Genome binding/occupancy profiling by high throughput sequencing
Summary
The transcription factor T-bet directs Th1 cell differentiation, but the molecular mechanisms that underlie this lineage-specific gene regulation are not completely understood. Here, we show that T-bet acts through super-enhancers in human and mouse Th1 cells to recruit Mediator and P-TEFb in the form of the super elongation complex (SEC). Th1-specific genes are poised in Th2 cells while T-bet-mediated recruitment of P-TEFb in Th1 cells activates transcriptional elongation. P-TEFb is recruited to both genes and super-enhancers, where it activates enhancer RNA transcription. P-TEFb inhibition and Mediator and SEC knockdown selectively block activation of T-bet target genes and P-TEFb inhibition abrogates Th1-associated experimental autoimmune uveitis. T-bet activity is independent of changes in NF-κB RelA and Brd4 binding, but T-bet- and NF-κB-mediated pathways converge to allow P-TEFb recruitment. These data support a model in which lineage-specifying factors allow recruitment of P-TEFb to poised genes to promote differentiation of alternative T cell fates.
Overall design
Indentification of P-TEFb binding sites in human Th1 and Th2 cells Indentification of RelA binding sites in human Th1 cells treated with BAY 11-7082 and DMSO control Indentification of P-TEFb binding sites in human Th1 cells treated with BAY 11-7082 and DMSO control Indentification of AFF4 binding sites in human Th1 cells treated with BAY 11-7082 and DMSO control Indentification of BRD4 binding sites in human Th1 cells treated with BAY 11-7082 and DMSO control Indentification of MED1 binding sites in human Th1 cells treated with BAY 11-7082 and DMSO control Indentification of P-TEFb binding sites in mouse wild-type and T-bet -/- Th1 and wild-type Th2 cells Indentification of RelA binding sites in mouse wild-type and T-bet -/- Th1 cells Indentification of Brd4 binding sites in mouse wild-type and T-bet -/- Th1 cells Indentification of Med1 binding sites in mouse wild-type and T-bet -/- Th1 cells Indentification of Aff4 binding sites in mouse wild-type and T-bet -/- Th1 cells Indentification of P-TEFb binding sites in EL4-GFP and EL4-T-bet cells Indentification of Flag-T-bet binding sites in EL4-T-bet-mPlum and EL4-Gata3-GFP cells Indentification of RelA binding sites in EL4-GFP and EL4-T-bet cells Indentification of Brd4 binding sites in EL4-GFP and EL4-T-bet cells Indentification of Med1 binding sites in EL4-GFP and EL4-T-bet cells Indentification of Aff4 binding sites in EL4-GFP and EL4-T-bet cells Indentification of RNA polymerase II binding sites in human Th1 and Th2 cells Mapping of H3K4me3 histone modifications in human Th1 and Th2 cells Mapping of H3K4me3 histone modifications in human CCR5+ memory Th1 Mapping of H3 histone in human CCR5+ memory Th1 Mapping of H3K27ac histone modifications in human Th1 and Th2 cells Mapping of H3K4me3 histone modifications in mouse wild-type and T-bet-/- Th1 cells Mapping of H3 histone in mouse wild-type and T-bet-/- Th1 cells
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