ArticleeLife2014
High-throughput engineering of a mammalian genome reveals building principles of methylation states at CG rich regions.
Article in eLife, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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Who cites it
55 citing papers in PubMed.
- Synthetic Regulatory Genomics.Annual review of genomics and human genetics · 2026Review
- Cumulative transcription factor binding and p300-mediated histone acetylation drive enhancer activation frequency.Nature genetics · 2026Article
- DNA base lesion-containing G-quadruplex mediates transcriptome reprogramming in EGFR-TKI resistance of non-small cell lung cancer.Journal of experimental & clinical cancer research : CR · 2026Article
- A tunable, ultrasensitive threshold in enzymatic activity governs the DNA methylation landscape.Biophysical journal · 2026Article
- Epigenetic Potential and Dispersal Propensity in a Free-Living Songbird: A Spatial and Temporal Approach.Molecular ecology · 2025Article
- DNA methylation shapes the Polycomb landscape during the exit from naive pluripotency.Nature structural & molecular biology · 2025Article
- The impact of the embryonic DNA methylation program on CTCF-mediated genome regulation.Nucleic acids research · 2024Article
- Genome access is transcription factor-specific and defined by nucleosome position.Molecular cell · 2024Article
- Epigenetics Research in Evolutionary Biology: Perspectives on Timescales and Mechanisms.Molecular biology and evolution · 2024Review
- The correlation between CpG methylation and gene expression is driven by sequence variants.Nature genetics · 2024Article
- CpG island turnover events predict evolutionary changes in enhancer activity.Genome biology · 2024Article
- Generating specificity in genome regulation through transcription factor sensitivity to chromatin.Nature reviews. Genetics · 2022Review
- DNA sequence and chromatin modifiers cooperate to confer epigenetic bistability at imprinting control regions.Nature genetics · 2022Article
- Local CpG density affects the trajectory and variance of age-associated DNA methylation changes.Genome biology · 2022Article
- Article
- Intragenic CpG Islands and Their Impact on Gene Regulation.Frontiers in cell and developmental biology · 2022Review
- A functional mutation associated with piglet diarrhea partially by regulating the transcription of porcineFrontiers in veterinary science · 2022Article
- Sequence determinants, function, and evolution of CpG islands.Biochemical Society transactions · 2021Review
- E2F6 initiates stable epigenetic silencing of germline genes during embryonic development.Nature communications · 2021Article
- High throughput screening identifies SOX2 as a super pioneer factor that inhibits DNA methylation maintenance at its binding sites.Nature communications · 2021Article
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4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The majority of mammalian promoters are CpG islands; regions of high CG density that require protection from DNA methylation to be functional. Importantly, how sequence architecture mediates this unmethylated state remains unclear. To address this question in a comprehensive manner, we developed a method to interrogate methylation states of hundreds of sequence variants inserted at the same genomic site in mouse embryonic stem cells. Using this assay, we were able to quantify the contribution of various sequence motifs towards the resulting DNA methylation state. Modeling of this comprehensive dataset revealed that CG density alone is a minor determinant of their unmethylated state. Instead, these data argue for a principal role for transcription factor binding sites, a prediction confirmed by testing synthetic mutant libraries. Taken together, these findings establish the hierarchy between the two cis-encoded mechanisms that define the DNA methylation state and thus the transcriptional competence of CpG islands.
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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.