Related Experiment Video
Updated: May 6, 2026
10:17
An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations
Published on: November 3, 2010
23.3K
Expression quantitative trait loci analysis identifies associations between genotype and gene expression in human
Boyko Kabakchiev1, Mark S Silverberg
1Zane Cohen Centre for Digestive Diseases, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada. kabakchiev@lunenfeld.ca
Gastroenterology
|March 12, 2013
Summary
This study identified thousands of expression quantitative trait loci (eQTL) in intestinal tissue, revealing new genetic links to inflammatory bowel disease and highlighting tissue-specific gene regulation.
Area of Science:
- Genetics
- Gastroenterology
- Molecular Biology
Background:
- Genome-wide association studies (GWAS) have advanced understanding of intestinal diseases but lack insight into genetic variation's phenotypic impact.
- Quantitative trait loci (QTL) link genetic variations to measurable traits, with expression QTL (eQTL) specifically connecting variations to gene expression levels.
- eQTL analysis offers a crucial bridge to understanding the biological relevance of GWAS findings in complex diseases.
Purpose of the Study:
- To conduct a comprehensive expression quantitative trait loci (eQTL) scan of human intestinal (ileal) tissue.
- To identify genetic variants that influence gene expression in the intestine.
- To explore the tissue-specific nature of eQTL and their association with intestinal diseases like inflammatory bowel disease (IBD).
Main Methods:
- RNA and DNA were extracted from ileal biopsy specimens and blood samples of 173 individuals.
- Cis- and trans-eQTL analyses were performed using a custom software pipeline.
- Expression levels of 19,047 autosomal genes and over 580,000 single nucleotide polymorphism (SNP) variants were analyzed.
Main Results:
- Over 15,000 statistically significant cis- and trans-eQTL were detected in intestinal tissue.
- A significant portion (30-40%) of identified eQTL were shared with other tissues (monocytes, liver, etc.), while many were novel and potentially tissue-specific.
- New associations between IBD susceptibility loci and gene expression were identified, confirming known eQTLs (e.g., rs2298428/UBE2L3) and discovering novel ones involved in cell division and antigen processing.
Conclusions:
- eQTL analysis in intestinal tissue reveals both conserved and location-specific gene expression patterns.
- The findings expand the catalog of genotypes associated with gene expression in the gut.
- This research provides valuable insights into the mechanisms underlying intestinal diseases and identifies potential therapeutic targets.
More Related Videos
07:39Author Spotlight: Investigating the Effects of Compounds on Intestinal Tissue Using 3D Human Cell Line Models
Published on: September 1, 2023
2.1K
08:23Author Spotlight: Integrating Single-Cell Transcriptomics with Organoid Cultures for Advanced Research and Therapeutic Insights
Published on: June 28, 2024
1.6K
Related Concept Videos
01:42What is Gene Expression?
133.1K
Overview
Gene expression is the process in which DNA directs the synthesis of functional products, that is, proteins. Cells can regulate gene expression at various stages. It allows organisms to generate different cell types and enables cells to adapt to internal and external factors.
Genetic Information Flows from DNA to RNA to Protein
A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is made up of nucleotides and proteins consist of amino...
Gene expression is the process in which DNA directs the synthesis of functional products, that is, proteins. Cells can regulate gene expression at various stages. It allows organisms to generate different cell types and enables cells to adapt to internal and external factors.
Genetic Information Flows from DNA to RNA to Protein
A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is made up of nucleotides and proteins consist of amino...
133.1K
02:11Reporter Genes
11.4K
Reporter genes are a type of protein-coding gene that are often tagged to a gene of interest. Once inside a target cell, reporter genes usually produce visually identifiable characteristics like fluorescence and luminescence when expressed along with the gene of interest. Thus, reporter genes “report” the presence or absence of genes of interest in an organism, determine the gene expression pattern, or track the physical location of a DNA segment or protein in the cell.
11.4K
02:24Ribosome Profiling
3.2K
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
3.2K
01:20Gene-Environment Interactions
1.5K
Gene expression is a dynamic process that is significantly influenced by environmental factors. This interaction underlies the complex nature of biological development and the phenotypic differences observed among individuals, even among those with identical genetic makeups. Factors such as radiation, temperature, behavior, nutrition, and stress play pivotal roles in determining how genes are expressed. The concept of the reaction range is central to understanding this interaction. It posits...
1.5K