Translesion synthesis polymerase kappa is recruited to ribosomal DNA to maintain rRNA transcription

Abstract

DNA polymerase kappa (POLK) is a Y-family translesion synthesis (TLS) polymerase that bypasses bulky DNA lesions, such as those induced by the carcinogen benzo[a]pyrene diol epoxide (BPDE). Although TLS polymerases are increasingly recognized to function at the intersection of replication, repair, and transcription, mapping their activity to specific genomic loci has remained technically challenging because all DNA polymerases incorporate canonical nucleotides. To overcome this obstacle, we employed the selective POLK substrate N2-(4-ethynylbenzyl)-2'-deoxyguanosine (EBndG) to capture proteins associated with POLK -synthesized DNA. POLK was unexpectedly found enriched in the nucleolus, and POLK - synthesized DNA is enriched with nucleolar proteins. DNA damage induced by BPDE triggered hallmarks of nucleolar stress, stabilized POLK, and increased its retention and activity on nucleolar DNA, including ribosomal DNA (rDNA). Additional nucleolar stressors, including mitomycin C, cisplatin, and actinomycin D, elicited similar effects. The POLK activity was independent of cell-cycle phase but required PCNA ubiquitination and was regulated by PARP1. These findings uncover novel interactions of POLK with nucleolar proteins, demonstrate its direct activity on rDNA, and establish its role in sustaining rRNA synthesis after DNA damage, thereby protecting cells from nucleolar stress and linking TLS polymerase function to nucleolar homeostasis.