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Related Concept Videos

The Eukaryotic Promoter Region02:40

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 Region02:40

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...
Transcription Initiation01:47

Transcription Initiation

Initiation is the first step of transcription in eukaryotes. Prokaryotic RNA Polymerase (RNAP) can bind to the template DNA and start transcribing. On the other hand, transcription in eukaryotes requires additional proteins, called transcription factors, to first bind to the promoter region in the DNA template. This binding helps recruit the specific RNAP that can assemble on the DNA and start transcription.
The promoters and enhancers and their accessory proteins allow tight regulation of...
Prokaryotic Gene Structure and Organization01:28

Prokaryotic Gene Structure and Organization

Prokaryotic genomes exhibit a streamlined organization of coding and non-coding regions essential for gene expression and protein synthesis. While coding regions contain the genetic instructions for proteins or functional RNAs, non-coding regions regulate the precise transcription and translation of these genes.Coding Regions: Proteins and RNAsThe primary coding regions, known as structural genes, include sequences transcribed into messenger RNA (mRNA) and ultimately translated into...
Structure of a Gene01:30

Structure of a Gene

A gene is the fundamental unit of heredity. Every individual has two copies of each gene, one inherited from each parent. Although most people contain the same genes, there is a small fraction that is slightly different amongst people. A gene with a small difference in its sequence of DNA bases forms different alleles, contributing to different phenotypes.
However, only 1% of the DNA is composed of genes that encode proteins; the rest, 99% is non-coding DNA. This non-coding DNA performs...
Bacterial Transcription01:53

Bacterial Transcription

RNA polymerase (RNAP) carries out DNA-dependent RNA synthesis in both bacteria and eukaryotes. Bacteria do not have a membrane-bound nucleus. So, transcription and translation occur simultaneously, on the same DNA template.
Transcription can be divided into three main stages, each involving distinct DNA sequences to guide the polymerase. These are:

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Related Experiment Video

Updated: Jul 9, 2026

Promoter Capture Hi-C: High-resolution, Genome-wide Profiling of Promoter Interactions
10:16

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

Published on: June 28, 2018

Determining promoter location based on DNA structure first-principles calculations.

J Ramon Goñi1, Alberto Pérez, David Torrents

  • 1Institute for Research in Biomedicine, Parc Científic de Barcelona, Josep Samitier, Barcelona 08028, Spain.

Genome Biology
|December 13, 2007
PubMed
Summary

A novel method predicts promoter regions using molecular dynamics simulations, independent of gene features. This approach reveals a hidden physical code influencing genome expression.

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Area of Science:

  • Genomics
  • Computational Biology
  • Biophysics

Background:

  • Predicting gene promoter regions is crucial for understanding genome regulation.
  • Current methods often rely on conserved gene structures or identifiable sequence motifs.

Purpose of the Study:

  • To develop a novel computational method for promoter region prediction.
  • To investigate the physical underpinnings of genome expression modulation.

Main Methods:

  • Utilized atomic molecular dynamics simulations.
  • Applied the method to small oligonucleotide sequences.
  • Developed a prediction model independent of gene structure and sequence features.

Main Results:

  • Successfully predicted promoter regions using the new method.
  • Demonstrated the method's independence from gene structure conservation and sequence motifs.
  • Confirmed the existence of a physical code governing genome expression.

Conclusions:

  • The developed method offers a new approach to promoter prediction.
  • Atomic molecular dynamics simulations can uncover hidden regulatory mechanisms.
  • A physical code plays a significant role in modulating genome expression.