Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Cis-regulatory Sequences02:02

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 Sequences02:02

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...
Cooperative Binding of Transcription Regulators02:13

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...
Cooperative Binding of Transcription Regulators02:13

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...
Co-activators and Co-repressors02:04

Co-activators and Co-repressors

Gene transcription is regulated by the synergistic action of several proteins that form a complex at a gene regulatory site. This is observed in eukaryotes, where the regulation of gene expression is a complex process. Regulatory proteins in eukaryotes can broadly be classified into two types – regulators that bind directly to specific DNA sequences and co-regulators that associate with regulatory proteins but cannot directly bind to the DNA. These co-regulators are further divided into...
Co-activators and Co-repressors02:04

Co-activators and Co-repressors

Gene transcription is regulated by the synergistic action of several proteins that form a complex at a gene regulatory site. This is observed in eukaryotes, where the regulation of gene expression is a complex process. Regulatory proteins in eukaryotes can broadly be classified into two types – regulators that bind directly to specific DNA sequences and co-regulators that associate with regulatory proteins but cannot directly bind to the DNA. These co-regulators are further divided into...

You might also read

Related Articles

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

Sort by
Same author

TALEs, TALENs, and TALE Base Editors: From Plant Pathology to Biotechnology.

Annual review of phytopathology·2026
Same author

Analyzing the digital customer journey: a novel framework for sequential behavior modeling.

Scientific reports·2026
Same author

Reanimating the past: From historical collections of the placenta and uterus to modern imaging, machine learning, and multiscale modeling.

Placenta·2026
Same author

CERTOMICS: trusted single-cell multiomics pipeline for high-resolution profiling of adoptive cellular immunotherapies.

Bioinformatics (Oxford, England)·2026
Same author

Improved reconstruction of transcripts and coding sequences from RNA-seq data.

Nucleic acids research·2026
Same author

Fast barcode calling based on <i>k</i>-mer distances.

PNAS nexus·2026

Related Experiment Video

Updated: Jul 13, 2026

Quantitative Comparison of cis-Regulatory Element (CRE) Activities in Transgenic Drosophila melanogaster
08:19

Quantitative Comparison of cis-Regulatory Element (CRE) Activities in Transgenic Drosophila melanogaster

Published on: December 19, 2011

Recognition of cis-regulatory elements with vombat.

Stefan Posch1, Jan Grau, Andre Gohr

  • 1Institute of Computer Science, University Halle, 06099 Halle (Saale), Germany.

Journal of Bioinformatics and Computational Biology
|July 20, 2007
PubMed
Summary

Variable order models significantly improve the identification of eukaryotic cis-regulatory elements, outperforming traditional methods. A new tool, VOMBATserver, facilitates their evaluation and genomic scanning.

More Related Videos

HOX Loci Focused CRISPR/sgRNA Library Screening Identifying Critical CTCF Boundaries
10:10

HOX Loci Focused CRISPR/sgRNA Library Screening Identifying Critical CTCF Boundaries

Published on: March 31, 2019

Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes
07:55

Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes

Published on: May 31, 2011

Related Experiment Videos

Last Updated: Jul 13, 2026

Quantitative Comparison of cis-Regulatory Element (CRE) Activities in Transgenic Drosophila melanogaster
08:19

Quantitative Comparison of cis-Regulatory Element (CRE) Activities in Transgenic Drosophila melanogaster

Published on: December 19, 2011

HOX Loci Focused CRISPR/sgRNA Library Screening Identifying Critical CTCF Boundaries
10:10

HOX Loci Focused CRISPR/sgRNA Library Screening Identifying Critical CTCF Boundaries

Published on: March 31, 2019

Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes
07:55

Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes

Published on: May 31, 2011

Area of Science:

  • Computational Biology
  • Bioinformatics
  • Genomics

Background:

  • Traditional models like position weight matrices struggle with complex cis-regulatory element recognition.
  • Variable order models have shown promise in prokaryotic binding site identification.

Purpose of the Study:

  • To assess the effectiveness of variable order models for eukaryotic cis-regulatory element recognition.
  • To introduce a computational tool for evaluating and scanning these elements.

Main Methods:

  • Application of variable order Markov models and variable order Bayesian trees.
  • Comparative analysis against traditional models for transcription factor binding sites.
  • Development and release of the VOMBATserver.

Main Results:

  • Variable order models demonstrated improved recognition of binding sites for all tested eukaryotic transcription factors.
  • The VOMBATserver enables systematic evaluation and genomic scanning using various model types.

Conclusions:

  • Variable order models offer a significant advancement in identifying eukaryotic cis-regulatory elements.
  • The VOMBATserver provides a valuable resource for researchers in the field.