NBCn1 interacts with DYNLL1 and regulates ciliary length and SUFU localization to control Sonic hedgehog signaling

Primary cilia integrate morphogen signaling with cellular physiology, yet how ion transporters contribute to ciliary organization and function remains poorly understood. Here, we identify the sodium-bicarbonate cotransporter NBCn1 (SLC4A7) as a previously unrecognized ciliary membrane component essential for regulating ciliary length and Sonic hedgehog (Shh) signaling. NBCn1 localizes to primary cilia through distinct Nand Cterminal targeting motifs and inhibition of dynein activity or loss of DLG1, a known NBCn1 interacting protein, augments its ciliary localization. Loss of NBCn1 shortens cilia without altering ciliation frequency or deciliation kinetics, indicating a selective role in ciliary elongation control rather than in ciliogenesis initiation or maintenance. NBCn1 deficiency or -inhibition leads to ciliary enrichment of SUFU even at basal level and markedly attenuates GLI1 transcriptional activation, despite intact SMO ciliary entry. Structural modeling and coimmunoprecipitation reveal that NBCn1 interacts with DYNLL1, VPS45, and the transitionzone protein TMEM216, suggesting that NBCn1 modulates ciliary length and Shh signaling through interactions with these proteins. Together, these findings uncover NBCn1 as a central regulator of ciliary length and Shh signaling, highlighting ion transport as a critical and underappreciated determinant of ciliary signaling competence. Significance statementPrimary cilia are essential cellular signaling hubs, yet the contribution of ion transporters and pH to ciliary architecture and function has remained unclear. This study identifies the bicarbonate transporter NBCn1 as a previously unrecognized regulator of ciliary length and Sonic hedgehog (Shh) signaling. We show that NBCn1 is actively trafficked into cilia through defined Nand Cterminal determinants, is exported from cilia via retrograde intraflagellar transport (IFT), and interacts directly with IFT dynein component DYNLL1. Loss of NBCn1 selectively shortens cilia while leaving ciliogenesis frequency and deciliation dynamics intact. NBCn1 deficiency disrupts the ciliary localization of the key Shh component SUFU, leading to impaired GLI transcriptional responses. By revealing how ion transport intersects with IFT and morphogen signaling, these findings establish NBCn1 as a central integrator of ciliary microenvironmental regulation and developmental signaling output, highlighting pH regulatory ion transport as a critical and underappreciated determinant of ciliary function.