ZFP281 coordinates DNMT3 and TET1 for transcriptional and epigenetic control in pluripotent state transitions

The progression from naive through formative to primed in vitro pluripotent stem cell states recapitulates the development of the epiblast in vivo during the peri-implantation period of mammalian development. Activation of the de novo DNA methyltransferases and reorganization of transcriptional and epigenetic landscapes are key events occurring during these pluripotent state transitions. However, the upstream regulators that coordinate these events are relatively underexplored. Here, using Zfp281 knockout mouse and degron knock-in cell models, we uncover the direct transcriptional activation of Dnmt3a/3b by ZFP281 in pluripotent stem cells. Chromatin co-occupancy of ZFP281 and DNA hydroxylase TET1, dependent on the formation of R loops in ZFP281-targeted gene promoters, undergoes a "high-low-high" bimodal pattern regulating dynamic DNA methylation and gene expression during the naive-formative-primed transitions. ZFP281 also safeguards DNA methylation in maintaining primed pluripotency. Our study demonstrates a previously unappreciated role for ZFP281 in coordinating DNMT3A/3B and TET1 functions to promote pluripotent state transitions. In BriefThe naive, formative, and primed pluripotent states and their interconversions recapitulate pluripotency continuum during early development. Huang and colleagues investigated the transcriptional programs during successive pluripotent state transitions and revealed an essential role for ZFP281 in coordinating DNMT3A/3B and TET1 to establish the DNA methylation and gene expression programs during the transitions. HighlightsO_LIZFP281 activates Dnmt3a/3b in vitro in pluripotent stem cells and in vivo in epiblast. C_LIO_LIZFP281 and TET1 undergo bimodal chromatin occupancy in pluripotent state transitions. C_LIO_LIChromatin-binding of ZFP281 and TET1 depends on the formation of R-loops at promoters. C_LIO_LIZFP281 is necessary for the establishment and maintenance of primed pluripotency. C_LI