RNA2020, 25th annual meeting of RNA Society

Abstract

Ribonucleotide (rNMP) incorporation in DNA generally occurs in all kingdoms of life, results in DNA structural change and genome instability. Previous studies in yeast showed that the rNMP presence in DNA is strongly induced by misincorporation of replicative DNA polymerases α, δ, and ε, particularly with low-fidelity mutants of these Pols. rNMP presence in DNA is more evident in cells with defects in ribonuclease (RNase) H2, which normally initiates rNMP removal from genomic DNA. The ribose-seq, EmRiboSeq, and RHII-HydEn-seq techniques are three established methods to capture the incorporated rNMPs in DNA. A large portion of rNMPs are incorporated around the autonomously replicating sequences (ARSs) in budding yeast, where the DNA replication process starts, and the leading and lagging strands are synthesized by the replicative Pols α, δ, and ε. Using published ribose-seq, EmRiboSeq, and RHII-HydEn-seq rNMP incorporation dataset, we performed a computational analysis of rNMP sites around ARSs. The analysis focuses on rNMP incorporation biases on the leading and lagging strands in both wild-type and RNase H2-mutant libraries. The results show an overall preference of rNMP incorporation on the leading strand in wild-type Pol and Pol ε low-fidelity mutant libraries. While Pol α or Pol δ low-fidelity mutant libraries display preference for rNMP incorporation on the lagging strand. All the rNMP preferences are reduced with increasing ARS firing time in RNase H2-mutant libraries. Moreover, at the beginning of DNA replication, the leading/lagging-strand ratio of rNMP incorporation increases in wild-type DNA Pol and Pol ε low-fidelity mutant libraries, and decreases in Pol α or Pol δ low-fidelity mutant libraries. Since the rNMP incorporation rate keeps steady in the lagging strand, the increase and decrease of the ratio reflect the replicative polymerase division of labor in the leading strand synthesis. Our results show that the leading strand synthesis is initiated by Pol α and followed by Pol δ. Then Pol ε synthesizes the remaining part. This work is supported by NIH, NIEHS R01 ES026243, and Howard Hughes Medical Institute Faculty Scholars Award, HHMI 55108574 to F. Storici.