An Alternative Splicing Switch Regulates Embryonic Stem Cell Pluripotency and Reprogramming [ChIP-Seq]

Alternative splicing (AS) is a key process underlying the expansion of proteomic diversity and the regulation of gene expression. However, the contribution of AS to the control of embryonic stem cell (ESC) pluripotency is not well understood. Here, we identify an evolutionarily conserved ESC-specific AS event that changes the DNA binding preference of the forkhead family transcription factor FOXP1. We show that the ESC-specific isoform of FOXP1 stimulates the expression of transcription factor genes required for pluripotency including OCT4, NANOG, NR5A2 and GDF3, while concomitantly repressing genes required for ESC differentiation. Remarkably, this isoform also promotes the maintenance of ESC pluripotency and the efficient reprogramming of somatic cells to induced pluripotent stem cells. These results thus reveal that an AS switch plays a pivotal role in the regulation of pluripotency and functions by controlling critical ESC-specific transcriptional programs. To identify genes potentially directly regulated by FOXP1-ES and FOXP1 in H9 ESCs, we performed chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-Seq). Using an antibody capable of efficiently immunoprecipitating both isoforms, >3400 significant ChIP-Seq peaks were detected across the human genome. To assess if these peaks are sites of FOXP1 and FOXP1-ES occupancy, we determined whether they are significantly enriched in individual PBM-derived 8-mers that bind to either or both isoforms.