Polymerase η Recruits DHX9 Helicase to Promote Replication across Guanine Quadruplex Structures

DNA polymerase η (Pol η) catalyzes accurate
bypass
of ultraviolet light-induced cyclobutane pyrimidine dimers, and it
also functions in several other related processes, including bypassing
DNA with unusual structures. Here, we performed unbiased proteome-wide
profiling of Pol η-interacting proteins by using two independent
approaches, i.e., proximity labeling and affinity pull-down followed
by LC-MS/MS analysis. We identified several helicases, including DHX9,
as novel Pol η-interacting proteins. Additionally, ChIP-Seq
analysis showed that Pol η is enriched at guanine quadruplex
(G4) structure sites in chromatin. Moreover, Pol η promotes
the recruitment of DHX9 to G4 structure loci in chromatin and facilitates
DHX9-mediated unwinding of G4 structures. Deficiency in Pol η
or DHX9 leads to attenuated replication across G4 regions in genomic
DNA. Together, we unveiled the interaction between Pol η and
DHX9 and demonstrated that the interaction promotes the replicative
bypass of G4 structures in chromatin.