Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

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...

Transcription Factors

Transcription Factors

Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...

Conserved Binding Sites

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...

Cooperative Binding of Transcription Regulators

Cooperative Binding of Transcription Regulators

Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome. Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form dimers that...

Organization of Genes

Organization of Genes

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

[Using the revised Chinese diet balance index Quality of Diet to evaluate the quality of diet among rural residents in Hanzhong, Shaanxi province and relative influencing factors].

Zhonghua liu xing bing xue za zhi = Zhonghua liuxingbingxue zazhi·2015

Same author

A highly sensitive and specific electrochemical sensing method for robust detection of Escherichia coli lac Z gene sequence.

Biosensors & bioelectronics·2015

Same author

Stereoselective intermolecular nitroaminoxylation of terminal aromatic alkynes: trapping alkenyl radicals by TEMPO.

Organic letters·2014

Same author

Correlation between red blood cell transfusion volume and mortality in patients with massive blood transfusion: A large multicenter retrospective study.

Experimental and therapeutic medicine·2014

Same author

[Sampling survey of schistosomiasis prevention knowledge among middle school students in endemic areas of Hubei Province].

Zhongguo xue xi chong bing fang zhi za zhi = Chinese journal of schistosomiasis control·2014

Same author

Synthesis of ultrahighly electron-deficient pyrrolo[3,4-d]pyridazine-5,7-dione by inverse electron demand Diels-Alder reaction and its application as electrochromic materials.

Organic letters·2014

Same journal

Tension on dsDNA bound to ssDNA-RecA filaments may play an important role in driving efficient and accurate homology recognition and strand exchange.

Physical review. E, Statistical, nonlinear, and soft matter physics·2016

Same journal

Publisher's Note: Amplitude-phase coupling drives chimera states in globally coupled laser networks [Phys. Rev. E 91, 040901(R) (2015)].

Physical review. E, Statistical, nonlinear, and soft matter physics·2016

Same journal

Erratum: Shapes of sedimenting soft elastic capsules in a viscous fluid [Phys. Rev. E 92, 033003 (2015)].

Physical review. E, Statistical, nonlinear, and soft matter physics·2016

Same journal

Erratum: Attenuation of excitation decay rate due to collective effect [Phys. Rev. E 90, 022142 (2014)].

Physical review. E, Statistical, nonlinear, and soft matter physics·2016

Same journal

Publisher's Note: Role of connectivity and fluctuations in the nucleation of calcium waves in cardiac cells [Phys. Rev. E 92, 052715 (2015)].

Physical review. E, Statistical, nonlinear, and soft matter physics·2016

Same journal

Publisher's Note: Lattice Boltzmann approach for complex nonequilibrium flows [Phys. Rev. E 92, 043308 (2015)].

Physical review. E, Statistical, nonlinear, and soft matter physics·2016

See all related articles

Search research articles

Related Experiment Video

Updated: Jun 18, 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

Finding human promoter groups based on DNA physical properties.

Jia Zeng¹, Xiao-Qin Cao, Hongya Zhao

¹Department of Computer Science, Hong Kong Baptist University, Kowloon Tong, Hong Kong. j.zeng@ieee.org

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics

|November 13, 2009

Summary

This summary is machine-generated.

This study reveals four distinct human promoter groups classified by DNA rigidity profiles. These groups show conserved rigidity at the TATA box and correlate with tissue-specific gene expression and function.

More Related Videos

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

An Integrated Workflow to Study the Promoter-Centric Spatio-Temporal Genome Architecture in Scarce Cell Populations

An Integrated Workflow to Study the Promoter-Centric Spatio-Temporal Genome Architecture in Scarce Cell Populations

Published on: April 21, 2023

Related Experiment Videos

Last Updated: Jun 18, 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

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

An Integrated Workflow to Study the Promoter-Centric Spatio-Temporal Genome Architecture in Scarce Cell Populations

An Integrated Workflow to Study the Promoter-Centric Spatio-Temporal Genome Architecture in Scarce Cell Populations

Published on: April 21, 2023

Area of Science:

Molecular Biology
Biophysics
Genomics

Background:

DNA rigidity, a property derived from its 3D structure, influences biological processes.
While general DNA rigidity patterns in human promoters are known, their specific roles in transcription remain unclear.

Purpose of the Study:

To identify distinct human promoter groups based on DNA rigidity profiles.
To investigate the functional implications of these promoter groups in gene regulation and expression.

Main Methods:

Clustering of human promoters based on similarity in their rigidity profiles.
Analysis of DNA rigidity at the TATA box region across different promoter groups.
Gene ontology annotation to determine shared biological functions of genes regulated by each promoter group.
Correlation analysis between promoter groups and tissue-specific gene expression data.

Main Results:

Four distinct human promoter groups were identified based on DNA rigidity profiles.
All identified promoter groups exhibit conserved DNA rigidity at the canonical TATA box.
Genes activated by each promoter group share significant biological functions.
These promoter groups demonstrate a correlation with tissue-specific gene expression patterns.

Conclusions:

DNA rigidity profiles can effectively classify human promoters into functionally distinct groups.
Conserved rigidity at the TATA box is a key feature across all promoter groups, important for transcription factor binding.
The identified promoter groups are linked to specific biological functions and tissue-specific gene expression, highlighting the role of DNA physical properties in gene regulation.