ArticleNature communications2021
Epigenomic profiling of primate lymphoblastoid cell lines reveals the evolutionary patterns of epigenetic activities in gene regulatory architectures.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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28 citing papers in PubMed, 39 citations in OpenAlex.
- Accelerated Evolution of Context-Dependent Gene Expression in Primate Immune Cells.bioRxiv : the preprint server for biology · 2026Article
- Cross-species prediction reveals chromatin regions with increased accessibility in humans.Science advances · 2026Article
- Ancestral chromatin state constrains the functional landscape of bivalent domains in mammalian spermatogenesis.bioRxiv : the preprint server for biology · 2026Article
- Complementary constraints in germ and immune cells shape evolution of gene regulation and phenotype.bioRxiv : the preprint server for biology · 2026Article
- A curated dataset of great ape genome diversity.Scientific data · 2025Article
- Comparative analysis of single-stranded and non-canonical DNA formation in human and other ape cells with telomere-to-telomere genomes.bioRxiv : the preprint server for biology · 2025Article
- Transposon invasion of primate genomes shaped human inflammatory enhancers and susceptibility to inflammatory diseases.Nature communications · 2025Article
- Distinct Co-methylation Patterns in African and European Populations and Their Genetic Associations.Genomics, proteomics & bioinformatics · 2025Article
- Addressing missing context in regulatory variation across primate evolution.Current opinion in genetics & development · 2025Review
- Genetic Architecture of Immune Cell DNA Methylation in the Rhesus Macaque.Molecular ecology · 2025Article
- Article
- Regulatory Plasticity of the Human Genome.Molecular biology and evolution · 2025Article
- Novelty versus innovation of gene regulatory elements in human evolution and disease.Current opinion in genetics & development · 2025Review
- A gene expression atlas ofFrontiers in plant science · 2025Article
- Deciphering the role of structural variation in human evolution: a functional perspective.Current opinion in genetics & development · 2024Review
- Epigenetics Research in Evolutionary Biology: Perspectives on Timescales and Mechanisms.Molecular biology and evolution · 2024Review
- Human gene regulatory evolution is driven by the divergence of regulatory element function in both cis and trans.Cell genomics · 2024Article
- Cell-type-specificeLife · 2024Article
- Evolutionarily conserved enhancer-associated features within theFrontiers in cell and developmental biology · 2024Article
- Article
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Authors and funding
13 authors at 5 institutions in 2 countries.
Funding
Abstract
Changes in the epigenetic regulation of gene expression have a central role in evolution. Here, we extensively profiled a panel of human, chimpanzee, gorilla, orangutan, and macaque lymphoblastoid cell lines (LCLs), using ChIP-seq for five histone marks, ATAC-seq and RNA-seq, further complemented with whole genome sequencing (WGS) and whole genome bisulfite sequencing (WGBS). We annotated regulatory elements (RE) and integrated chromatin contact maps to define gene regulatory architectures, creating the largest catalog of RE in primates to date. We report that epigenetic conservation and its correlation with sequence conservation in primates depends on the activity state of the regulatory element. Our gene regulatory architectures reveal the coordination of different types of components and highlight the role of promoters and intragenic enhancers (gE) in the regulation of gene expression. We observe that most regulatory changes occur in weakly active gE. Remarkably, novel human-specific gE with weak activities are enriched in human-specific nucleotide changes. These elements appear in genes with signals of positive selection and human acceleration, tissue-specific expression, and particular functional enrichments, suggesting that the regulatory evolution of these genes may have contributed to human adaptation.
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