E proteins orchestrate dynamic transcriptional cascades implicated in the suppression of the differentiation of group 2 innate lymphoid cells [RNA-Seq]
Group 2 innate lymphoid cells (ILC2s) represent a subset of newly discovered immune cells that are involved in immune reactions against microbial pathogens, host allergic reactions as well as tissue repair.  The basic helix-loop-helix transcription factors collectively called E proteins powerfully suppress the differentiation of ILC2s from bone marrow and thymic progenitors while promoting the development of B and T lymphocytes.  How E proteins exert the suppression is not well understood.  Here we investigated the underlying molecular mechanisms using inducible gain and loss of function approaches in ILC2s and their precursors, respectively.  Cross-examination of RNA sequencing and ATAC sequencing data obtained at different time points reveals a set of genes which are likely direct targets of E proteins.  Consequently, a widespread down-regulation of chromatin accessibility occurs at a later time point, possibly due to the activation of transcriptional repressor genes such as Cbfa2t3 and Jdp2.  The large number of genes repressed by gain of E protein function leads to the down-regulation of a transcriptional network important for ILC2 differentiation. Overall design: RNA-seq was performed on thymic ILC2 cells isolated from Id1 transgenic mice, which were transduced with retroviruses expressing either GFP alone or together with an E47-ER fusion protein after stimulation with ILC2, IL-7, IL-25 and IL-33.  Transduced cells were sorted for GFP and expanded in ILC2, IL-7, IL-25 and IL-33.  The cells were then treated with 4-hydroxy-Tamoxifen for 4 or 16 hours before harvested for RNA isolation.