Related Experiment Video
Updated: Aug 6, 2026
10:16
Promoter Capture Hi-C: High-resolution, Genome-wide Profiling of Promoter Interactions
Published on: June 28, 2018
Promoter strength and position govern promoter competition through transcript-dependent insulation
Mervenaz Koska1,2, Masahiro Nagano3,4,5,6, Tomek Swigut1
1Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA.
Nature Genetics
|July 20, 2026
Summary
Inserted promoters can compete with endogenous genes, with stronger promoters causing greater reduction in Sox2 expression. This competition effect, influenced by transcript length and genomic position, can be blocked by HUSH-mediated silencing.
Area of Science:
- Genetics
- Molecular Biology
- Epigenetics
Background:
- Long-range promoter competition impacts gene regulation in development and disease.
- The factors determining promoter competition are not fully understood.
Purpose of the Study:
- To investigate the rules governing promoter competition within a shared regulatory landscape.
- To determine how promoter strength, transcript length, and genomic context influence competition.
Main Methods:
- Insertion of diverse promoters into the Sox2 locus.
- Measurement of endogenous Sox2 expression levels.
- Analysis of the role of transcription, transcript length, and HUSH-mediated silencing.
Main Results:
- Competition level correlates with inserted promoter strength.
- Transcription from the inserted promoter is essential for competition.
- Longer transcripts lead to increased competition.
- Competition is position-dependent and acts as an insulator.
- HUSH-mediated silencing counteracts promoter competition.
Conclusions:
- Transcriptional units can mediate insulation independently of CTCF and cohesin.
- Promoter competition is a key mechanism for tuning gene expression.
- Understanding promoter competition offers insights into genome evolution.
More Related Videos
Related Concept Videos
02:36RNA Polymerase II Accessory Proteins
Proteins that regulate transcription can do so either via direct contact with RNA Polymerase or through indirect interactions facilitated by adaptors, mediators, histone-modifying proteins, and nucleosome remodelers. Direct interactions to activate transcription is seen in bacteria as well as in some eukaryotic genes. In these cases, upstream activation sequences are adjacent to the promoters, and the activator proteins interact directly with the transcriptional machinery. For example, in...
02:40The Eukaryotic Promoter Region
The eukaryotic promoter region is a segment of DNA located upstream of a gene. It contains an RNA polymerase binding site, a transcription start site, and several cis-regulatory sequences. The proximal promoter region is located in the vicinity of the gene and has cis-regulatory sequences and the core promoter. The core promoter is the binding site for RNA polymerase and is usually located between -35 and +35 nucleotides from the transcription start site. The distal promoter regions are...
02:40The Eukaryotic Promoter Region
The eukaryotic promoter region is a segment of DNA located upstream of a gene. It contains an RNA polymerase binding site, a transcription start site, and several cis-regulatory sequences. The proximal promoter region is located in the vicinity of the gene and has cis-regulatory sequences and the core promoter. The core promoter is the binding site for RNA polymerase and is usually located between -35 and +35 nucleotides from the transcription start site. The distal promoter regions are...
02:04Co-activators and Co-repressors
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...
02:04Co-activators and Co-repressors
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...
02:13Cooperative Binding of Transcription Regulators
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 dimers that...