ArticleGenome biology2011
A comparative analysis of DNA methylation across human embryonic stem cell lines.
Article in Genome biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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Who cites it
52 citing papers in PubMed, 100 citations in OpenAlex.
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- Human non-CpG methylation patterns display both tissue-specific and inter-individual differences suggestive of underlying function.Epigenetics · 2022Article
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- DNA methylation mediated RSPO2 to promote follicular development in mammals.Cell death & disease · 2021Article
- Systematic benchmarking of tools for CpG methylation detection from nanopore sequencing.Nature communications · 2021Article
- An integrated epigenomic-transcriptomic landscape of lung cancer reveals novel methylation driver genes of diagnostic and therapeutic relevance.Theranostics · 2021Article
- Insight Between the Epigenetics and Transcription Responding of Cotton Hypocotyl Cellular Elongation Under Salt-Alkaline Stress.Frontiers in plant science · 2021Article
- Neural precursors cells expanded in a 3D micro-engineered niche present enhanced therapeutic efficacyNanotheranostics · 2021Article
- The Needle in the Haystack-Searching for Genetic and Epigenetic Differences in Monozygotic Twins Discordant for Tetralogy of Fallot.Journal of cardiovascular development and disease · 2020Article
- The Impact and Mechanism of Methylated Metabotropic Glutamate Receptors 1 and 5 in the Hippocampus on Depression-Like Behavior in Prenatal Stress Offspring Rats.Journal of clinical medicine · 2018Article
- Transcriptional Regulation by CpG Sites Methylation in the Core Promoter Region of the Bovine SIX1 Gene: Roles of Histone H4 and E2F2.International journal of molecular sciences · 2018Article
- Single-base resolution methylomes of upland cotton (Gossypium hirsutum L.) reveal epigenome modifications in response to drought stress.BMC genomics · 2017Article
- Hypermethylated LTR retrotransposon exhibits enhancer activity.Epigenetics · 2017Article
- The elephant shark methylome reveals conservation of epigenetic regulation across jawed vertebrates.F1000Research · 2017Article
- Mammalian non-CG methylations are conserved and cell-type specific and may have been involved in the evolution of transposon elements.Scientific reports · 2016Article
- Gene and transposable element methylation in great tit (Parus major) brain and blood.BMC genomics · 2016Article
- Non-CG DNA methylation is a biomarker for assessing endodermal differentiation capacity in pluripotent stem cells.Nature communications · 2016Article
- CpG methylation differences between neurons and glia are highly conserved from mouse to human.Human molecular genetics · 2016Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
backgroundWe performed a comparative analysis of the genome-wide DNA methylation profiles from three human embryonic stem cell (HESC) lines. It had previously been shown that HESC lines had significantly higher non-CG methylation than differentiated cells, and we therefore asked whether these sites were conserved across cell lines.
resultsWe find that heavily methylated non-CG sites are strongly conserved, especially when found within the motif TACAG. They are enriched in splice sites and are more methylated than other non-CG sites in genes. We next studied the relationship between allele-specific expression and allele-specific methylation. By combining bisulfite sequencing and whole transcriptome shotgun sequencing (RNA-seq) data we identified 1,020 genes that show allele-specific expression, and 14% of CG sites genome-wide have allele-specific methylation. Finally, we asked whether the methylation state of transcription factor binding sites affects the binding of transcription factors. We identified variations in methylation levels at binding sites and found that for several transcription factors the correlation between the methylation at binding sites and gene expression is generally stronger than in the neighboring sequences.
conclusionsThese results suggest a possible but as yet unknown functional role for the highly methylated conserved non-CG sites in the regulation of HESCs. We also identified a novel set of genes that are likely transcriptionally regulated by methylation in an allele-specific manner. The analysis of transcription factor binding sites suggests that the methylation state of cis-regulatory elements impacts the ability of factors to bind and regulate transcription.
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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.