ArticlePloS one2016
Identifying Causal Genes at the Multiple Sclerosis Associated Region 6q23 Using Capture Hi-C.
Article in PloS one, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 34 citations in OpenAlex.
- Aberrant Enhancer Regulation, Phase Separation, and Autoimmune Diseases.Clinical reviews in allergy & immunology · 2025Review
- Primary osteoarthritis chondrocyte map of chromatin conformation reveals novel candidate effector genes.Annals of the rheumatic diseases · 2024Article
- Analysis of long-range chromatin contacts, compartments and looping between mouse embryonic stem cells, lens epithelium and lens fibers.Epigenetics & chromatin · 2024Article
- 3D genome organization and epigenetic regulation in autoimmune diseases.Frontiers in immunology · 2023Review
- The importance of considering regulatory domains in genome-wide analyses - the nearest gene is often wrong!Biology open · 2022Review
- Transcriptomic analysis of LMH cells in response to the overexpression of a protein ofFrontiers in veterinary science · 2022Article
- Integrating Multimorbidity into a Whole-Body Understanding of Disease Using Spatial Genomics.Results and problems in cell differentiation · 2022Article
- Combination of Genomic and Transcriptomic Approaches Highlights Vascular and Circadian Clock Components in Multiple Sclerosis.International journal of molecular sciences · 2021Article
- Seeing the forest through the trees: prioritising potentially functional interactions from Hi-C.Epigenetics & chromatin · 2021Review
- Chromatin Looping Links Target Genes with Genetic Risk Loci for Dermatological Traits.The Journal of investigative dermatology · 2021Article
- Using functional genomics to advance the understanding of psoriatic arthritis.Rheumatology (Oxford, England) · 2020Review
- Functional effects of variation in transcription factor binding highlight long-range gene regulation by epromoters.Nucleic acids research · 2020Article
- DNA Rchitect: an R based visualizer for network analysis of chromatin interaction data.Bioinformatics (Oxford, England) · 2020Article
- One protein to rule them all: The role of CCCTC-binding factor in shaping human genome in health and disease.Seminars in cell & developmental biology · 2019Review
- CRISPR/cas9 mediated knockout of an intergenic variant rs6927172 identified IL-20RA as a new risk gene for multiple autoimmune diseases.Genes and immunity · 2019Article
- GOPHER: Generator Of Probes for capture Hi-C Experiments at high Resolution.BMC genomics · 2019Article
- Genome-wide association study of response to tumour necrosis factor inhibitor therapy in rheumatoid arthritis.The pharmacogenomics journal · 2018Article
- Chromosome contacts in activated T cells identify autoimmune disease candidate genes.Genome biology · 2017Article
Corrections and comments
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Authors and funding
11 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundThe chromosomal region 6q23 has been found to be associated with multiple sclerosis (MS) predisposition through genome wide association studies (GWAS). There are four independent single nucleotide polymorphisms (SNPs) associated with MS in this region, which spans around 2.5 Mb. Most GWAS variants associated with complex traits, including these four MS associated SNPs, are non-coding and their function is currently unknown. However, GWAS variants have been found to be enriched in enhancers and there is evidence that they may be involved in transcriptional regulation of their distant target genes through long range chromatin looping.
aimThe aim of this work is to identify causal disease genes in the 6q23 locus by studying long range chromatin interactions, using the recently developed Capture Hi-C method in human T and B-cell lines. Interactions involving four independent associations unique to MS, tagged by rs11154801, rs17066096, rs7769192 and rs67297943 were analysed using Capture Hi-C Analysis of Genomic Organisation (CHiCAGO).
resultsWe found that the pattern of chromatin looping interactions in the MS 6q23 associated region is complex. Interactions cluster in two regions, the first involving the rs11154801 region and a second containing the rs17066096, rs7769192 and rs67297943 SNPs. Firstly, SNPs located within the AHI1 gene, tagged by rs11154801, are correlated with expression of AHI1 and interact with its promoter. These SNPs also interact with other potential candidate genes such as SGK1 and BCLAF1. Secondly, the rs17066096, rs7769192 and rs67297943 SNPs interact with each other and with immune-related genes such as IL20RA, IL22RA2, IFNGR1 and TNFAIP3. Finally, the above-mentioned regions interact with each other and therefore, may co-regulate these target genes.
conclusionThese results suggest that the four 6q23 variants, independently associated with MS, are involved in the regulation of several genes, including immune genes. These findings could help understand mechanisms of disease and suggest potential novel therapeutic targets.
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