Functional Genomics of the 9p21.3 Locus for Atherosclerosis: Clarity or Confusion?
Abstract
The 9p21.3 locus was the first to yield to genome-wide association studies (GWAS) seeking common genetic variants predisposing to increased risk of coronary artery atherosclerotic disease (CAD). The 59 single nucleotide polymorphisms that show highest association with CAD are clustered in a region 100,000 to 150,000 base pairs 5' to the cyclin-dependent kinase inhibitors CDKN2B (coding for p15(ink4b)) and CDKN2A (coding for p16(ink4a) and p14(ARF)). This region also covers the 3' end of a long noncoding RNA transcribed antisense to CDKN2B (CDKN2BAS, aka ANRIL for antisense noncoding RNA at the ink4 locus) whose expression has been linked to chromatin remodeling at the locus. Despite intensive investigation over the past 7 years, the functional significance of the 9p21.3 locus remains elusive. Other variants at this locus have been associated with glaucoma, glioma, and type 2 diabetes mellitus, diseases that implicate tissue-resident macrophages. Here, we review the evidence that genetic variants at 9p21.3 disrupt tissue-specific enhancers and propose new insights to guide future studies.
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Chromatin conformation capture in human vascular endothelial cells identified short-range interactions between sequences at the 9p21.3 locus and sequences near CDKN2A, CDKN2B and MTAP, and long-range interactions with IFNW1 and IFNA21 approximately one million base pairs upstream on chromosome 9.
“Chromatin conformation capture in this region in human vascular endothelial cells identified short-range interactions between sequences at the 9p21.3 locus and sequences in the vicinity of the genes encoding CDKN2A, CDKN2B, and MTAP, and long-range interactions with IFNW1 and IFNA21 approximately one million base pairs upstream on chromosome 9 (ref. 56).”
From Meta-analysis identifies five novel loci associated with endometriosis highlighting key genes involved in hormone metabolism (2017) · cites this paper as [56]
Functional studies in mammalian cells show that ANRIL overexpression accelerated proliferation, increased adhesion and decreased apoptosis.
“Functional studies in mammalian cells show that ANRIL overexpression accelerated proliferation, increased adhesion and decreased apoptosis5456.”
From Meta-analysis identifies five novel loci associated with endometriosis highlighting key genes involved in hormone metabolism (2017) · cites this paper as [56]
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Sapkota, Y., Steinthorsdottir, V., Morris, A. P., Fassbender, A., Rahmioglu, N., De Vivo, I., Buring, J. E., Zhang, F., Edwards, T. L., Jones, S., et al. (2017) · Nature Communications · doi:10.1038/ncomms15539 · Cited by 344 · see citing works
Noncoding RNAs regulate NF-κB signaling to modulate blood vessel inflammation
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- Authors
- Chen, H.-H., Almontashiri, N. A. M., Antoine, D., & Stewart, A. F. R.
- Affiliations
- Ottawa Hospital Research Institute (CA)
- Ottawa Heart Institute (CA)
- Corresponding author
- Stewart, Alexandre F. R.
- Venue
- Current Cardiology Reports
- Published
- 2014-06-04
- Volume
- 16
- Issue
- 7
- Pages
- 502-502
- ISSN
- 1523-3782 (ISSN-L)
- 1534-3170
- OpenAlex
- W2006450437
- Cited by
- 45
- References
- 101
- Citations by year
- 2024: 2 · 2023: 2 · 2021: 1 · 2020: 5 · 2019: 3 · 2018: 8 · 2017: 9 · 2016: 7 · 2015: 5 · 2014: 3
- FWCI
- 1.06
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Current Cardiology Reports (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Immunology and Microbiology › Immunology › Atherosclerosis and Cardiovascular Diseases
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- 9p21.3 locus, coronary artery atherosclerosis, CDKN2B, CDKN2A, ANRIL, long non-coding RNA, tissue-specific enhancers, genetic variants, macrophages, chromatin remodeling, functional genomics
- MeSH terms
- Chromosomes, Human, Pair 9, Humans, Phenotype, Signal Transduction, Genomics, Atherosclerosis, Genome-Wide Association Study
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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