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Related Concept Videos

Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

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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...
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Co-activators and Co-repressors02:04

Co-activators and Co-repressors

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Gene transcription is regulated by the synergistic action of several proteins that form a complex at a gene regulatory site. This is observed in eukaryotes, where the regulation of gene expression is a complex process. Regulatory proteins in eukaryotes can broadly be classified into two types – regulators that bind directly to specific DNA sequences and co-regulators that associate with regulatory proteins but cannot directly bind to the DNA. These co-regulators are further divided into...
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Cis-regulatory Sequences02:02

Cis-regulatory Sequences

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Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
10.0K
Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

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Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome.  Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form...
6.5K
Master Transcription Regulators02:23

Master Transcription Regulators

7.0K
Master transcription regulators are regulatory proteins that are predominantly responsible for regulating the expression of multiple genes. Often these genes work in concert to drive a  complex process. Activation of a master transcription regulator can lead to a cascade of transcriptional activation necessary for that outcome. These regulators can directly bind to the regulatory sequences of the various genes involved, or they can indirectly regulate transcription by binding to regulatory...
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Regulation of Expression Occurs at Multiple Steps02:24

Regulation of Expression Occurs at Multiple Steps

23.0K
Gene expression can be regulated at almost every step from gene to protein. Transcription is the step that is most commonly regulated. This involves the binding of proteins to short regulatory sequences on the DNA. This association can either promote or inhibit the transcription of a gene associated with the respective sequence.
Transcription results in the generation of precursor (pre-mRNA) that consists of both exons and introns, which needs further processing before being translated to a...
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Related Experiment Video

Updated: Aug 17, 2025

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

Published on: November 3, 2010

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The missing link between genetic association and regulatory function.

Noah J Connally1,2,3, Sumaiya Nazeen1,2,4, Daniel Lee1,2,3

  • 1Department of Biomedical Informatics, Harvard Medical School, Boston, United States.

Elife
|December 14, 2022
PubMed
Summary
This summary is machine-generated.

Most complex traits are polygenic, influenced by non-coding genetic variants. This study found limited evidence that baseline gene expression explains these associations, challenging current models and highlighting the need for new regulatory frameworks.

Keywords:
colocalizationeQTLgene regulationgeneticsgenomicshumannon-coding variants

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Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA
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Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA

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Large-Scale Multi-Omics Genome-Wide Association Studies Mo-GWAS: Guidelines for Sample Preparation and Normalization
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Last Updated: Aug 17, 2025

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Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA
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Large-Scale Multi-Omics Genome-Wide Association Studies Mo-GWAS: Guidelines for Sample Preparation and Normalization
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Large-Scale Multi-Omics Genome-Wide Association Studies Mo-GWAS: Guidelines for Sample Preparation and Normalization

Published on: July 27, 2021

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Area of Science:

  • Genetics
  • Genomics
  • Molecular Biology

Background:

  • Complex traits are polygenic, with non-coding variants assumed to regulate cis-linked genes.
  • Despite available data, few variant-to-gene links have been established for complex traits.
  • Uncertainty exists whether sparse results stem from data/method limitations or flawed underlying models.

Purpose of the Study:

  • To investigate the relationship between genetic variants, gene expression, and complex traits.
  • To test the hypothesis that complex trait-associated variants regulate baseline expression of nearby genes.
  • To identify potential shortcomings in current models of genetic regulation for complex traits.

Main Methods:

  • Identified 220 gene-trait pairs where protein-coding variants influence complex traits.
  • Applied a gene-based approach using colocalization, transcription-wide association studies (TWAS), and regulatory annotations.
  • Assessed evidence for baseline expression of trait-related genes explaining genome-wide association study (GWAS) associations.

Main Results:

  • Limited evidence found that baseline gene expression explains GWAS associations for complex traits.
  • Colocalization methods implicated 8% of genes, TWAS implicated 2%, and regulatory annotations/distance implicated 4%.
  • Results contradict the hypothesis that complex trait variants align with homeostatic expression quantitative trait loci (eQTLs).

Conclusions:

  • Current models assuming variants regulate baseline gene expression may be insufficient for complex traits.
  • The 'missing regulation' in complex trait genetics requires novel explanatory frameworks.
  • Further research is needed to develop and validate new models for understanding genetic architecture of complex traits.