ArticleNucleic acids research2014
CpG domains downstream of TSSs promote high levels of gene expression.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 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
20 citing papers in PubMed, 36 citations in OpenAlex.
- Genomic and cellular context-dependent expression of the human ELMO1 gene transcript variants.Gene · 2025Article
- Genome-Wide Study of Colocalization between Genomic Stretches: A Method and Applications to the Regulation of Gene Expression.Biology · 2022Article
- Screening thousands of transcribed coding and non-coding regions reveals sequence determinants of RNA polymerase II elongation potential.Nature structural & molecular biology · 2022Article
- Targeting HIF-2α in the Tumor Microenvironment: Redefining the Role of HIF-2α for Solid Cancer Therapy.Cancers · 2022Review
- Hypermethylation of PDX1, EN2, and MSX1 predicts the prognosis of colorectal cancer.Experimental & molecular medicine · 2022Article
- Epigenetic Dysregulation of Trophoblastic Gene Expression in Gestational Trophoblastic Disease.Biomedicines · 2021Article
- Identification of long regulatory elements in the genome of Plasmodium falciparum and other eukaryotes.PLoS computational biology · 2021Article
- Genome-wide role of codon usage on transcription and identification of potential regulators.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Predicting transfer RNA gene activity from sequence and genome context.Genome research · 2020Article
- Limited expression of non-integrating CpG-free plasmid is associated with increased nucleosome enrichment.PloS one · 2020Article
- Codon usage regulates human KRAS expression at both transcriptional and translational levels.The Journal of biological chemistry · 2018Article
- Formaldehyde-assisted Isolation of Regulatory Elements to Measure Chromatin Accessibility in Mammalian Cells.Journal of visualized experiments : JoVE · 2018Article
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- Optimizing a Human Papillomavirus Type 16 L1-Based Chimaeric Gene for Expression in Plants.Frontiers in bioengineering and biotechnology · 2018Article
- The Effects of CpG Densities around Transcription Start Sites on Sex-Biased Gene Expression in Poecilia reticulata.Genome biology and evolution · 2017Article
- MeDIP-seq and nCpG analyses illuminate sexually dimorphic methylation of gonadal development genes with high historic methylation in turtle hatchlings with temperature-dependent sex determination.Epigenetics & chromatin · 2017Article
- Codon usage is an important determinant of gene expression levels largely through its effects on transcription.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
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- 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
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
CpG dinucleotides are known to play a crucial role in regulatory domains, affecting gene expression in their natural context. Here, we demonstrate that intragenic CpG frequency and distribution impacts transgene and genomic gene expression levels in mammalian cells. As shown for the Macrophage Inflammatory Protein 1α, de novo RNA synthesis correlates with the number of CpG dinucleotides, whereas RNA splicing, stability, nuclear export and translation are not affected by the sequence modification. Differences in chromatin accessibility in vivo and altered nucleosome positioning in vitro suggest that increased CpG levels destabilize the chromatin structure. Moreover, enriched CpG levels correlate with increased RNA polymerase II elongation rates in vivo. Interestingly, elevated CpG levels particularly at the 5' end of the gene promote efficient transcription. We show that this is a genome-wide feature of highly expressed genes, by identifying a domain of ∼700 bp with high CpG content downstream of the transcription start site, correlating with high levels of transcription. We suggest that these 5' CpG domains are required to distort the chromatin structure and to increase gene activity.
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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.