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Cis-regulatory Sequences

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 Sequences

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...

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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)

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

Published on: October 5, 2018

Robust 4C-seq data analysis to screen for regulatory DNA interactions.

Harmen J G van de Werken¹, Gilad Landan, Sjoerd J B Holwerda

¹Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), Utrecht, The Netherlands.

|September 11, 2012

Summary

This summary is machine-generated.

We developed a cost-effective method using chromosome conformation capture (4C-seq) to map physical interactions between DNA elements. This technique robustly characterizes the 3D genome organization, aiding gene regulation studies.

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

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

Published on: October 5, 2018

A Quantitative Assay to Study Protein:DNA Interactions, Discover Transcriptional Regulators of Gene Expression, and Identify Novel Anti-tumor Agents

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Generation of High Quality Chromatin Immunoprecipitation DNA Template for High-throughput Sequencing (ChIP-seq)

Generation of High Quality Chromatin Immunoprecipitation DNA Template for High-throughput Sequencing (ChIP-seq)

Published on: April 19, 2013

Area of Science:

Genomics
Molecular Biology
Epigenetics

Background:

Gene expression is regulated by distal DNA elements interacting physically.
Understanding these 3D genome structures is crucial for deciphering gene regulation.

Purpose of the Study:

To present a cost-effective methodology for characterizing physical interactions around functional genomic elements.
To enable robust analysis of the 3D genome organization using chromosome conformation capture combined with high-throughput sequencing (4C-seq).

Main Methods:

Developed a streamlined 4C-seq protocol for efficient capture of DNA interactions.
Integrated a computational analysis pipeline for robust data processing and interpretation.
Demonstrated multiplexing capabilities for simultaneous analysis of multiple genomic regions.

Main Results:

Successfully characterized the physical organization around selected promoters and functional elements.
Provided a cost-effective and robust approach for 3D genome analysis.
Validated the integration of 4C-seq with other functional genomics assays.

Conclusions:

The presented 4C-seq methodology offers a powerful tool for physical characterization of gene regulation.
This approach facilitates a deeper understanding of genome architecture and its role in controlling gene expression.
The method is adaptable and can be routinely integrated into functional genomics workflows.