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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...
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...
Global Regulatory Systems01:28

Global Regulatory Systems

Global regulatory systems in bacteria enable rapid and coordinated responses to environmental changes by integrating sensory inputs with gene expression, ensuring efficient adaptation to fluctuating conditions. Key global regulatory mechanisms include regulons, two-component systems, sigma factors, and secondary messengers.Regulons and Global RegulatorsA regulon is a collection of genes and operons controlled by a common global regulator. These regulators enable bacteria to prioritize resource...
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...

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Related Experiment Video

Updated: Jun 25, 2026

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

Published on: April 21, 2023

Understanding the regulatory genome.

M Eva Alonso1, Bárbara Pernaute, Miguel Crespo

  • 1Instituto de Investigaciones Biomédicas CSIC-UAM, Madrid, Spain.

The International Journal of Developmental Biology
|February 28, 2009
PubMed
Summary
This summary is machine-generated.

Understanding the regulatory genome is key to deciphering organism development and evolution. This review explores genomic approaches, methods, and phylogenetic footprinting for discovering gene regulatory codes.

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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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Area of Science:

  • Genomics
  • Developmental Biology
  • Evolutionary Biology

Background:

  • Whole genome sequencing reveals organism blueprints and evolutionary history.
  • Current understanding is limited to gene identification and protein function.
  • The regulatory genome governs spatiotemporal gene product production for organism development.

Purpose of the Study:

  • To review current knowledge of gene regulation from a genomic perspective.
  • To examine in silico, in vitro, and in vivo methods for studying transcriptional regulation.
  • To highlight phylogenetic footprinting for identifying regulatory elements.

Main Methods:

  • Genomic analysis
  • In silico computational approaches
  • In vitro experimental assays
  • In vivo studies
  • Phylogenetic footprinting

Main Results:

  • Gene regulation is complex and requires understanding the regulatory genome.
  • Various methodologies offer insights but have limitations.
  • Phylogenetic footprinting aids in discovering regulatory elements.
  • Large-scale studies and data analysis are crucial for deciphering genomic regulatory systems.

Conclusions:

  • A comprehensive understanding of the regulatory genome is essential for developmental and evolutionary biology.
  • Integrating diverse methodologies, especially large-scale data analysis, is key to uncovering regulatory codes.
  • Future research should focus on deciphering the complex language of genomic regulatory systems.