ArticleGenome research2010
Genome architecture marked by retrotransposons modulates predisposition to DNA methylation in cancer.
Article in Genome research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers, 1 of them a synthesis that pooled it.
What it found
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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.
The trial behind it
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
51 citing papers in PubMed, 1 synthesis or guideline pooled it, 87 citations in OpenAlex.
- DNA methylation screening identifies driver epigenetic events of cancer cell survival.Cancer cell · 2012Pooled it
- Phase I/II study of decitabine in patients with myelodysplastic syndrome: a multi-center study in Japan.Cancer science · 2012Trial
- Non-pathogenic microbiota accelerate age-related CpG Island methylation in colonic mucosa.Epigenetics · 2023Article
- Computational Methods for Single-cell DNA Methylome Analysis.Genomics, proteomics & bioinformatics · 2023Review
- Methylation Markers in Cutaneous Melanoma: Unravelling the Potential Utility of Their Tracking by Liquid Biopsy.Cancers · 2021Review
- DNA methylation aging clocks: challenges and recommendations.Genome biology · 2019Review
- Emerging Role of Migration and Invasion Enhancer 1 (MIEN1) in Cancer Progression and Metastasis.Frontiers in oncology · 2019Review
- RBPJ binds to consensus and methylated cis elements within phased nucleosomes and controls gene expression in human aortic smooth muscle cells in cooperation with SRF.Nucleic acids research · 2018Article
- An annotated list of bivalent chromatin regions in human ES cells: a new tool for cancer epigenetic research.Oncotarget · 2017Article
- 5-methylcytosine-sensitive variants of Thermococcus kodakaraensis DNA polymerase.Nucleic acids research · 2016Article
- MIEN1 is tightly regulated by SINE Alu methylation in its promoter.Oncotarget · 2016Article
- 6-Substituted 2-Aminopurine-2'-deoxyribonucleoside 5'-Triphosphates that Trace Cytosine Methylation.Chembiochem : a European journal of chemical biology · 2016Article
- Modified Nucleotides for Discrimination between Cytosine and the Epigenetic Marker 5-Methylcytosine.Angewandte Chemie (International ed. in English) · 2016Article
- Liquid Biopsies for Assessing Metastatic Melanoma Progression.Critical reviews in oncogenesis · 2016Review
- Article
- Retrotransposition creates sloping shores: a graded influence of hypomethylated CpG islands on flanking CpG sites.Genome research · 2015Article
- Evolving insights on how cytosine methylation affects protein-DNA binding.Briefings in functional genomics · 2015Review
- Article
- Positive Darwinian selection in the singularly large taste receptor gene family of an 'ancient' fish, Latimeria chalumnae.BMC genomics · 2014Article
- Direct sensing of 5-methylcytosine by polymerase chain reaction.Angewandte Chemie (International ed. in English) · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
15 authors at 5 institutions in 3 countries.
Funding
Abstract
Epigenetic silencing plays an important role in cancer development. An attractive hypothesis is that local DNA features may participate in differential predisposition to gene hypermethylation. We found that, compared with methylation-resistant genes, methylation-prone genes have a lower frequency of SINE and LINE retrotransposons near their transcription start site. In several large testing sets, this distribution was highly predictive of promoter methylation. Genome-wide analysis showed that 22% of human genes were predicted to be methylation-prone in cancer; these tended to be genes that are down-regulated in cancer and that function in developmental processes. Moreover, retrotransposon distribution marks a larger fraction of methylation-prone genes compared to Polycomb group protein (PcG) marking in embryonic stem cells; indeed, PcG marking and our predictive model based on retrotransposon frequency appear to be correlated but also complementary. In summary, our data indicate that retrotransposon elements, which are widespread in our genome, are strongly associated with gene promoter DNA methylation in cancer and may in fact play a role in influencing epigenetic regulation in normal and abnormal physiological states.
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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.