Structural basis for competitive binding of productive and degradative co-transcriptional effectors to the nuclear cap-binding complex

The nuclear cap-binding complex (CBC) coordinates co-transcriptional maturation, transport, or degradation of nascent RNA polymerase II (Pol II) transcripts. CBC with its partner ARS2 forms mutually exclusive complexes with diverse “effectors” that promote either productive or destructive outcomes. Combining AlphaFold predictions with structural and biochemical validation, we show how effectors NCBP3, NELF-E, ARS2, PHAX, and ZC3H18 form competing binary complexes with CBC and how PHAX, NCBP3, ZC3H18, and other effectors compete for binding to ARS2. In ternary CBC-ARS2 complexes with PHAX, NCBP3, or ZC3H18, ARS2 is responsible for the initial effector recruitment but inhibits their direct binding to the CBC. We show that in vivo ZC3H18 binding to both CBC and ARS2 is required for nuclear RNA degradation. We propose that recruitment of PHAX to CBC-ARS2 can lead, with appropriate cues, to competitive displacement of ARS2 and ZC3H18 from the CBC, thus promoting a productive rather than a degradative RNA fate. [Display omitted] •Tryptophan-containing helices of RNA effectors NCBP3, PHAX, and ZC3H18 compete to bind to CBC•NCBP3, PHAX, and ZC3H18 compete to interact with ARS2 via their ARM motifs•After effector recruitment by ARS2, their access to CBC is blocked•ZC3H18 binding to both CBC and ARS2 is required for RNA degradation of NEXT targets in vivo RNA effectors, such as NCBP3, PHAX, and ZC3H18, competitively interact with the nuclear CBC-ARS2 complex during transcription to guide nascent transcripts for processing, export, or degradation. Dubiez et al. use biochemical and structural methods to reveal high-resolution details of effector interactions with both CBC and ARS2.