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Related Concept Videos

Cis-regulatory Sequences02:02

Cis-regulatory Sequences

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...
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

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...
Regulation of Expression Occurs at Multiple Steps02:24

Regulation of Expression Occurs at Multiple Steps

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...
Regulation of Expression Occurs at Multiple Steps02:24

Regulation of Expression Occurs at Multiple Steps

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...
Regulation of Expression at Multiple Steps01:23

Regulation of Expression at Multiple Steps

The gene expression in cells is regulated at different stages: (i) transcription, (ii) RNA processing, (iii) RNA localization, and (iv) translation. Transcriptional regulation is mediated by regulatory proteins such as transcription factors, activators, or repressors—these control gene expression by initiating or inhibiting the transcription of genes. Once a precursor or pre-mRNA is produced, it undergoes post-transcriptional modification, including 5' capping, splicing, and the addition of a...
Constitutive and Regulated Gene Expression01:27

Constitutive and Regulated Gene Expression

Gene expression in prokaryotes is governed by constitutive and regulated systems, allowing cells to balance the production of essential proteins with adaptive responses to environmental changes.Constitutive Gene ExpressionConstitutive, or housekeeping, genes are continuously expressed as they encode proteins vital for fundamental cellular processes. These include enzymes for glycolysis, ribosomal components for protein synthesis, and proteins involved in DNA replication. Their constant...

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Dissecting Innate Immune Signaling in Viral Evasion of Cytokine Production
08:32

Dissecting Innate Immune Signaling in Viral Evasion of Cytokine Production

Published on: March 2, 2014

Genes Induced by Reovirus Infection Have a Distinct Modular Cis-Regulatory Architecture.

R Lapadat1, R L Debiasi, G L Johnson

  • 1Department of Pharmacology, University of Colorado Health Sciences Center, Denver, Colorado.

Current Genomics
|January 22, 2013
PubMed
Summary
This summary is machine-generated.

This study introduces a bioinformatics strategy to analyze gene regulation during viral infection. It identifies conserved DNA "modules" and "super-modules" that control gene expression in response to reovirus.

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Using Reverse Genetics to Manipulate the NSs Gene of the Rift Valley Fever Virus MP-12 Strain to Improve Vaccine Safety and Efficacy
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Using Reverse Genetics to Manipulate the NSs Gene of the Rift Valley Fever Virus MP-12 Strain to Improve Vaccine Safety and Efficacy

Published on: November 1, 2011

Related Experiment Videos

Last Updated: May 15, 2026

Dissecting Innate Immune Signaling in Viral Evasion of Cytokine Production
08:32

Dissecting Innate Immune Signaling in Viral Evasion of Cytokine Production

Published on: March 2, 2014

Using Reverse Genetics to Manipulate the NSs Gene of the Rift Valley Fever Virus MP-12 Strain to Improve Vaccine Safety and Efficacy
09:13

Using Reverse Genetics to Manipulate the NSs Gene of the Rift Valley Fever Virus MP-12 Strain to Improve Vaccine Safety and Efficacy

Published on: November 1, 2011

Area of Science:

  • Genomics and Bioinformatics
  • Molecular Virology
  • Systems Biology

Background:

  • Complete genome sequences and gene expression profiling enable complex genetic regulatory system analysis.
  • Understanding cis-regulatory elements is crucial for deciphering gene expression control.
  • Viral infections trigger significant changes in host cell gene expression.

Purpose of the Study:

  • To develop and apply a bioinformatics strategy to analyze the cis-regulatory design of genes affected by viral infection.
  • To identify conserved sequence patterns (modules and super-modules) in the regulatory regions of differentially expressed genes.
  • To associate these regulatory patterns with biological processes involved in the host cell's response to reovirus.

Main Methods:

  • Global gene expression profiling of human embryonic kidney (HEK293) cells infected with reovirus using Affymetrix HU-95Av2 gene arrays.
  • Bioinformatic analysis of 5' upstream sequences of differentially expressed genes to identify conserved regions ('modules').
  • Statistical over-representation analysis to detect higher-order patterns ('super-modules') and their association with transcription factor binding sites.

Main Results:

  • Identification of highly preserved sequence regions ('modules') within the 5' upstream sequences of differentially expressed genes.
  • Discovery of 'super-modules', which are over-represented patterns containing multiple transcription factor binding sites.
  • Association of super-modules with genes involved in reovirus infection-related processes like signal transduction, transcriptional regulation, cell cycle control, and apoptosis.

Conclusions:

  • The supermodular design of cis-regulatory regions encodes a logic for controlling gene expression in response to viral stimuli.
  • This computational approach provides novel insights into pathogen-host interactions by linking gene expression changes to regulatory elements.
  • The strategy facilitates the study of integrated cellular responses, including apoptosis and cell cycle control, during viral infections.