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Inferring differential protein binding from time-series chromatin accessibility data
Sneha Mitra1, Alexander J Hartemink1,2
1Department of Computer Science, Duke University, Durham, NC 27708-0129, United States.
Bioinformatics Advances
|April 29, 2025
Summary
DynaCOP analyzes chromatin accessibility data to reveal dynamic changes in transcription factor binding and nucleosome positioning. This method helps understand how epigenomic changes impact gene expression under stress conditions.
Area of Science:
- Genomics
- Epigenetics
- Molecular Biology
Background:
- The epigenomic landscape dynamically changes, influencing gene expression.
- Chromatin accessibility data, like MNase-seq, offer insights into this landscape.
- Analyzing multiple datasets reveals dynamic chromatin occupancy changes.
Purpose of the Study:
- Introduce DynaCOP, a novel method for analyzing dynamic chromatin occupancy.
- Identify differentially binding transcription factors and changes in nucleosome occupancy/positioning.
- Investigate chromatin changes in yeast under cadmium stress.
Main Methods:
- DynaCOP processes multiple chromatin occupancy profiles.
- Generates nucleosome-guided difference profiles.
- Applies DynaCOP to time-series MNase-seq data.
Main Results:
- DynaCOP successfully identifies differential transcription factor binding.
- Reveals significant changes in nucleosome occupancy and positioning.
- Observed chromatin changes correlate strongly with transcriptional changes in yeast under cadmium stress.
Conclusions:
- DynaCOP is an effective tool for studying dynamic epigenomic changes.
- Provides insights into stress-induced transcriptional regulation.
- Highlights the link between chromatin dynamics and gene expression alterations.
