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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Correlative approaches can partially overcome this, but such links remain inferential.
“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]
The Results section, “Correlations in activity profiles link enhancers to target genes” (page not provided), says the authors correlated enhancer activity with gene expression across cell types to link enhancers probabilistically to target genes. The Discussion calls these interactions “inferred,” supporting the claim that the links remain inferential. This paper does not describe the specific example of correlating open-chromatin status between promoters and enhancers. (LLM, conf=0.83)
Experimental — accuracy not yet measuredH3K4me1, 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 H3K27ac.
“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]
The Results section, “Systematic mapping of chromatin marks in multiple cell types” (page unavailable), says H3K4me1 is preferentially associated with enhancers and H3K27ac with active regulatory regions. The copy does not establish the claimed association of H3K4me1 with Trithorax/MLL binding, or explicitly identify it as a hallmark of both primed and active enhancers. (LLM, conf=0.84)
Experimental — accuracy not yet measuredChIPseq in human neurons identified at least four major transcriptional start sites within the SYNE1 locus, one of which, P3, lies immediately upstream of the p.L3206M mutation.
“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
The majority of disease-associated non-coding variation occurs in the vicinity of enhancers and thus likely impacts these enhancers' target genes.
“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
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.
“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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Raznahan, A., Parikshak, N. N., Chandran, V., Blumenthal, J. D., Clasen, L. S., Alexander-Bloch, A. F., Zinn, A. R., Wangsa, D., Wise, J., Murphy, D. G. M., et al. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1802889115 · Cited by 179 · see citing works
Cancers with wrong HATs: the impact of acetylation
Di Cerbo, V., & Schneider, R. (2013) · Briefings in Functional Genomics · doi:10.1093/bfgp/els065 · Cited by 178 · see citing works
Reorganization of chromosome architecture in replicative cellular senescence
Criscione, S. W., De Cecco, M., Siranosian, B., Zhang, Y., Kreiling, J. A., Sedivy, J. M., & Neretti, N. (2016) · Science Advances · doi:10.1126/sciadv.1500882 · Cited by 164 · see citing works
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Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions
Ernst, J., Melnikov, A., Zhang, X., Wang, L., Rogov, P., Mikkelsen, T. S., & Kellis, M. (2016) · Nature Biotechnology · doi:10.1038/nbt.3678 · Cited by 162 · see citing works
Self-citation
- 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
- 66
- 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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