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Related Experiment Video

Updated: May 31, 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

Decoding the genome with an integrative analysis tool: combinatorial CRM Decoder.

Keunsoo Kang¹, Joomyeong Kim, Jae Hoon Chung

¹Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.

Nucleic Acids Research

|July 5, 2011

Summary

This summary is machine-generated.

A new tool, combinatorial CRM decoder (CCD), identifies genome-wide cis-regulatory modules (CRMs) and their epigenetic features. This method aids in understanding gene regulatory networks by cataloging thousands of CRMs, including multi-functional ones.

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Area of Science:

Genomics
Epigenetics
Bioinformatics

Background:

Understanding gene regulatory networks requires identifying genome-wide cis-regulatory modules (CRMs) and their epigenetic features.
Current integrative analysis methods are limited by a lack of novel methodologies.

Purpose of the Study:

To develop a comprehensive analysis tool, combinatorial CRM decoder (CCD), for identifying and characterizing genome-wide CRMs.
To utilize publicly available genome-wide data for CRM discovery.

Main Methods:

CCD defines a 'trace code' of epigenetic features associated with known CRMs.
This trace code is then used to identify putative CRMs across the genome.
The tool was validated using 61 datasets from 17 mouse studies.

Main Results:

CCD catalogued approximately 12,600 CRMs across five distinct classes.
Identified CRMs include polycomb repressive complex 2 target sites and imprinting control regions.
Approximately 4% of CRMs were multi-functional, indicating roles in spatiotemporal gene regulation.

Conclusions:

CCD is a versatile tool applicable to various genome-wide datasets for CRM discovery.
The tool facilitates the unveiling of genome-wide CRMs across different species.
The identification of multi-functional CRMs highlights their significance in gene expression regulation.