ArticleNucleic acids research2014
Characterizing the strand-specific distribution of non-CpG methylation in human pluripotent cells.
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 35 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
35 citing papers in PubMed, 60 citations in OpenAlex.
- Integrative multi-omics analysis of DNA methylome and transcriptome in a tyrosine kinase inhibitor LPM4870108-induced rat model of obesity.International journal of obesity (2005) · 2026Article
- DNA methylation shapes transcription factor binding beyond canonical CpG contexts.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- DNA methylation and hydroxymethylation characterize the identity of D1 and D2 striatal projection neurons.Communications biology · 2022Article
- Human non-CpG methylation patterns display both tissue-specific and inter-individual differences suggestive of underlying function.Epigenetics · 2022Article
- Transposable element regulation and expression in cancer.The FEBS journal · 2022Review
- TET3 dioxygenase modulates gene conversion at the avian immunoglobulin variable region via demethylation of non-CpG sites in pseudogene templates.Genes to cells : devoted to molecular & cellular mechanisms · 2021Article
- Transposable Element Dynamics and Regulation during Zygotic Genome Activation in Mammalian Embryos and Embryonic Stem Cell Model Systems.Stem cells international · 2021Review
- Developmental Accumulation of Gene Body and Transposon Non-CpG Methylation in the Zebrafish Brain.Frontiers in cell and developmental biology · 2021Article
- The Absence of C-5 DNA Methylation inMicroorganisms · 2020Article
- Epigenetic pacemaker: closed form algebraic solutions.BMC genomics · 2020Article
- Asymmetric Inheritance of Cell Fate Determinants: Focus on RNA.Non-coding RNA · 2019Review
- Article
- T-ALL leukemia stem cell 'stemness' is epigenetically controlled by the master regulator SPI1.eLife · 2018Article
- Epigenetic perspectives on the evolution and domestication of polyploid plant and crops.Current opinion in plant biology · 2018Review
- Comparison of whole-genome bisulfite sequencing library preparation strategies identifies sources of biases affecting DNA methylation data.Genome biology · 2018Article
- CGmapTools improves the precision of heterozygous SNV calls and supports allele-specific methylation detection and visualization in bisulfite-sequencing data.Bioinformatics (Oxford, England) · 2018Article
- Alpha-Lipoic Acid Downregulates IL-1β and IL-6 by DNA Hypermethylation in SK-N-BE Neuroblastoma Cells.Antioxidants (Basel, Switzerland) · 2017Article
- Genome-wide, Single-Cell DNA Methylomics Reveals Increased Non-CpG Methylation during Human Oocyte Maturation.Stem cell reports · 2017Article
- Genome-wide DNA methylation profiles reveal novel candidate genes associated with meat quality at different age stages in hens.Scientific reports · 2017Article
- Genome-wide DNA methylation reprogramming in response to inorganic arsenic links inhibition of CTCF binding, DNMT expression and cellular transformation.Scientific reports · 2017Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
Abstract
DNA methylation is an important defense and regulatory mechanism. In mammals, most DNA methylation occurs at CpG sites, and asymmetric non-CpG methylation has only been detected at appreciable levels in a few cell types. We are the first to systematically study the strand-specific distribution of non-CpG methylation. With the divide-and-compare strategy, we show that CHG and CHH methylation are not intrinsically different in human embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs). We also find that non-CpG methylation is skewed between the two strands in introns, especially at intron boundaries and in highly expressed genes. Controlling for the proximal sequences of non-CpG sites, we show that the skew of non-CpG methylation in introns is mainly guided by sequence skew. By studying subgroups of transposable elements, we also found that non-CpG methylation is distributed in a strand-specific manner in both short interspersed nuclear elements (SINE) and long interspersed nuclear elements (LINE), but not in long terminal repeats (LTR). Finally, we show that on the antisense strand of Alus, a non-CpG site just downstream of the A-box is highly methylated. Together, the divide-and-compare strategy leads us to identify regions with strand-specific distributions of non-CpG methylation in humans.
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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.