ROQUIN-1 binding to the transcriptome of T cells reveals conserved targets in the control of lymphopoiesis

Defining the RNA targets of ROQUIN-1 is essential for understanding post-transcriptional gene regulation in immunity, autoimmunity, and cancer immunotherapy. We systematically mapped transcriptome-wide ROQUIN-1/RNA interactions in mouse and human lymphocytes. Novel targets were enriched in signaling molecules, transcription factors, epigenetic regulators, and mediators of immune cell differentiation. Cross-species analysis revealed conservation at binding sites, suggesting evolutionary preservation of ROQUIN-mediated regulation. Notably, ROQUIN-1 bound all mRNAs of the Id1–Id4 gene family—transcriptional regulators critical for lymphocyte differentiation. Functional perturbation through Id1-3 overexpression impaired thymocyte and B cell development. Similarly, inactivation of Roquin-1/2 increased Id3 expression in thymocytes and developing B cells, delayed double-negative thymocyte progression and blocked B cell development before the pro-B cell stage. Uncovering Roquin's role in controlling gene expression driving lymphocyte development, our dataset also provides a valuable resource for functional genomics to dissect RNA-based regulation in immunity and offers mechanistic insights into ROQUIN function across species.