Alternative splicing of a chromatin modifier alters the transcriptional regulatory programs of stem cell maintenance and neuronal differentiation

Development of embryonic stem cells (ESCs) into neurons requires intricate regulation of transcription, splicing, and translation, but how these processes interconnect is not understood. We found that polypyrimidine tract binding protein 1 (PTBP1) controls splicing of DPF2, a subunit of BRG1/BRM-associated factor (BAF) chromatin remodeling complexes. Dpf2 exon 7 splicing is inhibited by PTBP1 to produce the DPF2-S isoform early in development. During neuronal differentiation, loss of PTBP1 allows exon 7 inclusion and DPF2-L expression. Different cellular phenotypes and gene expression programs were induced by these alternative DPF2 isoforms. We identified chromatin binding sites enriched for each DPF2 isoform, as well as sites bound by both. In ESC, DPF2-S preferential sites were bound by pluripotency factors. In neuronal progenitors, DPF2-S sites were bound by nuclear factor I (NFI), while DPF2-L sites were bound by CCCTC-binding factor (CTCF). DPF2-S sites exhibited enhancer modifications, while DPF2-L sites showed promoter modifications. Thus, alternative splicing redirects BAF complex targeting to impact chromatin organization during neuronal development. [Display omitted] •PTBP1 controls splicing of chromatin remodeler DPF2 to create a neuronal isoform•Loss of neuronal DPF2 isoform perturbs neuronal differentiation in culture•DPF2 isoforms exhibit both common and distinct chromatin target sites•DPF2 isoforms associate with distinct transcription factors and chromatin marks Nazim et al. investigate the molecular mechanisms and functional consequences of an alternative splicing switch in the chromatin modifier, DPF2. The study reveals that the developmental switch from the DPF2-S to DPF2-L isoform impacts transcriptional and chromatin regulatory programs involved in stem cell maintenance and neuronal development.