Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters
Open accessAbstract
Long-range interactions between regulatory elements and gene promoters play key roles in transcriptional regulation. The vast majority of interactions are uncharted, constituting a major missing link in understanding genome control. Here, we use promoter capture Hi-C to identify interacting regions of 31,253 promoters in 17 human primary hematopoietic cell types. We show that promoter interactions are highly cell type specific and enriched for links between active promoters and epigenetically marked enhancers. Promoter interactomes reflect lineage relationships of the hematopoietic tree, consistent with dynamic remodeling of nuclear architecture during differentiation. Interacting regions are enriched in genetic variants linked with altered expression of genes they contact, highlighting their functional role. We exploit this rich resource to connect non-coding disease variants to putative target promoters, prioritizing thousands of disease-candidate genes and implicating disease pathways. Our results demonstrate the power of primary cell promoter interactomes to reveal insights into genomic regulatory mechanisms underlying common diseases.
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Capture Hi-C analyses in multiple cell types consistently detect enhancer-promoter contacts that cross TAD boundaries.
“Capture Hi-C analyses in multiple cell types consistently detect enhancer–promoter contacts that cross TAD boundaries [141, 243].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [243]
The Results (Promoter Capture Hi-C; page not provided) report that about a third of PCHi-C interactions crossed TAD boundaries in all eight cell types examined. But that analysis covers promoter interactions generally; it does not establish that the boundary-crossing contacts specifically joined enhancers to promoters. (LLM, conf=0.85)
Experimental — accuracy not yet measuredPCHi-C showed that active promoters contacted a median of two active enhancers in human primary blood cells.
“PCHi-C showed that active promoters contacted a median of two active enhancers in human primary blood cells [243].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [243]
The Results section, “Promoter Capture Hi-C” (page unavailable), reports PCHi-C experiments in 17 human primary blood cell types, but gives a median of four interactions per promoter fragment per cell type. The paper also discusses contacts between active promoters and active enhancers, but the passages found do not establish a median of two active enhancers per active promoter. (LLM, conf=0.85)
Experimental — accuracy not yet measuredA similar network of contacts is detectable between active promoters of multiple histone genes in many mammalian cell types.
“A similar network of contacts is also detectable between the active promoters of multiple histone genes in many mammalian cell types [243, 279, 471, 492].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [243]
The Results section, “Promoter Capture Hi-C” (page unavailable), reports promoter-to-promoter contacts across 17 human primary blood cell types. It does not identify a network among active histone-gene promoters or establish its presence in many mammalian cell types. (LLM, conf=0.82)
Experimental — accuracy not yet measuredThe number of enhancers correlates with the expression level of a gene across cell types.
“the number of enhancers correlates with the expression level of a gene across cell types [243, 278, 279, 349].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [243]
The Results section (“Enhancer Activity Associates with Lineage-Specific Gene Expression”; page not provided) reports that promoter interactions with active enhancers have an additive association with gene expression across cell types. The STAR Methods section specifies that the analysis counted interacting active enhancers, not enhancers generally, and was restricted to genes with active promoters in all samples. The claim omits those qualifications. (LLM, conf=0.83)
Experimental — accuracy not yet measured3C-derived methods have detected multitudes of enhancer-promoter loops in many human and mouse cell types.
“These enrichment methods have detected multitudes of enhancer–promoter loops in many human and mouse cell types [243, 286–291].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [243]
Enhancers vastly outnumber promoters in human and mouse genomes, and promoters often contact more than one enhancer in the same cell type.
“Enhancers vastly outnumber promoters in human and mouse genomes [131], and consistently promoters often contact more than one enhancer in the same cell type [141, 243, 278, 279].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [243]
Disease-associated SNPs in non-coding areas of the genome influence genes associated with diseases including Alzheimer's Disease (AD).
“disease-associated SNPs in non-coding areas of the genome influence genes associated with diseases including Alzheimer’s Disease (AD)”
From Neuronal DNA double-strand breaks lead to genome structural variations and 3D genome disruption in neurodegeneration (2023) · cites this paper as [50]
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- Authors
- Javierre, B. M., Burren, O. S., Wilder, S. P., Kreuzhuber, R., Hill, S. M., Sewitz, S., Cairns, J., Wingett, S. W., Várnai, C., Thiecke, M. J., Burden, F., Farrow, S., Cutler, A. J., Rehnström, K., Downes, K., Grassi, L., Kostadima, M., Freire-Pritchett, P., Wang, F., Martens, J. H., Kim, B., Sharifi, N., Janssen-Megens, E. M., Yaspo, M.-L., Linser, M., Kovacsovics, A., Clarke, L., Richardson, D., Datta, A., Flicek, P., Stunnenberg, H. G., Todd, J. A., Zerbino, D. R., Stegle, O., Ouwehand, W. H., Frontini, M., Wallace, C., Spivakov, M., & Fraser, P.
- Affiliations
- Babraham Institute (GB)
- University of Cambridge (GB)
- European Bioinformatics Institute (GB)
- National Health Service (GB)
- MRC Biostatistics Unit (GB)
- Radboud University Nijmegen (NL)
- Corresponding author
- Frontini, Mattia
- Wallace, Chris
- Spivakov, Mikhail
- Fraser, Peter
- ORCID
- Javierre, Biola M.
- Burren, Oliver S.
- Wilder, Steven P.
- Kreuzhuber, Roman
- Sewitz, Sven
- Cairns, Jonathan
- Wingett, Steven W.
- Várnai, Csilla
- Thiecke, Michiel J.
- Burden, Frances
- Cutler, Antony J.
- Downes, Kate
- Grassi, Luigi
- Kostadima, Myrto
- Freire-Pritchett, Paula
- Wang, Fan
- Martens, Joost H.
- Yaspo, Marie-Laure
- Clarke, Laura
- Richardson, David
- Datta, Avik
- Flicek, Paul
- Stunnenberg, Hendrik G.
- Zerbino, Daniel R.
- Stegle, Oliver
- Ouwehand, Willem H.
- Frontini, Mattia
- Wallace, Chris
- Spivakov, Mikhail
- Fraser, Peter
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2016-11
- Volume
- 167
- Issue
- 5
- Pages
- 1369-1384.e19
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC5123897
- OpenAlex
- W2553838260
- Cited by
- 1,046
- References
- 87
- Citations by year
- 2026: 59 · 2025: 84 · 2024: 102 · 2023: 113 · 2022: 116 · 2021: 135 · 2020: 126 · 2019: 130 · 2018: 117 · 2017: 59 · 2016: 4
- FWCI
- 53.72
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Cell (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- UCL Discovery (University College London) (submittedVersion)
- University of Birmingham Research Portal (University of Birmingham) (submittedVersion, cc-by)
- Radboud Repository (Radboud University) (submittedVersion)
- Apollo (University of Cambridge) (submittedVersion, cc-by)
- Radboud Repository (Radboud University) (submittedVersion, other-oa)
- Apollo (cc-by)
- Funders
- Biotechnology and Biological Sciences Research Council (BB/J004480/1)
- National Institute for Health Research (PG-0310-1002)
- Wellcome Trust (107212, 107881, 089989, 091157, 095908, 100140)
- Seventh Framework Programme (282510, 241447)
- European Research Council
- Medical Research Council (MC_UP_1302/3, MC_UP_1302/5, MC_UP_1302/1, MR/L007150/1)
- European Molecular Biology Laboratory
- British Heart Foundation (RG/09/12/28096)
- Juvenile Diabetes Research Foundation United States of America (5-SRA-2015-130, 9-2011-253)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer-related molecular mechanisms research
- Keywords
- enhancer-promoter interactions, long-range chromatin interactions, promoter capture Hi-C, hematopoietic lineage, enhancers, transcriptional regulation
- MeSH terms
- Blood Cells, Cell Separation, Chromatin, Disease, Enhancer Elements, Genetic, Hematopoiesis, Humans, Promoter Regions, Genetic, Cell Lineage, Genetic Predisposition to Disease, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Genome-Wide Association Study, Epigenomics
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