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bioRxiv · 10.1101/2021.04.13.439211

Genomic patterns of transcription-replication interactions in mouse primary B cells

St Germain, C. P.·Zhao, H.·Sinha, V.·Sanz, L. A.·Chedin, F.·Barlow, J. H.
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Abstract

Conflicts between transcription and replication machinery are a potent source of replication stress and genome stability; however, no technique currently exists to identify endogenous genomic locations prone to transcription-replication interactions. Here, we report a novel method to identify genomic loci prone to transcription-replication interactions termed transcription-replication immunoprecipitation on nascent DNA sequencing, TRIPn-Seq. TRIPn-Seq employs the sequential immunoprecipitation of RNA polymerase 2 phosphorylated at serine 5 (RNAP2s5) followed by enrichment of nascent DNA previously labeled with bromodeoxyuridine. Using TRIPn-Seq, we mapped 1,009 unique transcription-replication interactions (TRIs) in mouse primary B cells characterized by a bimodal pattern of RNAP2s5, bidirectional transcription, an enrichment of RNA:DNA hybrids, and a high probability of forming G-quadruplexes. While TRIs themselves map to early replicating regions, they exhibit enhanced Replication Protein A association and replication fork termination, marks of replication stress. TRIs colocalize with double-strand DNA breaks, are enriched for deletions, and accumulate mutations in tumors. We propose that replication stress at TRIs induces mutations potentially contributing to age-related disease, as well as tumor formation and development.

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St Germain, C. P., Zhao, H., Sinha, V., Sanz, L. A., Chedin, F., Barlow, J. H.. 2021-04-13. Genomic patterns of transcription-replication interactions in mouse primary B cells. https://doi.org/10.1101/2021.04.13.439211

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