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Mapping and analysis of chromatin state dynamics in nine human cell types
Open accessAbstract
Chromatin profiling has emerged as a powerful means of genome annotation and detection of regulatory activity. The approach is especially well suited to the characterization of non-coding portions of the genome, which critically contribute to cellular phenotypes yet remain largely uncharted. Here we map nine chromatin marks across nine cell types to systematically characterize regulatory elements, their cell-type specificities and their functional interactions. Focusing on cell-type-specific patterns of promoters and enhancers, we define multicell activity profiles for chromatin state, gene expression, regulatory motif enrichment and regulator expression. We use correlations between these profiles to link enhancers to putative target genes, and predict the cell-type-specific activators and repressors that modulate them. The resulting annotations and regulatory predictions have implications for the interpretation of genome-wide association studies. Top-scoring disease single nucleotide polymorphisms are frequently positioned within enhancer elements specifically active in relevant cell types, and in some cases affect a motif instance for a predicted regulator, thus suggesting a mechanism for the association. Our study presents a general framework for deciphering cis-regulatory connections and their roles in disease.
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“To some degree this can be overcome by correlative approaches (e.g. correlating open chromatin status between promoters and enhancers across large numbers of cell types) but such links remain inferential45,134,135.”
From Towards a comprehensive catalogue of validated and target-linked human enhancers (2020) · cites this paper as [135]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
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“Currently mono-methylation of histone H3 lysine 4 (H3K4me1), associated with the binding of Trithorax/MLL complexes, is taken to be the hallmark of both ‘primed’ and active enhancers, whilst active enhancers additionally tend to associate with the acetylation of histone H3 lysine 27 (H3K27ac) [133–137].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [134]
Experimental — accuracy not yet measuredIn the citing paper
“ChIPseq using antibodies to H3K4Me3, a mark associated with active promoter sites (Ernst et al., 2011), and to H3K27Ac, a mark associated with enhancer elements (Heintzman et al., 2009), demonstrated mapped read peaks corresponding to at least four major transcriptional start sites within the SYNE1 locus (P1–P4), one of which (P3) lies immediately upstream of the p.L3206M mutation (Figure 3E).”
From Using Whole-Exome Sequencing to Identify Inherited Causes of Autism (2013) · cites this paper as Ernst et al., 2011
In the citing paper
“This mystery, which we will call the enhancer-gene specificity conundrum, is important to solve because the majority of disease-associated non-coding variation occurs in the vicinity of enhancers and thus likely impacts these enhancers’ target genes (Ernst et al., 2011; Farh et al., 2015; Hnisz et al., 2013; Maurano et al., 2012).”
From Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control (2016) · cites this paper as Ernst et al., 2011
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“Tens of thousands of non-coding genetic variants have been linked with various human diseases and traits in genome-wide association studies (GWAS), and the majority of these variants occur in enhancers (Ernst et al., 2011; Farh et al., 2015; Hnisz et al., 2013; Maurano et al., 2012).”
From Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control (2016) · cites this paper as Ernst et al., 2011
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Metadata
- Authors
- Ernst, J., Kheradpour, P., Mikkelsen, T. S., Shoresh, N., Ward, L. D., Epstein, C. B., Zhang, X., Wang, L., Issner, R., Coyne, M., Ku, M., Durham, T., Kellis, M., & Bernstein, B. E.
- Affiliations
- Broad Institute (US)
- Corresponding author
- Kellis, Manolis
- ORCID
- Venue
- Nature
- Published
- 2011-03-23
- Volume
- 473
- Issue
- 7345
- Pages
- 43-49
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC3088773
- OpenAlex
- W2117792884
- Cited by
- 2,898
- References
- 67
- Citations by year
- 2026: 47 · 2025: 62 · 2024: 109 · 2023: 130 · 2022: 141 · 2021: 179 · 2020: 203 · 2019: 191 · 2018: 216 · 2017: 237 · 2016: 237 · 2015: 306 · 2014: 260 · 2013: 287 · 2012: 225
- FWCI
- 108.00
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc-sa)
- eScholarship (California Digital Library) (submittedVersion)
- PubMed Central
- Funders
- Howard Hughes Medical Institute
- Broad Institute
- National Institutes of Health (5u54hg004570-04)
- National Human Genome Research Institute (RC1HG005334, U54-HG004570, R01HG004037)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Keywords
- histone modifications, cell type-specific chromatin, enhancers, promoter, insulators, cis-regulatory elements, transcriptional activators and repressors, genome-wide association study, human cell types
- MeSH terms
- Binding Sites, Cell Line, Cell Physiological Phenomena, Cells, Cultured, Chromatin, Chromosome Mapping, Gene Expression Regulation, Humans, Promoter Regions, Genetic, Transcription Factors, Reproducibility of Results, Genome, Human, Cell Line, Tumor, Hep G2 Cells
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