KCTD10 is a sensor for co-directional transcription-replication conflicts

During DNA replication, the replisome must remove barriers and roadblocks including the transcription machinery. Transcription-replication conflicts (TRCs) occur when there are collisions between the replisome and transcription machinery, and are increasingly recognized as an important source of mammalian genome instability. How cells facilitate replisome bypass at sites of TRCs is incompletely understood. Here we show that the CUL3-KCTD10 E3 ligase senses TRCs and promotes remodeling of the RNA polymerase complex to allow replisome bypass. We found that the substrate adaptor KCTD10 interacts with the replisome and the transcription machinery and regulates both in unstressed conditions. These bivalent interactions allow KCTD10 to detect co-directional TRCs and facilitate higher-order assembly of KCTD10 complexes that recruit CUL3 to induce the ubiquitination and removal of the RNA polymerase factor TCEA2. In the absence of KCTD10, there is increased retention of TCEA2 and the RNA polymerase complex, causing an accumulation of TRCs and increased DNA damage. Our results demonstrate how replication can proceed through transcriptionally active regions, utilizing a unique bridging function of the CUL3-KCTD10 complex. These findings provide a framework for how the coordination between transcription and replication may contribute to the maintenance of genome stability. Overall design: The submission includes samples from CUT&RUN experiments performed using HeLa cells expressing FLAG-tagged KCTD10. The primary objective of the study is to determine the location of KCTD10 binding genome-wide.