ChIP-seq data for studying the transcription activities of PRDL factors in HEK293 cells.

Embryonic genome activation (EGA) is a critical process that occurs during the early stages ofhuman development and is characterized by the initiation of de novo transcription. Despite itsimportance, the regulation of EGA and the transcription factors involved in this process arepoorly understood. Previous transcriptome sequencing studies have identified differentialexpression of thousands of genes during EGA and the downregulation of transcripts specific tooocytes. Paired-like homeobox (PRDL) family proteins have been implicated as a potentialtranscriptional regulator of EGA. To investigate the function of PRDL proteins, we set out toidentify the molecular interactions and the functions of a subset family the Eutherian TotipotentCell Homeobox (ETCHbox) proteins, seven other PRDL family proteins and six othertranscription factors (TFs) all indicated to participate in transcriptional regulation duringpreimplantation. We used mass spectrometry-based interactomics methods, AP-MS andproximity-dependentbiotin labeling, and chromatin immunoprecipitation sequencing to derivecomprehensive regulatory networks of these preimplantation transcription factors. Using theseinteractomics tools we identify more than a thousand high-confidence interactions for the21studied bait proteins with more than 300 interacting proteins. The majority of these interactingproteins were linked to transcriptional regulation, chromatin modification and/or epigeneticregulation. We also established that TPRX2, currently assignedas pseudogene, is a strongtranscriptional activator.Our results provide new insights into the protein interaction networksand functions of the ETCHbox family, which are important for understanding EGA and thedevelopment of early stage embryos.