iCLIP data from TAF15 bound transcript regulated by the cAMP-dependent Protein Kinase A. Phosphorylation of the compartmentalized PKA substrate TAF15 regulates RNA:Protein interactions

Spatiotemporal-controlled second messengers alter molecular interactions of central signaling nodes for ensuring physiological signal transmission. One prototypical second messenger molecule which modi-fies kinase-centered signalosomes is the cyclic-adenosine monophosphate (cAMP). The main proteino-genic cellular effectors of cAMP are compartmentalized protein kinase A (PKA) complexes. Their cell-type specific compositions precisely coordinate substrate phosphorylation and proper signal prop-agation which is indispensable for numerous cell-type specific functions. In label-free affini-ty-isolations of endogenous PKA complexes from colorectal cancer cell lines, we found a substantial enrichment of RNA-binding proteins. Among these, we identified TAF15, which is implicated in the etiology of amyotrophic lateral sclerosis, to be a novel nuclear PKA substrate. TAF15 contains a spe-cific PKA phosphorylation in one of its RNA-binding domains. In cross-linking and immunoprecipita-tion experiments (iCLIP) we showed that TAF15 phosphorylation alters the binding to target transcripts related to mRNA maturation, splicing and protein-binding related functions. TAF15 appears to be one of multiple PKA substrates that may undergo RNA-binding dynamics via phosphorylation. Further-more, we observed that cAMP elevation modifies the RNA-binding pattern of the TAF15 transcripts and changes the distribution of the TAF15 RNA-binding sites. We assume that phosphorylation of RNA binding domains adds another layer of regulation to binary protein-RNAs interactions with conse-quences to RNA features including binding specificities, localization, abundance and composition.