Alphafold2 modeling of KCTD10 interactions with RNAPII machinery

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 investigated the role of the CUL3-KCTD10 E3 ligase as a sensor for TRCs. We found that the substrate adaptor KCTD10 interacts with both the replisome and 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 can recruit CUL3 to ubiquitinate the RNA polymerase factor TCEA2. In the absence of KCTD10 there is increased retention of TCEA2 and RNA polymerase complex, causing an accumulation of TRCs and increased DNA damage. These ..., , # Alphafold2 modeling of KCTD10 interactions with RNAPII machinery

Dataset DOI: [10.5061/dryad.15dv41p7z](10.5061/dryad.15dv41p7z)

## Description of the data and file structure

Screening for KCTD10 interaction partners

FASTA sequences belonging to the gene ontology term “transcription by RNA polymerase II” (GO:0006366) were retrieved from the European Bioinformatics Institute (EMBL-EBI) Gene Ontology and GO Annotations database ([www.ebi.ac.uk/QuickGO/](http://www.ebi.ac.uk/QuickGO/)). Using linux shell commands, the FASTAs were split, concatenated with the full length FASTA sequence for KCTD10 (UniprotKB ID: Q9H3F6), and then pooled into batches of 100 files. Each batch was run through ColabFold (v1.5.5)9–11 using Tesla T4 GPUs as a first pass, then larger complexes were completed using Tesla A100 GPUs. One protein could not be completed due to limitations of Alphafold2 (CHD7). To prioritize top hits, an iPTM score > 0.4 was chosen, corresponding to > 1 standard deviation above the...,