A chromatin-associated long non-coding RNA is required for effective replication stress signaling [RNAseq_HUtreatment]

Despite the well-characterized protein network involved in replication stress response, several regulatory RNAs have been shown to be involved in this process; however, it has remained elusive the presence of such RNAs on the replication fork, and how they locally act in this critical process. Here, we identified lncREST, a previously uncharacterized lncRNA among a set of chromatin-associated transcripts induced by hydroxyurea. We show that lncREST localizes on stressed replication forks. Specifically, during replication stress, lncREST interacts with NCL in the nucleus, to help engage its interaction with RPA. Consequently, lncREST loss is associated to reduction of NCL-RPA interaction and decreased RPA on chromatin, leading to a defective replication stress signaling. lncREST depleted cells suffer sustained replication fork progression and accumulate un-signaled DNA damage. These findings uncover a structural function of a lncRNA acting as anchoring point for replication proteins foci on sites of DNA replication. Overall design: Comparative gene expression profiling analysis of RNA-seq data for chromatin and total RNA fractions of HCT116 cells treated with hydroxyurea versus control non-treated