Genomic patterns of transcription-replication interactions in mouse primary B cells
Commodore P St Germain1,2, Hongchang Zhao1, Vrishti Sinha1
1Department of Microbiology and Molecular Genetics, University of California Davis, One Shields Avenue, Davis, CA 95616, USA.
Nucleic Acids Research
|January 31, 2022
Summary
Scientists developed a new method, TRIPn-Seq, to find where DNA transcription and replication conflict. These conflicts, called transcription-replication interactions (TRIs), can cause genome instability and mutations linked to aging and cancer.
Area of Science:
- Genomics
- Molecular Biology
- Cellular Biology
Background:
- Transcription and replication conflicts are major drivers of replication stress and genomic instability.
- Existing methods cannot identify endogenous genomic sites prone to these transcription-replication interactions.
Purpose of the Study:
- To develop and validate a novel technique for identifying genomic loci prone to transcription-replication interactions.
- To characterize the genomic features and implications of these interactions in mouse primary B cells.
Main Methods:
- Developed transcription-replication immunoprecipitation on nascent DNA sequencing (TRIPn-Seq).
- Employed sequential immunoprecipitation of phosphorylated RNA polymerase 2 (RNAP2s5) and nascent DNA enrichment.
- Mapped transcription-replication interactions (TRIs) in mouse primary B cells.
Main Results:
- Identified 1009 unique TRIs characterized by specific RNAP2s5 patterns, bidirectional transcription, RNA:DNA hybrids, and G-quadruplex formation.
- TRIs are enriched at transcription start sites, early replicating regions, and show markers of replication stress (e.g., Replication Protein A association).
- TRIs colocalize with DNA breaks, deletions, and mutations, particularly in tumors.
Conclusions:
- TRIPn-Seq is a novel method to map transcription-replication interactions.
- Replication stress at TRIs contributes to mutations, potentially driving age-related diseases and tumorigenesis.
- Understanding TRIs is crucial for insights into genome instability and associated pathologies.
