Histone demethylase Lsd1 regulates multiple repressive gene programs during T cell development

Analysis of the transcriptional profiles of developing thymocytes has shown that T lineage commitment is associated with loss of stem cell and early progenitor gene signatures and the acquisition of T cell gene signatures. Less well understood are the epigenetic alterations that accompany or enable these transcriptional changes. Here, we show that the histone demethylase Lsd1 (Kdm1a) performs a key role in extinguishing stem/progenitor transcriptional programs in addition to key repressive gene programs during thymocyte maturation. Deletion of Lsd1 caused a block in late T cell development and resulted in overexpression of interferon response genes as well as genes regulated by the Gfi1, Bcl6, and, most prominently, Bcl11b transcriptional repressors in CD4+CD8+ thymocytes. Transcriptional overexpression in Lsd1-deficient thymocytes was not always associated with increased H3K4 trimethylation at gene promoters, indicating that Lsd1 indirectly affects the expression of many genes. Together, these results identify a critical function for Lsd1 in the epigenetic regulation of multiple repressive gene signatures during T cell development. RNA-Seq: 2 genotypes (Lsd1-KO, WT) x 2 conditions (CD69-, CD69+) x 4 biological replicates = 16 samples (x 2 technical replicates). ChIP-Seq: 1) H3K4me1 - 2 genotypes (Lsd1-ko, WT) x 2 biological replicates = 4 IP samples (x 2 technical replicates) + 2 input (Lsd1-KO, WT). 2) H3K4me2 - 2 genotypes (Lsd1-KO, WT) x 2 biological replicates = 4 IP samples + 4 input samples (Lsd1-KO, WT x 2 replicates). 3) H3K4me3 - 2 genotypes (Lsd1-KO, WT) x 3 biological replicates = 6 IP samples + 2 input (Lsd1-KO, WT) = 22 samples. scRNA-Seq: 2 genotypes (Lsd1 fl/fl, CD2-iCre; Lsd1 fl/fl) x 2 biological replicates = 4 samples.