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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...

Cell Specific Gene Expression

Cell Specific Gene Expression

Multicellular organisms contain a variety of structurally and functionally distinct cell types, but the DNA in all the cells originated from the same parent cells. The differences in the cells can be attributed to the differential gene expression. Liver cells, whose functions include detoxification of blood, production of bile to metabolize fats, and synthesis of proteins essential for metabolism, must express a specific set of genes to perform their functions. Gene expression also varies with...

Eukaryotic Transcription Activators

Eukaryotic Transcription Activators

Transcription activators are proteins that promote the transcription of genes from DNA to RNA. In most cases, these proteins contain two separate domains ‒ a domain that binds to DNA and a domain for activating transcription; however, in some cases, a single domain is responsible for both binding and activation of transcription, as seen in the glucocorticoid receptor and MyoD.
The binding domains are capable of recognizing and interacting with regulatory sequences on the DNA. These domains are...

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Related Experiment Video

Updated: Jul 17, 2026

A Web-Based Workflow for Selecting Gene- and Tissue-Specific Enhancers

A Web-Based Workflow for Selecting Gene- and Tissue-Specific Enhancers

Published on: July 18, 2025

EnhancerDB 2.0: a comprehensive cross-species enhancer atlas.

Junnuo Zheng¹, Yukun Li¹, Xingyi Du¹

¹School of Life Sciences and Engineering, Southwest Jiaotong University, Chengdu China.

Molecular Biology and Evolution

|July 15, 2026

Summary

EnhancerDB 2.0 is a powerful database for studying enhancers, which regulate gene expression. This updated resource expands to five species and offers extensive multi-omics data for biological and medical research.

Keywords:

TFBS database enhancers genes miRNAs

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Last Updated: Jul 17, 2026

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Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Enhancers are crucial cis-regulatory elements controlling gene expression during development and adaptation.
Large-scale omics data necessitates advanced tools for analyzing enhancer regulatory networks.
Existing resources may lack multi-species coverage and comprehensive annotation.

Purpose of the Study:

To update and expand EnhancerDB 1.0 into EnhancerDB 2.0 for enhanced profiling of enhancer regulatory networks.
To facilitate multi-omics interpretation of gene regulation by enhancers.
To provide a comprehensive, user-friendly platform for enhancer research.

Main Methods:

Expanded EnhancerDB 2.0 to include five species: human, mouse, zebrafish, fruit fly, and yeast.
Integrated extensive annotations including transcription factor binding sites, target genes/miRNAs/lncRNAs, SNPs, CRISPR-Cas9 sites, chromatin accessibility, repeat regions, methylation sites, and GWAS entries.
Developed an improved search function and a new analysis module for generating publication-quality charts.

Main Results:

EnhancerDB 2.0 now contains 1,605,856 enhancer entries across five species.
Nearly 100 million annotated entries provide rich functional and regulatory information.
The platform offers enhanced search capabilities and data visualization tools.

Conclusions:

EnhancerDB 2.0 is a significantly expanded and enriched resource for studying enhancer function and regulation.
It serves as a valuable, user-friendly platform for researchers in biology, medicine, and genetics.
The database supports comprehensive analysis of enhancer-mediated gene regulation across multiple species.