ArticleBMC genomics2014
Relating gene expression evolution with CpG content changes.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 25 citations in OpenAlex.
- Article
- Epigenetic Potential and Dispersal Propensity in a Free-Living Songbird: A Spatial and Temporal Approach.Molecular ecology · 2025Article
- DNA hypomethylation characterizes genes encoding tissue-dominant functional proteins in liver and skeletal muscle.Scientific reports · 2023Article
- Expression regulation of genes is linked to their CpG density distributions around transcription start sites.Life science alliance · 2022Article
- Simplified MethylRAD Sequencing to Detect Changes in DNA Methylation at Enhancer Elements in Differentiating Embryonic Stem Cells.Epigenomes · 2020Article
- Intrachromosomal colocalization strengthens co-expression, co-modification and evolutionary conservation of neighboring genes.BMC genomics · 2018Article
- 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
- Core Promoter Plasticity Between Maize Tissues and Genotypes Contrasts with Predominance of Sharp Transcription Initiation Sites.The Plant cell · 2015Article
- Neighboring Genes Show Correlated Evolution in Gene Expression.Molecular biology and evolution · 2015Article
- What to compare and how: Comparative transcriptomics for Evo-Devo.Journal of experimental zoology. Part B, Molecular and developmental evolution · 2015Review
Corrections and comments
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Authors and funding
3 authors at 3 institutions in 2 countries.
Funding
Abstract
backgroundPrevious studies have shown that CpG dinucleotides are enriched in a subset of promoters and the CpG content of promoters is positively correlated with gene expression levels. But the relationship between divergence of CpG content and gene expression evolution has not been investigated. Here we calculate the normalized CpG (nCpG) content in DNA regions around transcription start site (TSS) and transcription terminal site (TTS) of genes in nine organisms, and relate them with expression levels measured by RNA-seq.
resultsThe nCpG content of TSS shows a bimodal distribution in all organisms except platypus, whereas the nCpG content of TTS only has a single peak. When the nCpG contents are compared between different organisms, we observe a different evolution pattern between TSS and TTS: compared with TTS, TSS exhibits a faster divergence rate between closely related species but are more conserved between distant species. More importantly, we demonstrate the link between gene expression evolution and nCpG content changes: up-/down- regulation of genes in an organism is accompanied by the nCpG content increase/decrease in their TSS and TTS proximal regions.
conclusionsOur results suggest that gene expression changes between different organisms are correlated with the alterations in normalized CpG contents of promoters. Our analyses provide evidences for the impact of nCpG content on gene expression evolution.
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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.