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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...

Cis-regulatory Sequences

Cis-regulatory Sequences

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...

Cis-regulatory Sequences

Cis-regulatory Sequences

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...

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...

Prokaryotic Transcriptional Activators and Repressors

Prokaryotic Transcriptional Activators and Repressors

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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In vivo Application of the REMOTE-control System for the Manipulation of Endogenous Gene Expression

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Finding new core promoter elements using backward-looking strategies.

Yin-Fu Huang¹, Yi-Chao Jhan, Sing-Wu Liou

¹Graduate School of Computer Science and Information Engineering, National Yunlin University of Science and Technology, 123 University Road, Section 3, Touliu, Yunlin, Taiwan 640, ROC. huangyf@el.yuntech.edu.tw

International Journal of Data Mining and Bioinformatics

|May 13, 2009

Summary

This summary is machine-generated.

A new framework successfully identified known Core Promoter Elements (CPEs) and discovered novel motifs in Drosophila and human genomes. This reliable system aids in understanding gene expression by revealing new regulatory elements.

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Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes

Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes

Published on: May 31, 2011

Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Core Promoter Elements (CPEs) are essential for initiating transcription.
Accurate identification of CPEs is vital for comprehending gene expression regulation.
Existing methods may not capture the full diversity of CPEs.

Purpose of the Study:

To propose and validate a novel computational framework for identifying Core Promoter Elements (CPEs).
To discover previously unknown CPEs in eukaryotic genomes.
To assess the reliability and feasibility of the proposed identification system.

Main Methods:

Development of a computational framework for CPE discovery.
Application of the framework to sequences from the Eukaryotic Promoter Database (EPD).
Comparative analysis of discovered motifs against known CPEs.

Main Results:

The framework successfully identified all known CPEs within the EPD dataset.
Five novel CPE motifs were discovered in Drosophila melanogaster sequences.
Three novel CPE motifs were identified in human sequences.

Conclusions:

The proposed framework is a feasible and reliable tool for identifying both known and novel Core Promoter Elements.
The newly discovered motifs represent potential regulatory elements warranting further experimental investigation.
This work enhances our understanding of gene transcription initiation and regulation.