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The Eukaryotic Promoter Region

The 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...

The Eukaryotic Promoter Region

The 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...

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Related Experiment Video

Updated: Jun 14, 2026

Promoter Capture Hi-C: High-resolution, Genome-wide Profiling of Promoter Interactions

Promoter Capture Hi-C: High-resolution, Genome-wide Profiling of Promoter Interactions

Published on: June 28, 2018

DistanceScan: a tool for promoter modeling.

Vladimir Shelest¹, Daniela Albrecht, Ekaterina Shelest

¹Research group Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Beutenbergstr. 11a, 07745 Jena, Germany.

Bioinformatics (Oxford, England)

|April 3, 2010

Summary

This study introduces a new R tool for promoter modeling in higher eukaryotes. It identifies functional combinations of transcription factor binding sites (TFBSs) by analyzing their distance distributions, improving promoter analysis.

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Area of Science:

Computational biology
Bioinformatics
Genomics

Background:

Current promoter modeling focuses on transcription factor binding site (TFBS) combinations rather than single sites.
Predicting functional TFBS combinations is crucial for understanding gene regulation in higher eukaryotes.

Purpose of the Study:

To develop and implement a novel computational tool for predicting functional TFBS pairs in eukaryotic promoters.
To enhance promoter modeling by filtering noise and identifying overrepresented TFBS combinations.

Main Methods:

Utilizes a previously developed method based on the distance distributions of TFBS pairs.
Models random distance distributions and compares them with observed distributions in query sequences.
Integrates with existing TFBS and motif prediction tools (Gibbs Sampler, Match, MEME/FIMO).

Main Results:

Identifies potentially functional TFBS combinations by filtering noise through profile comparison.
Outputs a list of predicted TFBS pairs with scores, P-values, and distribution plots.
The approach is validated as an effective filtering technique for promoter modeling.

Conclusions:

The developed R tool advances the state of the art in promoter modeling for higher eukaryotes.
The method effectively identifies overrepresented TFBS pairs, aiding in the discovery of functional regulatory elements.
The tool provides a valuable resource for researchers in computational biology and genomics.