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Related Concept Videos

Combinatorial Gene Control02:33

Combinatorial Gene Control

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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Related Experiment Video

Updated: May 30, 2026

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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Systematic targeted integration to study Albumin gene control elements.

Sanchari Bhattacharyya1, Jianmin Tian, Eric E Bouhassira

  • 1Department of Pathology, Albert Einstein College of Medicine, Bronx, New York, United States of America.

Plos One
|August 23, 2011
PubMed
Summary
This summary is machine-generated.

Researchers studied transcriptional regulation by distant enhancers using reporter plasmids in HuH7 cells. Chromosomal integration revealed novel enhancers and complex interactions, differing from transient assays.

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Genome-wide Analysis using ChIP to Identify Isoform-specific Gene Targets
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Last Updated: May 30, 2026

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay (EMSA) and DNA-affinity Precipitation Assay (DAPA)
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Genome-wide Analysis using ChIP to Identify Isoform-specific Gene Targets
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Published on: July 7, 2010

Area of Science:

  • Molecular Biology
  • Genetics
  • Cell Biology

Background:

  • Understanding transcriptional regulation by enhancers is crucial for gene expression studies.
  • Distant enhancers play a significant role in controlling gene activity.
  • HuH7 cells, a human hepatocellular carcinoma line, provide a model for studying gene regulation.

Purpose of the Study:

  • To investigate transcriptional regulation by distant enhancers using a novel reporter plasmid system.
  • To analyze the function of enhancers in their natural chromosomal context versus transient expression.
  • To identify and characterize novel enhancers of the rat albumin gene.

Main Methods:

  • Development of easily modified reporter plasmids for single-copy integration into HuH7 cells.
  • Testing transcriptional function of a 35-kb region of the rat albumin gene and its flanking sequences.
  • Analysis of integrated constructs in two orientations, compared to transient transfection assays.
  • Deletion analysis to localize enhancer regions and assess their function.

Main Results:

  • Identification of two new enhancers (E2 at -13 kb and E4 at +1.2 kb) in addition to the known enhancer (E1 at -10 kb).
  • All three enhancers (E1, E2, E4) showed function in both transient and integrated assays.
  • Chromosomal integration revealed differences from transient expression, such as altered gene region requirements for enhancer E2 function.
  • A region (E3 at -0.7 kb) acted as an enhancer in transient assays but inhibited E1 and E2 function upon integration.
  • Enhancers did not exhibit additive or synergistic behavior, suggesting promoter competition or inhibitory interactions.
  • Serum starvation-induced growth arrest stimulated some integrated enhancers, potentially related to cell cycle-dependent enhancer-promoter looping.

Conclusions:

  • Chromosomal integration provides a more accurate model for studying enhancer function than transient assays.
  • Novel enhancers of the rat albumin gene were identified and characterized.
  • Complex regulatory interactions, including inhibition and competition, occur between enhancers within the chromosome.
  • Cell cycle status influences enhancer activity, highlighting the dynamic nature of transcriptional regulation.