Transcription-replication conflicts as a source of common fragile site instability caused by BMI1-RNF2 deficiency

Abstract

Common fragile sites (CFSs) are breakage-prone genomic loci, and are considered to be hotspots for genomic rearrangements frequently observed in cancers. Understanding the underlying mechanisms for CFS instability will lead to better insight on cancer etiology. Here we show that Polycomb group proteins BMI1 and RNF2 are suppressors of transcription-replication conflicts (TRCs) and CFS instability. Cells depleted of BMI1 or RNF2 showed slower replication forks and elevated fork stalling. These phenotypes are associated with increase occupancy of RNA Pol II (RNAPII) at CFSs, suggesting that the BMI1-RNF2 complex regulate RNAPII elongation at these fragile regions. Using proximity ligase assays, we showed that depleting BMI1 or RNF2 causes increased associations between RNAPII with EdU-labeled nascent forks and replisomes, suggesting increased TRC incidences. Increased occupancy of a fork protective factor FANCD2 and R-loop resolvase RNH1 at CFSs are observed in RNF2 CRISPR-KO cells, which are consistent with increased transcription-associated replication stress in RNF2-deficient cells. Depleting FANCD2 or FANCI proteins further increased genomic instability and cell death of the RNF2-deficient cells, suggesting that in the absence of RNF2, cells depend on these fork-protective factors for survival. These data suggest that the Polycomb proteins have non-canonical roles in suppressing TRC and preserving genomic integrity.Author summaryIncreasing evidence suggest that instabilities at common fragile sites (CFSs), breakage-prone genomic loci, may be source of genomic aberration seen in cancer cells. Among the proposed mechanisms that can cause CFSs instabilities is the conflict between transcription and replication, and the mechanisms or factors that resolve the possible conflicts are only beginning to be understood. Here we found that deficiency in the Polycomb group proteins BMI1 or RNF2 leads to the CFS instability, and is associated with transcription-associated replication fork stresses. We further found that in the absence of RNF2, cells depend on the Fanconi Anemia fork-protective proteins for genome maintenance and survival. These results underscore that the Polycomb proteins are important for genome maintenance.

Histone dynamics during DNA replication stress

“…In line with this mechanism, a recent study showed that SLX4, a tumor suppressor, directs the recruitment of FANCD2 (a critical FA complex member) to RNA polymerase II, and this action is necessary for prevention of TRCs in unstressed cells [62]. Polycomb group proteins BMI1 and RNF2 were recently revealed to suppress TRCs as well [63]. Lastly, transcription-coupled R-loops can also be resolved by RNA exosomes [64], RPA function [65], and the ATR-CHK1 pathway [44].…”

The prognostic significance and regulatory networks of DAP3 in hepatocellular carcinoma microenvironment based on bioinformatics analysis

“…Cancer cells have features of genomic instability and mutagenesis, and transcription factors can help stabilize and repair genomic DNA, and inhibit cell cycle progression [27,28]. Thus, we seek to characterize the kinase targets of DAP3 in HCC and nd that DAP3 in HCC is associated with a network of kinases including PDPK1, MAPK3, RPS6KA1, PTK6, and LYN1.…”

Hypertranscription and replication stress in cancer

“…TOP3B loss is potentially associated with renal cancer [133]. Loss of Polycomb group transcriptional repressor proteins such as BMI1 or RNF2, which keep chromatin in a silenced state, slows replication fork progression and leads to increased 53BP1 focus formation and genomic instability [134]. The p53 inhibitor and proto-oncogene MDM2 also interacts with the Polycomb repressive complex.…”