A bifunctional, moonlighting RNA coordinates pathways to regulate human embryonic development [scRNA-seq]
Early embryogenesis and cellular differentiation require complex choreography between nuclear and cytoplasmic pathways. Through integrative analysis and a short open reading frame functional screen, sORF-seq, we identified lncPRESS1, a bifunctional long-non-coding RNA that also encodes a microprotein. In the nucleus, lncPRESS1 binds BRG1 to regulate chromatin remodeling and modulate the expression of pluripotency and differentiation genes. In the cytoplasm, lncPRESS1 is translated into a microprotein that binds to IFT57, regulating ciliogenesis and SHH signaling pathways to control lineage commitment. Together, these results reveal a novel mechanism where the dual functions of lncPRESS1 simultaneously coordinate chromatin remodeling and signaling pathways. This coordination co-regulates the initial developmental decisions specifying neuroectoderm and mesoderm fates during human embryonic development, underscoring the underappreciated complexity of multifunctional RNAs. Overall design: The lncPRESS1 WT, KO, and ?ATG hESCs were pretreated with 3.25 uM of CHIR99021 for 24 hours and then 0.5 uM of CHIR99021 for 72 hours to develop 3D gastruloids. These gastruloids were dissociated into single cells using ACCUTASE and then sent for scRNA-seq analysis.