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Related Concept Videos

Cis-regulatory Sequences02:02

Cis-regulatory Sequences

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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...
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Global Regulatory Systems01:28

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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...
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Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

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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...
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Related Experiment Video

Updated: Mar 22, 2026

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq
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Connecting the regulatory genome.

John Stamatoyannopoulos1

  • 1Departments of Genome Sciences and Medicine at the University of Washington and at the Altius Institute for Biomedical Sciences, Seattle, Washington, USA.

Nature Genetics
|April 28, 2016
PubMed
Summary

Researchers developed a new computational method to predict how distal regulatory elements interact with target genes across the genome. This approach addresses a key challenge in understanding gene regulation and chromatin architecture.

Area of Science:

  • Genomics
  • Molecular Biology
  • Computational Biology

Background:

  • Understanding gene regulation is crucial for deciphering cellular function.
  • Mapping genome-wide distal regulatory elements and their target genes remains a significant challenge.
  • Advances in chromatin architecture studies provide context but lack direct interaction prediction.

Purpose of the Study:

  • To present a novel computational approach for predicting interactions between distal regulatory elements and target genes.
  • To provide a tool for better understanding genome-wide gene regulation.

Main Methods:

  • Development of a new computational algorithm.
  • Utilizing existing data on chromatin architecture and regulatory elements.
  • Prediction modeling for element-gene connections.

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Main Results:

  • The study successfully developed and validated a computational approach.
  • The method enables prediction of distal element-gene interactions.
  • The findings offer insights into regulatory networks.

Conclusions:

  • The developed computational approach is effective for predicting distal element-gene interactions.
  • This method advances the understanding of genome-wide regulatory networks.
  • The tool has potential applications in various fields of molecular biology and genomics.