FUS and TAF15 safeguard the critical functions of the ribonucleoprotein network formed by EWSR1 and newly synthesized RNA

SUMMARY The FET family of RNA-binding proteins, FUS, EWSR1, and TAF15, contribute to transcriptional regulation and RNA maturation, but their core functions remain unclear. Chromosomal rearrangements involving FUS, EWSR1, or TAF15 drive multiple cancers, and mutations in the genes encoding the FET proteins are associated with neurodegenerative disease. Here, using nanoscale imaging, we show that endogenous EWSR1 and newly synthesized RNA exhibit a network-like organization with EWSR1 foci forming the nodes of this ribonucleoprotein network. Acute depletion of EWSR1 causes a rapid but transient reduction in nascent RNA levels and cellular metabolic activity without affecting active transcription. Notably, loss of EWSR1 induces a compensatory mechanism involving the reorganization of FUS and TAF15 to closely resemble that of EWSR1, including enhanced clustering with newly synthesized RNA. Together, our findings reveal functional redundancy within the FET protein family that is critical for the homeostatic regulation of nascent RNA levels. In brief Sundara Rajan et al. show that endogenous EWSR1 and nascent RNA form a ribonucleoprotein network. EWSR1 depletion transiently reduces nascent RNA and metabolic activity without impairment of transcriptional elongation. Loss of EWSR1 induces compensatory reorganization of FUS and TAF15, revealing a protein family mechanism required for the homeostatic regulation of nascent RNA levels. Highlights EWSR1 and nascent RNA form a ribonucleoprotein network EWSR1 loss transiently reduces nascent RNA and metabolic activity FUS and TAF15 undergo compensatory nuclear reorganization upon EWSR1 loss FUS and TAF15 functionally replace EWSR1 GRAPHICAL ABSTRACT