ortholog, and H3K4me3 modification in both C. elegans and human genomes.
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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.