Disentangaling the gene expression programs controlled by ciliary and cytosolic cAMP signaling

Primary cilia are tiny membrane protrusions emanating from the surface of almost all mammalian cell types. Recently, a picture has emerged of the primary cilium functioning as a cellular antenna that senses extracellular stimuli via receptors, locally processes the signal using cilia-specific signalling pathways, and transduces this information into a cellular response. Components of the cyclic AMP (cAMP) signalling cascade have been proposed to be part of the ciliary signalling pathways. We aimed to shed light on whether ciliary cAMP signaling controls gene expression, and if yes, which gene expression program is particularly targeted by ciliary cAMP signaling. To this end, we targeted an optogenetic tool to increase cAMP levels (bPAC) to the primary cilium in murine, kidney-derived inner medullary collecting duct (mIMCD-3) cells (mIMCD-3 cilia-bPAC cells). As controls, we used cells were bPAC is targeted to the cytosol (mIMCD-3 cyto-bPAC cells) and wild-type cells (mIMCD-3 WT cells). We increased cAMP levels by light stimulation and next analysed gene expression using bulk RNA-sequencing. As an additional control, we also included WT cells treated with the compound Forskolin, which targets endogeneous adenylyl cyclases and thus, in principle, is believed to increase cAMP levels in both compartments, cilium and cell soma. Overall design: The whole experiment including all conditions was performed four times independently. The experimentID characteristics links conditions from the same experiment day.