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Identification of Enhancer-Promoter Contacts in Embryoid Bodies by Quantitative Chromosome Conformation Capture 4C
Published on: April 29, 2020
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K-mer Content Changes with Node Degree in Promoter-Enhancer Network of Mouse ES Cells
Kinga Szyman1,2, Bartek Wilczyński2, Michał Dąbrowski1
1Laboratory of Bioinformatics, Nencki Institute of Experimental Biology, 02-093 Warsaw, Poland.
International Journal of Molecular Sciences
|August 7, 2021
Summary
This study reveals that gene regulatory elements like promoters and enhancers exhibit distinct sequence compositions. Higher connectivity in these elements correlates with increased GC content and CpG counts, influencing their sequence similarity.
Area of Science:
- Genomics
- Epigenetics
- Computational Biology
Background:
- Gene regulation involves interactions between promoters and enhancers.
- Analyzing these interactions as networks reveals structural and compositional properties.
Purpose of the Study:
- To investigate if sequence composition and similarity differentiate promoter and enhancer nodes in interaction networks.
- To determine how node degree (connectivity) relates to sequence characteristics.
Main Methods:
- Utilized Hi-C contact maps to construct promoter-enhancer networks.
- Analyzed sequence composition using k-mer counts (k=4).
- Measured sequence similarity via k-mer distance.
Main Results:
- Promoters are GC-rich; enhancers are enriched in S/MARs and CpG-depleted.
- Promoters show higher sequence similarity to their interacting enhancers than vice-versa.
- GC content and CpG counts increase with node degree for both promoters and enhancers.
- High-degree enhancers become more promoter-like; high-degree promoters become less enhancer-like.
Conclusions:
- Sequence composition and similarity are linked to the functional roles and connectivity of cis-regulatory elements.
- Node degree is a significant factor shaping the sequence properties of interacting promoters and enhancers.
- Findings hold true across different cell types, including mouse embryonic stem cells and human keratinocytes.
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