Genomic Footprinting Analyses from DNase-seq Data to Construct Gene Regulatory Networks
Tomás C Moyano1,2,3, Rodrigo A Gutiérrez4,5,6, José M Alvarez7,8
1ANID-Millennium Science Initiative Program- Millenium Institute for Integrative Biology (iBio), Santiago, Chile.
Methods in Molecular Biology (Clifton, N.J.)
|July 12, 2021
Summary
This study presents a pipeline for building gene regulatory networks using DNase sequencing (DNase-seq) data. It identifies transcription factor footprints to map regulatory interactions in any sequenced organism.
Area of Science:
- Genomics and Molecular Biology
- Gene Regulation and Epigenetics
Background:
- Chromatin accessibility correlates with gene transcription in eukaryotes.
- DNase I hypersensitive sites (DHSs) mark accessible regulatory regions.
- DNase-seq identifies DHSs and transcription factor (TF) footprints at single-base resolution.
Purpose of the Study:
- To provide a step-by-step pipeline for constructing gene regulatory networks from DNase-seq data.
- To enable the mapping of TF regulatory interactions by identifying differential TF footprints between conditions.
Main Methods:
- DNase I digestion followed by high-throughput DNA sequencing (DNase-seq).
- Bioinformatic pipeline for DHS calling and TF footprint identification.
- Differential footprint analysis to detect changes between treatment and control conditions.
Main Results:
- A comprehensive workflow for analyzing DNase-seq data is presented.
- The pipeline facilitates the identification of TF binding and regulatory interactions.
- Gene regulatory networks can be constructed from differential TF footprinting data.
Conclusions:
- The developed pipeline effectively builds gene regulatory networks using DNase-seq data.
- This method allows for the mapping of TF regulatory interactions across different conditions.
- The workflow is adaptable to DNase-seq data from any organism with a sequenced genome.
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