Detours to Replication: Functions of Specialized DNA Polymerases during Oncogene-induced Replication Stress

Abstract

Incomplete and low-fidelity genome duplication contribute to genomic instability and cancer development. Difficult-to-Replicate Sequences, or DiToRS, are natural impediments in the genome that require specialized DNA polymerases and repair pathways to complete and maintain faithful DNA synthesis. DiToRS include non B-DNA secondary structures formed by repetitive sequences, for example within chromosomal fragile sites and telomeres, which inhibit DNA replication under endogenous stress conditions. Oncogene activation alters DNA replication dynamics and creates oncogenic replication stress, resulting in persistent activation of the DNA damage and replication stress responses, cell cycle arrest, and cell death. The response to oncogenic replication stress is highly complex and must be tightly regulated to prevent mutations and tumorigenesis. In this review, we summarize types of known DiToRS and the experimental evidence supporting replication inhibition, with a focus on the specialized DNA polymerases utilized to cope with these obstacles. In addition, we discuss different causes of oncogenic replication stress and its impact on DiToRS stability. We highlight recent findings regarding the regulation of DNA polymerases during oncogenic replication stress and the implications for cancer development.

Keywords: Difficult-to-Replicate Sequences; Microsatellites; Polymerase eta; Polymerase kappa; common fragile sites; genome instability; non-B DNA; replication stress.

Figure 1

Specialized DNA Polymerase Gene Alterations in Cancer. Thirty tumor groups (n = 65,690 samples) were queried using cBioportal (www.cbioportal.org) and public datasets available as of 1 September 2018. (A) The total number of POLH, POLK, REV3L, and REV1 gene alterations found in all tumor types are categorized into mutations (green bars), amplifications (red bars), deep deletions (blue bars), fusions (orange bars). Fusion events found in tumors were extremely rare: POLH has 2; POLK has 3; REV1 has 3; REV3L has 5. Multiple alterations with mutations were classified as mutations. Multiple alterations with fusions only occurred with amplifications and thus were designated as amplifications. (B) Correlation of POLH gene expression with copy number status. Individual TCGA PanCancer Atlas datasets for each type of cancer with mRNA expression from RNA-seq data sets were extracted as RSEM and graphed as box-and-whisker plots.

Figure 2

Oncogenes induce origin licensing and E2F transcriptional activity to drive G1/S transition and DNA hyper-replication. Myc and Cyclin E directly increase origin licensing by facilitating recruitment of pre-initiation complex (pre-IC) factors, including Cdt1, Cdc6, and MCMs. High levels of Ras, Myc or Cyclin E lead to increased CDK phosphorylation activity and E2F signaling that promotes the G1/S transition and initiation of DNA synthesis.

Figure 3

Conceptual framework for the role of specialized polymerases in oncogene induced replication stress. Oncogene activation promotes DNA replication thereby increasing replication fork encounters with DiToRS. Fork stalling activates the ATR/Chk1 axis and the subsequent recruitment of specialized DNA polymerase to resolve impediments. Rad18-mediated ubiquitination of PCNA is responsible, in part, for the recruitment of specialized DNA polymerase for distinct forms of DiToRS depending on the oncogenic cellular context. Engagement of specialized polymerases allows fork progression past DiToRS and continued cell cycle progression.