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The Eukaryotic Promoter Region

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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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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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The organization of prokaryotic genes in their genome is notably different from that of eukaryotes. Prokaryotic genes are organized, such that the genes for proteins involved in the same biochemical process or function are located together in groups. This group of genes, along with their regulatory elements, are collectively known as an operon. The functional genes in an operon are transcribed together to give a single strand of mRNA known as polycistronic mRNA.
Transcription of prokaryotic...

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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

ElemeNT: a computational tool for detecting core promoter elements.

Anna Sloutskin¹, Yehuda M Danino, Yaron Orenstein

¹a The Mina and Everard Goodman Faculty of Life Sciences ; Bar-Ilan University ; Ramat Gan , Israel.

|July 31, 2015

Summary

This summary is machine-generated.

This study introduces the Elements Navigation Tool (ElemeNT) and CORE database for identifying core promoter elements. These resources automate the detection of key DNA sequences regulating gene expression, aiding in biological sequence annotation.

Keywords:

BRE BRE downstream of the TATA box; BREu BRE upstream of the TATA box; DCE DPE MTE RNA Polymerase II; TBP RNAP II transcription TATA box TATA box-binding protein; TAFs TBP-associated factors; TSS TCT TFIIB recognition element; BREd computational tool core promoter elements/motifs downstream core element; DPE downstream core promoter element; Inr initiator initiator; MTE motif 10 element; PWM position weight matrix; RNAP II promoter prediction transcription start site.

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Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Core promoter elements are crucial for gene transcription but are often manually identified.
Accurate detection of these elements is essential for understanding gene regulation.

Purpose of the Study:

To develop automated tools for detecting and curating core promoter elements.
To facilitate the analysis of core promoter composition and its role in gene expression.

Main Methods:

Development of the Elements Navigation Tool (ElemeNT), a web-based interactive platform for predicting core promoter elements.
Creation of the CORE database, which aggregates ElemeNT predictions near transcription start sites (TSSs) defined by CAGE and RNA-seq data in Drosophila melanogaster.
ElemeNT predictions are based on biologically functional elements and do not require prior knowledge of TSS positions.

Main Results:

ElemeNT provides user-friendly prediction and display of putative core promoter elements and their combinations.
The CORE database offers a curated summary of predicted core promoter elements.
These tools enable the inference of core promoter compositions and assist in the annotation of novel sequences.

Conclusions:

The ElemeNT tool and CORE database streamline the identification of core promoter elements.
These resources enhance the study of gene regulation by providing accessible methods for detecting key transcriptional control regions.
Automated detection of core promoter elements facilitates deeper insights into gene expression mechanisms.