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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...
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...
Combinatorial Gene Control02:33

Combinatorial Gene Control

Combinatorial gene control is the synergistic action of several transcriptional factors to regulate the expression of a single gene. The absence of one or more of these factors may lead to a significant difference in the level of gene expression or repression.
The expression of more than 30,000 genes is controlled by approximately 2000-3000 transcription factors. This is possible because a single transcription factor can recognize more than one regulatory sequence. The specificity in gene...

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Related Experiment Video

Updated: May 18, 2026

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)
09:06

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)

Published on: October 5, 2018

Comparative genomics-based identification and analysis of cis-regulatory elements.

Hajime Ogino1, Haruki Ochi, Chihiro Uchiyama

  • 1Graduate School of Biological Sciences, Nara Institute of Science and Technology (NAIST), Ikoma, Nara, Japan. ogino@bs.naist.jp

Methods in Molecular Biology (Clifton, N.J.)
|September 8, 2012
PubMed
Summary

This study presents a simple method to identify gene enhancers by comparing genomes and testing their activity in Xenopus embryos. This approach aids in understanding gene regulation and targeted gene expression experiments.

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High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)
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Published on: October 5, 2018

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

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Published on: May 31, 2011

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Area of Science:

  • Genomics
  • Developmental Biology
  • Molecular Biology

Background:

  • Identifying cis-regulatory elements like enhancers and promoters is crucial for gene regulatory network analysis.
  • These elements are also valuable tools for targeted gene expression studies.

Purpose of the Study:

  • To introduce a straightforward and dependable method for predicting gene enhancers.
  • To validate enhancer activity using a co-transgenesis technique in Xenopus embryos.

Main Methods:

  • Comparative genomics analysis of mammalian and Xenopus sequences using publicly available web tools.
  • Co-transgenesis assay in Xenopus embryos utilizing polymerase chain reaction products for rapid screening.

Main Results:

  • The bioinformatics approach is accessible to bench biologists without specialized computational skills.
  • The co-transgenesis assay allows for cloning-free screening of candidate enhancer activity.

Conclusions:

  • This combined bioinformatics and experimental approach provides an efficient way to identify and validate functional enhancers.
  • The method facilitates research in gene regulation and targeted gene expression applications.