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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

C4S DB: Comprehensive Collection and Comparison for ChIP-Seq Database.

Hayato Anzawa¹, Kengo Kinoshita²

¹Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan; Department of System Bioinformatics, Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki-Aza-Aoba, Aoba-ku, Sendai 980-8579, Japan.

Journal of Molecular Biology

|May 27, 2023

Summary

This summary is machine-generated.

The Comprehensive Collection and Comparison for ChIP-Seq Database (C4S DB) integrates over 16,000 ChIP-seq experiments. It enables researchers to explore combined DNA-binding element profiles and regulatory relationships.

Keywords:

DNA-binding proteins histone modifications quality control transcription factors transcriptional regulation

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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
Molecular Biology
Bioinformatics

Background:

Understanding complex biological systems requires integrating multiple binding profiles, including transcription factors and histone modifications.
Existing chromatin immunoprecipitation followed by sequencing (ChIP-seq) databases often focus on individual experiments, hindering the analysis of coordinated regulation by DNA-binding elements.

Purpose of the Study:

To develop a comprehensive database (C4S DB) for analyzing combined DNA-binding element profiles using quality-assessed public ChIP-seq data.
To provide interactive web interfaces for discovering relationships between ChIP-seq experiments, facilitating the study of gene regulation.

Main Methods:

Aggregated and quality-assessed over 16,000 human ChIP-seq experiments.
Developed a "Gene browser" to visualize binding element distributions around specific genes.
Implemented a "global similarity" feature using hierarchical clustering heatmaps to analyze genome-wide relationships between ChIP-seq experiments.

Main Results:

The C4S DB offers tools to identify gene-specific and genome-wide colocalization or mutually exclusive localization of regulatory elements.
Interactive web interfaces enable efficient searching and aggregation of large-scale ChIP-seq data.
The database facilitates the evaluation of regulatory element interactions.

Conclusions:

The C4S DB provides valuable insights into the combinatorial nature of DNA-binding elements and their regulatory roles.
This resource enhances the ability of researchers to elucidate complex gene regulation mechanisms through integrated ChIP-seq data analysis.