ArticleJournal of visualized experiments : JoVE2016
Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay (EMSA) and DNA-affinity Precipitation Assay (DAPA).
Article in Journal of visualized experiments : JoVE, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
13 citing papers in PubMed, 15 citations in OpenAlex.
- A plausibly causal functional lupus-associated risk variant in the STAT1-STAT4 locus.Human molecular genetics · 2018Trial
- Update on the genetics of allergic diseases.The Journal of allergy and clinical immunology · 2025Review
- The regulatory variant rs1950834 confers the risk of depressive disorder by reducing LRFN5 expression.BMC medicine · 2025Article
- High-throughput identification of functional regulatory SNPs in systemic lupus erythematosus.Nature communications · 2024Article
- Repression ofJournal of bacteriology · 2024Article
- Identification of a regulatory pathway governing TRAF1 via an arthritis-associated non-coding variant.Cell genomics · 2023Article
- A functional mechanism for a non-coding variant near AGTR2 associated with risk for preterm birth.BMC medicine · 2023Article
- Regulatory variants at 2q33.1 confer schizophrenia risk by modulating distal gene TYW5 expression.Brain : a journal of neurology · 2022Article
- A DNA Regulatory Element Haplotype at Zinc Finger Genes Is Associated with Host Resilience to Small Ruminant Lentivirus in Two Sheep Populations.Animals : an open access journal from MDPI · 2021Article
- SLE non-coding genetic risk variant determines the epigenetic dysfunction of an immune cell specific enhancer that controls disease-critical microRNA expression.Nature communications · 2021Article
- The Effect of Single CpG Demethylation on the Pattern of DNA-Protein Binding.International journal of molecular sciences · 2019Article
- Genetic variants with gene regulatory effects are associated with diisocyanate-induced asthma.The Journal of allergy and clinical immunology · 2018Article
- Genetics of eosinophilic esophagitis.Mucosal immunology · 2017Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
Population and family-based genetic studies typically result in the identification of genetic variants that are statistically associated with a clinical disease or phenotype. For many diseases and traits, most variants are non-coding, and are thus likely to act by impacting subtle, comparatively hard to predict mechanisms controlling gene expression. Here, we describe a general strategic approach to prioritize non-coding variants, and screen them for their function. This approach involves computational prioritization using functional genomic databases followed by experimental analysis of differential binding of transcription factors (TFs) to risk and non-risk alleles. For both electrophoretic mobility shift assay (EMSA) and DNA affinity precipitation assay (DAPA) analysis of genetic variants, a synthetic DNA oligonucleotide (oligo) is used to identify factors in the nuclear lysate of disease or phenotype-relevant cells. For EMSA, the oligonucleotides with or without bound nuclear factors (often TFs) are analyzed by non-denaturing electrophoresis on a tris-borate-EDTA (TBE) polyacrylamide gel. For DAPA, the oligonucleotides are bound to a magnetic column and the nuclear factors that specifically bind the DNA sequence are eluted and analyzed through mass spectrometry or with a reducing sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) followed by Western blot analysis. This general approach can be widely used to study the function of non-coding genetic variants associated with any disease, trait, or phenotype.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.