Multiple levels of transcriptional regulation by PLZF in NKT cell development [Mouse430_2]. Mus musculus

To identify genes that require PLZF for their regulation in NKT cells, we compared the developmental stages of thymic NKT cells from wildtype and PLZF-deficient mice The transcription factor PLZF is induced during the development of innate and innate-like lymphocytes to direct their acquisition of a T helper effector program, but the molecular mechanisms involved are poorly understood. Using biotinylation-based ChIP-seq and microarray analysis of both NKT and PLZF-transgenic thymocytes, we identified several layers of regulation of the innate-like NKT effector program: first, PLZF bound and regulated genes encoding cytokine receptors as well as homing and adhesion receptors; second, PLZF bound and activated T helper-specific transcription factor genes that in turn control T helper specific programs; finally, PLZF bound and suppressed the transcription of Bach2, a potent general repressor of effector differentiation in naive T cells. These findings reveal the architecture of the transcriptional program recruited by PLZF and elucidate how a single transcription factor can drive the developmental acquisition of a broad effector program. Overall design: FACS-sorted stage 1 NKT (CD1d tetramer+ CD24low CD44- NK1.1-) from the thymi of Valpha14 TCR transgenic mice or PLZF-deficient Luxoid mutant mice that were also Valpha14 TCR transgenic and CD4SP (CD4+ CD8-) thymocytes from wildtype mice. 3 biological replicates of stage 1 NKT from PLZF-deficient Valpha14 transgenic mice, 2 biological replicates of stage 1 NKT from PLZF-sufficient Valpha14 transgenic mice and 2 biological replicates of CD4SP thymocytes from wildtype mice were compared using Mouse Genome 430 2.0 microarrays.