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Related Concept Videos

DNA Microarrays02:34

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
Ribosome Profiling02:24

Ribosome Profiling

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 helps...
Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
RNA-seq03:21

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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Related Experiment Video

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An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations
10:17

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations

Published on: November 3, 2010

Genome-wide allele- and strand-specific expression profiling.

Julien Gagneur1, Himanshu Sinha, Fabiana Perocchi

  • 1Gene Expression Unit, European Molecular Biology Laboratory, Heidelberg, Germany.

Molecular Systems Biology
|June 19, 2009
PubMed
Summary

This study introduces a novel method for measuring allele- and strand-specific gene expression in yeast. The findings reveal complex differential expression patterns and identify regulatory variants, advancing our understanding of genome-wide transcription.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Most of the genome is transcribed, often on both DNA strands.
  • Allele-specific expression levels influence how genetic variations impact phenotypes in diploid organisms.
  • Accurate quantification of allele- and strand-specific expression is crucial for understanding gene regulation.

Purpose of the Study:

  • To develop and pilot a method for measuring allele- and strand-specific expression in yeast.
  • To identify transcripts with significant allelic differential expression.
  • To explore the relationship between allele-specific expression and regulatory variants.

Main Methods:

  • Utilized a custom-designed tiling array for high-resolution expression analysis.
  • Developed a novel computational approach for quantitative expression estimation.
  • Integrated allele-specific expression data with linkage mapping.

Main Results:

  • Achieved confident quantitative estimates for allele-specific expression in approximately 50% of transcripts.
  • Identified 371 transcripts (13%) with significant allelic differential expression (>1.5-fold).
  • Observed complex allelic differential expression patterns on opposite DNA strands.

Conclusions:

  • This study provides the first high-resolution analysis of differential expression across all four strands of an eukaryotic genome.
  • The developed methodology enables precise quantification of allele- and strand-specific expression.
  • The findings highlight the intricate nature of gene expression regulation at the allelic and strand level.