H3K27ac Profiling in LIRIL2R-Deficient and LIRIL2R-Sufficient Induced Regulatory T Cells
Factors that determine the epigenetic landscape of regulatory T cells (Tregs), which is critical for their function, remain poorly understood. Long intergenic noncoding RNAs (LincRNA)s are important for shaping and maintaining the epigenetic landscape in different cell types. We identified a novel uncharacterised lincRNA, which we named LincRNA regulator of IL2RA (LIRIL2R), that is upregulated during early differentiation of human Tregs. RNA sequencing (RNA-seq) and data independent (DIA) proteomic analysis of LIRIL2R-deficient Tregs, with genome-wide chromatin occupancy analysis, identified IL2RA as direct LIRIL2R target. This nuclear lincRNA directly binds upstream of IL2RA locus and regulates its transcription by facilitating the accessibility of the locus. LIRIL2R-deficient Tregs had reduced expression of Treg-related genes, including FOXP3, IL2RA, STAT5, CTLA4 and PDCD1, as well as reduced suppressive capacity. Modulating LIRIL2R expression may hold promise for better therapeutic strategies against autoimmunity and cancer. Overall design: CD4 T cells were isolated from human umbilical cord blood.  Cells were treated with either control non targeting (NT) antisense loked nucleic acid oligos (LNAs) or two LNAs (LNA1 and LNA2) targeting LIRIL2R. The cells were rested for 24 h followed by differentiation under iTreg conditions for 48 hours and CUT&Tag-seq was performed using H3K27ac antibody or control IgG antibody.