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Introducing the EpG2 System: Epigenomic Processes and the Emergent Genome
1Department of Nutritional Sciences, University of Michigan School of Public Health, 2867 SPH I, 1415 Washington Heights, Ann Arbor, MI 48109, USA.
Epigenomes
|December 24, 2025
Summary
Genomic identity emerges from epigenomic processes, not just DNA sequence. The Epigenome-Genome (EpG²) system reframes the genome as an emergent entity driven by epigenomic regulation.
Area of Science:
- Genomics
- Epigenetics
- Systems Biology
Background:
- Current genomics research focuses on DNA sequence, overlooking the epigenome's role in establishing genomic identity.
- A DNA-centric view obscures the fundamental role of epigenomic processes in defining the genome.
Purpose of the Study:
- To propose a new theoretical framework, the Epigenome-Genome (EpG²) system.
- To reinterpret existing findings through the lens of epigenomic processes.
Main Methods:
- Integration of evidence from enhancer biology, genomic functions, and zygotic genome activation.
- Reinterpretation of published data using epigenomic principles.
Main Results:
- Enhancers arise from the interaction of DNA sequence, transcription factors, and chromatin.
- Zygote genome emergence (ZGE) involves coordinated epigenomic reprogramming.
- Risk alleles exhibit context-dependent effects influenced by changing epigenomic landscapes.
Conclusions:
- The EpG² system presents the genome as a dynamic, emergent entity regulated by epigenomic processes.
- This framework offers a new paradigm for understanding genomic variation beyond DNA sequence alone.
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