Alternative enhancer usage and targeted Polycomb marking hallmark promoter choice during T cell differentiation

To characterize the regulatory landscape of developing T-cells, we performed a wide epigenetic and transcriptional analysis of mouse primary thymocytes and ex-vivo differentiated T-helper cells. Based on this data, we portrayed extensively the enhancer and promoter landscape used during differentiation. Our investigations shed light to a very dynamic putative enhancer landscape, many of which we could validate genome-wide using CapStarr-seq. Using our data, we could also show that RNA polymerase II occupancy can be used as an excellent proxy for enhancer activity, when combined with H3K4me1 and H3K27ac epigenetic marks. We further show that enhancer dynamicity is in contrast to more modest variations in gene expression and long-distance interactions. However and interestingly, we found that genes using multiple promoters during differentiation display increased enhancer usage, suggesting that apparent 'enhancer redundancy' might relate to isoform selection. Furthermore, in the case of the Runx3 locus, we could identify that each of its two active promoters display long-range interactions with specific enhancers. Finally, our analyses reveal that the control of promoter usage is also associated to the PRC2-deposited H3K27me3 signal at the vicinity of the promoter that is apparently repressed, suggesting a novel function for this complex whereby it contributes to regulation of specific isoform expression. Overall design: This study was performed in a primary and in vitro differentiated mouse T cells. It contains ChIP-seq data for RNA Pol II, H3K4me1, H3K4me3, H3K27ac and H3K27me3 as well as RNAseq, capSTARRseq, and 4C-seq data.