ArticleGenome research2020
A comparison of gene expression and DNA methylation patterns across tissues and species.
Article in Genome research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 81 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
81 citing papers in PubMed, 139 citations in OpenAlex.
- Effects of 6-months of SSRI use on DNA-methylation and gene expression in blood.Brain, behavior, and immunity · 2026Trial
- Accelerated Evolution of Context-Dependent Gene Expression in Primate Immune Cells.bioRxiv : the preprint server for biology · 2026Article
- Positive selection on brain cis-regulatory elements in the human lineage drives changes in gene expression and susceptibility to neuropsychiatric disorders.HGG advances · 2026Article
- Non-Invasive Measures of DNA Methylation Capture Molecular Aging in Wild Capuchin Monkeys.Molecular ecology · 2026Article
- A comprehensive full-length transcriptome atlas across multiple organs of an Indian yak breed-Arunachali.Mammalian genome : official journal of the International Mammalian Genome Society · 2026Article
- Influence ofGenome research · 2026Article
- TiSMeD: A tissue-specific methylation and expression database for biomarker and translational applications.Molecular therapy. Nucleic acids · 2026Article
- CrossFilt: a cross-species filtering tool that eliminates alignment bias in comparative genomics studies of primates.Genome biology · 2026Article
- Systematic identification of pan-cancer single-gene expression biomarkers in drug high-throughput screens.PloS one · 2026Article
- Conserved Gene Expression Plasticity in Development Is More Pervasive Than Expression Divergence Between Species of Caenorhabditis Nematodes.Evolution & development · 2025Article
- Cell-type specific global reprogramming of the transcriptome and epigenome in induced neurons with the 16p11.2 neuropsychiatric CNVs.European journal of human genetics : EJHG · 2025Article
- An ancient regulatory variant of ACSF3 influences the coevolution of increased human height and basal metabolic rate via metabolic homeostasis.Cell genomics · 2025Article
- Cost-effective solutions for high-throughput enzymatic DNA methylation sequencing.PLoS genetics · 2025Article
- DNA methylation confers a cerebellum-specific identity in non-human primates.Zoological research · 2025Article
- Sexual dimorphism in the DNA methylation pattern after immune stimulation in the zebrafish (Frontiers in cell and developmental biology · 2025Article
- Inferring DNA methylation in non-skeletal tissues of ancient specimens.Nature ecology & evolution · 2025Article
- Predicting Differentially Methylated Cytosines in TET and DNMT3 Knockout Mutants via a Large Language Model.bioRxiv : the preprint server for biology · 2024Article
- Epigenetics Research in Evolutionary Biology: Perspectives on Timescales and Mechanisms.Molecular biology and evolution · 2024Review
- Century-old chromatin architecture revealed in formalin-fixed vertebrates.Nature communications · 2024Article
- A multiomic atlas of the aging hippocampus reveals molecular changes in response to environmental enrichment.Nature communications · 2024Article
21 more citing papers are in PubMed but not listed here.
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Authors and funding
10 authors at 4 institutions in 3 countries.
Funding
Abstract
Previously published comparative functional genomic data sets from primates using frozen tissue samples, including many data sets from our own group, were often collected and analyzed using nonoptimal study designs and analysis approaches. In addition, when samples from multiple tissues were studied in a comparative framework, individuals and tissues were confounded. We designed a multitissue comparative study of gene expression and DNA methylation in primates that minimizes confounding effects by using a balanced design with respect to species, tissues, and individuals. We also developed a comparative analysis pipeline that minimizes biases attributable to sequence divergence. Thus, we present the most comprehensive catalog of similarities and differences in gene expression and DNA methylation levels between livers, kidneys, hearts, and lungs, in humans, chimpanzees, and rhesus macaques. We estimate that overall, interspecies and inter-tissue differences in gene expression levels can only modestly be accounted for by corresponding differences in promoter DNA methylation. However, the expression pattern of genes with conserved inter-tissue expression differences can be explained by corresponding interspecies methylation changes more often. Finally, we show that genes whose tissue-specific regulatory patterns are consistent with the action of natural selection are highly connected in both gene regulatory and protein-protein interaction networks.
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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.