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Fun2Fountain: Investigating transcription-replication conflicts in 3D genome
1Gilbert S. Omenn Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Electrical and Computer Engineering, University of Michigan, Ann Arbor, MI 48109, USA.
Molecular Cell
|May 21, 2026
Summary
Researchers developed Repli-MiC and Fun2 to study DNA replication and transcription conflicts. This helps understand how gene activity impacts the replication process and chromatin organization.
Area of Science:
- Molecular Biology
- Genomics
- Epigenetics
Background:
- Transcription and DNA replication are essential cellular processes.
- Conflicts between transcription and replication can lead to genomic instability.
- Understanding these conflicts is crucial for comprehending genome regulation.
Purpose of the Study:
- To investigate transcription-replication conflicts.
- To develop novel methods for analyzing chromatin dynamics during DNA replication.
- To assess the impact of transcription directionality on chromatin fountains.
Main Methods:
- Development of Repli-MiC, an experimental technique for chromatin analysis.
- Development of Fun2, a computational algorithm for identifying replication-associated chromatin structures.
- Measurement of chromatin fountains under co-directional and head-on transcription conditions.
Main Results:
- Identification of chromatin fountains linked to DNA replication.
- Quantification of transcription-replication conflicts using Repli-MiC and Fun2.
- Demonstration of differential effects of co-directional and head-on transcription on chromatin fountains.
Conclusions:
- Repli-MiC and Fun2 provide powerful tools for studying genome organization and dynamics.
- Transcription directionality significantly influences chromatin fountains and replication processes.
- This work advances the understanding of molecular mechanisms underlying transcription-replication conflicts.
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