DNA topoisomerase I (TOP1) has an important role in maintaining DNA topology by relaxing supercoiled DNA. Here we show that the K391 and K436 residues of TOP1 are SUMOylated by the PIAS1-SRSF1 E3 ligase complex in the chromatin fraction containing active RNA polymerase II (RNAPIIo). This modification is necessary for the binding of TOP1 to RNAPIIo and for the recruitment of RNA splicing factors to the actively transcribed chromatin, thereby reducing the formation of R-loops that lead to genome instability. RECQ5 helicase promotes TOP1 SUMOylation by facilitating the interaction between PIAS1, SRSF1 and TOP1. Unexpectedly, the topoisomerase activity is compromised by K391/K436 SUMOylation, and this provides the first in vivo evidence that TOP1 activity is negatively regulated at transcriptionally active chromatin to prevent TOP1-induced DNA damage. Therefore, our data provide mechanistic insight into how TOP1 SUMOylation contributes to genome maintenance during transcription.

Mitochondrial DNA (mtDNA) encodes genes important for ATP biogenesis. Therefore, changes in mtDNA copy number will have profound consequences on cell survival and proliferation. RECQ4 DNA helicase plays important roles in both nuclear and mtDNA synthesis. However, the mechanism that balances the distribution of RECQ4 in the nucleus and mitochondria is unknown. Here, we show that RECQ4 forms protein complexes with Protein Phosphatase 2A (PP2A), nucleophosmin (NPM) and mitochondrial p32 in different cellular compartments. Critically, the interaction with p32 negatively controls the transport of both RECQ4 and its chromatin-associated replication factor MCM10 from the nucleus to mitochondria. Amino acids (Ala420-Ala463), which are deleted in the most common cancer-induced RECQ4 mutation, are required for the interaction with p32. Hence, this RECQ4 mutant, which is no longer regulated by p32 and is enriched in the mitochondria, interacts with the mitochondrial replication helicase PEO1 and induces abnormally high levels of mtDNA synthesis.

The replication licensing factor CDC6 recruits the MCM2-7 replicative helicase to the replication origin, where MCM2-7 is activated to initiate DNA replication. MCM2-7 is activated by both the CDC7-Dbf4 kinase and cyclin-dependent kinase and via interactions with CDC45 and go-ichi-ni-san complex (GINS) to form the CDC45⅐MCM2-7⅐GINS (CMG) helicase complex. TIMELESS (TIM) is important for the subsequent coupling of CMG activity to DNA polymerases for efficient DNA synthesis. However, the mechanism by which TIM regulates CMG activity for proper replication fork progression remains unclear. Here we show that TIM interacts with MCM2-7 prior to the initiation of DNA replication. TIM depletion in various human cell lines results in the accumulation of aberrant CMG helicase complexes on chromatin. Importantly, the presence of these abnormal CMG helicase complexes is not restricted to cells undergoing DNA synthesis. Furthermore, even though these aberrant CMG complexes interact with the DNA polymerases on human chromatin, these complexes are not phosphorylated properly by cyclin-dependent kinase/CDC7-Dbf4 kinase and exhibit reduced DNA unwinding activity. This phenomenon coincides with a significant accumulation of the p27 and p21 replication inhibitors, reduced chromatin association of CDC6 and cyclin E, and a delay in S phase entry. Our results provide the first evidence that TIM is required for the correct chromatin association of the CMG complex to allow efficient DNA replication.During cell growth, faithful DNA duplication is essential for correctly transmitting genetic material to daughter cells during cell division, and defects in this process can result in genome instability, tumorigenesis, or cell death. During DNA replication, double-stranded DNA must be unwound by the MCM2-7 a hexameric helicase to generate ssDNA, 2 which is then used as the template for DNA synthesis by DNA polymerase. However, even though there is an abundance of MCM2-7 protein on the chromatin throughout the cell cycle, most of the MCM2-7 is kept inactive, and only a small population is recruited and associated with active replicons to participate in DNA synthesis (1-3). During early G 1 phase, the MCM2-7 protein is recruited to the active replication origins, where it forms part of the pre-replication complex, and its recruitment requires the CDC6 and CDT1 licensing factors (4, 5). To ensure the accurate timing of replication initiation, the activity of the chromatin-bound MCM2-7 protein is tightly regulated both by post-translational modifications and protein-protein interactions. Specifically, the catalytic activity of the MCM2-7 helicase is suppressed during G 1 phase and can only be activated both via the interaction with GINS and CDC45, which forms the CMG complex, and via phosphorylation by DDK and CDK during replication initiation (6, 7). Mammalian TIM is an essential protein for embryonic development (8). TIM and its interacting protein, TIPIN, are highly conserved replication factors that directly interact with the MCM2-7 helicase...