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Related Concept Videos

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...
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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...
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General Transcription Factors01:30

General Transcription Factors

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Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...
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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...
7.4K
Combinatorial Gene Control02:33

Combinatorial Gene Control

8.4K
Combinatorial gene control is the synergistic action of several transcriptional factors to regulate the expression of a single gene. The absence of one or more of these factors may lead to a significant difference in the level of gene expression or repression.
The expression of more than 30,000 genes is controlled by approximately 2000-3000 transcription factors. This is possible because a single transcription factor can recognize more than one regulatory sequence. The specificity in gene...
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Regulation of Expression at Multiple Steps01:23

Regulation of Expression at Multiple Steps

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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...
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Related Experiment Video

Updated: Jul 24, 2025

Author Spotlight: An Integrated Workflow to Study the Promoter-Centric Spatio-Temporal Genome Architecture in Scarce Cell Populations
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Cis-regulatory Landscape Size, Constraint, and Tissue Specificity Associate with Gene Function and Expression.

Mary Lauren Benton1, Douglas M Ruderfer2, John A Capra3

  • 1Department of Computer Science, Baylor University, Waco, Texas, USA.

Genome Biology and Evolution
|July 6, 2023
PubMed
Summary

Genes with larger regulatory element landscapes are more likely to be expressed and have specific functions. This landscape size influences gene regulation and evolutionary conservation, impacting genetic variant effects.

Keywords:
cis-regulatory elementgene regulationregulatory landscapetissue-specific gene expression

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Quantitative Comparison of cis-Regulatory Element CRE Activities in Transgenic Drosophila melanogaster
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Quantitative Comparison of cis-Regulatory Element CRE Activities in Transgenic Drosophila melanogaster
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Area of Science:

  • Genomics
  • Gene Regulation
  • Evolutionary Biology

Background:

  • Distal cis-regulatory elements (CREs) cooperate to regulate gene expression, potentially offering robustness.
  • The relationship between a gene's CRE landscape and its expression, function, and constraint remains unclear.

Purpose of the Study:

  • To investigate how CRE landscape composition relates to gene function, constraint, and expression patterns.
  • To quantify CRE landscapes genome-wide across multiple human tissues.

Main Methods:

  • Integration of 3D chromatin conformation and functional genomics data.
  • Genome-wide analysis of CRE landscapes in ten human tissues.
  • Correlation analysis between CRE landscape attributes and gene properties.

Main Results:

  • Expressed genes possess larger CRE landscapes than nonexpressed genes.
  • Tissue-specific CREs correlate with tissue-specific gene expression.
  • Genes under strong constraint show more conserved CRE sequences, not necessarily smaller landscapes.
  • Larger CRE landscapes associate with fewer expression quantitative trait loci (eQTLs).

Conclusions:

  • CRE landscape features reflect gene function, expression dynamics, and evolutionary constraint.
  • Understanding CRE landscapes is crucial for interpreting gene expression and noncoding variant effects.