DDX5 regulates chromatin lncRNAs to direct T cell programs

Abstract Recent studies uncovered the growing role of long non-coding RNAs (lncRNAs) in T cell biology. However, little is known about the lncRNAs that localize on the T cell chromatin (T-chrRNAs) with critical roles in gene expressions at the transcription and post-transcriptional level. Using the GRID-seq approach, we uncovered the top 18 T-chrRNAs and their chromatin occupancy in primary mouse CD4+ T helper cells in both the naïve and differentiated states. The chromatin binding of these T-chrRNAs revealed surprising stage-specific clustering patterns and mobilization during development and T cell differentiation. Our eCLIP assay showed that many of these T-chrRNAs interact directly with the DDX5, a nuclear residing RNA binding protein with ATPase activity. Th17 are unique CD4+ T-cell subset characterized by production of IL-17 and play an important role in inflammation and autoimmunity. At low TGFβ concentration, DDX5 is required for proper Th17 cytokine expression. Our ATAC-seq results suggest that DDX5 knockout Th17 cells fail to maintain chromatin accessibility at numerous regulatory regions, including the super-enhancer at the Il17a-Il17f locus. Moreover, GRID-seq data on WT and DDX5 knockout Th17 cells identified a subset of T-chrRNAs dependent on DDX5 for their proper chromatin localization. In particular, Malat1 is recruited to key Th17 loci in a DDX5 dependent manner. Similar to the DDX5-knockout Th17 cells, CRISPR-Cas targeting of the DDX5 bound regions of Malat1 results in loss of Th17 effector function. Better understanding of the localizations, functions, and upstream regulatory mechanisms governing T-chrRNAs physiology will provide new opportunities for therapeutic intervention to treating T cell mediated diseases.