ArticleGenome biology and evolution2014
Sequence-level mechanisms of human epigenome evolution.
Article in Genome biology and evolution, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers, 1 of them a synthesis that pooled it.
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Who cites it
9 citing papers in PubMed, 1 synthesis or guideline pooled it, 17 citations in OpenAlex.
- Risk alleles of genes with monoallelic expression are enriched in gain-of-function variants and depleted in loss-of-function variants for neurodevelopmental disorders.Molecular psychiatry · 2017Pooled it
- Cytosine Methylation Affects the Mutability of Neighboring Nucleotides in Germline and Soma.Genetics · 2020Article
- Does the Presence of Transposable Elements Impact the Epigenetic Environment of Human Duplicated Genes?Genes · 2019Article
- Warning SINEs: Alu elements, evolution of the human brain, and the spectrum of neurological disease.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2018Review
- Alu-miRNA interactions modulate transcript isoform diversity in stress response and reveal signatures of positive selection.Scientific reports · 2016Article
- The transposable element environment of human genes is associated with histone and expression changes in cancer.BMC genomics · 2016Article
- Evolution of Epigenetic Regulation in Vertebrate Genomes.Trends in genetics : TIG · 2016Review
- One-pot multienzyme (OPME) systems for chemoenzymatic synthesis of carbohydrates.Organic & biomolecular chemistry · 2016Article
- DNA Methylation: Insights into Human Evolution.PLoS genetics · 2015Review
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
DNA methylation and chromatin states play key roles in development and disease. However, the extent of recent evolutionary divergence in the human epigenome and the influential factors that have shaped it are poorly understood. To determine the links between genome sequence and human epigenome evolution, we examined the divergence of DNA methylation and chromatin states following segmental duplication events in the human lineage. Chromatin and DNA methylation states were found to have been generally well conserved following a duplication event, with the evolution of the epigenome largely uncoupled from the total number of genetic changes in the surrounding DNA sequence. However, the epigenome at tissue-specific, distal regulatory regions was observed to be unusually prone to diverge following duplication, with particular sequence differences, altering known sequence motifs, found to be associated with divergence in patterns of DNA methylation and chromatin. Alu elements were found to have played a particularly prominent role in shaping human epigenome evolution, and we show that human-specific AluY insertion events are strongly linked to the evolution of the DNA methylation landscape and gene expression levels, including at key neurological genes in the human brain. Studying paralogous regions within the same sample enables the study of the links between genome and epigenome evolution while controlling for biological and technical variation. We show DNA methylation and chromatin divergence between duplicated regions are linked to the divergence of particular genetic motifs, with Alu elements having played a disproportionate role in the evolution of the epigenome in the human lineage.
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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.