The SMAD2/3 interactome reveals that TGFβ controls m ⁶A mRNA methylation in pluripotency

Abstract

The TGFβ pathway plays an essential role in embryonic development, organ homeostasis, tissue repair, and disease 1, 2. This diversity of tasks is achieved through the intracellular effector SMAD2/3, whose canonical function is to control activity of target genes by interacting with transcriptional regulators 3. Nevertheless, a complete description of the factors interacting with SMAD2/3 in any given cell type is still lacking. Here we address this limitation by describing the interactome of SMAD2/3 in human pluripotent stem cells (hPSCs). This analysis reveals that SMAD2/3 is involved in multiple molecular processes in addition to its role in transcription. In particular, we identify a functional interaction with the METTL3-METTL14-WTAP complex, which deposits N ⁶-methyladenosine (m6A) 4. We uncover that SMAD2/3 promotes binding of the m6A methyltransferase complex onto a subset of transcripts involved in early cell fate decisions. This mechanism destabilizes specific SMAD2/3 transcriptional targets, including the pluripotency factor NANOG, thereby poising them for rapid downregulation upon differentiation to enable timely exit from pluripotency. Collectively, these findings reveal the mechanism by which extracellular signalling can induce rapid cellular responses through regulations of the epitranscriptome. These novel aspects of TGFβ signalling could have far-reaching implications in many other cell types and in diseases such as cancer 5.