ArticleCell2012
Comparative epigenomic annotation of regulatory DNA.
Article in Cell, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 123 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
123 citing papers in PubMed, 222 citations in OpenAlex.
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- Complementary constraints in germ and immune cells shape evolution of gene regulation and phenotype.bioRxiv : the preprint server for biology · 2026Article
- Splicing retention and enhancer divergence govern the evolutionary fate of ohnologues following whole-genome duplication in rainbow trout.Scientific reports · 2026Article
- DMN-seq enriches DNA hypomethylated regions for biomarker discovery using 5-methylcytosine glycosylase.Genome biology · 2026Article
- Farm animal evolution demonstrates hidden molecular basis of human traits.bioRxiv : the preprint server for biology · 2026Article
- Comparative transcriptomics analysis of histone deacetylases, transcription factors, and ion channel genes in human iPSC-cardiomyocytes vs. the adult human heart.bioRxiv : the preprint server for biology · 2026Article
- Unveiling causal regulatory mechanisms through cell-state parallax.Nature communications · 2025Article
- iPSCs and iPSC-derived cells as a model of human genetic and epigenetic variation.Nature communications · 2025Article
- Functional annotation of regulatory elements in rainbow trout uncovers roles of the epigenome in genetic selection and genome evolution.GigaScience · 2024Article
- Learning functional conservation between human and pig to decipher evolutionary mechanisms underlying gene expression and complex traits.Cell genomics · 2023Article
- DNA methylation networks underlying mammalian traits.Science (New York, N.Y.) · 2023Article
- Harnessing male germline epigenomics for the genetic improvement in cattle.Journal of animal science and biotechnology · 2023Review
- Comparative analysis reveals epigenomic evolution related to species traits and genomic imprinting in mammals.Innovation (Cambridge (Mass.)) · 2023Article
- Comparing genomic and epigenomic features across species using the WashU Comparative Epigenome Browser.Genome research · 2023Article
- Comparative epigenomics reveals the impact of ruminant-specific regulatory elements on complex traits.BMC biology · 2022Article
- Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements.Nature genetics · 2022Article
- The CpG Island-Binding Protein SAMD1 Contributes to an Unfavorable Gene Signature in HepG2 Hepatocellular Carcinoma Cells.Biology · 2022Article
- Granger causal inference on DAGs identifies genomic loci regulating transcription.... International Conference on Learning Representations · 2022Article
- Enhancer RNA: What we know and what we can achieve.Cell proliferation · 2022Review
- Interplay between chromatin marks in development and disease.Nature reviews. Genetics · 2022Review
63 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
12 authors at 2 institutions in 1 country.
Funding
Abstract
Despite the explosive growth of genomic data, functional annotation of regulatory sequences remains difficult. Here, we introduce "comparative epigenomics"-interspecies comparison of DNA and histone modifications-as an approach for annotation of the regulatory genome. We measured in human, mouse, and pig pluripotent stem cells the genomic distributions of cytosine methylation, H2A.Z, H3K4me1/2/3, H3K9me3, H3K27me3, H3K27ac, H3K36me3, transcribed RNAs, and P300, TAF1, OCT4, and NANOG binding. We observed that epigenomic conservation was strong in both rapidly evolving and slowly evolving DNA sequences, but not in neutrally evolving sequences. In contrast, evolutionary changes of the epigenome and the transcriptome exhibited a linear correlation. We suggest that the conserved colocalization of different epigenomic marks can be used to discover regulatory sequences. Indeed, seven pairs of epigenomic marks identified exhibited regulatory functions during differentiation of embryonic stem cells into mesendoderm cells. Thus, comparative epigenomics reveals regulatory features of the genome that cannot be discerned from sequence comparisons alone.
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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.